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    Aapro, M. Optimising antiemetic therapy: what are the problems and how can they be overcome? {2005} CURRENT MEDICAL RESEARCH AND OPINION
    Vol. {21}({6}), pp. {885-897} 
    article DOI  
    Abstract: Background: Management of chemotherapy- or radiotherapy-induced emesis has improved significantly following the introduction of the 5-HT3-receptor antagonists. Prophylactic use of these agents is recommended for the prevention of both chemotherapy- and radiotherapy-induced nausea and vomiting, given with a corticosteroid. Despite these advances, nausea and vomiting remain among the most feared and debilitating adverse effects of cytotoxic therapy. The shift towards a more elderly population of patients with cancer presents additional considerations for supportive care, with an emphasis on achieving control of nausea and vomiting, whilst minimising toxicity and avoiding drug-drug interactions. This review presents some of the key issues for consideration in optimising antiemetic therapy. The PubMed search engine was used to search for relevant literature (up to December 2004) and relevant international congress materials collected during 2003 and 2004. Scope: While the early stages of nausea and vomiting are 5-HT-mediated, identification of a role for substance P in late emesis has led to the development of the NK1-receptor antagonist, aprepitant. As a new agent, the clinical profile of aprepitant is still being explored, including its interaction with concomitant medications. Patients who achieve good control of acute and late-acute nausea and vomiting have a reduced risk of experiencing delayed onset symptoms, emphasising the importance of prophylactic management with effective agents. Although the 5-HT3-receptor antagonists are widely considered to have equivalent efficacy, they vary in half-life and the nature of antagonism at receptors. Their metabolic profiles also differ, with cytochrome P450 (CYP) metabolism affecting their propensity for drug-drug interactions. Several sets of guidelines are available that outline recommendations for selection and use of antiemetic therapy. However, under-use of 5-HT3-receptor antagonists has been reported in both the radiotherapy and chemotherapy settings, and some commonly used doses may be suboptimal. Conclusion: In optimising antiemetic therapy, wider implementation of guidelines is desirable, as is consideration of each patient's individual needs. Safety and tolerability of supportive care medications should be a key consideration, and cardiovascular warnings and the possibility of drug-drug interactions should be given sufficient consideration, particularly in view of the older age of the population with cancer.
    BibTeX:
    @article{Aapro2005,
      author = {Aapro, M},
      title = {Optimising antiemetic therapy: what are the problems and how can they be overcome?},
      journal = {CURRENT MEDICAL RESEARCH AND OPINION},
      year = {2005},
      volume = {21},
      number = {6},
      pages = {885-897},
      doi = {{10.1185/030079905X46313}}
    }
    
    Abdelmoty, A., Smart, P., Jones, C., Fu, G. & Finch, D. A critical evaluation of ontology languages for geographic information retrieval on the Internet {2005} JOURNAL OF VISUAL LANGUAGES AND COMPUTING
    Vol. {16}({4}), pp. {331-358} 
    article DOI  
    Abstract: A geo-ontology has a key role to play in the development of a spatially aware search engine, with regard to providing Support for query disambiguation, query term expansion, relevance ranking and web resource annotation. This paper reviews those functions and identifies the challenges arising in the construction and maintenance of such an ontology. Two current contenders for the representation of the geo-ontology are GML, a specific markup language for geographic domains and OWL, a generic ontology representation language. Both languages are used to model the geo-ontology designed for supporting web retrieval of geographic concepts. The powers and limitations of the languages are identified. In particular, the paper highlights the lack of representation and reasoning abilities for different types of rules needed for supporting the geo-ontology. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Abdelmoty2005,
      author = {Abdelmoty, AI and Smart, PD and Jones, CB and Fu, GH and Finch, D},
      title = {A critical evaluation of ontology languages for geographic information retrieval on the Internet},
      journal = {JOURNAL OF VISUAL LANGUAGES AND COMPUTING},
      year = {2005},
      volume = {16},
      number = {4},
      pages = {331-358},
      doi = {{10.1016/j.jvlc.2004.11.001}}
    }
    
    Accomazzi, A., Eichhorn, G., Kurtz, M., Grant, C. & Murray, S. The NASA Astrophysics Data System: Architecture {2000} ASTRONOMY & ASTROPHYSICS SUPPLEMENT SERIES
    Vol. {143}({1}), pp. {85-109} 
    article  
    Abstract: The powerful discovery capabilities available in the ADS bibliographic services are possible thanks to the design of a flexible search and retrieval system based on a relational database model. Bibliographic records are stared as a corpus of structured documents containing fielded data and metadata, while discipline-specific knowledge is segregated in a set of files independent of the bibliographic data itself. This ancillary information is used by the database management software to compile field-specific index files used by the ADS search engine to resolve user queries into lists of relevant documents. The creation and management of links to both internal and external resources associated with each bibliography in the database is made possible by representing them as a set of document properties and their attributes. The resolution of links available from different locations has been generalized to allow its control through a site- and user-specific preference database. To improve global access to the ADS data holdings, a number of mirror sites have been created by cloning the database contents and software on a variety of hardware and software platforms. The procedures used to create and manage the database and its mirrors have been written as a set of scripts that can be run in either an interactive or unsupervised fashion. The modular approach we followed in software development has allowed a high degree of freedom in prototyping and customization, malting our system rich of features and yet simple enough to be easily modified on a day-to-day basis, We conclude discussing the impact that new datasets, technologies and collaborations is expected to have on the ADS and its possible role in an integrated environment of networked resources in astronomy. The ADS can be accessed at: http://adswww.harvard.edu.
    BibTeX:
    @article{Accomazzi2000,
      author = {Accomazzi, A and Eichhorn, G and Kurtz, MJ and Grant, CS and Murray, SS},
      title = {The NASA Astrophysics Data System: Architecture},
      journal = {ASTRONOMY & ASTROPHYSICS SUPPLEMENT SERIES},
      year = {2000},
      volume = {143},
      number = {1},
      pages = {85-109}
    }
    
    Adamic, L. The small World Web {1999}
    Vol. {1696}RESEARCH AND ADVANCED TECHNOLOGY FOR DIGITAL LIBRARIES, PROCEEDINGS, pp. {443-452} 
    inproceedings  
    Abstract: I show that the World Wide Web is a small world, in the sense that sites are highly clustered yet the path length between them is small. I also demonstrate the advantages of a search engine which;makes use of the fact that pages corresponding to a particular search query can form small world networks, In a further application, the search engine uses the small-worldness of its search results to measure the connectedness between communities on the Web.
    BibTeX:
    @inproceedings{Adamic1999,
      author = {Adamic, LA},
      title = {The small World Web},
      booktitle = {RESEARCH AND ADVANCED TECHNOLOGY FOR DIGITAL LIBRARIES, PROCEEDINGS},
      year = {1999},
      volume = {1696},
      pages = {443-452},
      note = {3rd European Conference on Research and Advanced Technology for Digital Libraries (ECDL 99), PARIS, FRANCE, SEP 22-24, 1999}
    }
    
    Agrafiotis, D. Stochastic algorithms for maximizing molecular diversity {1997} JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
    Vol. {37}({5}), pp. {841-851} 
    article  
    Abstract: A common problem in the emerging field of combinatorial drug design is the selection of an appropriate subset of compounds for chemical synthesis and biological evaluation. In this paper, we introduce a new family of selection algorithms that combine a stochastic search engine with a user-defined objective function that encodes any desirable selection criterion. The method is applied to the problem of maximizing molecular diversity, and the results are visualized using Sammon's nonlinear mapping algorithm. By separating the search method from the performance metric, the method can be easily extended to perform complex multiobjective selections in advanced decision-support systems.
    BibTeX:
    @article{Agrafiotis1997,
      author = {Agrafiotis, DK},
      title = {Stochastic algorithms for maximizing molecular diversity},
      journal = {JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES},
      year = {1997},
      volume = {37},
      number = {5},
      pages = {841-851}
    }
    
    Ahonen, E.Q., Benavides, F.G. & Benach, J. Immigrant populations, work and health - a systematic literature review {2007} SCANDINAVIAN JOURNAL OF WORK ENVIRONMENT & HEALTH
    Vol. {33}({2}), pp. {96-104} 
    article  
    Abstract: Objectives This paper summarizes the information on immigrant occupational health available from recent studies, incorporating varied study designs. Methods A systematic search was carried out in PubMed employing terms of interest to the study and related terms supplied by the same search engine. Articles were selected through the following process: (i) reading the title and abstract, in English or Spanish, for the period 1990-2005, (ii) reading of the entire text of selected articles; (iii) making a manual search of the relevant citations in the selected articles; (iv) eliminating articles without a focus on the themes of central interest (immigration, work, and health), and (v) reading and analyzing the definitive article set. No quality criteria were used in the article selection. Results The location of studies was not straightforward and required careful thought about the search terms. The included 48 papers were often multifaceted and difficult to categorize. They generally came from countries historically associated with immigration and described occupational risk factors, health consequences, and the social, economic, and cultural influences on worker health. They were also based on data, surveillance, training, and preventive measures that were inadequate. Conclusions Increased migration is a reality in industrialized countries all over the world, and it has social, political, and economic consequences for migrating groups, as well as for their sending and host societies. More reliable data, targeted appropriate interventions, and enforcement of existing regulations are necessary to improve the health of immigrant workers. Furthermore, studies in sending and developing countries should be encouraged to form a more complete understanding of this complex situation.
    BibTeX:
    @article{Ahonen2007,
      author = {Ahonen, Emily Q. and Benavides, Fernando G. and Benach, Joan},
      title = {Immigrant populations, work and health - a systematic literature review},
      journal = {SCANDINAVIAN JOURNAL OF WORK ENVIRONMENT & HEALTH},
      year = {2007},
      volume = {33},
      number = {2},
      pages = {96-104}
    }
    
    Aldea, A., Banares-Alcantara, R., Jimenez, L., Moreno, A., Martinez, J. & Riano, D. The scope of application of multi-agent systems in the process industry: three case studies {2004} EXPERT SYSTEMS WITH APPLICATIONS
    Vol. {26}({1}), pp. {39-47} 
    article DOI  
    Abstract: It has been suggested that multi-agent systems (MAS) are specially adequate for the solution of problems with a dynamic, uncertain and distributed nature. Within industrial applications, there is a wide spectrum of problems with these characteristics, in particular those covering the modelling of artifacts, methodologies and organisations. Three case studies on the application of MAS in the process industry are presented. All of them relate to tools that are being developed to support very diverse core tasks in the process industry (and, by extension, the petroleum industry): An intelligent search system composed of Internet information agents which are able to gather, compile and classify data available in web pages related to a specific technological domain. This search engine is the first step towards the construction of a knowledge management platform that will allow chemical process industries to improve their capabilities to monitor, predict and respond to technological trends and challenges. A system to support the concurrent design of processes, to ease communication between engineers who perform design and keep them informed about the progress of the design process. A tool to support the configuration of work teams. This tool will assist in the configuration of the most suitable team for a specific project. It takes into account the ideal size of the team (2 to n members); its specific composition (managers, engineers/scientists, assistants, etc.); and the proposed type of organisation (centralised, tree hierarchy, etc.). These case studies are representative of a large variety of the possible applications of agent based systems in the process industry. (C) 2003 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Aldea2004,
      author = {Aldea, A and Banares-Alcantara, R and Jimenez, L and Moreno, A and Martinez, J and Riano, D},
      title = {The scope of application of multi-agent systems in the process industry: three case studies},
      journal = {EXPERT SYSTEMS WITH APPLICATIONS},
      year = {2004},
      volume = {26},
      number = {1},
      pages = {39-47},
      note = {1st Workshop on Intelligent Computing in the Petroleum Industry, MEXICO CITY, MEXICO, NOV 24-25, 2002},
      doi = {{10.1016/S0957-47174(03)00105-2}}
    }
    
    Ansani, N., Vogt, M., Henderson, B., McKaveney, T., Weber, R., Smith, R., Burda, M., Kwoh, C., Osial, T. & Starz, T. Quality of arthritis information on the Internet {2005} AMERICAN JOURNAL OF HEALTH-SYSTEM PHARMACY
    Vol. {62}({11}), pp. {1184-1189} 
    article  
    Abstract: Purpose. The quality and reliability of Internet-based arthritis information were studied. Methods. The search terms ``arthritis,'' ``osteoarthritis,'' and ``rheumatoid arthritis'' were entered into the AOL, MSN, Yahoo, Google, and Lycos search engines. The Web sites for the first 40 matches generated by each search engine were grouped by URL suffix and evaluated on the basis of four categories of criteria: disease and medication information content, Web-site navigability, required literacy level, and currentness of information. Ratings were assigned by using an assessment tool derived from published literature (maximum score of 15 points). Results. Of the 600 arthritis Web sites identified, only 69 were unique and included in the analysis. Fifty-seven percent were .com sites, 20% .org sites, 7% .gov sites, 6% .edu sites, and 10% other sites. Total scores for individual sites reviewed ranged from 3 to 14. Eighty percent of .gov sites, 75% of .edu sites, 29% of other sites, 36% of .com sites, and 21% of .org sites were within the top tertile of scores. No Web site met the criterion for being understandable to people with no more than a sixth-grade reading ability. .Gov sites scored significantly higher overall than .com sites, .org sites, and other sites. .Edu sites also scored relatively well. Conclusion. The quality of arthritis information on the Internet varied widely. Sites with URLs having suffixes of .gov and .edu were ranked higher than other types of sites.
    BibTeX:
    @article{Ansani2005,
      author = {Ansani, NT and Vogt, M and Henderson, BAF and McKaveney, TP and Weber, RJ and Smith, RB and Burda, M and Kwoh, CK and Osial, TA and Starz, T},
      title = {Quality of arthritis information on the Internet},
      journal = {AMERICAN JOURNAL OF HEALTH-SYSTEM PHARMACY},
      year = {2005},
      volume = {62},
      number = {11},
      pages = {1184-1189}
    }
    
    Ansary, T.F., Daoudi, M. & Vandeborre, J.-P. A Bayesian 3-D search engine using adaptive views clustering {2007} IEEE TRANSACTIONS ON MULTIMEDIA
    Vol. {9}({1}), pp. {78-88} 
    article DOI  
    Abstract: In this paper, we propose a method for three-dimensional (3-D)-model indexing based on two-dimensional (2-D) views, which we call adaptive views clustering (AVC). The goal of this method is to provide an ``optimal'' selection of 2-D views from a 3-D model, and a probabilistic Bayesian method for 3-D-model retrieval from these views. The characteristic view selection algorithm is based on an adaptive clustering algorithm and uses statistical model distribution scores to select the optimal number of views. Starting from the fact that all views do not have equal importance, we also introduce a novel Bayesian approach to improve the retrieval. Finally, we present our results and compare our method to some state-of-the-art 3-D retrieval descriptors on the Princeton 3-D Shape Benchmark database and a 3-D-CAD-models database supplied by the car manufacturer Renault.
    BibTeX:
    @article{Ansary2007,
      author = {Ansary, Tarik Filali and Daoudi, Mohamed and Vandeborre, Jean-Philippe},
      title = {A Bayesian 3-D search engine using adaptive views clustering},
      journal = {IEEE TRANSACTIONS ON MULTIMEDIA},
      year = {2007},
      volume = {9},
      number = {1},
      pages = {78-88},
      doi = {{10.1109/TMM.2006.886359}}
    }
    
    Anselmo, M., Lash, K., Stieb, E. & Haver, K. Cystic fibrosis on the Internet: A survey of site adherence to AMA guidelines {2004} PEDIATRICS
    Vol. {114}({1}), pp. {100-103} 
    article  
    Abstract: Objectives. The Internet permits unprecedented and mostly unrestricted access to medical knowledge; however, concerns exist regarding viewer privacy, accountability of authorship, accuracy of information, and patient safety. To address these issues, the American Medical Association (AMA) has developed guidelines concerning web site content and visitor rights. Cystic fibrosis (CF) is the most common genetically inherited lethal disease in North America. Many Internet sites that provide information on CF have been developed, although adherence to validated guidelines for online health information is not required. The purpose of this study was to assess systematically web sites with content pertaining to CF for adherence to the published AMA guidelines. Methods. The search term ``cystic fibrosis'' was entered into a commonly used search engine (Google), and the first 100 eligible sites were reviewed. Each site was examined for adherence to the AMA Guidelines for Medical and Health Information Sites on the Internet using a series of adapted questions. There were 15 questions divided into the following main categories: 1) site structure and viewer privacy, 2) author accountability, 3) scientific citation, and 4) patient safety. The number of positives for each question was tabulated. Results. With respect to site structure, fewer than half (45 of the reviewed sites indicated a date of last revision. Only 11 (11 carried an explicit privacy policy. A responsible author or group was listed in only 43 (43 of 100 sites. Presented data regarding CF was supported by references, sources, or expert review in only 38 (38 of 100 sites. A medical disclaimer noting that information provided does not substitute for evaluation by a health care team was evident in only 37 (37 sites. Conclusions. The majority of easily accessible CF informational web sites do not adhere to guidelines published by the AMA. Patients and families who use the Internet as a CF information resource should examine the web sites carefully and be familiar with the guidelines established by the AMA. Personal information is not protected, and few sites provide explicit privacy guarantees. Finally, CF care teams should inquire about Internet use by patients and families and be prepared to discuss findings from the Internet to heighten patient safety and awareness.
    BibTeX:
    @article{Anselmo2004,
      author = {Anselmo, MA and Lash, KM and Stieb, ES and Haver, KE},
      title = {Cystic fibrosis on the Internet: A survey of site adherence to AMA guidelines},
      journal = {PEDIATRICS},
      year = {2004},
      volume = {114},
      number = {1},
      pages = {100-103}
    }
    
    Armellini, D. & von Fraunhofer, J. The shortened dental arch: A review of the literature {2004} JOURNAL OF PROSTHETIC DENTISTRY
    Vol. {92}({6}), pp. {531-535} 
    article DOI  
    Abstract: The functional demands of patients are highly variable and individual, requiring dental treatment to be tailored to the individual's needs and adaptive capability. The World Health Organization indicates that a functional, esthetic, natural dentition has at least 20 teeth, while the literature indicates that dental arches comprising the anterior and premolar regions meet the requirements of a functional dentition. The English-language peer-reviewed literature pertaining to the short dental arch (SDA) was identified through the Medline search engine covering the period between 1966 and the present and critically reviewed. This treatment option for the partially dentate patient may provide oral functionality, improved oral hygiene, comfort, and, possibly, reduced costs.
    BibTeX:
    @article{Armellini2004,
      author = {Armellini, D and von Fraunhofer, JA},
      title = {The shortened dental arch: A review of the literature},
      journal = {JOURNAL OF PROSTHETIC DENTISTRY},
      year = {2004},
      volume = {92},
      number = {6},
      pages = {531-535},
      doi = {{10.1016/j.prosdent.2004.08.013}}
    }
    
    Arthur, J., Thongboonkerd, V., Scherzer, J., Cai, J., Pierce, W. & Klein, J. Differential expression of proteins in renal cortex and medulla: A proteomic approach {2002} KIDNEY INTERNATIONAL
    Vol. {62}({4}), pp. {1314-1321} 
    article  
    Abstract: Background. Western blotting has previously been used to identify changes in protein expression in renal tissue. However, only a few proteins can be studied in each experiment by Western blot. We have used proteomic tools to construct protein maps of rat kidney cortex and medulla. Methods. Expression of proteins was determined by silver stain after two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Protein spots were excised and digested with trypsin. Peptide masses were identified by MALDI-TOF mass spectrometry. The Mascot search engine was used to analyze the peptide masses and identify the proteins. Results. Seventy-two proteins were identified (54 unique proteins) out of approximately 1000 spots visualized on each gel. Most of the spots were expressed both in cortex and medulla. Of the identified proteins, three were expressed only in medulla and one only in cortex. Nine proteins were expressed in both regions but to a greater extent in cortex and three proteins were expressed more in medulla. Differential expression was confirmed for three proteins by Western blot. Conclusions. A large group of proteins and their relative expression levels from cortical and medullary portions of rat kidneys were found. Sixteen proteins are differentially expressed. Proteomics can be used to identify differential expression of proteins in the kidney on a large scale. Proteomics should be useful to detect changes in renal protein expression in response to a large range of physiological and pathophysiological stimuli.
    BibTeX:
    @article{Arthur2002,
      author = {Arthur, JM and Thongboonkerd, V and Scherzer, JA and Cai, J and Pierce, WM and Klein, JB},
      title = {Differential expression of proteins in renal cortex and medulla: A proteomic approach},
      journal = {KIDNEY INTERNATIONAL},
      year = {2002},
      volume = {62},
      number = {4},
      pages = {1314-1321}
    }
    
    ASHRAFIUON, H. DESIGN OPTIMIZATION OF AIRCRAFT ENGINE-MOUNT SYSTEMS {1993} JOURNAL OF VIBRATION AND ACOUSTICS-TRANSACTIONS OF THE ASME
    Vol. {115}({4}), pp. {463-467} 
    article  
    Abstract: Design optimization of aircraft engine-mount systems for vibration isolation is presented. The engine is modeled as a rigid body connected to a flexible base representing the nacelle. The base (nacelle) is modeled with mass and stiffness matrices and structural damping using finite element modeling. The mounts are modeled as three-dimensional springs with hysteresis damping. The objective is to select the stiffness coefficients and orientation angles of the individual mounts in order to minimize the transmitted forces from the engine to the nacelle. Meanwhile, the mounts have to be stiff enough not to allow the engine deflection to exceed its limits under static and low frequency loadings. It is shown that with an optimal system the transmitted forces may be reduced significantly particularly when orientation angles are also treated as design variables. The optimization problems are solved using a constraint variable metric approach. The closed form derivatives of the engine vibrational amplitudes with respect to design variables are derived in order to determine the objective function gradients and consequently a more effective optimization search technique.
    BibTeX:
    @article{ASHRAFIUON1993,
      author = {ASHRAFIUON, H},
      title = {DESIGN OPTIMIZATION OF AIRCRAFT ENGINE-MOUNT SYSTEMS},
      journal = {JOURNAL OF VIBRATION AND ACOUSTICS-TRANSACTIONS OF THE ASME},
      year = {1993},
      volume = {115},
      number = {4},
      pages = {463-467}
    }
    
    Augustine, S. & Greene, C. Discovering how students search a library Web site: A usability case study {2002} COLLEGE & RESEARCH LIBRARIES
    Vol. {63}({4}), pp. {354-365} 
    article  
    Abstract: Have Internet search engines influenced the way students search library Web pages? The results of this usability study reveal that students consistently and frequently use the library Web site's internal search engine to find information rather than navigating through pages. If students are searching rather than navigating, library Web page designers must make metadata and powerful search engines priorities. The study also shows that students have difficulty interpreting library terminology, experience confusion discerning difference amongst library resources, and prefer to seek human assistance when encountering problems online. These findings imply that library Web sites have not alleviated some of the basic and long-range problems that have challenged librarians in the past.
    BibTeX:
    @article{Augustine2002,
      author = {Augustine, S and Greene, C},
      title = {Discovering how students search a library Web site: A usability case study},
      journal = {COLLEGE & RESEARCH LIBRARIES},
      year = {2002},
      volume = {63},
      number = {4},
      pages = {354-365}
    }
    
    Avrahami, T., Yau, L., Si, L. & Callan, J. The FedLemur project: Federated search in the real world {2006} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {57}({3}), pp. {347-358} 
    article DOI  
    Abstract: Federated search and distributed information retrieval systems provide a single user interface for searching multiple full-text search engines. They have been an active area of research for more than a decade, but in spite of their success as a research topic, they are still rare in operational environments. This article discusses a prototype federated search system developed for the U.S. government's FedStats Web portal, and the issues addressed in adapting research solutions to this operational environment. A series of experiments explore how well prior research results, parameter settings, and heuristics apply in the FedStats environment. The article concludes with a set of lessons learned from this technology transfer effort, including observations about search engine quality in the ``real world.''
    BibTeX:
    @article{Avrahami2006,
      author = {Avrahami, TT and Yau, L and Si, L and Callan, J},
      title = {The FedLemur project: Federated search in the real world},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2006},
      volume = {57},
      number = {3},
      pages = {347-358},
      doi = {{10.1002/asi.20283}}
    }
    
    Bach, J., Fuller, C., Gupta, A., Hampapur, A., Horowitz, B., Humphrey, R., Jain, R. & Shu, C. The Virage image search engine: An open framework for image management {1996}
    Vol. {2670}STORAGE AND RETRIEVAL FOR STILL IMAGE AND VIDEO DATABASES IV, pp. {76-87} 
    inproceedings  
    BibTeX:
    @inproceedings{Bach1996,
      author = {Bach, JR and Fuller, C and Gupta, A and Hampapur, A and Horowitz, B and Humphrey, R and Jain, R and Shu, CF},
      title = {The Virage image search engine: An open framework for image management},
      booktitle = {STORAGE AND RETRIEVAL FOR STILL IMAGE AND VIDEO DATABASES IV},
      year = {1996},
      volume = {2670},
      pages = {76-87},
      note = {Conference on Storage and Retrieval for Still Image and Video Databases IV, SAN JOSE, CA, FEB 01-02, 1996}
    }
    
    BADDELEY, A. A THEORY OF REHABILITATION WITHOUT A MODEL OF LEARNING IS A VEHICLE WITHOUT AN ENGINE - A COMMENT {1993} NEUROPSYCHOLOGICAL REHABILITATION
    Vol. {3}({3}), pp. {235-244} 
    article  
    Abstract: While the search for a theory of rehabilitation by Caramazza and Hillis is welcomed, the model they propose is criticised on the grounds that it offers little more than a recommendation that we should wait until rehabilitation has occurred, and then attempt to understand it. The theme of this comment is to propose that it is necessary not only to understand the systems being treated, but also to have a model of how they can be changed by experience. Examples are given of ways in which recent developments in the cognitive neuropsychology of learning and memory may contribute to improved rehabilitation methods. It is suggested that an adequate theory of rehabilitation must combine a knowledge of the systems undergoing treatment with an understanding of how the principles of learning may be applied to their modification.
    BibTeX:
    @article{BADDELEY1993,
      author = {BADDELEY, A},
      title = {A THEORY OF REHABILITATION WITHOUT A MODEL OF LEARNING IS A VEHICLE WITHOUT AN ENGINE - A COMMENT},
      journal = {NEUROPSYCHOLOGICAL REHABILITATION},
      year = {1993},
      volume = {3},
      number = {3},
      pages = {235-244}
    }
    
    BaezaYates, R., Hurtado, C. & Mendoza, M. Query recommendation using query logs in search engines {2004}
    Vol. {3268}CURRENT TRENDS IN DATABASE TECHNOLOGY - EDBT 2004 WORKSHOPS, PROCEEDINGS, pp. {588-596} 
    inproceedings  
    Abstract: In this paper we propose a method that, given a query submitted to a search engine, suggests a list of related queries. The related queries are based in previously issued queries, and can be issued by the user to the search engine to tune or redirect the search process. The method proposed is based on a query clustering process in which groups of semantically similar queries are identified. The clustering process uses the content of historical preferences of users registered in the query log of the search engine. The method not only discovers the related queries, but also ranks them according to a relevance criterion. Finally, we show with experiments over the query log of a search engine the effectiveness of the method.
    BibTeX:
    @inproceedings{BaezaYates2004,
      author = {BaezaYates, R and Hurtado, C and Mendoza, M},
      title = {Query recommendation using query logs in search engines},
      booktitle = {CURRENT TRENDS IN DATABASE TECHNOLOGY - EDBT 2004 WORKSHOPS, PROCEEDINGS},
      year = {2004},
      volume = {3268},
      pages = {588-596},
      note = {9th Internatioal Conference on Extending Database Technology (EDBT 2004), Iraklion, GREECE, MAR 14-18, 2004}
    }
    
    BaezaYates, R., Hurtado, C. & Mendoza, M. Query clustering for boosting web page ranking {2004}
    Vol. {3034}ADVANCES IN WEB INTELLIGENCE, PROCEEDINGS, pp. {164-175} 
    inproceedings  
    Abstract: Over the past few years, there has been a great deal of research on the use of content and links of Web pages to improve the quality of Web page rankings returned by search engines. However, few formal approaches have considered the use of search engine logs to improve the rankings. In this paper we propose a ranking algorithm that uses the logs of search engines to boost their retrieval quality. The relevance of Web pages is estimated using the historical preferences of users that appear in the logs. The algorithm is based on a clustering process in which groups of semantically similar queries are identified. The method proposed is simple, has low computational cost, and we show with experiments that achieves good results.
    BibTeX:
    @inproceedings{BaezaYates2004a,
      author = {BaezaYates, R and Hurtado, C and Mendoza, M},
      title = {Query clustering for boosting web page ranking},
      booktitle = {ADVANCES IN WEB INTELLIGENCE, PROCEEDINGS},
      year = {2004},
      volume = {3034},
      pages = {164-175},
      note = {2nd International Altantic Web Intelligence Conference (AWIC 2004), Cancun, MEXICO, MAY 16-19, 2004}
    }
    
    Baggerman, G., Liu, F., Wets, G. & Schoofs, L. Bioinformatic analysis of peptide precursor proteins {2005}
    Vol. {1040}TRENDS IN COMPARATIVE ENDOCRINOLOGY AND NEUROBIOLOGY, pp. {59-65} 
    inproceedings DOI  
    Abstract: Neuropeptides are among the most important signal molecules in animals. Traditional identification of peptide hormones through peptide purification is a tedious and time-consuming process. With the advent of the genome sequencing projects, putative peptide precursor can be mined from the genome. However, because bioactive peptides are usually quite short in length and because the active core of a peptide is often limited to only a few amino acids, using the BLAST search engine to identify neuropeptide precursors in the genome is difficult and sometimes impossible. To overcome these shortcomings, we subject the entire set of all known Drosophila melanogaster peptide precursor sequences to motif-finding algorithms in search of a motif that is common for all prepropeptides and that could be used in the search for new peptide precursors.
    BibTeX:
    @inproceedings{Baggerman2005,
      author = {Baggerman, G and Liu, F and Wets, G and Schoofs, L},
      title = {Bioinformatic analysis of peptide precursor proteins},
      booktitle = {TRENDS IN COMPARATIVE ENDOCRINOLOGY AND NEUROBIOLOGY},
      year = {2005},
      volume = {1040},
      pages = {59-65},
      note = {Conference on Trends in Comparative Endocrinology and Neurobiology, Uppsala, SWEDEN, AUG 24-28, 2004},
      doi = {{10.1196/annals.1327.006}}
    }
    
    Balota, D.A., Yap, M.J., Cortese, M.J., Hutchison, K.A., Kessler, B., Loftis, B., Neely, J.H., Nelson, D.L., Simpson, G.B. & Treiman, R. The English Lexicon Project {2007} BEHAVIOR RESEARCH METHODS
    Vol. {39}({3}), pp. {445-459} 
    article  
    Abstract: The English Lexicon Project is a multiuniversity effort to provide a standardized behavioral and descriptive data set for 40,481 words and 40,481 nonwords. It is available via the Internet at elexicon.wustl.edu. Data from 816 participants across six universities were collected in a lexical decision task (approximately 3400 responses per participant), and data from 444 participants were collected in a speeded naming task (approximately 2500 responses per participant). The present paper describes the motivation for this project, the methods used to collect the data, and the search engine that affords access to the behavioral measures and descriptive lexical statistics for these stimuli.
    BibTeX:
    @article{Balota2007,
      author = {Balota, David A. and Yap, Melvin J. and Cortese, Michael J. and Hutchison, Keith A. and Kessler, Brett and Loftis, Bjorn and Neely, James H. and Nelson, Douglas L. and Simpson, Greg B. and Treiman, Rebecca},
      title = {The English Lexicon Project},
      journal = {BEHAVIOR RESEARCH METHODS},
      year = {2007},
      volume = {39},
      number = {3},
      pages = {445-459}
    }
    
    Bar-Ilan, J. Informetrics at the beginning of the 21st century - A review {2008} JOURNAL OF INFORMETRICS
    Vol. {2}({1}), pp. {1-52} 
    article DOI  
    Abstract: This paper reviews developments in informetrics between 2000 and 2006. At the beginning of the 21st century we witness considerable growth in webometrics, mapping and visualization and open access. A new topic is comparison between citation databases, as a result of the introduction of two new citation databases Scopus and Google Scholar. There is renewed interest in indicators as a result of the introduction of the h-index. Traditional topics like citation analysis and informetric theory also continue to develop. The impact factor debate, especially outside the informetric literature continues to thrive. Ranked lists (of journal, highly cited papers or of educational institutions) are of great public interest. (C) 2007 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Bar-Ilan2008,
      author = {Bar-Ilan, Judit},
      title = {Informetrics at the beginning of the 21st century - A review},
      journal = {JOURNAL OF INFORMETRICS},
      year = {2008},
      volume = {2},
      number = {1},
      pages = {1-52},
      doi = {{10.1016/j.joi.2007.11.001}}
    }
    
    Bar-Ilan, J. Comparing rankings of search results on the Web {2005} INFORMATION PROCESSING & MANAGEMENT
    Vol. {41}({6}), pp. {1511-1519} 
    article DOI  
    Abstract: The Web has become an information source for professional data gathering. Because of the vast amounts of information on almost all topics, one cannot systematically go over the whole set of results, and therefore must rely on the ordering of the results by the search engine. It is well known that search engines on the Web have low overlap in terms of coverage. In this study we measure how similar are the rankings of search engines on the overlapping results. We compare rankings of results for identical queries retrieved from several search engines. The method is based only on the set of URLs that appear in the answer sets of the engines being compared. For comparing the similarity of rankings of two search engines, the Spearman correlation coefficient is computed. When comparing more than two sets Kendall's W is used. These are well-known measures and the statistical significance of the results can be computed. The methods are demonstrated on a set of 15 queries that were submitted to four large Web search engines. The findings indicate that the large public search engines on the Web employ considerably different ranking algorithms. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Bar-Ilan2005,
      author = {Bar-Ilan, J},
      title = {Comparing rankings of search results on the Web},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2005},
      volume = {41},
      number = {6},
      pages = {1511-1519},
      doi = {{10.1016/j.ipm.2005.03.008}}
    }
    
    Bar-Ilan, J. Methods for measuring search engine performance over time {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({4}), pp. {308-319} 
    article DOI  
    Abstract: This study introduces methods for evaluating search engine performance over a time period. Several measures are defined, which as a whole describe search engine functionality over time. The necessary setup for such studies is described, and the use of these measures is illustrated through a specific example. The set of measures introduced here may serve as a guideline for the search engines for testing and improving their functionality. We recommend setting up a standard suite of measures for evaluating search engine performance.
    BibTeX:
    @article{Bar-Ilan2002,
      author = {Bar-Ilan, J},
      title = {Methods for measuring search engine performance over time},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {4},
      pages = {308-319},
      doi = {{10.1002/asi.10047}}
    }
    
    Bar-Ilan, J. On the overlap, the precision and estimated recall of search engines, a case study of the query ``Erdos'' {1998} SCIENTOMETRICS
    Vol. {42}({2}), pp. {207-228} 
    article  
    Abstract: In this paper we investigate the retrieval capabilities of six Internet search engines on a simple query. As a case study the query ``Erdos'' was chosen. Paul Erdos was a world famous Hungarian mathematician, who passed away in September 1996. Existing work on search engine evaluation considers only the first ten or twenty results returned by the search engine, therefore approximation of the recalls of the engines has not been considered so far. In this work we retrieved all 6681 documents that the search engines pointed at and thoroughly examined them. Thus we could calculate the precision of the whole retrieval process, study the overlap between the results of the engines and give an estimate on the recall of the searches. The precision of the engines is high, recall is very low and the overlap is minimal.
    BibTeX:
    @article{Bar-Ilan1998,
      author = {Bar-Ilan, J},
      title = {On the overlap, the precision and estimated recall of search engines, a case study of the query ``Erdos''},
      journal = {SCIENTOMETRICS},
      year = {1998},
      volume = {42},
      number = {2},
      pages = {207-228}
    }
    
    Bar-Ilan, J., Mat-Hassan, M. & Levene, M. Methods for comparing rankings of search engine results {2006} COMPUTER NETWORKS
    Vol. {50}({10, Sp. Iss. SI}), pp. {1448-1463} 
    article DOI  
    Abstract: In this paper we present a number of measures that compare rankings of search engine results. We apply these measures to five queries that were monitored daily for two periods of 14 or 21 days each. Rankings of the different search engines (Google, Yahoo! and Teoma for text searches and Google, Yahoo! and Picsearch for image searches) are compared on a daily basis, in addition to longitudinal comparisons of the same engine for the same query over time. The results and rankings of the two periods are compared as well. (c) 2005 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Bar-Ilan2006,
      author = {Bar-Ilan, J and Mat-Hassan, M and Levene, M},
      title = {Methods for comparing rankings of search engine results},
      journal = {COMPUTER NETWORKS},
      year = {2006},
      volume = {50},
      number = {10, Sp. Iss. SI},
      pages = {1448-1463},
      doi = {{10.1016/j.comnet.2005.10.020}}
    }
    
    Batzias, F. & Marcoulaki, E. Restructuring the keywords interface to enhance CAPE knowledge acquisition via an intelligent agent {2002}
    Vol. {10}EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING - 12, pp. {829-834} 
    inproceedings  
    Abstract: This work proposes an improved KeyWord Interface (KWI) to enhance the efficiency of information retrieval when using an advanced search engine, as an intelligent agent. This can be achieved by restructuring the KWI into a new hierarchical structure based on an n domains by 3 levels arrangement of keywords (nx3 KWI), forming a loose/adaptive semantic network. The hierarchical levels used in the suggested implementation are set of species, logical category, and holistic entity. As an illustration, the method is applied to an example of literature survey concerning a well-documented process engineering field. The results of the proposed technology are compared with the outcome of general-purpose search-engines built in common academic publication databases. The comparison reveals the advantage of intelligent searching in creating a local base according to the orders/interests of the researcher.
    BibTeX:
    @inproceedings{Batzias2002,
      author = {Batzias, FA and Marcoulaki, EC},
      title = {Restructuring the keywords interface to enhance CAPE knowledge acquisition via an intelligent agent},
      booktitle = {EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING - 12},
      year = {2002},
      volume = {10},
      pages = {829-834},
      note = {12th European Symposium on Computer Aided Process Engineering (ESCAPE-12), THE HAGUE, NETHERLANDS, MAY 20-29, 2002}
    }
    
    Baujard, O., Baujard, V., Aurel, S., Boyer, C. & Appel, R. MARVIN, multi-agent softbot to retrieve multilingual medical information on the Web {1998} MEDICAL INFORMATICS
    Vol. {23}({3}), pp. {187-191} 
    article  
    Abstract: The World-Wide Web is an unstructured, multimedia and multilingual information network. While most efforts have addressed the structuring issue, very few attempts have been proposed to provide support for mutilingual information retrieval. Pet, medical information is now available all over the world. The MARVIN (Multi-Agent Retrieval Vagabond on Information Network) softbot and its associated medical search engine MedHunt (Medical Hunter) are a solution for helping people, who only understand a few languages, to access multilingual information.
    BibTeX:
    @article{Baujard1998,
      author = {Baujard, O and Baujard, V and Aurel, S and Boyer, C and Appel, RD},
      title = {MARVIN, multi-agent softbot to retrieve multilingual medical information on the Web},
      journal = {MEDICAL INFORMATICS},
      year = {1998},
      volume = {23},
      number = {3},
      pages = {187-191}
    }
    
    Berland, G., Elliott, M., Morales, L., Algazy, J., Kravitz, R., Broder, M., Kanouse, D., Munoz, J., Puyol, J., Lara, M., Watkins, K., Yang, H. & McGlynn, E. Health information on the Internet - Accessibility, quality, and readability in English and Spanish {2001} JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
    Vol. {285}({20}), pp. {2612-2621} 
    article  
    Abstract: Context Despite the substantial amount of health-related information available on the Internet, little is known about the accessibility, quality, and reading grade level of that health information. Objective To evaluate health information on breast cancer, depression, obesity, and childhood asthma available through English- and Spanish-language search engines and Web sites. Design and Setting Three unique studies were performed from July 2000 through December 2000, Accessibility of 14 search engines was assessed using a structured search experiment. Quality of 25 health Web sites and content provided by 1 search engine was evaluated by 34 physicians using structured implicit review (interrater reliability >0.90). The reading grade level of text selected for structured implicit review was established using the Fry Readability Graph method. Main Outcome Measures For the accessibility study, proportion of links leading to relevant content; for quality, coverage and accuracy of key clinical elements; and grade level reading formulas. Results Less than one quarter of the search engine's first pages of links led to relevant content (20% of English and 12% of Spanish). On average, 45% of the clinical elements on English- and 22% on Spanish-language Web sites were more than minimally covered and completely accurate and 24% of the clinical elements on English- and 53% on Spanish-language Web sites were not covered at all. All English and 86% of Spanish Web sites required high school level or greater reading ability. Conclusion Accessing health information using search engines and simple search terms is not efficient. Coverage of key information on English- and Spanish-language Web sites is poor and inconsistent, although the accuracy of the information provided is generally good. High reading levels are required to comprehend Web-based health information.
    BibTeX:
    @article{Berland2001,
      author = {Berland, GK and Elliott, MN and Morales, LS and Algazy, JI and Kravitz, RL and Broder, MS and Kanouse, DE and Munoz, JA and Puyol, JA and Lara, M and Watkins, KE and Yang, H and McGlynn, EA},
      title = {Health information on the Internet - Accessibility, quality, and readability in English and Spanish},
      journal = {JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION},
      year = {2001},
      volume = {285},
      number = {20},
      pages = {2612-2621}
    }
    
    Bernstam, E.V., Waiji, M.F., Sagaram, S., Sagaram, D., Johnson, C.W. & Meric-Bernstam, F. Commonly cited website quality criteria are not effective at identifying inaccurate online information about breast cancer {2008} CANCER
    Vol. {112}({6}), pp. {1206-1213} 
    article DOI  
    Abstract: BACKGROUND. Consumers increasingly consult the Internet for breast cancer information. Concerned about accuracy, multiple organizations developed quality criteria for online content. However, the effectiveness of these tools is unknown. The authors determined whether existing quality criteria can identify inaccurate breast cancer information online. METHODS. The authors identified 343 unique webpages by using 15 breast cancer-related queries on 5 popular web search-engines. Each page was assessed for 15 quality criteria and 3 website characteristics, link type (sponsored or not), search engine used to find the page, and domain extension. Two clinician-reviewers independently assessed accuracy and topics covered. The authors then determined whether quality criteria, website characteristics, and topics were associated with the presence of inaccurate statements. RESULTS. The authors found 41 inaccurate statements on 18 webpages (5.2. No quality criteria or website characteristic, singly or in combination, reliably identified inaccurate information. The total number of quality criteria met by a website accounted for a small fraction of the variability in the presence of inaccuracies (point biserial r = -0.128; df = 341; P =.018; r(2) = 0.016). However, webpages containing information on complementary and alternative medicine (CAM) were significantly more likely to contain inaccuracies compared with pages without CAM information (odds ratio [OR], 15.6; P <.001). CONCLUSIONS. Most breast cancer information that consumers are likely to encounter online is accurate. However, commonly cited quality criteria do not identify inaccurate information. Webpages that contain information about CAM are relatively likely to contain inaccurate statements. Consumers searching for health information online should still consult a clinician before taking action.
    BibTeX:
    @article{Bernstam2008,
      author = {Bernstam, Elmer V. and Waiji, Muhammad F. and Sagaram, Smitha and Sagaram, Deepak and Johnson, Craig W. and Meric-Bernstam, Funda},
      title = {Commonly cited website quality criteria are not effective at identifying inaccurate online information about breast cancer},
      journal = {CANCER},
      year = {2008},
      volume = {112},
      number = {6},
      pages = {1206-1213},
      doi = {{10.1002/cncr.23308}}
    }
    
    Bessell, T., Silagy, C., Anderson, J., Hiller, J. & Sansom, L. Quality of global e-pharmacies: can we safeguard consumers? {2002} EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY
    Vol. {58}({9}), pp. {567-572} 
    article DOI  
    Abstract: Objective: E-pharmacies are web sites selling prescription-only medicines and other products including non-prescription and complementary medicines to consumers via the internet. This study aims to evaluate the quality of global e-pharmacies, discuss whether e-pharmacies support the safe and appropriate use of medicines, and consider how we can protect consumers in the future. Methods: A survey of public information published on global e-pharmacy web sites was conducted between July and September 2001. We used a meta-search engine, Copernic, and the search terms of `online' or `internet', and `pharmacy', `pharmacies' and `medicines' to identify a sampling frame of global e-pharmacies. We surveyed all web sites in the sampling frame except those under construction or only offering electronic refills, members-only and non-English web sites. Survey data included country of origin, range of medicines sold, prescription requirements, availability of online medical consultations and pharmacists' advice, quality accreditation seals, policies and advertisements. Results: E-pharmacies operated in at least 13 countries; however, the country of origin could not be identified for 22 web sites. Twenty web sites (19 appeared to supply prescription-only medicines with no prescription required. Only 12% of e-pharmacies displayed quality accreditation seals. We observed information published on e-pharmacy web sites that potentially undermines the safe and appropriate use of medicines. Conclusion: Safeguarding consumers and ensuring the quality of web sites that sell medicines across state and national boundaries is both complex and difficult. Strategies to improve the quality of e-pharmacies include independent third-party regulation of providers, evaluation and enforcement of sanctions in cases of dissemination of fraudulent or harmful information and practices, self-regulation and consumer education. The development of internet regulatory technologies themselves and the resolution of jurisdictional issues offer future solutions but international co-operation is vital.
    BibTeX:
    @article{Bessell2002,
      author = {Bessell, TL and Silagy, CA and Anderson, JN and Hiller, JE and Sansom, LN},
      title = {Quality of global e-pharmacies: can we safeguard consumers?},
      journal = {EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY},
      year = {2002},
      volume = {58},
      number = {9},
      pages = {567-572},
      doi = {{10.1007/s00228-002-0519-5}}
    }
    
    Bhaduri, A., Pugalenthi, G. & Sowdhamini, R. PASS2: an automated database of protein alignments organised as structural superfamilies {2004} BMC BIOINFORMATICS
    Vol. {5} 
    article  
    Abstract: Background: The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. Description: An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. Conclusions: The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/similar tofaculty/mini/campass/pass2.html.
    BibTeX:
    @article{Bhaduri2004,
      author = {Bhaduri, A and Pugalenthi, G and Sowdhamini, R},
      title = {PASS2: an automated database of protein alignments organised as structural superfamilies},
      journal = {BMC BIOINFORMATICS},
      year = {2004},
      volume = {5}
    }
    
    Bharat, K. & Broder, A. A technique for measuring the relative size and overlap of public Web search engines {1998} COMPUTER NETWORKS AND ISDN SYSTEMS
    Vol. {30}({1-7}), pp. {379-388} 
    article  
    Abstract: Search engines are among the most useful and popular services on the Web. Users are eager to know how they compare. Which one has the largest coverage? Have they indexed the same portion of the Web? How many pages are out there? Although these questions have been debated in the popular and technical press, no objective evaluation methodology has been proposed and few clear answers have emerged. In this paper we describe a standardized, statistical way of measuring search engine coverage and overlap through random queries. Our technique does not require privileged access to any database. It can be implemented by third-party evaluators using only public query interfaces. We present results from our experiments showing size and overlap estimates for HotBot, AltaVista, Excite, and Infoseek as percentages of their total joint coverage in mid 1997 and in November 1997. Our method does not provide absolute values. However using data from other sources we estimate that as of November 1997 the number of pages indexed by HotBot, AltaVista, Excite, and Infoseek were respectively roughly 77M, 100M, 32M, and 17M and the joint total coverage was 160 million pages. We further conjecture that the size of the static, public Web as of November was over 200 million pages. The most startling finding is that the overlap is very small: less than 1.4% of the total coverage, or about 2.2 million pages were indexed by all four engines. (C) 1998 Published by Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Bharat1998,
      author = {Bharat, K and Broder, A},
      title = {A technique for measuring the relative size and overlap of public Web search engines},
      journal = {COMPUTER NETWORKS AND ISDN SYSTEMS},
      year = {1998},
      volume = {30},
      number = {1-7},
      pages = {379-388},
      note = {7th International World Wide Web Conference, BRISBANE, AUSTRALIA, APR 14-18, 1998}
    }
    
    Bilal, D. Children's use of the yahooligans! - Web search engine. III. Cognitive and physical behaviors on fully self-generated search tasks {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({13}), pp. {1170-1183} 
    article DOI  
    Abstract: This article presents the third part of a research project that investigated the information-seeking behavior and success of seventh-grade science children in using the Yahooligans! Web search engine/directory. In parts 1 and 2, children performed fully assigned tasks to pursue in the engine. In the present study, children generated their tasks fully. Children's information seeking was captured from the cognitive, physical, and affective perspectives using both quantitative and qualitative inquiry methods. Their information-seeking behavior and success on the fully self-generated task was compared to the behavior and success they exhibited in the two fully assigned tasks. Children were more successful on the fully self-generated task than the two fully assigned tasks. Children preferred the fully self-generated task to the two fully assigned tasks due to their ability to find the information sought and satisfaction with search results rather than the nature of the task in itself (i.e., self-generated aspect). Children were more successful when they browsed than when they searched by keyword on the three tasks. Yahooligans! design, especially its poor keyword searching, contributed to the breakdowns children experienced. Implications for system design improvement and Web training are discussed.
    BibTeX:
    @article{Bilal2002,
      author = {Bilal, D},
      title = {Children's use of the yahooligans! - Web search engine. III. Cognitive and physical behaviors on fully self-generated search tasks},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {13},
      pages = {1170-1183},
      doi = {{10.1002/asi.10145}}
    }
    
    Bilal, D. Children's use of the Yahooligans! Web search engine: II. Cognitive and physical behaviors on research tasks {2001} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {52}({2}), pp. {118-136} 
    article  
    Abstract: This study reports the results of Part II of a research project that investigated the cognitive and physical behaviors of middle school students in using Yahooligans! Seventeen students in the seventh grade searched Yahooligans! to locate relevant information for an assigned research task. Sixty-nine percent partially succeeded, while 31% failed. Children had difficulty completing the task mainly because they lacked adequate level of research skills and approached the task by seeking specific answers. Children's cognitive and physical behaviors varied by success levels. Similarities and differences in children's cognitive and physical behaviors were found between the research task and the fact-based task they performed in the previous study. The present study considers the impact of prior experience in using the Web, domain knowledge, topic knowledge, and reading ability on children's success. It reports the overall patterns of children's behaviors, including searching and browsing moves, backtracking and looping moves, and navigational styles, as well as the time taken to complete the research task. Children expressed their information needs and provided recommendations for improving the interface design of Yahooligans! Implications for formal Web training and system design improvements are discussed.
    BibTeX:
    @article{Bilal2001,
      author = {Bilal, D},
      title = {Children's use of the Yahooligans! Web search engine: II. Cognitive and physical behaviors on research tasks},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2001},
      volume = {52},
      number = {2},
      pages = {118-136}
    }
    
    Bilal, D. Children's use of the Yahooligans! Web search engine: I. Cognitive, physical, and affective behaviors on fact-based search tasks {2000} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE
    Vol. {51}({7}), pp. {646-665} 
    article  
    Abstract: This study reports on the first part of a research project that investigated children's cognitive, affective, and physical behaviors as they use the Yahooligans! search engine to find information on a specific search task. Twenty-two seventh-grade science children from a middle school located in Knoxville, Tennessee participated in the project. Their cognitive and physical behaviors were captured using Lotus ScreenCam, a Windows-based software package that captures and replays activities recorded in Web browsers, such as Netscape. Their affective states were captured via a one-on-one exit interview, A new measure called ``Web Traversal Measure'' was developed to measure children's ``weighted'' traversal effectiveness and efficiency scores, as well as their quality moves in Yahooligans! Children's prior experience in using the Internet/Web and their knowledge of the Yahooligans! interface were gathered via a questionnaire. The findings provided insights into children's behaviors and success, as their weighted traversal effectiveness and efficiency scores, as well as quality moves. Implications for user training and system design are discussed.
    BibTeX:
    @article{Bilal2000,
      author = {Bilal, D},
      title = {Children's use of the Yahooligans! Web search engine: I. Cognitive, physical, and affective behaviors on fact-based search tasks},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE},
      year = {2000},
      volume = {51},
      number = {7},
      pages = {646-665}
    }
    
    Bilal, D. Children's search processes in using World Wide Web search engines: An exploratory study {1998} PROCEEDINGS OF THE ASIS ANNUAL MEETING
    Vol. {35}, pp. {45-53} 
    article  
    Abstract: This paper reports the results of part one of a multi-faceted research project that is investigating children's information seeking behavior in using World Wide Web search engines, with reference to Yahooligans. It examines children's search processes, patterns of exploration of returned results, success in finding and retrieving relevant information, persistence in finding information, and the kind of errors that occur during searching. It explores children's information seeking behavior from both cognitive and affective domains. It makes implications for end-user training and search engine design and development.
    BibTeX:
    @article{Bilal1998,
      author = {Bilal, D},
      title = {Children's search processes in using World Wide Web search engines: An exploratory study},
      journal = {PROCEEDINGS OF THE ASIS ANNUAL MEETING},
      year = {1998},
      volume = {35},
      pages = {45-53},
      note = {61st ASIS Annual Meeting, PITTSBURGH, PENNSYLVANIA, OCT 24-29, 1998}
    }
    
    Bilal, D. & Kirby, J. Differences and similarities in information seeking: children and adults as Web users {2002} INFORMATION PROCESSING & MANAGEMENT
    Vol. {38}({5, Sp. Iss. SI}), pp. {649-670} 
    article  
    Abstract: This study examined the success and information seeking behaviors of seventh-grade science students and graduate students in information science in using Yahooligans! Web search engine/directory. It investigated these users cognitive, affective, and physical behaviors as they sought the answer for a fact-finding task. It analyzed and compared the overall patterns of children's and graduate students' Web activities, including searching moves, browsing moves, backtracking moves, looping moves, screen scrolling, target location and deviation moves, and the time they took to complete the task. The authors applied Bilal's Web Traversal Measure to quantify these uscrs effectiveness, efficiency, and quality of moves they made. Results were based on 14 children's Web sessions and nine graduate students' sessions. Both groups' Web activities were captured online using Lotus ScreenCam, a software package that records and replays online activities in Web browsers. Children's affective states were captured via exit interviews. Graduate students' affective states were extracted from the journal writings they kept during the traversal process. The study findings reveal that 89% of the graduate students found the correct answer to the search task as opposed to 50 of the children. Based on the Measure, graduate students' weighted effectiveness, efficiency, and quality of the Web moves they made were much higher than those of the children. Regardless of success and weighted scores, however, similarities and differences in information seeking were found between the two groups. Yahooligans! poor structure of keyword searching was a major factor that contributed to the ``breakdowns'' children and graduate students experienced. Unlike children, graduate students were able to recover from ``breakdowns'' quickly and effectively. Three main factors influenced these users' performance: ability to recover from ``breakdowns'', navigational style, and focus on task. Children and graduate students made recommendations for improving Yahooligans! interface design. Implications for Web user training and system design improvements are made. (C) 2002 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Bilal2002a,
      author = {Bilal, D and Kirby, J},
      title = {Differences and similarities in information seeking: children and adults as Web users},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2002},
      volume = {38},
      number = {5, Sp. Iss. SI},
      pages = {649-670}
    }
    
    Billoud, B., Kontic, M. & Viari, A. Palingol: A declarative programming language to describe nucleic acids' secondary structures and to sequence databases {1996} NUCLEIC ACIDS RESEARCH
    Vol. {24}({8}), pp. {1395-1403} 
    article  
    Abstract: At the RNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus ion `what to search for' while the language engine takes care of `how to look for it'. Therefore, it becomes simpler to write a scanning grogram and the structural constraints that define the required structure are more clearly identified.
    BibTeX:
    @article{Billoud1996,
      author = {Billoud, B and Kontic, M and Viari, A},
      title = {Palingol: A declarative programming language to describe nucleic acids' secondary structures and to sequence databases},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {1996},
      volume = {24},
      number = {8},
      pages = {1395-1403}
    }
    
    Birru, M., Monaco, V., Charles, L., Drew, H., Njie, V., Bierria, T., Detlefsen, E. & Steinman, R. Internet usage by low-literacy adults seeking health information: An observational analysis {2004} JOURNAL OF MEDICAL INTERNET RESEARCH
    Vol. {6}({3}), pp. {66-76} 
    article  
    Abstract: Background: Adults with low literacy may encounter informational obstacles on the Internet when searching for health information, in part because most health Web sites require at least a high-school reading proficiency for optimal access. Objective: The purpose of this study was to 1) determine how low-literacy adults independently access and evaluate health information on the Internet, 2) identify challenges and areas of proficiency in the Internet-searching skills of low-literacy adults. Methods: Subjects (n=8) were enrolled in a reading assistance program at Bidwell Training Center in Pittsburgh, PA, and read at a 3rd to 8th grade level. Subjects conducted self-directed Internet searches for designated health topics while utilizing a think-aloud protocol. Subjects' keystrokes and comments were recorded using Camtasia Studio screen-capture software. The search terms used to find health information, the amount of time spent on each Web site, the number of Web sites accessed, the reading level of Web sites accessed, and the responses of subjects to questionnaires were assessed. Results: Subjects collectively answered 8 out of 24 questions correctly. Seven out of 8 subjects selected ``sponsored sites''-paid Web advertisements-over search engine-generated links when answering health questions. On average, subjects accessed health Web sites written at or above a 10th grade reading level. Standard methodologies used for measuring health literacy and for promoting subjects to verbalize responses to Web-site form and content had limited utility in this population. Conclusion: This study demonstrates that Web health information requires a reading level that prohibits optimal access by some low-literacy adults. These results highlight the low-literacy adult population as a potential audience for Web health information, and indicate some areas of difficulty that these individuals face when using the Internet and health Web sites to find information on specific health topics.
    BibTeX:
    @article{Birru2004,
      author = {Birru, MS and Monaco, VM and Charles, L and Drew, H and Njie, V and Bierria, T and Detlefsen, E and Steinman, RA},
      title = {Internet usage by low-literacy adults seeking health information: An observational analysis},
      journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
      year = {2004},
      volume = {6},
      number = {3},
      pages = {66-76}
    }
    
    Bjorneborn, L. & Ingwersen, P. Perspectives of webometrics {2001} SCIENTOMETRICS
    Vol. {50}({1}), pp. {65-82} 
    article  
    Abstract: Since the mid-1990s has emerged a new research field, webometrics, investigating the nature and properties of the Web drawing on modern informetric methodologies. The article attempts to point to selected areas of webometric research that demonstrate interesting progress and space for development as well as to some currently less promising areas. Recent investigations of search engine coverage and performance are reviewed as a frame for selected quality and content analyses. Problems with measuring Web Impact Factors (Web-IF) are discussed. Concluding the article. new directions of webometrics are outlined for performing knowledge discovery and issue tracking on the Web, partly based on bibliometric methodologies used in bibliographic and citation databases. In this framework graph theoretic approaches, including path analysis, transversal links, ``weak ties'' and ``small-world'' phenomena are integrated.
    BibTeX:
    @article{Bjorneborn2001,
      author = {Bjorneborn, L and Ingwersen, P},
      title = {Perspectives of webometrics},
      journal = {SCIENTOMETRICS},
      year = {2001},
      volume = {50},
      number = {1},
      pages = {65-82}
    }
    
    Black, P. & Penson, D. Prostate cancer on the Internet - Information or misinformation? {2006} JOURNAL OF UROLOGY
    Vol. {175}({5}), pp. {1836-1842} 
    article DOI  
    Abstract: Purpose: We assessed the quality of information available to patients on prostate cancer on the Internet. Materials and Methods: The search engine Webcrawler (R) was used with the search term ``prostate cancer'' to generate a list of 75 websites which were reviewed for currency, disclosure, attribution, interactivity and content. A rating tool was designed including 50 elements considered essential for a comprehensive review of prostate cancer, and each website was judged for degree of coverage and accuracy (each rated on a scale of 1 to 3) of information for each element. Results: Of the 75 sites 39 contained information about prostate cancer. Only 9 sites indicated a date of last update within 6 months. References were rarely given (in 5) and a disclaimer was provided on less than half of the sites (18). The sites covered a mean of 24 elements (range 6 to 43) with a mean coverage rating of 1.0 to 2.6 (1.8 overall). Of 943 elements covered on 39 sites, 94% were completely correct, 5% were mostly correct and 1% was mostly incorrect. Conclusions: The information on the Internet is of sufficient quality to aid in patient decision making. However, there are numerous shortcomings especially related to currency, disclosure and attribution. Degree of coverage is highly variable and there is a deficiency in balance of evidence found on many sites. The urologist needs to be aware of such shortcomings when counseling patients on prostate cancer.
    BibTeX:
    @article{Black2006,
      author = {Black, PC and Penson, DF},
      title = {Prostate cancer on the Internet - Information or misinformation?},
      journal = {JOURNAL OF UROLOGY},
      year = {2006},
      volume = {175},
      number = {5},
      pages = {1836-1842},
      doi = {{10.1016/S0022-5347(05)00996-1}}
    }
    
    Blanchard, D., Erblich, J., Montgomery, G. & Bovbjerg, D. Read all about it: The over-representation of breast cancer in popular magazines {2002} PREVENTIVE MEDICINE
    Vol. {35}({4}), pp. {343-348} 
    article DOI  
    Abstract: Background. While women are far more likely to develop and die from cardiovascular disease (CVD) than breast cancer, research has shown that they markedly overestimate their personal risks of breast cancer and underestimate their CVD risks. The source of this disparity is not yet known, although increased media attention to breast cancer relative to CVD has been suggested to play a role. The purpose of the present study was to provide a first critical test of this possibility. Two hypotheses were tested: (a) the number of breast cancer articles would be greater than the number of CVD articles; and (b) this disparity in coverage would increase over the years. Methods. A web-based search engine was used to quantify all breast cancer and cardiovascular disease articles (keyword search) in 73 popular magazines on a annual basis for a 10-year interval (1990-1999). Results. Consistent with study hypotheses, breast cancer articles outnumbered CVD articles, and this disparity widened over the years (P < 0.0001). This disparity was not limited to specific magazine categories (e.g., women's interest). Conclusions. Over-representation of breast cancer vis-a-vis CVD is pervasive in popular magazines. Future research should investigate how such disparities in the media may influence risk perceptions, adoption of preventive health behaviors, and compliance with screening guidelines. (C) 2002 American Health Foundation and Elsevier Science (USA).
    BibTeX:
    @article{Blanchard2002,
      author = {Blanchard, D and Erblich, J and Montgomery, GH and Bovbjerg, DH},
      title = {Read all about it: The over-representation of breast cancer in popular magazines},
      journal = {PREVENTIVE MEDICINE},
      year = {2002},
      volume = {35},
      number = {4},
      pages = {343-348},
      doi = {{10.1006/pmed.2002.1088}}
    }
    
    Bouyssie, D., de Peredo, A.G., Mouton, E., Albigot, R., Roussel, L., Ortega, N., Cayrol, C., Burlet-Schiltz, O., Girard, J.-P. & Monsarrat, B. Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses {2007} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {6}({9}), pp. {1621-1637} 
    article DOI  
    Abstract: Proteomics strategies based on nanoflow ( nano-) LCMS/ MS allow the identification of hundreds to thousands of proteins in complex mixtures. When combined with protein isotopic labeling, quantitative comparison of the proteome from different samples can be achieved using these approaches. However, bioinformatics analysis of the data remains a bottleneck in large scale quantitative proteomics studies. Here we present a new software named Mascot File Parsing and Quantification ( MFPaQ) that easily processes the results of the Mascot search engine and performs protein quantification in the case of isotopic labeling experiments using either the ICAT or SILAC ( stable isotope labeling with amino acids in cell culture) method. This new tool provides a convenient interface to retrieve Mascot protein lists; sort them according to Mascot scoring or to user- defined criteria based on the number, the score, and the rank of identified peptides; and to validate the results. Moreover the software extracts quantitative data from raw files obtained by nanoLC- MS/ MS, calculates peptide ratios, and generates a non- redundant list of proteins identified in a multisearch experiment with their calculated averaged and normalized ratio. Here we apply this software to the proteomics analysis of membrane proteins from primary human endothelial cells ( ECs), a cell type involved in many physiological and pathological processes including chronic inflammatory diseases such as rheumatoid arthritis. We analyzed the EC membrane proteome and set up methods for quantitative analysis of this proteome by ICAT labeling. EC microsomal proteins were fractionated and analyzed by nano- LC- MS/ MS, and database searches were performed with Mascot. Data validation and clustering of proteins were performed with MFPaQ, which allowed identification of more than 600 unique proteins. The software was also successfully used in a quantitative differential proteomics analysis of the EC membrane proteome after stimulation with a combination of proinflammatory mediators ( tumor necrosis factor- alpha, interferon- gamma, and lymphotoxin alpha/beta) that resulted in the identification of a full spectrum of EC membrane proteins regulated by inflammation.
    BibTeX:
    @article{Bouyssie2007,
      author = {Bouyssie, David and de Peredo, Anne Gonzalez and Mouton, Emmanuelle and Albigot, Renaud and Roussel, Lucie and Ortega, Nathalie and Cayrol, Corinne and Burlet-Schiltz, Odile and Girard, Jean-Philippe and Monsarrat, Bernard},
      title = {Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2007},
      volume = {6},
      number = {9},
      pages = {1621-1637},
      doi = {{10.1074/mcp.T600069-MCP200}}
    }
    
    BOWER, G., RICHSTONE, D., BOTHUN, G. & HECKMAN, T. A SEARCH FOR DEAD QUASARS AMONG NEARBY LUMINOUS GALAXIES .1. THE STELLAR KINEMATICS IN THE NUCLEI OF NGC-2613, NGC-4699, NGC-5746, AND NGC-7331 {1993} ASTROPHYSICAL JOURNAL
    Vol. {402}({1, Part 1}), pp. {76-94} 
    article  
    Abstract: present observations and analysis of the rotation velocities and velocity dispersions along the major and minor axes of the spiral galaxies NGC 2613, NGC 4699, NGC 5746, and NGC 7331. This work represents the initial results of a project to search for supermassive black holes in the nuclei of nearby galaxies with similar morphological types and luminosities as QSO host galaxies. We analyze the observed stellar kinematics using maximum entropy dynamical models that allow for the possibility of an anisotropic velocity distribution function. The models of each galaxy are compared to the observational data after projection onto the sky and convolution with the point-spread function. We find that for all four galaxies, models without central black holes and with constant M/L as a function or radius are able to fit the observational data. Thus, none of these galaxies shows particularly compelling evidence of harboring a approximately 10(9) M. black hole, the presumed central engine of a QSO. Dynamical models that include a central black hole with this mass are able to fit the observations of NGC 2613, NGC 4699, and NGC 5746 but do not fit the observations of NGC 7331. The dynamical models of all four galaxies that include the greatest central black hole mass consistent with the observations show velocity distribution functions that are significantly anisotropic inside radii of a few arcseconds.
    BibTeX:
    @article{BOWER1993,
      author = {BOWER, GA and RICHSTONE, DO and BOTHUN, GD and HECKMAN, TM},
      title = {A SEARCH FOR DEAD QUASARS AMONG NEARBY LUMINOUS GALAXIES .1. THE STELLAR KINEMATICS IN THE NUCLEI OF NGC-2613, NGC-4699, NGC-5746, AND NGC-7331},
      journal = {ASTROPHYSICAL JOURNAL},
      year = {1993},
      volume = {402},
      number = {1, Part 1},
      pages = {76-94}
    }
    
    Bradlow, E. & Schmittlein, D. The little engines that could: Modeling the performance of World Wide Web search engines {2000} MARKETING SCIENCE
    Vol. {19}({1}), pp. {43-62} 
    article  
    Abstract: This research examines the ability of six popular Web search engines, individually and collectively, to locate Web pages containing common marketing/management phrases. We propose and validate a model for search engine performance that is able to represent key patterns of coverage and overlap among the engines. The model enables us to estimate the typical additional benefit of using multiple search engines, depending on the particular set of engines being considered. It also provides an estimate of the number of relevant Web pages not found by any of the engines. For a typical marketing/management phrase we estimate that the ``best'' search engine locates about 50% of the pages, and all six engines together find about 90% of the total. The model is also used to examine how properties of a Web page and characteristics of a phrase affect the probability that a given search engine will find a given page. For example, we find that the number of Web page links increases the prospect that each of the six search engines will find it. Finally, we summarize the relationship between major structural characteristics of a search engine and its performance in locating relevant Web pages.
    BibTeX:
    @article{Bradlow2000,
      author = {Bradlow, ET and Schmittlein, DC},
      title = {The little engines that could: Modeling the performance of World Wide Web search engines},
      journal = {MARKETING SCIENCE},
      year = {2000},
      volume = {19},
      number = {1},
      pages = {43-62}
    }
    
    Brandon, M., Lott, M., Nguyen, K., Spolim, S., Navathe, S., Baldi, P. & Wallace, D. MITOMAP: a human mitochondrial genome database - 2004 update {2005} NUCLEIC ACIDS RESEARCH
    Vol. {33}({Sp. Iss. SI}), pp. {D611-D613} 
    article  
    Abstract: MITOMAP (http://www.MITOMAP.org), a database for the human mitochondrial genome, has grown rapidly in data content over the past several years as interest in the role of mitochondrial DNA (mtDNA) variation in human origins, forensics, degenerative diseases, cancer and aging has increased dramatically. To accommodate this information explosion, MITOMAP has implemented a new relational database and an improved search engine, and all programs have been rewritten. System administrative changes have been made to improve security and efficiency, and to make MITOMAP compatible with a new automatic mtDNA sequence analyzer known as Mitomaster.
    BibTeX:
    @article{Brandon2005,
      author = {Brandon, MC and Lott, MT and Nguyen, KC and Spolim, S and Navathe, SB and Baldi, P and Wallace, DC},
      title = {MITOMAP: a human mitochondrial genome database - 2004 update},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2005},
      volume = {33},
      number = {Sp. Iss. SI},
      pages = {D611-D613}
    }
    
    Bright, J., Claydon, M., Soufian, M. & Gordon, D. Rapid typing of bacteria using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and pattern recognition software {2002} JOURNAL OF MICROBIOLOGICAL METHODS
    Vol. {48}({2-3, Sp. Iss. SI}), pp. {127-138} 
    article  
    Abstract: Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) of intact microorganisms, also known as intact cell MALDI-TOF-MS (ICM-MS), has been shown to produce characteristic mass spectral fingerprints of moieties desorbed from the cell surface. ICM-MS spectra can be obtained in minutes after removal of a colony from a culture plate. The similarity of ICM-MS spectra of replicate samples and of two different batches of the same bacterial strain demonstrates, in this study, the reproducibility of the technique. We have developed the Manchester Metropolitan University Search Engine (MUSE(TM)) to rapidly build and search databases of ICM-MS spectra. A database of 35 strains, representing 20 species and 12 genera. was built with MUSE(TM) and used to identify 212 isolates. The database was created in 26 s and loaded in 10 s, ready for searching, which took less than 1 s per isolate. Correct matches were made in 79 84% and 89% of the 212 samples at strain, species and genus levels, respectively. At least 50% of the replicates of 42 of the 45 isolates matched the correct strain, and the most commonly identified species for 43 of the 45 isolates was the correct one. The close match of the Escherichia coli strains containing the O157 antigen and the E. coli strains containing the K1 antigen suggests that these antigens may have a dominating influence on the ICM-MS fingerprints of these strains. We now have the ability to acquire ICM-MS fingerprints of bacteria and to search a database of these Fingerprints within minutes, so that the rapid identification of bacteria to the strain level can be realised. (C) 2002 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Bright2002,
      author = {Bright, JJ and Claydon, MA and Soufian, M and Gordon, DB},
      title = {Rapid typing of bacteria using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and pattern recognition software},
      journal = {JOURNAL OF MICROBIOLOGICAL METHODS},
      year = {2002},
      volume = {48},
      number = {2-3, Sp. Iss. SI},
      pages = {127-138},
      note = {4th International Symposium on the Interface between Analytical Chemistry and Microbiology, BRETAGNE, FRANCE, JUN 04-08, 2000}
    }
    
    Brin, S. & Page, L. The anatomy of a large-scale hypertextual Web search engine {1998} COMPUTER NETWORKS AND ISDN SYSTEMS
    Vol. {30}({1-7}), pp. {107-117} 
    article  
    Abstract: In this paper, we present Google, a prototype of a large-scale search engine which makes heavy use of the structure present in hypertext. Google is designed to crawl and index the Web efficiently and produce much more satisfying search results than existing systems. The prototype with a full text and hyperlink database of at least 24 million pages is available at http://google.stanford.edu/ To engineer a search engine is a challenging task. Search engines index tens to hundreds of millions of Web pages involving a comparable number of distinct terms. They answer tens of millions of queries every day. Despite the importance of large-scale search engines on the Web, very little academic research has been done on them. Furthermore, due to rapid advance in technology and Web proliferation, creating a Web search engine today is very different from three years ago. This paper provides an in-depth description of our large-scale Web search engine - the first such detailed public description we know of to date. Apart from the problems of scaling traditional search techniques to data of this magnitude, there are new technical challenges involved with using the additional information present in hypertext to produce better search results. This paper addresses this question of how to build a practical large-scale system which can exploit the additional information present in hypertext. Also we look at the problem of how to effectively deal with uncontrolled hypertext collections where anyone can publish anything they want. (C) 1998 Published by Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Brin1998,
      author = {Brin, S and Page, L},
      title = {The anatomy of a large-scale hypertextual Web search engine},
      journal = {COMPUTER NETWORKS AND ISDN SYSTEMS},
      year = {1998},
      volume = {30},
      number = {1-7},
      pages = {107-117},
      note = {7th International World Wide Web Conference, BRISBANE, AUSTRALIA, APR 14-18, 1998}
    }
    
    Broder, A. Identifying and filtering near-duplicate documents {2000}
    Vol. {1848}COMBINATORIAL PATTERN MATCHING, pp. {1-10} 
    inproceedings  
    Abstract: The informal notion of syntactic similarity. The resemblance can be estimated using a fixed size ``sketch'' for each document. For a large collection of documents (say hundreds of millions) the size of this sketch is of the order of a few hundred bytes per document. However, for efficient large scale web indexing it is not necessary to determine the actual resemblance value: it suffices to determine whether newly encountered documents are duplicates or near-duplicates of documents already indexed. In other words, it suffices to determine whether the resemblance is above a certain threshold. In this talk we show how this determination can be made using a ``sample'' of less than 50 bytes per document. The basic approach for computing resemblance has two aspects: first, resemblance is expressed as a set (of strings) intersection problem, and second, the relative size of intersections is evaluated by a process of random sampling that can be done independently for each document. The process of estimating the relative size of intersection of sets and the threshold test discussed above can be applied to arbitrary sets, and thus might be of independent interest. The algorithm for filtering near-duplicate documents discussed here has been successfully implemented and has been used for the last three years in the context of the Alta Vista search engine.
    BibTeX:
    @inproceedings{Broder2000,
      author = {Broder, AZ},
      title = {Identifying and filtering near-duplicate documents},
      booktitle = {COMBINATORIAL PATTERN MATCHING},
      year = {2000},
      volume = {1848},
      pages = {1-10},
      note = {11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000), MONTREAL, CANADA, JUN 21-23, 2000}
    }
    
    Brophy, J. & Bawden, D. Is Google enough? Comparison of an internet search engine with academic library resources {2005} ASLIB PROCEEDINGS
    Vol. {57}({6}), pp. {498-512} 
    article DOI  
    Abstract: Purpose - The purpose of the study was to compare an internet search engine, Google, with appropriate library databases and systems, in order to assess the relative value, strengths and weaknesses of the two sorts of system. Design/methodology/approach - A case study approach was used, with detailed analysis and failure checking of results. The performance of the two systems was assessed in terms of coverage, unique records, precision, and quality and accessibility of results. A novel form of relevance assessment, based on the work of Saracevic and others was devised. Findings - Google is superior for coverage and accessibility. Library systems are superior for quality of results. Precision is similar for both systems. Good coverage requires use of both, as both have many unique items. Improving the skills of the searcher is likely to give better results from the library systems, but not from Google. Research limitations/implications - Only four case studies were included. These were limited to the kind of queries likely to be searched by university students. Library resources were limited to those in two UK academic libraries. Only the basic Google web search functionality was used, and only the top ten records examined. Practical implications - The results offer guidance for those providing support and training for use of these retrieval systems, and also provide evidence for debates on the ``Google phenomenon''. Originality/value - This is one of the few studies which provide evidence on the relative performance of internet search engines and library databases, and the only one to conduct such in-depth case studies. The method for the assessment of relevance is novel.
    BibTeX:
    @article{Brophy2005,
      author = {Brophy, J and Bawden, D},
      title = {Is Google enough? Comparison of an internet search engine with academic library resources},
      journal = {ASLIB PROCEEDINGS},
      year = {2005},
      volume = {57},
      number = {6},
      pages = {498-512},
      doi = {{10.1108/00012530510634235}}
    }
    
    Brunn, S. & Dodge, M. Mapping the ``worlds'' of the World Wide Web - (Re)structuring global commerce through hyperlinks {2001} AMERICAN BEHAVIORAL SCIENTIST
    Vol. {44}({10}), pp. {1717-1739} 
    article  
    Abstract: The World Wide Web is barely 10 years old and already spans the globe, comprising more than a billion public pages and 3 million servers. It is a decentralized information space, created and controlled by many different authors, and has much lower barriers to entry than conventional information media. The authors analyze the connections between 180 different Internet ``nations'' using data on the number of Web pages and hyperlinks gathered from a commercial search Engine in 1998. They also analyze and describe the geography of the hyperlinks, revealing the most and least connected regions and countries, with a particular focus an African and Central Asian countries. A metric is created the Hyperlink Index, which is similar to the Export-Import Index common in economics and used to measure the flows of physical goods.
    BibTeX:
    @article{Brunn2001,
      author = {Brunn, SD and Dodge, M},
      title = {Mapping the ``worlds'' of the World Wide Web - (Re)structuring global commerce through hyperlinks},
      journal = {AMERICAN BEHAVIORAL SCIENTIST},
      year = {2001},
      volume = {44},
      number = {10},
      pages = {1717-1739}
    }
    
    Bruno, N., Gravano, L. & Marian, A. Evaluating Top-k queries over web-accessible Databases {2002} 18TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING, PROCEEDINGS, pp. {369-380}  inproceedings  
    Abstract: A query to a web search engine usually, consists of a list of keywords, to which the search engine responds with the best or ``top'' k pages for the query. This top-k query, model is prevalent over multimedia collections in general, but also over plain relational data for certain applications. For exampie, consider a relation with information on available restaurants, including their location, price range for one diner, and overall food rating. A Laser who queries such a relation might simply specify the user's location and target price range, and expect in return the best 10 restaurants in terms of some combination of proximity, to the user closeness of match to the target price range, and overall food rating. Processing such top-k queries efficiently, is challenging for a number of reasons. One critical such reason is that, in many web applications, the relation attributes might not be available other than through external web-accessible form interfaces, which we will have to query, repeatedly for a potentially, large set of candidate objects. In this paper, we steady, how to process top-k queries efficiently, in this setting, where the attributes for which users specify target values might be handled by external, autonomous sources with a variety of access interfaces. We present several algorithms for processing such queries, and evaluate them thoroughly using both synthetic arid real web-accessible data.
    BibTeX:
    @inproceedings{Bruno2002,
      author = {Bruno, N and Gravano, L and Marian, A},
      title = {Evaluating Top-k queries over web-accessible Databases},
      booktitle = {18TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING, PROCEEDINGS},
      year = {2002},
      pages = {369-380},
      note = {18th International Conference on Data Engineering, SAN JOSE, CA, FEB 26-MAR 01, 2002}
    }
    
    Bucci, G., Cagnoni, S. & DeDominicis, R. Integrating content-based retrieval in a medical image reference database {1996} COMPUTERIZED MEDICAL IMAGING AND GRAPHICS
    Vol. {20}({4}), pp. {231-241} 
    article  
    Abstract: Image reference databases (RDBs) are a recurrent research topic in medical imaging. Most IRDBs are designed to help experienced physicians in diagnostic tasks and require that users have prior extensive knowledge of the field for their use to be fruitful. Therefore, the educational potential of such image collections cannot be exploited thoroughly. In this paper we propose an image-indexing method to extend the functionalities of an existing medical IRDB and allow for ifs use in educational applications, as well as in computer-assisted diagnosis. Our method, based on the Kahrunen-Loeve transform, has been used to develop a content-based search engine for tomographic image databases on which we are presently experimenting and which we aim to integrate into a working radiological IRDB installed at the University of Florence. Results achieved in our preliminary tests are also reported. Copyright (C) 1996 Elsevier Science Ltd.
    BibTeX:
    @article{Bucci1996,
      author = {Bucci, G and Cagnoni, S and DeDominicis, R},
      title = {Integrating content-based retrieval in a medical image reference database},
      journal = {COMPUTERIZED MEDICAL IMAGING AND GRAPHICS},
      year = {1996},
      volume = {20},
      number = {4},
      pages = {231-241}
    }
    
    Buriol, L., Franca, P. & Moscato, P. A new memetic algorithm for the asymmetric traveling salesman problem {2004} JOURNAL OF HEURISTICS
    Vol. {10}({5}), pp. {483-506} 
    article  
    Abstract: This paper introduces a new memetic algorithm specialized for the asymmetric instances of the traveling salesman problem (ATSP). The method incorporates a new local search engine and many other features that contribute to its effectiveness, such as: (i) the topological organization of the population as a complete ternary tree with thirteen nodes; (ii) the hierarchical organization of the population in overlapping clusters leading to the special selection scheme; (iii) efficient data structures. Computational experiments are conducted on all ATSP instances available in the TSPLIB, and on a set of larger asymmetric instances with known optimal solutions. The comparisons show that the results obtained by our method compare favorably with those obtained by several other algorithms recently proposed for the ATSP.
    BibTeX:
    @article{Buriol2004,
      author = {Buriol, L and Franca, PM and Moscato, P},
      title = {A new memetic algorithm for the asymmetric traveling salesman problem},
      journal = {JOURNAL OF HEURISTICS},
      year = {2004},
      volume = {10},
      number = {5},
      pages = {483-506}
    }
    
    BURKOWSKI, F. AN ALGEBRA FOR HIERARCHICALLY ORGANIZED TEXT-DOMINATED DATABASES {1992} INFORMATION PROCESSING & MANAGEMENT
    Vol. {28}({3}), pp. {333-348} 
    article  
    Abstract: Structured documents are usually comprised of nested text elements; for example, reports contain chapters, chapters contain sections, . . . , sentences contain words. The containment relationships of these text elements define a text hierarchy that can be exploited during search activities such as database browsing and full-text retrieval. During a database load the system typically constructs concordance lists, each list maintaining the locations of all occurrences of a particular type of text element. Although not necessarily constructed in practice, a complete set of concordance lists would constitute an equivalent representation of the database, namely its inverted form. This paper describes an algebra based on various primitive operators that use concordance lists as operands. These primitives can be used to define higher level filter operators that specify whether a contiguous text extent will be selected or rejected during a search. The main contribution of the paper is the presentation of this algebra as a theoretical model that can be used to define a conceptual schema for the database. This theoretical model provides both a mathematically well defined abstraction for the database and a basis for database implementation since it may be utilized to formally define the search protocols between the database query facilities and the underlying retrieval engine.
    BibTeX:
    @article{BURKOWSKI1992,
      author = {BURKOWSKI, FJ},
      title = {AN ALGEBRA FOR HIERARCHICALLY ORGANIZED TEXT-DOMINATED DATABASES},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {1992},
      volume = {28},
      number = {3},
      pages = {333-348},
      note = {RIAO 91 : CONF ON INTELLIGENT TEXT AND IMAGE HANDLING, BARCELONA, SPAIN, APR 02-05, 1991}
    }
    
    Caballero, J. & Nahata, M. Atomoxetine hydrochloride for the treatment of attention-deficit/hyperactivity disorder {2003} CLINICAL THERAPEUTICS
    Vol. {25}({12}), pp. {3065-3083} 
    article  
    Abstract: Background: Attention-deficit/hyperactivity disorder (ADHD) occurs in similar to3% to 10% of the pediatric population. Most of the drugs typically used to treat ADHD are stimulants, which, because of their addictive properties and potential for abuse, are controlled substances. Although these drugs are the mainstay of treatment for ADHD, nearly one third of patients may not respond to or be able to tolerate them. Atomoxetine hydrochloride, a nonstimulant approved by the US Food and Drug Administration for the treatment of ADHD, may provide an alternative to the use of stimulants. Objective: The goal of this review was to describe the chemistry, mechanism of action, pharmacokinetics, drug interactions, and efficacy and safety profiles of atomoxetine in pediatric and adult patients with ADHD, as well as relevant pharmacoeconomic considerations. Methods: Relevant publications were identified through a search of the English-language literature indexed on PreMEDLINE and MEDLINE (1966-May 2003) using the search terms atomoxetine, tomoxetine, and LY139603. These terms were also applied to the Google search engine. All articles were reviewed for suitability for inclusion. The manufacturer of atomoxetine provided both published and unpublished data. Results: in the. data reviewed, atomoxetine was more efficacious than placebo in patients with ADHD (P < 0.05 to P < 0.01). Therapeutic doses ranged from 1.2 to 1.4 mg/kg per day (maximum 100 mg/d) in children and were similar to80 mg/d in adults. Among the common adverse effects of atomoxetine were decreased appetite, somnolence, dizziness, and vomiting. Thus far, atomoxetine has shown no abuse potential and is therefore an alternative for parents seeking nonstimulants for their children. The cost of atomoxetine is greater than that of the generic versions of first-line agents and, depending on the dose, is comparable to or more expensive than that of brand-name methylphenidate or amphetamine products. Conclusions: Based on the available data, the nonstimulant atomoxetine is superior to placebo in children aged >6 years and adults with ADHD. Studies are needed that compare atomoxetine with stimulants and amphetamines in children and adults. Atomoxetine provides an alternative for patients with ADHD who prefer to use a noncontrolled drug, who cannot tolerate first-line agents, or whose previous treatment has failed. Adverse effects appear to be similar to those of the stimulants. Because of the lack of comparative trials against other drugs, limited clinical experience, and potentially higher drug costs, atomoxetine should be considered a second-line agent in patients with ADHD.Copyright (C) 2003 Excerpta Medica, Inc.
    BibTeX:
    @article{Caballero2003,
      author = {Caballero, J and Nahata, MC},
      title = {Atomoxetine hydrochloride for the treatment of attention-deficit/hyperactivity disorder},
      journal = {CLINICAL THERAPEUTICS},
      year = {2003},
      volume = {25},
      number = {12},
      pages = {3065-3083}
    }
    
    Callan, J. & Connell, M. Query-based sampling of text databases {2001} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {19}({2}), pp. {97-130} 
    article  
    Abstract: The proliferation of searchable text databases on corporate networks and the Internet causes a database selection problem for many people. Algorithms such as gGlOSS and CORI can automatically select which text databases to search for a given information need, but only if given a set of resource descriptions that accurately represent the contents of each database. The existing techniques for acquiring resource descriptions have significant limitations when used in wide-area networks controlled by many parties. This paper presents query-based sampling, a new technique for acquiring accurate resource descriptions. Query-based sampling does not require the cooperation of resource providers, nor does it require that resource providers use a particular search engine or representation technique. An extensive set of experimental results demonstrates that accurate resource descriptions are created, that computation and communication costs are reasonable, and that the resource descriptions do in fact enable accurate automatic database selection.
    BibTeX:
    @article{Callan2001,
      author = {Callan, J and Connell, M},
      title = {Query-based sampling of text databases},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2001},
      volume = {19},
      number = {2},
      pages = {97-130}
    }
    
    Camilo, F., Ransom, S., Gaensler, B., Slane, P., Lorimer, D., Reynolds, J., Manchester, R. & Murray, S. PSR J1833-1034: Discovery of the central young pulsar in the supernova remnant G21.5-0.9 {2006} ASTROPHYSICAL JOURNAL
    Vol. {637}({1, Part 1}), pp. {456-465} 
    article  
    Abstract: We have discovered the pulsar associated with the supernova remnant G21.5-0.9. PSR J1833-1034, with spin period P = 61.8 ms and dispersion measure 169 cm(-3) pc, is very faint, with pulse-averaged flux density of approximate to 70 mu Jy at a frequency of 1.4 GHz, and was first detected in a deep search with the Parkes telescope. Subsequent observations with Parkes and the Green Bank Telescope have confirmed this detection and yield a period derivative. P 2.02 x 10(-13). These spin parameters imply a characteristic age tau(c) = 4.8 kyr and a spin-down luminosity E 3: 3; 10(37) ergs s(-1), the latter value exceeded only by the Crab pulsar among the rotation-powered pulsars known in our Galaxy. The pulsar has an unusually steep radio spectrum in the 0.8-2.0 GHz range, with power-law index approximate to 3.0, and a narrow single-peaked pulse profile with FWHM of 0.04P. We have analyzed 350 ks of archival Chandra X-Ray Observatory HRC data and find a pointlike source of luminosity approximate to 3 x 10(-5). E, offset from the center of an elliptical region of size approximate to 70''5'' and luminosity approximate to 10(-3). E within which likely lies the pulsar wind termination shock. We have searched for X-ray pulsations in a 30 ks HRC observation without success, deriving a pulsed fraction upper limit for a sinusoidal pulse shape of about 70% of the pulsar flux. We revisit the distance to G21.5-0.9 based on H (I) and CO observations, arguing that it is 4.7 +/- 0.4 kpc. We use existing X-ray and radio observations of the pulsar wind nebula, along with the measured properties of its engine and a recent detection of the supernova remnant shell, to argue that G21.5-0.9 and PSR J1833-1034 are much younger than tau(c) and likely their true age is <= 1000 yr. In that case, the initial spin period of the pulsar was >= 55 ms.
    BibTeX:
    @article{Camilo2006,
      author = {Camilo, F and Ransom, SM and Gaensler, BM and Slane, PO and Lorimer, DR and Reynolds, J and Manchester, RN and Murray, SS},
      title = {PSR J1833-1034: Discovery of the central young pulsar in the supernova remnant G21.5-0.9},
      journal = {ASTROPHYSICAL JOURNAL},
      year = {2006},
      volume = {637},
      number = {1, Part 1},
      pages = {456-465}
    }
    
    Campbell, M., Hoane, A. & Hsu, F. Deep blue {2002} ARTIFICIAL INTELLIGENCE
    Vol. {134}({1-2}), pp. {57-83} 
    article  
    Abstract: Deep Blue is the chess machine that defeated then-reigning World Chess Champion Garry Kasparov in a six-game match in 1997. There were a number of factors that contributed to this success, including: a single-chip chess search engine, a massively parallel system with multiple levels of parallelism, a strong emphasis on search extensions, a complex evaluation function, and effective use of a Grandmaster game database. This paper describes the Deep Blue system, and gives some of the rationale that went into the design decisions behind Deep Blue. (C) 2001 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Campbell2002,
      author = {Campbell, M and Hoane, AJ and Hsu, FH},
      title = {Deep blue},
      journal = {ARTIFICIAL INTELLIGENCE},
      year = {2002},
      volume = {134},
      number = {1-2},
      pages = {57-83}
    }
    
    Cappellaro, E., Evans, R. & Turatto, M. A new determination of supernova rates and a comparison with indicators for galactic star formation {1999} ASTRONOMY AND ASTROPHYSICS
    Vol. {351}({2}), pp. {459-466} 
    article  
    Abstract: We have computed new estimates of the local rates of supernovae (SNe) adding the updated log of Evans' visual search to our SN search database. In this way, we have accumulated the largest SN statistics ever assembled for this purpose. The new SN rates are corrected on an empirical basis for the bias in the inner regions of galaxies and that in inclined spirals. We also tested an alternative approach based on the simple model proposed by Hatano et al. (1998) for the SN and dust distribution in spirals. It turns out that, although the two approaches give similar average rates, the Hatano et al. model appears to overcorrect the SN rate of distant galaxies. We used these updated statistics to probe the SN rates with different tracers of the star formation activity in galaxies, namely integrated colors, infrared luminosities and nuclear activities. We found a clear relation between the core-collapse SN rate and the integrated galaxy color, which appears consistent with the prediction of galaxy evolutionary models. We also compared SN rates in galaxies with different L-FIR with unfavorable outcome, and we argue that L-FIR is not a universal measurement of SFR. Finally, we confirm that the SN rate is not enhanced in AGN host galaxies which indicates that the nuclear engine does not significantly stimulate the extranuclear SF.
    BibTeX:
    @article{Cappellaro1999,
      author = {Cappellaro, E and Evans, R and Turatto, M},
      title = {A new determination of supernova rates and a comparison with indicators for galactic star formation},
      journal = {ASTRONOMY AND ASTROPHYSICS},
      year = {1999},
      volume = {351},
      number = {2},
      pages = {459-466}
    }
    
    Casper, R. & Mitwally, M. Review: Aromatase inhibitors for ovulation induction {2006} JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
    Vol. {91}({3}), pp. {760-771} 
    article DOI  
    Abstract: Context: For the last 40 yr, the first line of treatment for anovulation in infertile women has been clomiphene citrate (CC). CC is a safe, effective oral agent but is known to have relatively common antiestrogenic endometrial and cervical mucous side effects that could prevent pregnancy in the face of successful ovulation. In addition, there is a significant risk of multiple pregnancy with CC, compared with natural cycles. Because of these problems, we proposed the concept of aromatase inhibition as a new method of ovulation induction that could avoid many of the adverse effects of CC. The objective of this review was to describe the different physiological mechanisms of action for CC and aromatase inhibitors (AIs) and compare studies of efficacy for both agents for ovulation induction. Evidence Acquisition: We conducted a systematic review of all the published studies, both controlled and noncontrolled, comparing CC and AI treatment, either alone or in combination with gonadotropins, for ovulation induction or augmentation, identified through the Entrez-PubMed search engine. Evidence Synthesis: Because of the recent acceptance of the concept of using AIs for ovulation induction, few controlled studies were identified, and the rest of the studies were pilot or preliminary comparisons. Based on these studies, it appears that AIs are as effective as CC in inducing ovulation, are devoid of any antiestrogenic side effects, result in lower serum estrogen concentrations, and are associated with good pregnancy rates with a lower incidence of multiple pregnancy than CC. When combined with gonadotropins for assisted reproductive technologies, AIs reduce the dose of FSH required for optimal follicle recruitment and improve the response to FSH in poor responders. Conclusions: Preliminary evidence suggests that AIs may replace CC in the future because of similar efficacy with a reduced side effect profile. Although worldwide experience with AIs for ovulation induction is increasing, at present, definitive studies in the form of randomized controlled trials comparing CC with AIs are lacking.
    BibTeX:
    @article{Casper2006,
      author = {Casper, RF and Mitwally, MFM},
      title = {Review: Aromatase inhibitors for ovulation induction},
      journal = {JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM},
      year = {2006},
      volume = {91},
      number = {3},
      pages = {760-771},
      doi = {{10.1210/jc.2005-1923}}
    }
    
    Castells, P., Fernandez, M. & Vallet, D. An adaptation of the vector-space model for ontology-based information retrieval {2007} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {19}({2}), pp. {261-272} 
    article  
    Abstract: Semantic search has been one of the motivations of the Semantic Web since it was envisioned. We propose a model for the exploitation of ontology-based knowledge bases to improve search over large document repositories. In our view of Information Retrieval on the Semantic Web, a search engine returns documents rather than, or in addition to, exact values in response to user queries. For this purpose, our approach includes an ontology-based scheme for the semiautomatic annotation of documents and a retrieval system. The retrieval model is based on an adaptation of the classic vector-space model, including an annotation weighting algorithm, and a ranking algorithm. Semantic search is combined with conventional keyword-based retrieval to achieve tolerance to knowledge base incompleteness. Experiments are shown where our approach is tested on corpora of significant scale, showing clear improvements with respect to keyword-based search.
    BibTeX:
    @article{Castells2007,
      author = {Castells, Pablo and Fernandez, Miriam and Vallet, David},
      title = {An adaptation of the vector-space model for ontology-based information retrieval},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2007},
      volume = {19},
      number = {2},
      pages = {261-272}
    }
    
    Chakrabarti, S., Dom, B., Kumar, S., Raghavan, P., Rajagopalan, S., Tomkins, A., Gibson, D. & Kleinberg, J. Mining the web's link structure {1999} COMPUTER
    Vol. {32}({8}), pp. {60+} 
    article  
    Abstract: Sifting through the growing mountain of Web data demands an increasingly discerning search engine, one that can reliably assess the quality of sites, not just their relevance.
    BibTeX:
    @article{Chakrabarti1999,
      author = {Chakrabarti, S and Dom, BE and Kumar, SR and Raghavan, P and Rajagopalan, S and Tomkins, A and Gibson, D and Kleinberg, J},
      title = {Mining the web's link structure},
      journal = {COMPUTER},
      year = {1999},
      volume = {32},
      number = {8},
      pages = {60+}
    }
    
    Chalkley, R., Baker, P., Huang, L., Hansen, K., Allen, N., Rexach, M. & Burlingame, A. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer - II. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets {2005} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {4}({8}), pp. {1194-1204} 
    article DOI  
    Abstract: A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine ``Mascot'' using a new results comparison program within Prospector named ``SearchCompare.'' The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines.
    BibTeX:
    @article{Chalkley2005,
      author = {Chalkley, RJ and Baker, PR and Huang, L and Hansen, KC and Allen, NP and Rexach, M and Burlingame, AL},
      title = {Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer - II. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2005},
      volume = {4},
      number = {8},
      pages = {1194-1204},
      doi = {{10.1074/mcp.D500002-MCP200}}
    }
    
    Chang, C., Christensen, M. & Zhang, T. Genetic algorithms for project management {2001} ANNALS OF SOFTWARE ENGINEERING
    Vol. {11}, pp. {107-139} 
    article  
    Abstract: The scheduling of tasks and the allocation of resource in medium to large-scale development projects is an extremely hard problem and is one of the principal challenges of project management due to its sheer complexity. As projects evolve any solutions, either optimal or near optimal, must be continuously scrutinized in order to adjust to changing conditions. Brute force exhaustive or branch-and-bound search methods cannot cope with the complexity inherent in finding satisfactory solutions to assist project managers. Most existing project management (PM) techniques, commercial PM tools, and research prototypes fall short in their computational capabilities and only provide passive project tracking and reporting aids. Project managers must make all major decisions based on their individual insights and experience, must build the project database to record such decisions and represent them as project nets, then use the tools to track progress, perform simple consistency checks, analyze the project net for critical path, etc., and produce reports in various formats such as Gantt or Pert charts. Our research has developed a new technique based on genetic algorithms (GA) that automatically determines, using a programmable goal function, a near-optimal allocation of resources and resulting schedule that satisfies a given task structure and resource pool. We assumed that the estimated effort for each task is known a priori and can be obtained from any known estimation method such as COCOMO. Based on the results of these algorithm, the software manager will be able to assign tasks to staff in an optimal manner and predict the corresponding future status of the project, including an extensive analysis on the time-and-cost variations in the solution space. Our experiments utilized Wall's GALib as the search engine. The algorithms operated on a richer, refined version of project management networks derived from Chao's seminal work on GA-based Software Project Management Net (SPMnet). Generalizing the results of Chao's solution, the new GA algorithms can operate on much more complex scheduling networks involving multiple projects. They also can deal with more realistic programmatic and organizational assumptions. The results of the GA algorithm were evaluated using exhaustive search for five test cases. In these tests our GA showed strong scalability and simplicity. Its orthogonal genetic form and modularized heuristic functions are well suited for complex conditional optimization problems, of which project management is a typical example.
    BibTeX:
    @article{Chang2001,
      author = {Chang, CK and Christensen, MJ and Zhang, T},
      title = {Genetic algorithms for project management},
      journal = {ANNALS OF SOFTWARE ENGINEERING},
      year = {2001},
      volume = {11},
      pages = {107-139}
    }
    
    Chang, S., Chen, W., Meng, H., Sundaram, H. & Zhong, D. A fully automated content-based video search engine supporting spatiotemporal queries {1998} IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
    Vol. {8}({5}), pp. {602-615} 
    article  
    Abstract: The rapidity with which digital information, particularly video, is being generated has necessitated the development of tools for efficient search of these media. Content-based visual queries hare been primarily focused on still image retrieval. In this paper, we propose a novel, interactive system on the Web, based on the visual paradigm, with spatiotemporal attributes playing a key role in video retrieval. We have developed innovative algorithms for automated video object segmentation and tracking, and use real-time video editing techniques while responding to user queries. The resulting system, called VideoQ (demo available at http://www.ctr.columbia.edu/VideoQ/) is the first on-line video search engine supporting automatic object-based indexing and spatiotemporal queries. The system performs well, with the user being able to retrieve complex video clips such as those of skiers and baseball players with ease.
    BibTeX:
    @article{Chang1998,
      author = {Chang, SF and Chen, W and Meng, HJ and Sundaram, H and Zhong, D},
      title = {A fully automated content-based video search engine supporting spatiotemporal queries},
      journal = {IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY},
      year = {1998},
      volume = {8},
      number = {5},
      pages = {602-615}
    }
    
    Chang, S., Eleftheriadis, A. & Mcclintock, R. Next-generation content representation, creation, and searching for new-media applications in education {1998} PROCEEDINGS OF THE IEEE
    Vol. {86}({5}), pp. {884-904} 
    article  
    Abstract: Content creation, editing, and searching are extremely time-consuming tasks that often require substantial training and experience, especially when high-quality audio and video are involved. ``New media'' represents a new paradigm for multimedia information representation and processing, in which the emphasis is placed on the actual content. It thus brings the tasks of content creation and searching much closer to actual users and enables them to be active producers of audio-visual information rather than passive recipients. We discuss the state of the art and present next-generation techniques for content representation, searching, creation, and editing. We discuss our experiences in developing a Web-based distributed compressed video editing and searching system (WebClip), a media-representation language (Flavor) and an object-based video-authoring system (Zest) based on it, and a large image/video search engine for the World Wide Web (WebSEEk). We also present a case study of new media applications based on specific planned multimedia education experiments with the above systems in several K-12 schools in Manhattan, NY.
    BibTeX:
    @article{Chang1998a,
      author = {Chang, SF and Eleftheriadis, A and Mcclintock, R},
      title = {Next-generation content representation, creation, and searching for new-media applications in education},
      journal = {PROCEEDINGS OF THE IEEE},
      year = {1998},
      volume = {86},
      number = {5},
      pages = {884-904}
    }
    
    Chao, H., Jenq, Y., Guo, X. & Lam, C. Design of packet-fair queuing schedulers using a RAM-based searching engine {1999} IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS
    Vol. {17}({6}), pp. {1105-1126} 
    article  
    Abstract: The implementation of packet-fair queuing (PFQ) schedulers, which aim at approximating the generalized processor sharing (GPS) policy, is a central issue for providing multimedia services with various quality-of-service (QoS) requirements in packet-switching networks. In the PFQ scheduler, packets are usually time stamped with a value based on some algorithm and are transmitted with an increasing order of the time-stamp values. One of the most challenging issues is to search for the smallest time-stamp value among hundreds of thousands of sessions, In this paper, we propose a novel RAM-based searching engine (RSE) to speed up the searching process by using the concept of hierarchical searching with a tree data structure. The time for searching the smallest time stamp is independent of the number of sessions in the system and is only bounded by the memory accesses needed. The RSE can be implemented with commercial memory and field programmable gate array (FPGA) chips in a cost-effective manner. With the extension of the RSE, we propose a two-dimensional (2-D) RSE architecture to implement a general shaper-scheduler. Other challenging issues, such as time-stamp overflow and aging, are also addressed in the paper.
    BibTeX:
    @article{Chao1999,
      author = {Chao, HJ and Jenq, YR and Guo, XL and Lam, CH},
      title = {Design of packet-fair queuing schedulers using a RAM-based searching engine},
      journal = {IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS},
      year = {1999},
      volume = {17},
      number = {6},
      pages = {1105-1126}
    }
    
    Chau, M., Fang, X. & Sheng, O. Analysis of the query logs of a web site search engine {2005} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {56}({13}), pp. {1363-1376} 
    article DOI  
    Abstract: A large number of studies have investigated the transaction log of general-purpose search engines such as Excite and AltaVista, but few studies have reported on the analysis of search logs for search engines that are limited to particular Web sites, namely, Web site search engines. In this article, we report our research on analyzing the search logs of the search engine of the Utah state government Web site. Our results show that some statistics, such as the number of search terms per query, of Web users are the same for general-purpose search engines and Web site search engines, but others, such as the search topics and the terms used, are considerably different. Possible reasons for the differences include the focused domain of Web site search engines and users' different information needs. The findings are useful for Web site developers to improve the performance of their services provided on the Web and for researchers to conduct further research in this area. The analysis also can be applied in e-government research by investigating how information should be delivered to users in government Web sites.
    BibTeX:
    @article{Chau2005,
      author = {Chau, M and Fang, X and Sheng, ORL},
      title = {Analysis of the query logs of a web site search engine},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2005},
      volume = {56},
      number = {13},
      pages = {1363-1376},
      doi = {{10.1002/asi.20210}}
    }
    
    Chau, M., Fang, X. & Yang, C.C. Web searching in Chinese: A study of a search engine in Hong Kong {2007} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {58}({7}), pp. {1044-1054} 
    article DOI  
    Abstract: The number of non-English resources has been increasing rapidly on the Web. Although many studies have been conducted on the query logs in search engines that are primarily English-based (e.g., Excite and AltaVista), only a few of them have studied the information-seeking behavior on the Web in non-English languages. In this article, we report the analysis of the search-query logs of a search engine that focused on Chinese. Three months of search-query logs of Timway, a search engine based in Hong Kong, were collected and analyzed. Metrics on sessions, queries, search topics, and character usage are reported. N-gram analysis also has been applied to perform character-based analysis. Our analysis suggests that some characteristics identified in the search log, such as search topics and the mean number of queries per sessions, are similar to those in English search engines; however, other characteristics, such as the use of operators in query formulation, are significantly different. The analysis also shows that only a very small number of unique Chinese characters are used in search queries. We believe the findings from this study have provided some insights into further research in non-English Web searching.
    BibTeX:
    @article{Chau2007,
      author = {Chau, Michael and Fang, Xiao and Yang, Christopher C.},
      title = {Web searching in Chinese: A study of a search engine in Hong Kong},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2007},
      volume = {58},
      number = {7},
      pages = {1044-1054},
      doi = {{10.1002/asi.20592}}
    }
    
    Chen, D., Muller, H.-M. & Sternberg, P.W. Automatic document classification of biological literature {2006} BMC BIOINFORMATICS
    Vol. {7} 
    article DOI  
    Abstract: Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusion: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.
    BibTeX:
    @article{Chen2006,
      author = {Chen, David and Muller, Hans-Michael and Sternberg, Paul W.},
      title = {Automatic document classification of biological literature},
      journal = {BMC BIOINFORMATICS},
      year = {2006},
      volume = {7},
      doi = {{10.1186/1471-2105-7-370}}
    }
    
    Chen, H., Fan, H., Chau, M. & Zeng, D. MetaSpider: Meta-searching and categorization on the Web {2001} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {52}({13}), pp. {1134-1147} 
    article  
    Abstract: It has become increasingly difficult to locate relevant information on the Web, even with the help of Web search engines. Two approaches to addressing the low precision and poor presentation of search results of current search tools are studied: meta-search and document categorization. Meta-search engines improve precision by selecting and integrating search results from generic or domain-specific Web search engines or other resources. Document categorization promises better organization and presentation of retrieved results. This article introduces MetaSpider, a meta-search engine that has real-time indexing and categorizing functions. We report in this paper the major components of MetaSpider and discuss related technical approaches. Initial results of a user evaluation study comparing MetaSpider, NorthernLight, and MetaCrawler in terms of clustering performance and of time and effort expended show that MetaSpider performed best in precision rate, but disclose no statistically significant differences in recall rate and time requirements. Our experimental study also reveals that MetaSpider exhibited a higher level of automation than the other two systems and facilitated efficient searching by providing the user with an organized, comprehensive view of the retrieved documents.
    BibTeX:
    @article{Chen2001,
      author = {Chen, HC and Fan, HY and Chau, M and Zeng, D},
      title = {MetaSpider: Meta-searching and categorization on the Web},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2001},
      volume = {52},
      number = {13},
      pages = {1134-1147}
    }
    
    Chen, J., Anderson, J., DeWeese-Scott, C., Fedorova, N., Geer, L., He, S., Hurwitz, D., Jackson, J., Jacobs, A., Lanczycki, C., Liebert, C., Liu, C., Madej, T., Marchler-Bauer, A., Marchler, G., Mazumder, R., Nikolskaya, A., Rao, B., Panchenko, A., Shoemaker, B., Simonyan, V., Song, J., Thiessen, P., Vasudevan, S., Wang, Y., Yamashita, R., Yin, J. & Bryant, S. MMDB: Entrez's 3D-structure database {2003} NUCLEIC ACIDS RESEARCH
    Vol. {31}({1}), pp. {474-477} 
    article DOI  
    Abstract: dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez' s 3D- structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez' s search engine provides several powerful features: ( i) links between databases, for example between a protein s sequence and structure; ( ii) precomputed sequence and structure neighbors; and ( iii) structure and sequence/ structure alignment visualization. Here, we focus on a new feature of Entrez' s Molecular Modeling Database ( MMDB) : Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http: / / www. ncbi. nlm. nih. gov/ Entrez/ structure. html.
    BibTeX:
    @article{Chen2003,
      author = {Chen, J and Anderson, JB and DeWeese-Scott, C and Fedorova, ND and Geer, LY and He, SQ and Hurwitz, DI and Jackson, JD and Jacobs, AR and Lanczycki, CJ and Liebert, CA and Liu, CL and Madej, T and Marchler-Bauer, A and Marchler, GH and Mazumder, R and Nikolskaya, AN and Rao, BS and Panchenko, AR and Shoemaker, BA and Simonyan, V and Song, JS and Thiessen, PA and Vasudevan, S and Wang, YL and Yamashita, RA and Yin, JJ and Bryant, SH},
      title = {MMDB: Entrez's 3D-structure database},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2003},
      volume = {31},
      number = {1},
      pages = {474-477},
      doi = {{10.1093/nar/gkg086}}
    }
    
    Chen, J.H., Linstead, E., Swamidass, S.J., Wang, D. & Baldi, P. ChemDB update - full-text search and virtual chemical space {2007} BIOINFORMATICS
    Vol. {23}({17}), pp. {2348-2351} 
    article DOI  
    Abstract: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure ( and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB. Availability: ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu. Contact: pfbaldi@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    BibTeX:
    @article{Chen2007,
      author = {Chen, Jonathan H. and Linstead, Erik and Swamidass, S. Joshua and Wang, Dennis and Baldi, Pierre},
      title = {ChemDB update - full-text search and virtual chemical space},
      journal = {BIOINFORMATICS},
      year = {2007},
      volume = {23},
      number = {17},
      pages = {2348-2351},
      doi = {{10.1093/bioinformatics/btm341}}
    }
    
    Chen, L., Zheng, J., Sun, F. & Wu, C. Power density analysis and optimization of a regenerated closed variable-temperature heat reservoir Brayton cycle {2001} JOURNAL OF PHYSICS D-APPLIED PHYSICS
    Vol. {34}({11}), pp. {1727-1739} 
    article  
    Abstract: In this paper, the power density, defined as the ratio of power output to the maximum specific volume in the cycle, is taken as the objective for performance analysis and optimization of an irreversible regenerated closed Brayton cycle coupled to variable-temperature heal reservoirs from the viewpoint of finite time thermodynamics (FTT) or entropy generation minimization (EGM). The analytical formulae about the relations between power density and pressure ratio are derived with the heat resistance losses in the hot- and cold-side heat exchangers and the regenerator, the it-reversible compression and expansion losses in the compressor and turbine, the pressure drop losses at the heater, cooler and regenerator as well as in the piping, and the effect of the finite thermal capacity rate of the heat reservoirs. The obtained results are compared with those results obtained by using the maximum power criterion, and the advantages and disadvantages of maximum power density design are analysed. The maximum power density optimization is performed in two stages. The first is to search the optimum heat conductance distribution corresponding to the optimum power density among the hot- and cold-side heat exchangers and the regenerator for a fixed total heat exchanger inventory. The second is to search the optimum thermal capacitance rate matching corresponding to the optimum power density between the working fluid and the high-temperature heat source for a fixed ratio of the thermal capacitance rates of two heat reservoirs. The influences of some design parameters, including the effectiveness of the regenerator, the inlet temperature ratio of the heat reservoirs, the effectiveness of the heat exchangers between the working fluid and the heat reservoirs, the efficiencies of the compressor and the turbine, and the pressure recovery coefficient, on the optimum heat conductance distribution, the optimum thermal capacitance rate matching, and the maximum power density are provided by numerical examples. The power plant design with optimization leads to a smaller size including the compressor, turbine, and the hot- and cold-side heat exchangers and the regenerator. When the heat transfers between the working fluid and the heat reservoirs are carried out ideally, the pressure drop loss may be neglected, and the thermal capacity rates of the heat reservoirs are infinite, the results of this paper then replicate those obtained in recent literature.
    BibTeX:
    @article{Chen2001a,
      author = {Chen, LG and Zheng, JL and Sun, FR and Wu, C},
      title = {Power density analysis and optimization of a regenerated closed variable-temperature heat reservoir Brayton cycle},
      journal = {JOURNAL OF PHYSICS D-APPLIED PHYSICS},
      year = {2001},
      volume = {34},
      number = {11},
      pages = {1727-1739}
    }
    
    Chen, T.-C., Chen, Y.-H., Tsai, S.-F., Chien, S.-Y. & Chen, L.-G. Fast algorithm and architecture design of low-power integer motion estimation for H.264/AVC {2007} IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
    Vol. {17}({5}), pp. {568-577} 
    article DOI  
    Abstract: In an H.264/AVC video encoder, integer motion estimation (RUE) requires 74.29% computational complexity and 77.49% memory access and becomes the most critical component for low-power applications. According to our analysis, an optimal low-power IME engine should be a parallel hardware architecture supporting fast algorithms and efficient data reuse (DR). In this paper, a hardware-oriented fast algorithm is proposed with the intra-/inter-candidate DR considerations. In addition, based on the systolic array and 2-D adder tree architecture, a ladder-shaped search window data arrangement and an advanced searching flow are proposed to efficiently support inter-candidate DR and reduce latency cycles. According to the implementation results, 97% computational complexity is saved by the proposed fast algorithm. In addition, 77.6% memory bandwidth is further saved with the proposed DR techniques at architecture level. In the ultra-low-power mode, the power consumption is 2.13 mW for real-time encoding CIF 30-fps videos at 13.5-MHz operating frequency.
    BibTeX:
    @article{Chen2007a,
      author = {Chen, Tung-Chien and Chen, Yu-Han and Tsai, Sung-Fang and Chien, Shao-Yi and Chen, Liang-Gee},
      title = {Fast algorithm and architecture design of low-power integer motion estimation for H.264/AVC},
      journal = {IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY},
      year = {2007},
      volume = {17},
      number = {5},
      pages = {568-577},
      doi = {{10.1109/TCSVT.2007.894044}}
    }
    
    Chen, Y., Kwon, S., Kim, S. & Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra {2005} JOURNAL OF PROTEOME RESEARCH
    Vol. {4}({3}), pp. {998-1005} 
    article DOI  
    Abstract: Quantitative proteomics relies on accurate protein identification, which often is carried out by automated searching of a sequence database with tandem mass spectra of peptides. When these spectra contain limited information, automated searches may lead to incorrect peptide identifications. It is therefore necessary to validate the identifications by careful manual inspection of the mass spectra. Not only is this task time-consuming, but the reliability of the validation varies with the experience of the analyst. Here, we report a systematic approach to evaluating peptide identifications made by automated search algorithms. The method is based on the principle that the candidate peptide sequence should adequately explain the observed fragment ions. Also, the mass errors of neighboring fragments should be similar. To evaluate our method, we studied tandem mass spectra obtained from tryptic digests of E. coli and HeLa cells. Candidate peptides were identified with the automated search engine Mascot and subjected to the manual validation method. The method found correct peptide identifications that were given low Mascot scores (e.g., 20-25) and incorrect peptide identifications that were given high Mascot scores (e.g., 40-50). The method comprehensively detected false results from searches designed to produce incorrect identifications. Comparison of the tandem mass spectra of synthetic candidate peptides to the spectra obtained from the complex peptide mixtures confirmed the accuracy of the evaluation method. Thus, the evaluation approach described here could help boost the accuracy of protein identification, increase number of peptides identified, and provide a step toward developing a more accurate next-generation algorithm for protein identification.
    BibTeX:
    @article{Chen2005,
      author = {Chen, Y and Kwon, SW and Kim, SC and Zhao, YM},
      title = {Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra},
      journal = {JOURNAL OF PROTEOME RESEARCH},
      year = {2005},
      volume = {4},
      number = {3},
      pages = {998-1005},
      doi = {{10.1021/pr049754t}}
    }
    
    Cheung, S. & Zakhor, A. Fast similarity search and clustering of video sequences on the world-wide-web {2005} IEEE TRANSACTIONS ON MULTIMEDIA
    Vol. {7}({3}), pp. {524-537} 
    article DOI  
    Abstract: We define similar video content as video sequences with almost identical content but possibly compressed at different qualities, reformatted to different sizes and frame-rates, undergone minor editing in either spatial or temporal domain, or summarized into keyframe sequences. Building a search engine to identify such similar content in the World-Wide Web requires: 1) robust video similarity measurements; 2) fast similarity search techniques on large databases; and 3) intuitive organization of search results. In a previous paper, we proposed a randomized technique called the video signature (ViSig) method for video similarity measurement. In this paper, we focus on the remaining two issues by proposing a feature extraction scheme for fast similarity search, and a clustering algorithm for identification of similar clusters. Similar to many other content-based methods, the ViSig method uses high-dimensional feature vectors to represent video. To warrant a fast response time for similarity searches on high dimensional vectors, we propose a novel nonlinear feature extraction scheme on arbitrary metric spaces that combines the triangle inequality with the classical Principal Component Analysis (PCA). We show experimentally that the proposed technique outperforms PCA, Fastmap, Triangle-Inequality Pruning, and Haar wavelet on signature data. To further improve retrieval performance, and provide better organization of similarity search results, we introduce a new graph-theoretical clustering algorithm on large databases of signatures. This algorithm treats all signatures as an abstract threshold graph, where the distance threshold is determined based on local data statistics. Similar clusters are then identified as highly connected regions in the graph. By measuring the retrieval performance against a ground-truth set, we show that our proposed algorithm outperforms simple thresholding, single-link and complete-link hierarchical clustering techniques.
    BibTeX:
    @article{Cheung2005,
      author = {Cheung, SCS and Zakhor, A},
      title = {Fast similarity search and clustering of video sequences on the world-wide-web},
      journal = {IEEE TRANSACTIONS ON MULTIMEDIA},
      year = {2005},
      volume = {7},
      number = {3},
      pages = {524-537},
      doi = {{10.1109/TMM.2005.846906}}
    }
    
    Chi, D., Costa, M., Zhao, L. & Badler, N. The EMOTE model for effort and shape {2000} SIGGRAPH 2000 CONFERENCE PROCEEDINGS, pp. {173-182}  inproceedings  
    Abstract: Human movements include limb gestures and postural attitude. Although many computer animation researchers have studied these classes of movements, procedurally generated movements still lack naturalness. We argue that looking only at the psychological notion of gesture is insufficient to capture movement qualities needed by animated characters. We advocate that the domain of movement observation science, specifically Laban Movement Analysis (LMA) and its Effort and Shape components, provides us with valuable parameters for the form and execution of qualitative aspects of movements. Inspired by some tenets shared among LMA proponents, we also point out that Effort and Shape phrasing across movements and the engagement of the whole body are essential aspects to be considered in the search for naturalness in procedurally generated gestures. Finally, we present EMOTE (Expressive MOTion Engine), a 3D character animation system that applies Effort and Shape qualities to independently defined underlying movements and thereby generates more natural synthetic gestures.
    BibTeX:
    @inproceedings{Chi2000,
      author = {Chi, D and Costa, M and Zhao, LW and Badler, N},
      title = {The EMOTE model for effort and shape},
      booktitle = {SIGGRAPH 2000 CONFERENCE PROCEEDINGS},
      year = {2000},
      pages = {173-182},
      note = {Computer Graphics Annual Conference, NEW ORLEANS, LA, JUL 23-28, 2000}
    }
    
    Chignell, M., Gwizdka, J. & Bodner, R. Discriminating meta-search: a framework for evaluation {1999} INFORMATION PROCESSING & MANAGEMENT
    Vol. {35}({3}), pp. {337-362} 
    article  
    Abstract: There was a proliferation of electronic information sources and search engines in the 1990s. Many of these information sources became available through the ubiquitous interface of the Web browser. Diverse information sources became accessible to information professionals and casual end users alike. Much of the information was also hyperlinked, so that information could be explored by browsing as well as searching, While vast amounts of information were now just a few keystrokes and mouseclicks away, as the choices multiplied, so did the complexity of choosing where and how to look for the electronic information. Much of the complexity in information exploration at the turn of the twenty-first century arose because there was no common cataloguing and control system across the various electronic information sources. In addition, the many search engines available differed widely in terms of their domain coverage, query methods and efficiency. Meta-search engines were developed to improve search performance by querying multiple search engines at once. In principle, meta-search engines could greatly simplify the search for electronic information by selecting a subset of first-level search engines and digital libraries to submit a query to based on the characteristics of the user, the query/topic, and the search strategy. This selection would be guided by diagnostic knowledge about which of the first-level search engines works best under what circumstances. Programmatic research is required to develop this diagnostic knowledge about first-level search engine performance. This paper introduces an evaluative framework for this type of research and illustrates its use in two experiments. The experimental results obtained are used to characterize some properties of leading search engines (as of 1998), Significant interactions were observed between search engine and two other factors (time of day and Web domain). These findings supplement those of earlier studies, providing preliminary information about the complex relationship between search engine functionality and performance in different contexts. While the specific results obtained represent a,time-dependent snapshot of search engine performance in 1998, the evaluative framework proposed should be generally applicable in the future. (C) 1999 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Chignell1999,
      author = {Chignell, MH and Gwizdka, J and Bodner, RC},
      title = {Discriminating meta-search: a framework for evaluation},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {1999},
      volume = {35},
      number = {3},
      pages = {337-362}
    }
    
    Childs, W., Dabiri, A., Al-Hinai, H. & Abdullah, H. VARI-RO solar-powered desalting technology {1999} DESALINATION
    Vol. {125}({1-3}), pp. {155-166} 
    article  
    Abstract: This paper reports on the innovative concepts study conducted for the Middle East Desalination Research Center (MEDRC) to determine the cost-effectiveness of new approaches to solar powered desalting. These approaches include combining of modem solar power conversion technology with newly developed, hydraulic-driven, pumping and energy recovery technology for brackish water and seawater desalting reverse osmosis (BWRO or SWRO) desalting. The study included a literature search of existing methods, preliminary concepting and assessment, technical analysis, and comparisons of water produced per quantity of solar energy insolation for various concepts. The hydraulic driven pumping and energy recovery system is known as the VARI-RO system (patent pending). Four new combinations of solar energy conversion and SWRO desalting systems were evaluated for comparison to existing methods, as follows: System A, solar photovoltaic-electric module with the VARI-RO electric motel: drive; System B, solar dish concentrator-Stirling engine electric module with the VARI-RO electric motor drive; System C, solar trough concentrator-thermal energy module with the VARI-RO direct drive engine. System D, sol:ar dish concentrator-thermal energy module with the VARI-RO direct drive engine. It was determined that the VARI-RO technology is uniquely suited for use with solar power because of (1) high efficiency of the pumping and energy recovery system, (2) high efficiency of the direct drive engine system, and (3) the capability to adjust the power consumption to match the solar power variations throughout the day. This study has shown that this solar powered desalination technology can provide substantial environmental benefits in the next century by supplying needed water to remote regions without extensive infrastructure, and also by reducing the environmental emissions (including CO2) for desalting saline water sources.
    BibTeX:
    @article{Childs1999,
      author = {Childs, WD and Dabiri, AE and Al-Hinai, HA and Abdullah, HA},
      title = {VARI-RO solar-powered desalting technology},
      journal = {DESALINATION},
      year = {1999},
      volume = {125},
      number = {1-3},
      pages = {155-166},
      note = {European Conference on Desalination and the Environment, LAS PALMAS, SPAIN, NOV 09-12, 1999}
    }
    
    Chipperfield, A. & Fleming, P. Multiobjective gas turbine engine controller design using genetic algorithms {1996} IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
    Vol. {43}({5}), pp. {583-587} 
    article  
    Abstract: This paper describes the use of multiobjective genetic algorithms (MOGA's) in the design of a multivariable control system for a gas turbine engine, The mechanisms employed to facilitate multiobjective search with the genetic algorithm are described with the aid of an example. It is shown that the MOGA confers a number of advantages over conventional multiobjective optimization methods by evolving a family of Pareto-optimal solutions rather than a single solution estimate, This allows the engineer to examine the trade-offs between the different design objectives and configurations during the course of an optimization. In addition, the paper demonstrates how the genetic algorithm can be used to search in both controller structure and parameter space thereby offering a potentially more general approach to optimization in controller design than traditional numerical methods, While the example in the paper deals with control system design, the approach described can be expected to be applicable to more general problems in the fields of computer aided design (CAD) and computer aided engineering (CAE).
    BibTeX:
    @article{Chipperfield1996,
      author = {Chipperfield, A and Fleming, P},
      title = {Multiobjective gas turbine engine controller design using genetic algorithms},
      journal = {IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS},
      year = {1996},
      volume = {43},
      number = {5},
      pages = {583-587}
    }
    
    Chiras, N., Evans, C. & Rees, D. Nonlinear gas turbine modeling using NARMAX structures {2001} IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
    Vol. {50}({4}), pp. {893-898} 
    article  
    Abstract: The estimation of a nonlinear autoregressive moving average with exogenous inputs (NARMAX) model of an aircraft gas turbine is presented. A method is proposed whereby periodic signals with certain harmonic content are used to qualify the nature of the nonlinearity of the engine in the frequency domain. The static behavior of the engine is investigated in the time domain to approximate the order of nonlinearity and this information is used a priori to restrict the search space of the potential NARMAX models. A forward-regression orthogonal estimation algorithm is then employed to select the model terms using the error reduction ratio. The performance of the estimated NARMAX model is illustrated against a range of small- and large-signal engine tests.
    BibTeX:
    @article{Chiras2001,
      author = {Chiras, N and Evans, C and Rees, D},
      title = {Nonlinear gas turbine modeling using NARMAX structures},
      journal = {IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT},
      year = {2001},
      volume = {50},
      number = {4},
      pages = {893-898},
      note = {Instrumentation and Measurement Technology Conference (IMTC 2000), BALTIMORE, MARYLAND, MAY 01-04, 2000}
    }
    
    Chung, W., Chen, H. & Nunamaker, J. A visual framework for knowledge discovery on the Web: An empirical study of business intelligence exploration {2005} JOURNAL OF MANAGEMENT INFORMATION SYSTEMS
    Vol. {21}({4}), pp. {57-84} 
    article  
    Abstract: Information overload often hinders knowledge discovery on the Web. Existing tools lack analysis and visualization capabilities. Search engine displays often overwhelm users with irrelevant information. This research proposes a visual framework for knowledge discovery on the Web. The framework incorporates Web mining, clustering, and visualization techniques to support effective exploration of knowledge. Two new browsing methods were developed and applied to the business intelligence domain: Web community uses a genetic algorithm to organize Web sites into a tree format; knowledge map uses a multidimensional scaling algorithm to place Web sites as points on a screen. Experimental results show that knowledge map outperformed Kartoo, a commercial search engine with graphical display, in terms of effectiveness and efficiency. Web community was found to be more effective, efficient, and usable than result list. Our visual framework thus helps to alleviate information overload on the Web and offers practical implications for search engine developers.
    BibTeX:
    @article{Chung2005,
      author = {Chung, W and Chen, H and Nunamaker, JF},
      title = {A visual framework for knowledge discovery on the Web: An empirical study of business intelligence exploration},
      journal = {JOURNAL OF MANAGEMENT INFORMATION SYSTEMS},
      year = {2005},
      volume = {21},
      number = {4},
      pages = {57-84}
    }
    
    Chung, W., Zhang, Y., Huang, Z., Wang, G., Ong, T. & Chen, H. Internet searching and browsing in a multilingual world: An experiment on the Chinese Business Intelligence Portal (CBizPort) {2004} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {55}({9}), pp. {818-831} 
    article DOI  
    Abstract: The rapid growth of the non- English-speaking Internet population has created a need for better searching and browsing capabilities in languages other than English. However, existing search engines may not serve the needs of many non-English-speaking Internet users. In this paper, we propose a generic and integrated approach to searching and browsing the Internet in a multilingual world. Based on this approach, we have developed the Chinese Business Intelligence Portal (CBizPort), a meta-search engine that searches for business information of mainland China, Taiwan, and Hong Kong. Additional functions provided by CBizPort include encoding conversion (between Simplified Chinese and Traditional Chinese), summarization, and categorization. Experimental results of our user evaluation study show that the searching and browsing performance of CBizPort was comparable to that of regional Chinese search engines, and CBizPort could significantly augment these search engines. Subjects' verbal comments indicate that CBizPort performed best in terms of analysis functions, cross-regional searching, and user-friendliness, whereas regional search engines were more efficient and more popular. Subjects especially liked CBizPort's summarizer and categorizer, which helped in understanding search results. These encouraging results suggest a promising future of our approach to Internet searching and browsing in a multilingual world.
    BibTeX:
    @article{Chung2004,
      author = {Chung, WY and Zhang, YW and Huang, Z and Wang, G and Ong, TH and Chen, HC},
      title = {Internet searching and browsing in a multilingual world: An experiment on the Chinese Business Intelligence Portal (CBizPort)},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2004},
      volume = {55},
      number = {9},
      pages = {818-831},
      doi = {{10.1002/asi.20025}}
    }
    
    Cilibrasi, R.L. & Vitanyi, P.M.B. The Google similarity distance {2007} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {19}({3}), pp. {370-383} 
    article  
    Abstract: Words and phrases acquire meaning from the way they are used in society, from their relative semantics to other words and phrases. For computers, the equivalent of ``society'' is ``database,'' and the equivalent of `` use'' is ``a way to search the database.'' We present a new theory of similarity between words and phrases based on information distance and Kolmogorov complexity. To fix thoughts, we use the World Wide Web (WWW) as the database, and Google as the search engine. The method is also applicable to other search engines and databases. This theory is then applied to construct a method to automatically extract similarity, the Google similarity distance, of words and phrases from the WWW using Google page counts. The WWW is the largest database on earth, and the context information entered by millions of independent users averages out to provide automatic semantics of useful quality. We give applications in hierarchical clustering, classification, and language translation. We give examples to distinguish between colors and numbers, cluster names of paintings by 17th century Dutch masters and names of books by English novelists, the ability to understand emergencies and primes, and we demonstrate the ability to do a simple automatic English-Spanish translation. Finally, we use the WordNet database as an objective baseline against which to judge the performance of our method. We conduct a massive randomized trial in binary classification using support vector machines to learn categories based on our Google distance, resulting in an a mean agreement of 87 percent with the expert crafted WordNet categories.
    BibTeX:
    @article{Cilibrasi2007,
      author = {Cilibrasi, Rudi L. and Vitanyi, Paul M. B.},
      title = {The Google similarity distance},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2007},
      volume = {19},
      number = {3},
      pages = {370-383},
      note = {IEEE Information Theory Workshop on Coding and Complexity, Rotorua, NEW ZEALAND, AUG-SEP, 2005}
    }
    
    Ciocca, G., Gagliardi, I. & Schettini, R. Quicklook(2): An integrated multimedia system {2001} JOURNAL OF VISUAL LANGUAGES AND COMPUTING
    Vol. {12}({1}), pp. {81-103} 
    article  
    Abstract: The need to retrieve visual information from large image collections is shared by many application domains. This paper describes the main features of the multimedia information retrieval engine of Quicklook(2). Quicklook(2) allows the user to query image and multimedia databases with the aid of sample images, or an impromptu sketch and/or textual descriptions, and progressively refine the system's response by indicating the relevance, or non-relevance of the retrieved items. The major innovation of the system is its relevance feedback mechanism that performs a statistical analysis of both the image and textual feature distributions of the retrieved items the user has judged relevant, or not relevant to identify what features the user has taken into account (and to what extent) in formulating this judgement, and then weigh their influence in the overall evaluation of similarity, as well as in the formulation of a new, single query that better expresses the user's multimedia information needs. Another important contribution is the design and integration with the relevance feedback mechanism of an indexing scheme based on triangle inequality to improve retrieval efficiency. The performance of the system is illustrated with examples from various application domains and for different types of queries (target search as well as similarity search). (C) 2001 Academic Press.
    BibTeX:
    @article{Ciocca2001,
      author = {Ciocca, G and Gagliardi, I and Schettini, R},
      title = {Quicklook(2): An integrated multimedia system},
      journal = {JOURNAL OF VISUAL LANGUAGES AND COMPUTING},
      year = {2001},
      volume = {12},
      number = {1},
      pages = {81-103}
    }
    
    Clark, J. Creatine and phosphocreatine: A review of their use in exercise and sport {1997} JOURNAL OF ATHLETIC TRAINING
    Vol. {32}({1}), pp. {45-51} 
    article  
    Abstract: Objective: Creatine and phosphocreatine (PCr) are important compounds in the normal energy metabolism of muscle. Recently, it has been shown that dietary creatine (5 to 20 g/day) can increase muscle creatine and PCr, with enhancement in anaerobic exercise performance after two weeks of administration caused by an increase in anaerobic capacity. Data Sources: MEDLINE was searched from 1983 to 1996 using key word `'creatine'' along with `'humans,'' `'muscle,'' `'exercise,'' and `'transport.'' Also, APStracts, the American Physiology Society search engine for abstracts, was searched from 1994 to 1996. Data Synthesis: Creatine is transported into the muscle cell by a specific transporter, resulting in increased intracellular creatine and PCr. The PCr is capable of acting as an energy buffer, protecting the adenosine triphosphate (ATP) concentration. Maintaining muscle nucleotides therefore enhances exercise performance and recovery, There have been reports that PCr protects the cells from ischemic damage and decreases the loss of nucleotides by stabilizing cell membranes, Indeed, intravenous PCr (2-4 g/day) has been administered to cyclists, resulting in a faster recovery time between training sessions. Conclusions/Recommendations: It is becoming evident that oral creatine supplementation may yield certain benefits to enhance the athlete's performance during maximal anaerobic exercise and interval training.
    BibTeX:
    @article{Clark1997,
      author = {Clark, JF},
      title = {Creatine and phosphocreatine: A review of their use in exercise and sport},
      journal = {JOURNAL OF ATHLETIC TRAINING},
      year = {1997},
      volume = {32},
      number = {1},
      pages = {45-51}
    }
    
    Clifford, R., Edmonson, M., Hu, Y., Nguyen, C., Scherpbier, T. & Buetow, K. Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project {2000} GENOME RESEARCH
    Vol. {10}({8}), pp. {1259-1265} 
    article  
    Abstract: SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. in addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a lava-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site [http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.
    BibTeX:
    @article{Clifford2000,
      author = {Clifford, R and Edmonson, M and Hu, Y and Nguyen, C and Scherpbier, T and Buetow, KH},
      title = {Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project},
      journal = {GENOME RESEARCH},
      year = {2000},
      volume = {10},
      number = {8},
      pages = {1259-1265}
    }
    
    Cobb, N.K. & Graham, A.L. Characterizing Internet searchers of smoking cessation information {2006} JOURNAL OF MEDICAL INTERNET RESEARCH
    Vol. {8}({3}) 
    article DOI  
    Abstract: Background: The Internet is a viable channel to deliver evidence-based smoking cessation treatment that has the potential to make a large population impact on reducing smoking prevalence. There is high demand for smoking cessation information and support on the Internet. Approximately 7% (10.2 million) of adult American Internet users have searched for information on quitting smoking. Little is known about these individuals, their smoking status, what type of cessation services they are seeking on the Internet, or how frequently these searches for cessation information are conducted. Objective: The primary goal of this study was to characterize individuals who search for smoking cessation information on the Internet to determine appropriate triage and treatment strategies. The secondary goal was to estimate the incidence of searches for cessation information using publicly available search engine data. Methods: We recruited individuals who clicked on a link to a leading smoking cessation website (QuitNet) from within the results of a search engine query. Individuals were ``intercepted'' before seeing the QuitNet home page and were invited to participate in the study. Those accepting the invitation were routed to an online survey about demographics, smoking characteristics, preferences for specific cessation services, and Internet search patterns. To determine the generalizability of our sample, national datasets on search engine usage patterns, market share, and keyword rankings were examined. These datasets were then used to estimate the number of queries for smoking cessation information each year. Results: During the 10-day study period, 2265 individuals were recruited and 29% (N = 655) responded. Of these, 59% were female and overall tended to be younger than the previously characterized general Internet population. Most (76 respondents were current smokers; 17% had quit within the last 7 days, and 7% had quit more than 7 days ago. Slightly more than half of active smokers (53 indicated that they were planning to quit in the next 30 days. Smokers were more likely to seek information on how to quit and on medications; former smokers were more interested in how to cope with withdrawal. All participants rated withdrawal information and individually tailored information as being more useful, while displaying little interest in telephone counseling, expert support, or peer support. Publicly available data from large search engines suggest that 4 million Americans search for resources on smoking cessation each year. Conclusions: This study adds to the limited data available on individuals who search for smoking cessation information on the Internet, supports the prior estimates of the size of the population, and indicates that these individuals are in appropriate stages for both active cessation interventions and aggressive relapse prevention efforts. Continued development and evaluation of online interventions is warranted, and organizations seeking to promote cessation should carefully evaluate the Internet as a possible modality for treatment and as a gateway to other traditional programs.
    BibTeX:
    @article{Cobb2006,
      author = {Cobb, Nathan K. and Graham, Amanda L.},
      title = {Characterizing Internet searchers of smoking cessation information},
      journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
      year = {2006},
      volume = {8},
      number = {3},
      doi = {{10.2196/jmir.8.3.e17}}
    }
    
    Coello, C., Christiansen, A. & Hernandez, F. A simple genetic algorithm for the design of reinforced concrete beams {1997} ENGINEERING WITH COMPUTERS
    Vol. {13}({4}), pp. {185-196} 
    article  
    Abstract: We present an optimization model for the design of rectangular reinforced concrete beams subject to a specified set of constraints. Our model is more realistic than previously published models because it minimizes the cost of the beam on strength design procedures, while also considering the costs of concrete, steel and shuttering. Thus our method leads to very practical designs. As there is an infinite number of possible beam dimensions and reinforcement ratios that yield the same moment of resistance, an efficient search technique is preferred over the more traditional iterative methods. We employ a simple genetic algorithm as the search engine, and we compare our results with those obtained via geometric programming. Since the adjustment of parameters in a genetic algorithm (e.g., population size, crossover and mutation rates, and maximum number of generations) is a significant problem for any application, we present our own methodology to deal with this problem. A prototype of this system is currently being tested in Mexico, in order to evaluate its potential as a reliable design tool for real world applications.
    BibTeX:
    @article{Coello1997,
      author = {Coello, CAC and Christiansen, AD and Hernandez, FS},
      title = {A simple genetic algorithm for the design of reinforced concrete beams},
      journal = {ENGINEERING WITH COMPUTERS},
      year = {1997},
      volume = {13},
      number = {4},
      pages = {185-196}
    }
    
    Cohen, W., Schapire, R. & Singer, Y. Learning to order things {1999} JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH
    Vol. {10}, pp. {243-270} 
    article  
    Abstract: There are many applications in which it is desirable to order rather than classify instances. Here we consider the problem of learning how to order instances given feedback in the form of preference judgments, i.e., statements to the effect that one instance should be ranked ahead of another. We outline a two-stage approach in which one first learns by conventional means a binary preference function indicating whether it is advisable to rank one instance before another. Here we consider an on-line algorithm for learning preference functions that is based on Freund and Schapire's ``Hedge'' algorithm. In the second stage, new instances are ordered so as to maximize agreement with the learned preference function. We show that the problem of finding the ordering that agrees best with a learned preference function is NP-complete. Nevertheless, we describe simple greedy algorithms that are guaranteed to find a good approximation. Finally, we show how metasearch can be formulated as an ordering problem, and present experimental results on learning a combination of ``search experts,'' each of which is a domain-specific query expansion strategy for a web search engine.
    BibTeX:
    @article{Cohen1999,
      author = {Cohen, WW and Schapire, RE and Singer, Y},
      title = {Learning to order things},
      journal = {JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH},
      year = {1999},
      volume = {10},
      pages = {243-270}
    }
    
    Coleman, D. Replacement migration, or why everyone is going to have to live in Korea: a fable for our times from the United Nations {2002} PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES
    Vol. {357}({1420}), pp. {583-598} 
    article DOI  
    Abstract: This paper considers international migration in the context of population ageing. In many Western countries, the search for appropriate responses to manage future population ageing and population decline has directed attention to international migration. It seems reasonable to believe that international migrants, mostly of young working age, can supply population deficits created by low birth rates, protect European society and economy from the economic costs of elderly dependency, and provide a worldforce to care for the elderly. Particular prominence has been given to this option through the publicity attendant on a report from the UN Population Division in 2000 on `replacement migration', which has been widely reported and widely misunderstood. Although immigration can prevent population decline, it is already well known that it can only prevent population ageing at unprecedented, unsustainable and increasing levels of inflow, which would generate rapid population growth and eventually displace the original population from its majority position. This paper reviews these arguments in the context of the causes and inevitability of population ageing, with examples mostly based on UK data. It discusses various options available in response to population ageing through workforce, productivity, pensions reform and other means. It concludes that there can be no `solution' to population ageing, which is to a considerable degree unavoidable. However, if the demographic regime of the United Kingdom continues to be relatively benign, future population ageing can be managed with tolerable inconvenience without recourse to increased immigration for `demographic' purposes. At present (2001), net immigration to the United Kingdom is already running at record levels and is now the main engine behind UK population and household growth. By itself, population stabilization, or even mild reduction, is probably to be welcomed in the United Kingdom, although the issue has attracted little attention since the 1970s.
    BibTeX:
    @article{Coleman2002,
      author = {Coleman, DA},
      title = {Replacement migration, or why everyone is going to have to live in Korea: a fable for our times from the United Nations},
      journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES},
      year = {2002},
      volume = {357},
      number = {1420},
      pages = {583-598},
      doi = {{10.1098/rstb.2001.1034}}
    }
    
    Cooper, L. A case study of information-seeking behavior in 7-year-old children in a semistructured situation {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({11}), pp. {904-922} 
    article DOI  
    Abstract: This article presents a case study of the information-seeking behavior of 7-year-old children in a semistructured situation in their school library media center. The study focuses on how young children who are in the process of learning to read cope with searching for information in a largely textual corpus, and how they make up for their deficit in textual experience. Children's search strategies are examined and discussed in the context of computer versus shelf searching, textual versus visual searching, and in comparison with adult search dimensions previously established.
    BibTeX:
    @article{Cooper2002,
      author = {Cooper, LZ},
      title = {A case study of information-seeking behavior in 7-year-old children in a semistructured situation},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {11},
      pages = {904-922},
      doi = {{10.1002/asi.10130}}
    }
    
    Corney, J., Rea, H., Clark, D., Pritchard, J., Breaks, M. & MacLeod, R. Coarse filters for shape matching {2002} IEEE COMPUTER GRAPHICS AND APPLICATIONS
    Vol. {22}({3}), pp. {65-74} 
    article  
    Abstract: We describe coarse shape filters that support our 3D, Internet-based search engine ShapeSifter, which we're developing to promote collaborative reuse of 3D engineering data.
    BibTeX:
    @article{Corney2002,
      author = {Corney, J and Rea, H and Clark, D and Pritchard, J and Breaks, M and MacLeod, R},
      title = {Coarse filters for shape matching},
      journal = {IEEE COMPUTER GRAPHICS AND APPLICATIONS},
      year = {2002},
      volume = {22},
      number = {3},
      pages = {65-74}
    }
    
    Cox, J., Matic, I., Hilger, M., Nagaraj, N., Selbach, M., Olsen, J.V. & Mann, M. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics {2009} NATURE PROTOCOLS
    Vol. {4}({5}), pp. {698-705} 
    article DOI  
    Abstract: MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high-resolution mass spectrometry (MS) data. Currently, Thermo LTQ-Orbitrap and LTQ-FT-ICR instruments are supported and Mascot is used as a search engine. This protocol explains step by step how to use MaxQuant on stable isotope labeling by amino acids in cell culture (SILAC) data obtained with double or triple labeling. Complex experimental designs, such as time series and drug-response data, are supported. A standard desktop computer is sufficient to fulfill the computational requirements. The workflow has been stress tested with more than 1,000 liquid chromatography/mass spectrometry runs in a single project. In a typical SILAC proteome experiment, hundreds of thousands of peptides and thousands of proteins are automatically and reliably quantified. Additional information for identified proteins, such as Gene Ontology, domain composition and pathway membership, is provided in the output tables ready for further bioinformatics analysis. The software is freely available at the MaxQuant home page.
    BibTeX:
    @article{Cox2009,
      author = {Cox, Juergen and Matic, Ivan and Hilger, Maximiliane and Nagaraj, Nagarjuna and Selbach, Matthias and Olsen, Jesper V. and Mann, Matthias},
      title = {A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics},
      journal = {NATURE PROTOCOLS},
      year = {2009},
      volume = {4},
      number = {5},
      pages = {698-705},
      doi = {{10.1038/nprot.2009.36}}
    }
    
    Creasy, D. & Cottrell, J. Error tolerant searching of uninterpreted tandem mass spectrometry data {2002} PROTEOMICS
    Vol. {2}({10}), pp. {1426-1434} 
    article  
    Abstract: An error tolerant mode for database matching of uninterpreted tandem mass spectrometry data is described. Selected database entries are searched without enzyme specificity, using a comprehensive list of chemical and post-translational modifications, together with a residue substitution matrix. The modifications are tested serially, to avoid the catastrophic loss of discrimination that would occur if all the permutations of large numbers of modifications in combination were possible. The new mode has been coded as an extension to the Mascot search engine, and tested against a number of Liquid chromatography-tandem mass spectrometry datasets. The results show a number of additional peptide matches, but require careful interpretation. The most significant limitation of this approach is that it can only reveal new matches to proteins that already have at least one significant peptide match.
    BibTeX:
    @article{Creasy2002,
      author = {Creasy, DM and Cottrell, JS},
      title = {Error tolerant searching of uninterpreted tandem mass spectrometry data},
      journal = {PROTEOMICS},
      year = {2002},
      volume = {2},
      number = {10},
      pages = {1426-1434}
    }
    
    Croft, D. & Peterson, M. An evaluation of the quality and contents of asthma education on the World Wide Web {2002} CHEST
    Vol. {121}({4}), pp. {1301-1307} 
    article  
    Abstract: Study objectives: To measure the accessibility and quality of currently available asthma education World Wide Web sites using the following criteria: accessibility by readability, language, and download time; information quality based on inclusion of core educational concepts and compliance with Health On the Net (HON) principles; and utilization of innovative technology. Design: Objective evaluation of 145 Web sites. Measurements and results: Four search engines or directories (Yahoo, HON, Alta Vista, and Healthfinder) were searched for ``asthma, patient information.'' A maximum of 50 Web sites from each search engine or directory was evaluated. Only 90 of the 145 Web sites actually contained asthma educational material. The mean (+/-SD) time necessary to open each Web site on a 28.800-bits-per-second modem was 33.6 (+/- 36.6) s. The mean number of graphics on the Web sites was 24.6 (+/- 30.2) files per page. The educational material required a mean reading level beyond the 10th grade. Only nine Web sites contained multilingual asthma education material. The mean number of HON principles with which the Web sites conformed was 6.3 (+/- 1.0) of 8 principles; 14 Web sites conformed to all the HON criteria. The average Web site contained 4.9 (+/- 2.5) of 8 core asthma educational concepts, and only 20 Web sites contained all 8 educational concepts. Very few Web sites utilized innovative educational technology. Conclusions: While patient asthma education Web sites are common, asthma educational material contains many accessibility barriers, is highly variable in quality and content, and takes little innovative use of technology. Patient educational material currently available on the World Wide Web fails to meet the information needs of patients.
    BibTeX:
    @article{Croft2002,
      author = {Croft, DR and Peterson, MW},
      title = {An evaluation of the quality and contents of asthma education on the World Wide Web},
      journal = {CHEST},
      year = {2002},
      volume = {121},
      number = {4},
      pages = {1301-1307}
    }
    
    Cui, H., Wen, J., Nie, J. & Ma, W. Query expansion by mining user logs {2003} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {15}({4}), pp. {829-839} 
    article  
    Abstract: Queries to search engines on the Web are usually short. They do not provide sufficient information for an effective selection of relevant documents. Previous research has proposed the utilization of query expansion to deal with this problem. However, expansion terms are usually determined on term co-occurrences within documents. In this study, we propose a new method for query expansion based on user interactions recorded in user logs. The central idea is to extract correlations between query terms and document terms by analyzing user logs. These correlations are then used to select high-quality expansion terms for new queries. Compared to previous query expansion methods, ours takes advantage of the user judgments implied in user logs. The experimental results show that the log-based query expansion method can produce much better results than both the classical search method and the other query expansion methods.
    BibTeX:
    @article{Cui2003,
      author = {Cui, H and Wen, JR and Nie, JY and Ma, WY},
      title = {Query expansion by mining user logs},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2003},
      volume = {15},
      number = {4},
      pages = {829-839},
      note = {11th International World Wide Web Conference, HONOLULU, HAWAII, MAY 07-11, 2002}
    }
    
    Cui, W., Ning, J., Naik, U. & Duncan, M. OptiRNAi, an RNAi design tool {2004} COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
    Vol. {75}({1}), pp. {67-73} 
    article DOI  
    Abstract: RNA interference (RNAi), a recently developed reverse genetics toot, has many advantages compared to traditional gene knockout methods. Appropriate selection of double stranded RNAs identical to a specific region(s) of the target gene is critical for the successful implementation of this technology. Recently, Elbashir et at. [Methods 26 (2002) 199] has established empirical criteria for siRNA sequence selection that significantly improved the success rate for RNAi attempts. We have developed OptiRNAi, a computational tool, which uses the Elbashir et at. criteria to predict appropriate target sequences for siRNA production. Specificity of these siRNAs for the target of interest can then be assessed by the investigator using the embedded Blast search engine optimized for RNAi design. Thus, OptiRNAi is an efficient and user friendly toot for RNAi design based on criteria that are more stringent than other available tools. (C) 2003 Elsevier Ireland Ltd. All rights reserved.
    BibTeX:
    @article{Cui2004,
      author = {Cui, WW and Ning, JC and Naik, UP and Duncan, MK},
      title = {OptiRNAi, an RNAi design tool},
      journal = {COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE},
      year = {2004},
      volume = {75},
      number = {1},
      pages = {67-73},
      doi = {{10.1016/j.cmpb.2003.09.002}}
    }
    
    Dagtas, S., Al-Khatib, W., Ghafoor, A. & Kashyap, R. Models for motion-based video indexing and retrieval {2000} IEEE TRANSACTIONS ON IMAGE PROCESSING
    Vol. {9}({1}), pp. {88-101} 
    article  
    Abstract: With the rapid proliferation of multimedia applications that require video data management, it is becoming more desirable to provide proper video data indexing techniques capable of representing the rich semantics in video data. In real-time applications, the need for efficient query processing is another reason for the use of such techniques, We present models that use the object motion information in order to characterize the events to allow subsequent retrieval. Algorithms for different spatiotemporal search cases in terms of spatial and temporal translation and scale invariance have been del eloped using various signal and image processing techniques. We have developed a prototype video search engine, PICTURESQUE (pictorial information and content transformation unified retrieval engine for spatiotemporal queries) to verify the proposed methods. Development of such technology will enable true multimedia search engines that will enable indexing and searching of the digital video data based on its true content.
    BibTeX:
    @article{Dagtas2000,
      author = {Dagtas, S and Al-Khatib, W and Ghafoor, A and Kashyap, RL},
      title = {Models for motion-based video indexing and retrieval},
      journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING},
      year = {2000},
      volume = {9},
      number = {1},
      pages = {88-101}
    }
    
    Darling, J. & Giovanelli, R. A search for OH megamasers at z > 0.1. II. Further results {2001} ASTRONOMICAL JOURNAL
    Vol. {121}({3}), pp. {1278-1293} 
    article  
    Abstract: We present current results of an ongoing survey for OH megamasers in luminous infrared galaxies at the Arecibo Observatory.(1) The survey is now two-thirds complete, and has resulted in the discovery of 35 new OH megamasers at z > 0.1, 24 of which are presented in this paper. We discuss the properties of each source in detail, including an exhaustive survey of the literature. We also place upper limits on the OH emission from 107 nondetections and list their IR, radio, and optical properties. The survey detection rate is one OH megamaser for every six candidates overall, but is a strong function of the far-IR luminosity of candidates and may depend on merger stage or on the central engine responsible for the IR luminosity in the merging galaxy pair. We also report the detection of IRAS 12032+1707, a new OH gigamaser.
    BibTeX:
    @article{Darling2001,
      author = {Darling, J and Giovanelli, R},
      title = {A search for OH megamasers at z > 0.1. II. Further results},
      journal = {ASTRONOMICAL JOURNAL},
      year = {2001},
      volume = {121},
      number = {3},
      pages = {1278-1293}
    }
    
    Dea-Ayuela, M.A., Perez-Castillo, Y., Meneses-Marcel, A., Ubeira, F.M., Bolas-Fernandez, F., Chou, K.-C. & Gonzalez-Diaz, H. HP-Lattice QSAR for dynein proteins: Experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence {2008} BIOORGANIC & MEDICINAL CHEMISTRY
    Vol. {16}({16}), pp. {7770-7776} 
    article DOI  
    Abstract: The toxicity and inefficacy of actual organic drugs against Leishmaniosis justify research projects to find new molecular targets in Leishmania species including Leishmania infantum ( L. infantum) and Leishmania major (L. major), both important pathogens. In this sense, quantitative structure-activity relationship (QSAR) methods, which are very useful in Bioorganic and Medicinal Chemistry to discover small-sized drugs, may help to identify not only new drugs but also new drug targets, if we apply them to proteins. Dyneins are important proteins of these parasites governing fundamental processes such as cilia and flagella motion, nuclear migration, organization of the mitotic splinde, and chromosome separation during mitosis. However, despite the interest for them as potential drug targets, so far there has been no report whatsoever on dyneins with QSAR techniques. To the best of our knowledge, we report here the first QSAR for dynein proteins. We used as input the Spectral Moments of a Markov matrix associated to the HP-Lattice Network of the protein sequence. The data contain 411 protein sequences of different species selected by ClustalX to develop a QSAR that correctly discriminates on average between 92.75% and 92.51% of dyneins and other proteins in four different train and cross-validation datasets. We also report a combined experimental and theoretic study of a new dynein sequence in order to illustrate the utility of the model to search for potential drug targets with a practical example. First, we carried out a 2D-electrophoresis analysis of L. infantum biological samples. Next, we excised from 2D-E gels one spot of interest belonging to an unknown protein or protein fragment in the region M < 20,200 and pI < 4. We used MASCOT search engine to find proteins in the L. major data base with the highest similarity score to the MS of the protein isolated from L. infantum. We used the QSAR model to predict the new sequence as dynein with probability of 99.99% without relying upon alignment. In order to confirm the previous function annotation we predicted the sequences as dynein with BLAST and the omniBLAST tools (96% alignment similarity to dyneins of other species). Using this combined strategy, we have successfully identified L. infantum protein containing dynein heavy chain, and illustrated the potential use of the QSAR model as a complement to alignment tools. (c) 2008 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Dea-Ayuela2008,
      author = {Dea-Ayuela, Maria Auxiliadora and Perez-Castillo, Yunierkis and Meneses-Marcel, Alfredo and Ubeira, Florencio M. and Bolas-Fernandez, Francisco and Chou, Kuo-Chen and Gonzalez-Diaz, Humberto},
      title = {HP-Lattice QSAR for dynein proteins: Experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence},
      journal = {BIOORGANIC & MEDICINAL CHEMISTRY},
      year = {2008},
      volume = {16},
      number = {16},
      pages = {7770-7776},
      doi = {{10.1016/j.bmc.2008.07.023}}
    }
    
    Deng, Z., Li, H., Tam, C., Shen, Q. & Love, P. An application of the Internet-based project management system {2001} AUTOMATION IN CONSTRUCTION
    Vol. {10}({2}), pp. {239-246} 
    article  
    Abstract: The great advance in information technologies (IT) and the availability of a wide range of software in recent years have brought many changes in the construction industry. The Internet, a new member of IT, offers a medium with new opportunities to manage construction projects. This paper describes an Internet-based project management system called ``Total Information Transfer System'' (TITS). TITS comprises six major functions including data exchange, information exchange, Internet chat, live video-cam, search engine and auxiliary services. TITS is demonstrated for project monitoring with a real-life project. (C) 2001 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Deng2001,
      author = {Deng, ZM and Li, H and Tam, CM and Shen, QP and Love, PED},
      title = {An application of the Internet-based project management system},
      journal = {AUTOMATION IN CONSTRUCTION},
      year = {2001},
      volume = {10},
      number = {2},
      pages = {239-246}
    }
    
    Dennis, S., Bruza, P. & McArthur, R. Web searching: A process-oriented experimental study of three interactive search paradigms {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({2}), pp. {120-133} 
    article  
    Abstract: This article compares search effectiveness when using query-based Internet search (via the Google search engine), directory-based search (via Yahoo), and phrase-based query reformulation-assisted search (via the Hyperindex browser) by means of a controlled, user-based experimental study. The focus was to evaluate aspects of the search process. Cognitive load was measured using a secondary digit-monitoring task to quantify the effort of the user in various search states; independent relevance judgements were employed to gauge the quality of the documents accessed during the search process and time was monitored as a function of search state. Results indicated directory-based search does not offer increased relevance over the query-based search (with or without query formulation assistance), and also takes longer. Query reformulation does significantly improve the relevance of the documents through which the user must trawl, particularly when the formulation of query terms is more difficult. However, the improvement in document relevance comes at the cost of increased search time, although this difference is quite small when the search is self-terminated. In addition, the advantage of the query reformulation seems to occur as a consequence of providing more discriminating terms rather than by increasing the length of queries.
    BibTeX:
    @article{Dennis2002,
      author = {Dennis, S and Bruza, P and McArthur, R},
      title = {Web searching: A process-oriented experimental study of three interactive search paradigms},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {2},
      pages = {120-133}
    }
    
    Ding, L., Pan, R., Finin, T., Joshi, A., Peng, Y. & Kolari, P. Finding and ranking knowledge on the Semantic Web {2005}
    Vol. {3729}SEMANTIC WEB - ISWC 2005, PROCEEDINGS, pp. {156-170} 
    inproceedings  
    Abstract: Swoogle helps software agents and knowledge engineers find Semantic Web knowledge encoded in RDF and OWL documents on the Web. Navigating such a Semantic Web on the Web is difficult due to the paucity of explicit hyperlinks beyond the namespaces in URIrefs and the few inter-document links like rdfs:seeAlso and owl:imports. In order to solve this issue, this paper proposes a novel Semantic Web navigation model providing additional navigation paths through Swoogle's search services such as the Ontology Dictionary. Using this model, we have developed algorithms for ranking the importance of Semantic Web objects at three levels of granularity: documents, terms and RDF graphs. Experiments show that Swoogle outperforms conventional web search engine and other ontology libraries in finding more ontologies, ranking their importance, and thus promoting the use and emergence of consensus ontologies.
    BibTeX:
    @inproceedings{Ding2005,
      author = {Ding, L and Pan, R and Finin, T and Joshi, A and Peng, Y and Kolari, P},
      title = {Finding and ranking knowledge on the Semantic Web},
      booktitle = {SEMANTIC WEB - ISWC 2005, PROCEEDINGS},
      year = {2005},
      volume = {3729},
      pages = {156-170},
      note = {4th International Semantic Web Conference (ISWC 2005), Galway, IRELAND, NOV 06-10, 2005}
    }
    
    Ding, Y.-S. & Zhang, T.-L. Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: An approach with immune genetic algorithm-based ensemble classifier {2008} PATTERN RECOGNITION LETTERS
    Vol. {29}({13}), pp. {1887-1892} 
    article DOI  
    Abstract: It is crucial to develop powerful tools to predict apoptosis protein locations for rapidly increasing gap between the number of known structural proteins and the number of known sequences in protein data-bank. In this study, based on the concept of pseudo amino acid (PseAA) composition originally introduced by Chou, a novel approximate entropy (ApEn) based PseAA composition is proposed to represent apoptosis protein sequences. An ensemble classifier is introduced, of which the basic classifier is the FKNN (fuzzy K-nearest neighbor) one, as prediction engine. Each basic classifier is trained in different dimensions of PseAA composition of protein sequences. The immune genetic algorithm (IGA) is used to search the optimal weight factors in generating the PseAA composition for crucial of weight factors in PseAA composition. The results obtained by jackknife test are quite encouraging, indicating that the proposed method might become a potentially useful tool for protein function, or at least can play a complimentary role to the existing methods in the relevant areas. (C) 2008 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Ding2008,
      author = {Ding, Yong-Sheng and Zhang, Tong-Liang},
      title = {Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: An approach with immune genetic algorithm-based ensemble classifier},
      journal = {PATTERN RECOGNITION LETTERS},
      year = {2008},
      volume = {29},
      number = {13},
      pages = {1887-1892},
      doi = {{10.1016/j.patrec.2008.06.007}}
    }
    
    Djajaputra, D., Wu, Q., Wu, Y. & Mohan, R. Algorithm and performance of a clinical IMRT beam-angle optimization system {2003} PHYSICS IN MEDICINE AND BIOLOGY
    Vol. {48}({19}), pp. {3191-3212} 
    article  
    Abstract: This paper describes the algorithm and examines the performance of an intensity-modulated radiation therapy (IMRT) beam-angle optimization (BAO) system. In this algorithm successive sets of beam angles are selected from a set of predefined directions using a fast simulated annealing (FSA) algorithm. An IMRT beam-profile optimization is performed on each generated set of beams. The IMRT optimization is accelerated by using a fast dose calculation method that utilizes a precomputed dose kernel. A compact kernel is constructed for each of the predefined beams prior to starting the FSA algorithm. The IMRT optimizations during the BAO are then performed using these kernels in a fast dose calculation engine. This technique allows the IMRT optimization to be performed more than two orders of magnitude faster than a similar optimization that uses a convolution dose calculation engine. Any type of optimization criterion present in the IMRT system can be used in this BAO system. An objective function based on clinically-relevant dose-volume (DV) criteria is used in this study. This facilitates the comparison between a BAO plan and the corresponding plan produced by a planner since the latter is usually optimized using a DV-based objective function. A simple prostate case and a complex head-and-neck (HN) case were used to evaluate the usefulness and performance of this BAO method. For the prostate case we compared the BAO results for three, five and seven coplanar beams with those of the same number of equispaced coplanar beams. For the HN case we compare the BAO results for seven and nine non-coplanar beams with that for nine equispaced coplanar beams. In each case the BAO algorithm was allowed to search up to 1000 different sets of beams. The BAO for the prostate cases were finished in about 1-2 h on a moderate 400 MHz workstation while that for the head-and-neck cases were completed in 13-17 h on a 750 MHz machine. No a priori beam-selection criteria have been used in achieving this performance. In both the prostate and the head-and-neck cases, BAO is shown to provide improvements in plan quality over that of the equispaced beams. The use of DV-based objective function also allows us to study the dependence of the improvement of plan quality offered by BAO on the DV criteria used in the optimization. We found that BAO is especially useful for cases that require strong DV criteria. The main advantages of this BAO system are its speed and its direct link to a clinical IMRT system.
    BibTeX:
    @article{Djajaputra2003,
      author = {Djajaputra, D and Wu, QW and Wu, Y and Mohan, R},
      title = {Algorithm and performance of a clinical IMRT beam-angle optimization system},
      journal = {PHYSICS IN MEDICINE AND BIOLOGY},
      year = {2003},
      volume = {48},
      number = {19},
      pages = {3191-3212}
    }
    
    Domingues, F., Lackner, P., Andreeva, A. & Sippl, M. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy {2000} JOURNAL OF MOLECULAR BIOLOGY
    Vol. {297}({4}), pp. {1003-1013} 
    article  
    Abstract: The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy. Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity. Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials. (C) 2000 Academic Press.
    BibTeX:
    @article{Domingues2000,
      author = {Domingues, FS and Lackner, P and Andreeva, A and Sippl, MJ},
      title = {Structure-based evaluation of sequence comparison and fold recognition alignment accuracy},
      journal = {JOURNAL OF MOLECULAR BIOLOGY},
      year = {2000},
      volume = {297},
      number = {4},
      pages = {1003-1013}
    }
    
    Dowd, S., Zaragoza, J., Rodriguez, J., Oliver, M. & Payton, P. Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST) {2005} BMC BIOINFORMATICS
    Vol. {6} 
    article DOI  
    Abstract: Background: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows. NET Distributed Basic Local Alignment Search Toolkit ( W. ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes ( 11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from http://liru.ars. usda. gov/ mainbioinformatics. html. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.
    BibTeX:
    @article{Dowd2005,
      author = {Dowd, SE and Zaragoza, J and Rodriguez, JR and Oliver, MJ and Payton, PR},
      title = {Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST)},
      journal = {BMC BIOINFORMATICS},
      year = {2005},
      volume = {6},
      doi = {{10.1186/1471-2105-6-93}}
    }
    
    Dralyuk, I., Brudno, M., Gelfand, M., Zorn, M. & Dubchak, I. ASDB: database of alternatively spliced genes {2000} NUCLEIC ACIDS RESEARCH
    Vol. {28}({1}), pp. {296-297} 
    article  
    Abstract: Version 2.1 of ASDB (Alternative Splicing Data Base) contains 1922 protein and 2486 DNA sequences. The protein entries from SWISS-PROT are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank, The search engine allows one to search over SWISS-PROT and GenBank fields and then follow the links to all variants. The database can be assessed at the URL http://cbcg.nersc.gov/asdb.
    BibTeX:
    @article{Dralyuk2000,
      author = {Dralyuk, I and Brudno, M and Gelfand, MS and Zorn, M and Dubchak, I},
      title = {ASDB: database of alternatively spliced genes},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2000},
      volume = {28},
      number = {1},
      pages = {296-297}
    }
    
    Dreilinger, D. & Howe, A. Experiences with selecting search engines using metasearch {1997} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {15}({3}), pp. {195-222} 
    article  
    Abstract: Search engines are among the most useful and high-profile resources on the Internet. The problem of finding information on the Internet has been replaced with the problem of knowing where search engines are, what they are designed to retrieve, and how to use them. This article describes and evaluates SavvySearch, a metasearch engine designed to intelligently select and interface with multiple remote search engines. The primary metasearch issue examined is the importance of carefully selecting and ranking remote search engines for user queries; We studied the efficacy of SavvySearch's incrementally acquired metaindex approach to selecting search engines by analyzing the effect of time and experience on performance. We also compared the metaindex approach to the simpler categorical approach and showed how much experience is required to surpass the simple scheme.
    BibTeX:
    @article{Dreilinger1997,
      author = {Dreilinger, D and Howe, AE},
      title = {Experiences with selecting search engines using metasearch},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {1997},
      volume = {15},
      number = {3},
      pages = {195-222}
    }
    
    Du, X., Sudjianto, A. & Chen, W. An integrated framework for optimization under uncertainty using inverse reliability strategy {2004} JOURNAL OF MECHANICAL DESIGN
    Vol. {126}({4}), pp. {562-570} 
    article DOI  
    Abstract: In this work, we propose an integrated framework for optimization under uncertainty that can bring both the design objective robustness and the probabilistic design constraints into account. The fundamental development of this work is the employment of an inverse reliability strategy that uses percentile performance for assessing both the objective robustness and probabilistic constraints. The percentile formulation for objective robustness provides us an accurate evaluation of the variation of an objective performance and a probabilistic measurement of the robustness. We can obtain more reasonable compound noise combinations for a robust design objective compared to using the traditional approach proposed by Taguchi. The proposed formulation is very efficient to solve since it only needs to evaluate the constraint functions at the required reliability levels. The other major development of this work is a new search algorithm for the Most Probable Point of Inverse Reliability (MPPIR) that can be used to efficiently evaluate percentile performances for both robustness and reliability assessments. Multiple strategies are employed in the MPPIR search, including using the steepest ascent direction and an arc search. The algorithm is applicable to general non-concave and non-convex performance functions of random variables following any continuous distributions. The effectiveness of the MPPIR search algorithm is verified using example problems. Overall, an engineering example on integrated robust and reliability design of a vehicle combustion engine piston is used to illustrate the benefits of our proposed method.
    BibTeX:
    @article{Du2004,
      author = {Du, XP and Sudjianto, A and Chen, W},
      title = {An integrated framework for optimization under uncertainty using inverse reliability strategy},
      journal = {JOURNAL OF MECHANICAL DESIGN},
      year = {2004},
      volume = {126},
      number = {4},
      pages = {562-570},
      doi = {{10.1115/1.1759358}}
    }
    
    Durand, P., Canard, L. & Mornon, J. Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT {1997} COMPUTER APPLICATIONS IN THE BIOSCIENCES
    Vol. {13}({4}), pp. {407-413} 
    article  
    Abstract: Motivation: When routinely analysing protein sequences, detailed analysis of database search results made with BLAST and FASTA becomes exceedingly time consuming and tedious work, as the resultant file may contain a list of hundreds of potential homologies. The interpretation of these results is usually carried out with a text editor which is not a convenient tool for this analysis, In addition, the format of data within BLAST and FASTA output files makes them difficult to read. Results: To facilitate and accelerate this analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.
    BibTeX:
    @article{Durand1997,
      author = {Durand, P and Canard, L and Mornon, JP},
      title = {Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT},
      journal = {COMPUTER APPLICATIONS IN THE BIOSCIENCES},
      year = {1997},
      volume = {13},
      number = {4},
      pages = {407-413}
    }
    
    Eastman, C. & Jansen, B. Coverage, relevance, and ranking: The impact of query operators on web search engine results {2003} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {21}({4}), pp. {383-411} 
    article  
    Abstract: Research has reported that about 10% of Web searchers utilize advanced query operators, with the other 90% using extremely simple queries. It is often assumed that the use of query operators, such as Boolean operators and phrase searching, improves the effectiveness of Web searching. We test this assumption by examining the effects of query operators on the performance of three major Web search engines. We selected one hundred queries from the transaction log of a Web search service. Each of these original queries contained query operators such as AND, OR, MUST APPEAR (+), or PHRASE ('' ``). We then removed the operators from these one hundred advanced queries. We submitted both the original and modified queries to three major Web search engines; a total of 600 queries were submitted and 5,748 documents evaluated. We compared the results from the original queries with the operators to the results from the modified queries without the operators. We examined the results for changes in coverage, relative precision, and ranking of relevant documents. The use of most query operators had no significant effect on coverage, relative precision, or ranking, although the effect varied depending on the search engine. We discuss implications for the effectiveness of searching techniques as currently taught, for future information retrieval system design, and for future research.
    BibTeX:
    @article{Eastman2003,
      author = {Eastman, CM and Jansen, BJ},
      title = {Coverage, relevance, and ranking: The impact of query operators on web search engine results},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2003},
      volume = {21},
      number = {4},
      pages = {383-411}
    }
    
    Eddleston, M., Szinicz, L., Eyer, P. & Buckley, N. Oximes in acute organophosphorus pesticide poisoning: a systematic review of clinical trials {2002} QJM-AN INTERNATIONAL JOURNAL OF MEDICINE
    Vol. {95}({5}), pp. {275-283} 
    article  
    Abstract: Background: Acute organophosphorus (OP) pesticide poisoning is widespread in the developing world. Standard treatment involves the administration of intravenous atropine and an oxime to counter acetylcholinesterase inhibition at the synapse, but the usefulness of oximes is uncertain. Aim: To assess the evidence on the use of oximes in OP poisoning. Design: Systematic review. Methods: We searched Medline, Embase, and Cochrane databases (last check 01/02/02) for `organophosphate' or `oxime' together with `poisoning' or `overdose'. We cross-referenced from other articles, and contacted experts to identify unpublished studies. A Web search engine [www.google.com] was also used, with the keywords `organophosphate', `oxime', and `trial' (last check 01/02/02). Results: We found two randomized controlled trials (RCTs) involving 182 patients treated with pralidoxime. The RCTs found no benefit with pralidoxime, and have been used to argue that pralidoxime should not be used in OP poisoning. Discussion: The RCT authors must be congratulated for attempting important studies in a difficult environment. However, their studies did not take into account recently clarified issues regarding outcome, and their methodology is unclear. A generalized statement that pralidoxime should not be used in OP poisoning is not supported by the published results. Oximes may well be irrelevant in the overwhelming self-poisoning typical of the tropics, but a large RCT comparing the current WHO-recommended pralidoxime regimen (>30 mg/kg bolus followed by >8 mg/kg/h infusion) with placebo is needed for a definitive answer. Such a study should be designed to identify any patient subgroups that might benefit from oximes.
    BibTeX:
    @article{Eddleston2002,
      author = {Eddleston, M and Szinicz, L and Eyer, P and Buckley, N},
      title = {Oximes in acute organophosphorus pesticide poisoning: a systematic review of clinical trials},
      journal = {QJM-AN INTERNATIONAL JOURNAL OF MEDICINE},
      year = {2002},
      volume = {95},
      number = {5},
      pages = {275-283}
    }
    
    Egelhofer, V., Gobom, J., Seitz, H., Giavalisco, P., Lehrach, H. & Nordhoff, E. Protein identification by MALDI-TOF-MS peptide mapping: A new strategy {2002} ANALYTICAL CHEMISTRY
    Vol. {74}({8}), pp. {1760-1771} 
    article DOI  
    Abstract: A new strategy for identifying proteins by MALDI-TOF-MS peptide mapping is reported. In contrast to current approaches, the strategy does not rely on a good relative or absolute mass accuracy as the criterion that discriminates false positive results. The protein sequence database is first searched for all proteins that match a minimum five of the submitted masses within the maximum expected relative errors when the default or externally determined calibration constants are used, for instance, +/- 500 ppm. Typicafly, this search retrieves many thousand candidate sequences. Assuming initially that each of these is the correct protein, the relative errors of the matching peptide masses are calculated for each candidate sequence. Linear regression analysis is then performed of the calculated relative errors as a function of m/z for each candidate sequence, and the standard deviation to the regression is used to distinguish the correct sequence among the candidates. We show that this parameter is independent of whether the mass spectrometric data were internally or externally calibrated. The result is a search engine that renders internal spectrum calibration unnecessary and adapts to the quality of the raw data without user interference. This is made possible by a dynamic scoring algorithm, which takes into account the number of matching peptide masses, the percentage of the protein's sequence covered by these peptides and, as new parameter, the determined standard deviation. The lower the standard deviation, the less cleavage peptides are required for identification and, ice versa. Performance of the new strategy is demonstrated and discussed. All necessary computing has been implemented in a computer program, free access to which is provided in the Internet.
    BibTeX:
    @article{Egelhofer2002,
      author = {Egelhofer, V and Gobom, J and Seitz, H and Giavalisco, P and Lehrach, H and Nordhoff, E},
      title = {Protein identification by MALDI-TOF-MS peptide mapping: A new strategy},
      journal = {ANALYTICAL CHEMISTRY},
      year = {2002},
      volume = {74},
      number = {8},
      pages = {1760-1771},
      doi = {{10.1021/ac011204g}}
    }
    
    Eichhorn, G., Kurtz, M., Accomazzi, A., Grant, C. & Murray, S. The NASA Astrophysics Data System: The search engine and its user interface {2000} ASTRONOMY & ASTROPHYSICS SUPPLEMENT SERIES
    Vol. {143}({1}), pp. {61-83} 
    article  
    Abstract: The ADS Abstract and Article Services pros ide access to the astronomical literature through the World Wide Web (WWW). The forms based user interface provides access to sophisticated searching capabilities that allow our users to find references in the fields of Astronomy, Physics/Geophysics, and astronomical Instrumentation and Engineering. The returned information includes links to other an-line information sources, creating an extensive astronomical digital library. Otter interfaces to the ADS databases provide direct access to the ADS data to allow developers of other data systems to integrate our data into their system. The search engine is a custom-built software system that is specifically tailored to search astronomical references. It includes an extensive synonym list that contains discipline specific knowledge about search term equivalences. Search request logs show the usage pattern of the various search system capabilities. Access logs show the world-wide distribution of ADS users. The ADS can be accessed at: http://adswww.harvard.edu.
    BibTeX:
    @article{Eichhorn2000,
      author = {Eichhorn, G and Kurtz, MJ and Accomazzi, A and Grant, CS and Murray, SS},
      title = {The NASA Astrophysics Data System: The search engine and its user interface},
      journal = {ASTRONOMY & ASTROPHYSICS SUPPLEMENT SERIES},
      year = {2000},
      volume = {143},
      number = {1},
      pages = {61-83}
    }
    
    Escobar-Morreale, H., Botella-Carretero, J., del Rey, F. & de Escobar, G. REVIEW: Treatment of hypothyroidism with combinations of levothyroxine plus liothyronine {2005} JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
    Vol. {90}({8}), pp. {4946-4954} 
    article DOI  
    Abstract: Context: Combined infusion of levothyroxine plus liothyronine, as opposed to levothyroxine alone, is the only way of restoring the concentrations of circulating TSH, T-4, and T-3 as well as those of both T-4 and T-3 in all tissues of thyroidectomized rats. Considering the substantial differences in thyroid hormone secretion, transport, and metabolism between rats and humans, whether or not combined levothyroxine plus liothyronine replacement therapy has advantages over treatment with levothyroxine alone in hypothyroid patients is still questioned. Evidence Acquisition: We conducted a systematic review of all the published controlled studies comparing treatment with levothyroxine alone with combinations of levothyroxine plus liothyronine in hypothyroid patients, identified through the Entrez-PubMed search engine. Evidence Synthesis: Nine controlled clinical trials were identified that compared treatment with levothyroxine alone and treatment with combinations of levothyroxine plus liothyronine and included a sufficient number of adult hypothyroid patients to yield meaningful results. In only one study did the combined therapy appear to have beneficial effects on the mood, quality of life, and psychometric performance of the patients over levothyroxine alone. These results have not been confirmed by later studies using either T-3 substitution protocols or approaches with fixed combinations of levothyroxine plus liothyronine, including those based on the physiological proportion in which T-3 and T-4 are secreted by the human thyroid. However, in some of these studies the patients preferred levothyroxine plus liothyronine combinations, for reasons not explained by changes in the psychological and psychometric tests employed. Yet patients' preference should be balanced against the possibility of adverse events resulting from the addition of liothyronine to levothyroxine, even in the small doses used in these studies. Conclusions: Until clear advantages of levothyroxine plus liothyronine are demonstrated, the administration of levothyroxine alone should remain the treatment of choice for replacement therapy of hypothyroidism.
    BibTeX:
    @article{Escobar-Morreale2005,
      author = {Escobar-Morreale, HF and Botella-Carretero, JI and del Rey, FE and de Escobar, GM},
      title = {REVIEW: Treatment of hypothyroidism with combinations of levothyroxine plus liothyronine},
      journal = {JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM},
      year = {2005},
      volume = {90},
      number = {8},
      pages = {4946-4954},
      doi = {{10.1210/jc.2005-0184}}
    }
    
    Faccioli, P., Ciceri, G.P., Provero, P., Stanca, A.M., Morcia, C. & Terzi, V. A combined strategy of ``in silico'' transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies {2007} PLANT MOLECULAR BIOLOGY
    Vol. {63}({5}), pp. {679-688} 
    article DOI  
    Abstract: Traditionally housekeeping genes have been employed as endogenous reference (internal control) genes for normalization in gene expression studies. Since the utilization of single housekeepers cannot assure an unbiased result, new normalization methods involving multiple housekeeping genes and normalizing using their mean expression have been recently proposed. Moreover, since a gold standard gene suitable for every experimental condition does not exist, it is also necessary to validate the expression stability of every putative control gene on the specific requirements of the planned experiment. As a consequence, finding a good set of reference genes is for sure a non-trivial problem requiring quite a lot of lab-based experimental testing. In this work we identified novel candidate barley reference genes suitable for normalization in gene expression studies. An advanced web search approach aimed to collect, from publicly available web resources, the most interesting information regarding the expression profiling of candidate housekeepers on a specific experimental basis has been set up and applied, as an example, on stress conditions. A complementary lab-based analysis has been carried out to verify the expression profile of the selected genes in different tissues and during heat shock response. This combined dry/wet approach can be applied to any species and physiological condition of interest and can be considered very helpful to identify putative reference genes to be shortlisted every time a new experimental design has to be set up.
    BibTeX:
    @article{Faccioli2007,
      author = {Faccioli, Primetta and Ciceri, Gian Paolo and Provero, Paolo and Stanca, Antonio Michele and Morcia, Caterina and Terzi, Valeria},
      title = {A combined strategy of ``in silico'' transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies},
      journal = {PLANT MOLECULAR BIOLOGY},
      year = {2007},
      volume = {63},
      number = {5},
      pages = {679-688},
      doi = {{10.1007/s11103-006-9116-9}}
    }
    
    Fagni, T., Perego, R., Silvestri, F. & Orlando, S. Boosting the performance of web search engines: Caching and prefetching query results by exploiting historical usage data {2006} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {24}({1}), pp. {51-78} 
    article  
    Abstract: This article discusses efficiency and effectiveness issues in caching the results of queries submitted to a Web search engine (WSE). We propose SDC ( Static Dynamic Cache), a new caching strategy aimed to efficiently exploit the temporal and spatial locality present in the stream of processed queries. SDC extracts from historical usage data the results of the most frequently submitted queries and stores them in a static, read-only portion of the cache. The remaining entries of the cache are dynamically managed according to a given replacement policy and are used for those queries that cannot be satisfied by the static portion. Moreover, we improve the hit ratio of SDC by using an adaptive prefetching strategy, which anticipates future requests by introducing a limited overhead over the back-end WSE. We experimentally demonstrate the superiority of SDC over purely static and dynamic policies by measuring the hit ratio achieved on three large query logs by varying the cache parameters and the replacement policy used for managing the dynamic part of the cache. Finally, we deploy and measure the throughput achieved by a concurrent version of our caching system. Our tests show how the SDC cache can be efficiently exploited by many threads that concurrently serve the queries of different users.
    BibTeX:
    @article{Fagni2006,
      author = {Fagni, T and Perego, R and Silvestri, F and Orlando, S},
      title = {Boosting the performance of web search engines: Caching and prefetching query results by exploiting historical usage data},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2006},
      volume = {24},
      number = {1},
      pages = {51-78}
    }
    
    Fan, W., Gordon, M. & Pathak, P. Genetic programming-based discovery of ranking functions for effective Web search {2005} JOURNAL OF MANAGEMENT INFORMATION SYSTEMS
    Vol. {21}({4}), pp. {37-56} 
    article  
    Abstract: Web search engines have become an integral part of the daily life of a knowledge worker, who depends on these search engines to retrieve relevant information from the Web or from the company's vast document databases. Current search engines are very fast in terms of their response time to a user query. But their usefulness to the user in terms of retrieval performance leaves a lot to be desired. Typically, the user has to sift through a lot of nonrelevant documents to get only a few relevant ones for the user's information needs. Ranking functions play a very important role in the search engine retrieval performance. In this paper, we describe a methodology using genetic programming to discover new ranking functions for the Web-based information-seeking task. We exploit the content as well as structural information in the Web documents in the discovery process. The discovery process is carried out for both the ad hoc task and the routing task in retrieval. For either of the retrieval tasks, the retrieval performance of these newly discovered ranking functions has been found to be superior to the performance obtained by well-known ranking strategies in the information retrieval literature.
    BibTeX:
    @article{Fan2005,
      author = {Fan, WG and Gordon, MD and Pathak, P},
      title = {Genetic programming-based discovery of ranking functions for effective Web search},
      journal = {JOURNAL OF MANAGEMENT INFORMATION SYSTEMS},
      year = {2005},
      volume = {21},
      number = {4},
      pages = {37-56}
    }
    
    Fan, W., Gordon, M. & Pathak, P. Discovery of context-specific ranking functions for effective information retrieval using genetic programming {2004} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {16}({4}), pp. {523-527} 
    article  
    Abstract: The Internet and corporate Intranets have brought a lot of information. People usually resort to search engines to find required information. However, these systems tend to use only one fixed ranking strategy regardless of the contexts. This poses serious performance problems when characteristics of different users, queries, and text collections are taken into account. In this paper, we argue that the ranking strategy should be context specific and we propose a new systematic method that can automatically generate ranking strategies for different contexts based on Genetic Programming (GP). The new method was tested on TREC data and the results are very promising.
    BibTeX:
    @article{Fan2004,
      author = {Fan, WG and Gordon, MD and Pathak, P},
      title = {Discovery of context-specific ranking functions for effective information retrieval using genetic programming},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2004},
      volume = {16},
      number = {4},
      pages = {523-527}
    }
    
    Feng, J., Bhargava, H.K. & Pennock, D.M. Implementing sponsored search in web search engines: Computational evaluation of alternative mechanisms {2007} INFORMS JOURNAL ON COMPUTING
    Vol. {19}({1}), pp. {137-148} 
    article DOI  
    Abstract: The practice of sponsored search advertising-where advertisers pay a fee to appear alongside particular Web search results-is now one of the largest and fastest growing source of revenue for Web search engines. We model and compare several mechanisms for allocating sponsored slots, including stylized versions of those used by Overture and Google, the two biggest brokers of sponsored search. The performance of these mechanisms depends on the degree of correlation between providers' willingness to pay and their relevance to the search term. Ranking providers based on the product of relevance and bid price performs well and is robust across varying degrees of correlation. Ranking purely based on bid price fares nearly as well when bids and relevance are positively correlated (the expected regime), and is further enhanced by adding an editorial filter. Regardless of the allocation mechanism, sponsored search revenues are lower when users' attention decays quickly at lower ranks, emphasizing the need to develop better user interfaces and control features. The search engine can address initial inscience of relevance scores by modifying rank allocations over time as it observes clickthroughs at each rank. We propose a rank-revision strategy that weights clicks on lower ranked items more than clicks on higher ranked items. This method is shown to converge to the optimal (maximum revenue) ordering faster and more consistently than other methods.
    BibTeX:
    @article{Feng2007,
      author = {Feng, Juan and Bhargava, Hemant K. and Pennock, David M.},
      title = {Implementing sponsored search in web search engines: Computational evaluation of alternative mechanisms},
      journal = {INFORMS JOURNAL ON COMPUTING},
      year = {2007},
      volume = {19},
      number = {1},
      pages = {137-148},
      doi = {{10.1287/ijoc.1050.0135}}
    }
    
    Fernandez, M., Kadiyska, Y., Suciu, D., Morishima, A. & Tan, W. SilkRoute: A framework for publishing relational data in XML {2002} ACM TRANSACTIONS ON DATABASE SYSTEMS
    Vol. {27}({4}), pp. {438-493} 
    article  
    Abstract: XML is the ``lingua franca'' for data exchange between interenterprise applications. In this work, we describe SilkRoute, a framework for publishing relational data in XML. In SilkRoute, relational data is published in three steps: the relational tables are presented to the database administrator in a canonical XML view; the database administrator defines in the XQuery query language a public, virtual XML view over the canonical XML view; and an application formulates an XQuery query over the public view. SilkRoute composes the application query with the public-view query, translates the result into SQL, executes this on the relational engine, and assembles the resulting tuple streams into an XML document. This work makes some key contributions to XML query processing. First, it describes an algorithm that translates an XQuery expression into SQL. The translation depends on a query representation that separates the structure of the output XML document from the computation that produces the document's content. The second contribution addresses the optimization problem of how to decompose an XML view over a relational database into an optimal set of SQL queries. We define formally the optimization problem, describe the search space, and propose a greedy, cost-based optimization algorithm, which obtains its cost estimates from the relational engine. Experiments confirm that the algorithm produces queries that are nearly optimal.
    BibTeX:
    @article{Fernandez2002,
      author = {Fernandez, M and Kadiyska, Y and Suciu, D and Morishima, A and Tan, WC},
      title = {SilkRoute: A framework for publishing relational data in XML},
      journal = {ACM TRANSACTIONS ON DATABASE SYSTEMS},
      year = {2002},
      volume = {27},
      number = {4},
      pages = {438-493}
    }
    
    Field, H., Fenyo, D. & Beavis, R. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database {2002} PROTEOMICS
    Vol. {2}({1}), pp. {36-47} 
    article  
    Abstract: RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring similar to40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user.
    BibTeX:
    @article{Field2002,
      author = {Field, HI and Fenyo, D and Beavis, RC},
      title = {RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database},
      journal = {PROTEOMICS},
      year = {2002},
      volume = {2},
      number = {1},
      pages = {36-47},
      note = {Meeting of the British-Electrophoresis-Society, YORK, ENGLAND, APR 04-06, 2001}
    }
    
    Filippenko, A., Li, W., Treffers, R. & Modjaz, M. The Lick Observatory Supernova Search with the Katzman Automatic Imaging Telescope {2001}
    Vol. {246}SMALL-TELESCOPE ASTRONOMY ON GLOBAL SCALES, pp. {121-130} 
    inproceedings  
    Abstract: The Katzman Automatic Imaging Telescope (KAIT) at Lick Observatory is a fully robotic 0.76-m reflector equipped with a CCD imaging camera. Its telescope control system checks the weather, opens the dome, points to the desired objects, finds and acquires guide stars, exposes, stores the data, and manipulates the data without human intervention. There is a 20-slot filter wheel, including UBVRI. Five-minute guided exposures yield detections of stars at R approximate to 20 mag when the seeing is good (less than or equal to 2''). One of our main goals is to discover nearby supernovae (SNe; redshifts generally less than 5000 km s(-1)), to be used for a variety of studies. Special emphasis is placed on finding them well before maximum brightness. A limit of similar to19 mag is reached in the 25-sec unfiltered, unguided exposures of our Lick Observatory Supernova Search (LOSS). We can observe over 1200 galaxies in a long night, and we try to cycle back to the same galaxies after 3 to 4 nights. Our software automatically subtracts template images from new observations and identifies supernova candidates that are subsequently examined by student research assistants. LOSS found 20 SNe in 1998, 40 in 1999, and 36 in 2000, making KAIT the world's most successful search engine for nearby SNe. We also find novae in the Local Group, comets, asteroids, and cataclysmic variables. Multi-filter follow-up photometry is conducted of the most important SNe, and all objects are monitored in unfiltered mode. A Web page describing LOSS is at http://astro.berkeley.edu/similar tobait/kait.html.
    BibTeX:
    @inproceedings{Filippenko2001,
      author = {Filippenko, AV and Li, WD and Treffers, RR and Modjaz, M},
      title = {The Lick Observatory Supernova Search with the Katzman Automatic Imaging Telescope},
      booktitle = {SMALL-TELESCOPE ASTRONOMY ON GLOBAL SCALES},
      year = {2001},
      volume = {246},
      pages = {121-130},
      note = {Colloquium on Small-Telescope Astronomy on Global Scales, KENTING, TAIWAN, JAN 04-08, 2001}
    }
    
    FISANICK, W., CROSS, K., FORMAN, J. & RUSINKO, A. EXPERIMENTAL SYSTEM FOR SIMILARITY AND 3D SEARCHING OF CAS REGISTRY SUBSTANCES .1. 3D SUBSTRUCTURE SEARCHING {1993} JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
    Vol. {33}({4}), pp. {548-559} 
    article  
    Abstract: Chemical Abstracts Service (CAS) is developing an experimental system for similarity and 3D searching on CAS Registry substances. The purpose of this system is to obtain user input on desirable capabilities and data content for such searching. Currently, the system supports 3D exact, substructure, and superstructure searching. The 3D coordinates for the system's databases were generated via the CONCORD program. These databases include a CAS 3D structure templates (CAST-3D) subset of over 365 000 substances with limited conformational flexibility. The experimental system utilizes a client-server architecture using client workstations for query framing and display and a single search engine compute server. Search levels include a screen step followed by atom-by-atom search (using a modified Ullman subgraph isomorphism algorithm), and, where appropriate, a geometric superimposition of the query and answer file substance. Two logical 3D substructure query types are supported: a general query, typically used for pharmacophore pattern matching, and a framework query, typically used in locating synthetic precursors that lead to a desired geometric orientation of substituents. Novel screens based on atom triangle and tetrangle distances as well as global and localized flexibility indices provide for effective and efficient screening. Also, user parameters can specify approximate local and global conformational flexibility characteristics for the matching file substances. This paper describes the features and capabilities that are currently available in the experimental system along with an illustrative application scenario.
    BibTeX:
    @article{FISANICK1993,
      author = {FISANICK, W and CROSS, KP and FORMAN, JC and RUSINKO, A},
      title = {EXPERIMENTAL SYSTEM FOR SIMILARITY AND 3D SEARCHING OF CAS REGISTRY SUBSTANCES .1. 3D SUBSTRUCTURE SEARCHING},
      journal = {JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES},
      year = {1993},
      volume = {33},
      number = {4},
      pages = {548-559},
      note = {SYMP ON STRUCTURE SEARCHING, AT THE 204TH NATIONAL MEETING OF THE AMERICAN CHEMICAL SOC, WASHINGTON, DC, AUG 24, 1992}
    }
    
    Fleming, D. & Wasserheit, J. From epidemiological synergy to public health policy and practice: the contribution of other sexually transmitted diseases to sexual transmission of HIV infection {1999} SEXUALLY TRANSMITTED INFECTIONS
    Vol. {75}({1}), pp. {3-17} 
    article  
    Abstract: Objectives: To review the scientific data on the role of sexually transmitted diseases (STDs) in sexual transmission of HIV infection and discuss the implications of these findings for HIV and STD prevention policy and practice. Methods: Articles were selected from a review of Medline, accessed with the OVID search engine. The search covered articles from January 1987 to September 1998 and yielded 2101 articles. Methods used to uncover articles which might have been missed included searching for related articles by author, and combing literature reviews. In addition, all abstracts under the category ``sexually transmitted diseases'' from the XI and XII International Conferences on AIDS (Vancouver 1996 and Geneva 1998) and other relevant scientific meetings were reviewed. Efforts were made to locate journal articles which resulted from the research reported in the identified abstracts. All original journal articles and abstracts which met one of the following criteria were included: (1) studies of the biological plausibility or mechanism of facilitation of HIV infectiousness or susceptibility by STDs, (2) prospective cohort studies (longitudinal or nested case-control) which estimate the risk of HIV infection associated with specific STDs or STD syndromes, or (3) intervention studies which quantitate the effect which STD treatment can have on HIV incidence. Results: Strong evidence indicates that both ulcerative and non-ulcerative STDs promote HIV transmission by augmenting HIV infectiousness and HIV susceptibility via a variety of biological mechanisms. These effects are reflected in the risk estimates found in numerous prospective studies from four continents which range from 2.0 to 23.5, with most clustering between 2 and 5. The relative importance of ulcerative and non-ulcerative STDs appears to be complex. Owing to the greater frequency of non-ulcerative STDs in many populations, these infections may be responsible for more HIV transmission than genital ulcers. However, the limited reciprocal impact of HIV infection on non-ulcerative STDs and the evidence that non-ulcerative STDs may increase risk primarily for the receptive partner (rather than bidirectionally) may modulate the impact of these diseases. The results of two community level randomised, controlled intervention trials conducted in Africa suggest that timely provision of STD services can substantially reduce HIV incidence, but raise additional questions about the optimal way to target and implement these services to achieve the greatest effect on HIV transmission. Conclusions: Available data leave little doubt that other STDs facilitate HN transmission through direct, biological mechanisms and that early STD treatment should be part of a high quality, comprehensive HIV prevention strategy. Policy makers, HIV prevention programme managers, and providers should focus initial implementation efforts on three key areas: (i) improving access to and quality of STD clinical services; (ii) promoting early and effective STD related healthcare behaviours; and (iii) establishing surveillance systems to monitor STD and HIV trends and their interrelations.
    BibTeX:
    @article{Fleming1999,
      author = {Fleming, DT and Wasserheit, JN},
      title = {From epidemiological synergy to public health policy and practice: the contribution of other sexually transmitted diseases to sexual transmission of HIV infection},
      journal = {SEXUALLY TRANSMITTED INFECTIONS},
      year = {1999},
      volume = {75},
      number = {1},
      pages = {3-17}
    }
    
    Fonseca, C. & Fleming, P. Multiobjective optimization and multiple constraint handling with evolutionary algorithms - Part II: Application example {1998} IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART A-SYSTEMS AND HUMANS
    Vol. {28}({1}), pp. {38-47} 
    article  
    Abstract: The evolutionary approach to multiple function optimization formulated in the first part of the paper [1] is applied to the optimization of the low-pressure spool speed governor of a Pegasus gas turbine engine, This study illustrates how a technique such as the multiobjective genetic algorithm can be applied, and exemplifies how design requirements can be refined as the algorithm runs, Several objective functions and associated goals express design concerns in direct form, i,e,, as the designer would state them, While such a designer-oriented formulation is very attractive, its practical usefulness depends heavily on the ability to search and optimize cost surfaces in a class much broader than usual, as already provided to a large extent by the genetic algorithm (GA), The two instances of the problem studied demonstrate the need for preference articulation in cases where many and highly competing objectives lead to a nondominated set too large for a finite population to sample effectively, It is shown that only a very small portion of the nondominated set is of practical relevance, which further substantiates the need to supply preference information to the GA, The paper concludes with a discussion of the results.
    BibTeX:
    @article{Fonseca1998,
      author = {Fonseca, CM and Fleming, PJ},
      title = {Multiobjective optimization and multiple constraint handling with evolutionary algorithms - Part II: Application example},
      journal = {IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART A-SYSTEMS AND HUMANS},
      year = {1998},
      volume = {28},
      number = {1},
      pages = {38-47}
    }
    
    Ford, N., Miller, D. & Moss, N. Web search strategies and retrieval effectiveness: an empirical study {2002} JOURNAL OF DOCUMENTATION
    Vol. {58}({1}), pp. {30-48} 
    article DOI  
    Abstract: This paper reports the results of a study funded by the Arts and Humanities. Research Board which sought to investigate links between Web search strategies and retrieval effectiveness. A total of 68 students, enrolled on masters programmes in librarianship, information management and information systems, searched for two topics using the AltaVista search engine. Logs of the resultant 341 queries, along with relevance judgements for over 4,000 retrieved items, were analysed using factor analysis and regression. The differing but complementary types and strengths of evidence produced by these two forms of analysis are discussed and presented. Retrieval effectiveness was associated Positively with best-match searching and negatively with Boolean searching. The implications of these findings for Web searching are discussed.
    BibTeX:
    @article{Ford2002,
      author = {Ford, N and Miller, D and Moss, N},
      title = {Web search strategies and retrieval effectiveness: an empirical study},
      journal = {JOURNAL OF DOCUMENTATION},
      year = {2002},
      volume = {58},
      number = {1},
      pages = {30-48},
      doi = {{10.1108/00220410210425395}}
    }
    
    Ford, N., Miller, D. & Moss, N. The role of individual differences in Internet searching: An empirical study {2001} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {52}({12}), pp. {1049-1066} 
    article  
    Abstract: This article reports the results of a study of the role of individual differences in Internet searching. The dimensions of individual differences forming the focus of the research consisted of: cognitive styles; levels of prior experience; Internet perceptions; study approaches; age; and gender. Sixty-nine Masters students searched for information on a prescribed topic using the AltaVista search engine. Results were assessed using simple binary relevance judgements. Factor analysis and multiple regression revealed interesting differences, retrieval effectiveness being linked to: male gender, low cognitive complexity; an imager (as opposed to verbalizer) cognitive style; and a number of Internet perceptions and study approaches grouped here as indicating low self-efficacy. The implications of these findings for system development and for future research are discussed.
    BibTeX:
    @article{Ford2001,
      author = {Ford, N and Miller, D and Moss, N},
      title = {The role of individual differences in Internet searching: An empirical study},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2001},
      volume = {52},
      number = {12},
      pages = {1049-1066}
    }
    
    Freeman, B., Chapman, S. & Rimmer, M. The case for the plain packaging of tobacco products {2008} ADDICTION
    Vol. {103}({4}), pp. {580-590} 
    article  
    Abstract: Aims The Framework Convention on Tobacco Control (FCTC) requires nations that have ratified the convention to ban all tobacco advertising and promotion. In the face of these restrictions, tobacco packaging has become the key promotional vehicle for the tobacco industry to interest smokers and potential smokers in tobacco products. This paper reviews available research into the probable impact of mandatory plain packaging and internal tobacco industry statements about the importance of packs as promotional vehicles. It critiques legal objections raised by the industry about plain packaging violating laws and international trade agreements. Methods Searches for available evidence were conducted within the internal tobacco industry documents through the online document archives; tobacco industry trade publications; research literature through the Medline and Business Source Premier databases; and grey literature including government documents, research reports and non-governmental organization papers via the Google internet search engine. Results Plain packaging of all tobacco products would remove a key remaining means for the industry to promote its products to billions of the world's smokers and future smokers. Governments have required large surface areas of tobacco packs to be used exclusively for health warnings without legal impediment or need to compensate tobacco companies. Conclusions Requiring plain packaging is consistent with the intention to ban all tobacco promotions. There is no impediment in the FCTC to interpreting tobacco advertising and promotion to include tobacco packs.
    BibTeX:
    @article{Freeman2008,
      author = {Freeman, Becky and Chapman, Simon and Rimmer, Matthew},
      title = {The case for the plain packaging of tobacco products},
      journal = {ADDICTION},
      year = {2008},
      volume = {103},
      number = {4},
      pages = {580-590}
    }
    
    Freyne, J., Smyth, B., Coyle, M., Balfe, E. & Briggs, P. Further experiments on collaborative ranking in community-based Web search {2004} ARTIFICIAL INTELLIGENCE REVIEW
    Vol. {21}({3-4}), pp. {229-252} 
    article  
    Abstract: As the search engine arms-race continues, search engines are constantly looking for ways to improve the manner in which they respond to user queries. Given the vagueness of Web search queries, recent research has focused on ways to introduce context into the search process as a means of clarifying vague, under-specified or ambiguous query terms. In this paper we describe a novel approach to using context in Web search that seeks to personalize the results of a generic search engine for the needs of a specialist community of users. In particular we describe two separate evaluations in detail that demonstrate how the collaborative search method has the potential to deliver significant search performance benefits to end-users while avoiding many of the privacy and security concerns that are commonly associated with related personalization research.
    BibTeX:
    @article{Freyne2004,
      author = {Freyne, J and Smyth, B and Coyle, M and Balfe, E and Briggs, P},
      title = {Further experiments on collaborative ranking in community-based Web search},
      journal = {ARTIFICIAL INTELLIGENCE REVIEW},
      year = {2004},
      volume = {21},
      number = {3-4},
      pages = {229-252},
      note = {14th Artificial Intelligence and Cognitive Science Conference (AICS 2003), Dublin, IRELAND, SEP 17-19, 2003}
    }
    
    Fu, Z., Rose, J. & Wang, B. SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination {2005} ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
    Vol. {61}({Part 7}), pp. {951-959} 
    article DOI  
    Abstract: SGXPro consists of four components. (i) A parallel workflow engine that was designed to automatically manage communication between the different processes and build systematic searches of algorithm/program/parameter space to generate the best possible result for a given data set. This is performed by offering the user a palette of programs and techniques commonly used in X-ray structure determination in an environment that lets the user choose programs in a mix-and-match manner, without worrying about inter-program communication and file formats, during the structure-determination process. The current SGXPro program palette includes 3DSCALE, SHELXD, ISAS, SOLVE/RESOLVE, DM, SOLOMON, DMMULTI, BLAST, AMoRe, EPMR, XTALVIEW, ARP/wARP and MAID. (ii) A client/server architecture that allows the user to utilize the best computing facility available. (iii) Plug-in-and-play design, which allows easily integration of new programs into the system. (iv) User-friendly interface.
    BibTeX:
    @article{Fu2005,
      author = {Fu, ZQ and Rose, J and Wang, BC},
      title = {SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination},
      journal = {ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY},
      year = {2005},
      volume = {61},
      number = {Part 7},
      pages = {951-959},
      doi = {{10.1107/S0907444905010541}}
    }
    
    Fuhr, N. & Grossjohann, K. XIRQL: An XML query language based on information retrieval concepts {2004} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {22}({2}), pp. {313-356} 
    article  
    Abstract: XIRQL (''circle'') is an XML query language that incorporates imprecision and vagueness for both structural and content-oriented query conditions. The corresponding uncertainty is handled by a consistent probabilistic model. The core features of XIRQL are ( 1) document ranking based on index term weighting, (2) specificity-oriented search for retrieving the most relevant parts of documents, (3) datatypes with vague predicates for dealing with specific types of content and (4) structural vagueness for vague interpretation of structural query conditions. A XIRQL database may contain several classes of documents, where all documents in a class conform to the same DTD; links between documents also are supported. XIRQL queries are translated into a path algebra, which can be processed by our HyREX retrieval engine.
    BibTeX:
    @article{Fuhr2004,
      author = {Fuhr, N and Grossjohann, K},
      title = {XIRQL: An XML query language based on information retrieval concepts},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2004},
      volume = {22},
      number = {2},
      pages = {313-356}
    }
    
    Funkhouser, T., Min, P., Kazhdan, M., Chen, J., Halderman, A., Dobkin, D. & Jacobs, D. A search engine for 3D models {2003} ACM TRANSACTIONS ON GRAPHICS
    Vol. {22}({1}), pp. {83-105} 
    article  
    Abstract: As the number of 3D models available on the Web grows, there is an increasing need for a search engine to help people find them. Unfortunately, traditional text-based search techniques are not always effective for 3D data. In this article, we investigate new shape-based search methods. The key challenges are to develop query methods simple enough for novice users and matching algorithms robust enough to work for arbitrary polygonal models. We present a Web-based search engine system that supports queries based on 3D sketches, 2D sketches, 3D models, and/or text keywords. For the shape-based queries, we have developed a new matching algorithm that uses spherical harmonics to compute discriminating similarity measures without requiring repair of model degeneracies or alignment of orientations. It provides 46 to 245% better performance than related shape-matching methods during precision-recall experiments, and it is fast enough to return query results from a repository of 20,000 models in under a second. The net result is a growing interactive index of 3D models available on the Web (i.e., a Google for 3D models).
    BibTeX:
    @article{Funkhouser2003,
      author = {Funkhouser, T and Min, P and Kazhdan, M and Chen, J and Halderman, A and Dobkin, D and Jacobs, D},
      title = {A search engine for 3D models},
      journal = {ACM TRANSACTIONS ON GRAPHICS},
      year = {2003},
      volume = {22},
      number = {1},
      pages = {83-105}
    }
    
    Gaglio, C. & Katz, J. The psychological basis of opportunity identification: Entrepreneurial alertness {2001} SMALL BUSINESS ECONOMICS
    Vol. {16}({2}), pp. {95-111} 
    article  
    Abstract: Opportunity identification represents a unique entrepreneurial behavior yet its processes and dynamics remain mysterious. Entrepreneurial alertness, a distinctive set of perceptual and information-processing skills, has been advanced as the cognitive engine driving the opportunity identification process. To date, empirical support has been equivocal; however, these early studies suffer from fundamental mistakes in theory and method. These mistakes are examined and addressed. A research agenda for the systematic and conceptually sound study of entrepreneurial alertness and opportunity identification is outlined.
    BibTeX:
    @article{Gaglio2001,
      author = {Gaglio, CM and Katz, JA},
      title = {The psychological basis of opportunity identification: Entrepreneurial alertness},
      journal = {SMALL BUSINESS ECONOMICS},
      year = {2001},
      volume = {16},
      number = {2},
      pages = {95-111}
    }
    
    Gal, R., Shamir, A. & Cohen-Or, D. Pose-oblivious shape signature {2007} IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
    Vol. {13}({2}), pp. {261-271} 
    article  
    Abstract: A 3D shape signature is a compact representation for some essence of a shape. Shape signatures are commonly utilized as a fast indexing mechanism for shape retrieval. Effective shape signatures capture some global geometric properties which are scale, translation, and rotation invariant. In this paper, we introduce an effective shape signature which is also pose-oblivious. This means that the signature is also insensitive to transformations which change the pose of a 3D shape such as skeletal articulations. Although some topology-based matching methods can be considered pose-oblivious as well, our new signature retains the simplicity and speed of signature indexing. Moreover, contrary to topology-based methods, the new signature is also insensitive to the topology change of the shape, allowing us to match similar shapes with different genus. Our shape signature is a 2D histogram which is a combination of the distribution of two scalar functions defined on the boundary surface of the 3D shape. The first is a definition of a novel function called the local-diameter function. This function measures the diameter of the 3D shape in the neighborhood of each vertex. The histogram of this function is an informative measure of the shape which is insensitive to pose changes. The second is the centricity function that measures the average geodesic distance from one vertex to all other vertices on the mesh. We evaluate and compare a number of methods for measuring the similarity between two signatures, and demonstrate the effectiveness of our pose-oblivious shape signature within a 3D search engine application for different databases containing hundreds of models.
    BibTeX:
    @article{Gal2007,
      author = {Gal, Ran and Shamir, Ariel and Cohen-Or, Daniel},
      title = {Pose-oblivious shape signature},
      journal = {IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS},
      year = {2007},
      volume = {13},
      number = {2},
      pages = {261-271}
    }
    
    Gandal, N. The dynamics of competition in the internet search engine market {2001} INTERNATIONAL JOURNAL OF INDUSTRIAL ORGANIZATION
    Vol. {19}({7}), pp. {1103-1117} 
    article  
    Abstract: Search engines hold the key to helping consumers access the wealth of information on the web. In this paper I examine the evolution of and competition in the internet search engine market. The goal of my analysis is to examine whether early entrants benefit in the long run from their first-mover position in internet markets, I End that while early entrants (Yahoo, Lycos, Excite, Infoseek, and Altavista) still have an advantage, the pure ``brand effect'' advantage has been declining over time. Yahoo has maintained its leadership position by providing a superior product. The success of a wave of recent new entrants suggests that entry barriers are still quite low in the internet search engine market. (C) 2001 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Gandal2001,
      author = {Gandal, N},
      title = {The dynamics of competition in the internet search engine market},
      journal = {INTERNATIONAL JOURNAL OF INDUSTRIAL ORGANIZATION},
      year = {2001},
      volume = {19},
      number = {7},
      pages = {1103-1117}
    }
    
    Garcia-Vallve, S., Guzman, E., Montero, M. & Romeu, A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes {2003} NUCLEIC ACIDS RESEARCH
    Vol. {31}({1}), pp. {187-189} 
    article DOI  
    Abstract: The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complet genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database contains 88 bacterial and archaeal complet genomes, including multiple chromosomes and strains. For each genome, the database provides statistical parameters for all the genes, as well as averages and standard deviations of G+C content, codon usage, relative synonymous codon usage and amino-acid content. It also provides information about correspondence analyses of the codon usage, plus lists of extraneous group of genes in terms of G+C content and lists of putatively acquired genes. With this information, researchers can explore the G+C content and codon usage of a gene when they find incongruities in sequence-based phylogenetic trees. A search engine that allows searches for gene names or keywords for a specific organism is also available. HGT-DB is freely accessible at http://www.fut.es/similar todebb/HGT.
    BibTeX:
    @article{Garcia-Vallve2003,
      author = {Garcia-Vallve, S and Guzman, E and Montero, MA and Romeu, A},
      title = {HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2003},
      volume = {31},
      number = {1},
      pages = {187-189},
      doi = {{10.1093/nar/gkg004}}
    }
    
    Ginsberg, J., Mohebbi, M.H., Patel, R.S., Brammer, L., Smolinski, M.S. & Brilliant, L. Detecting influenza epidemics using search engine query data {2009} NATURE
    Vol. {457}({7232}), pp. {1012-U4} 
    article DOI  
    Abstract: Seasonal influenza epidemics are a major public health concern, causing tens of millions of respiratory illnesses and 250,000 to 500,000 deaths worldwide each year(1). In addition to seasonal influenza, a new strain of influenza virus against which no previous immunity exists and that demonstrates human- to- human transmission could result in a pandemic with millions of fatalities(2). Early detection of disease activity, when followed by a rapid response, can reduce the impact of both seasonal and pandemic influenza(3,4). One way to improve early detection is to monitor health- seeking behaviour in the form of queries to online search engines, which are submitted by millions of users around the world each day. Here we present a method of analysing large numbers of Google search queries to track influenza- like illness in a population. Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza- like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. This approach may make it possible to use search queries to detect influenza epidemics in areas with a large population of web search users.
    BibTeX:
    @article{Ginsberg2009,
      author = {Ginsberg, Jeremy and Mohebbi, Matthew H. and Patel, Rajan S. and Brammer, Lynnette and Smolinski, Mark S. and Brilliant, Larry},
      title = {Detecting influenza epidemics using search engine query data},
      journal = {NATURE},
      year = {2009},
      volume = {457},
      number = {7232},
      pages = {1012-U4},
      doi = {{10.1038/nature07634}}
    }
    
    Glover, E., Lawrence, S., Birmingham, W. & Giles, C. Architecture of a metasearch engine that supports user information needs {1999} PROCEEDINGS OF THE EIGHTH INTERNATIONAL CONFERENCE ON INFORMATION KNOWLEDGE MANAGEMENT, CIKM'99, pp. {210-216}  inproceedings  
    Abstract: When a query is submitted to a metasearch engine, decisions are made with respect to the underlying search engines to be used, what modifications will be made to the query, and how to score the results. These decisions are typically made by considering only the user's keyword query, neglecting the larger information need. Users with specific needs, such as ``research papers'' or ``homepages,'' are not able to express these needs in a way that affects the decisions made by the metasearch engine. fn this paper, we describe a metasearch engine architecture that considers the user's information need for each decision. Users with different needs, but the same keyword query, may search different sub-search engines, have different modifications made to their query, and have results ordered differently. Our architecture combines several powerful approaches together in a single general purpose metasearch engine.
    BibTeX:
    @inproceedings{Glover1999,
      author = {Glover, EJ and Lawrence, S and Birmingham, WP and Giles, CL},
      title = {Architecture of a metasearch engine that supports user information needs},
      booktitle = {PROCEEDINGS OF THE EIGHTH INTERNATIONAL CONFERENCE ON INFORMATION KNOWLEDGE MANAGEMENT, CIKM'99},
      year = {1999},
      pages = {210-216},
      note = {8th International Conference on Information Knowledge Management (CIKM 99), KANSAS CITY, MO, NOV 02-06, 1999}
    }
    
    Glovsky, M., Miguel, A. & Cass, G. Particulate air pollution: Possible relevance in asthma {1997} ALLERGY AND ASTHMA PROCEEDINGS
    Vol. {18}({3}), pp. {163-166} 
    article  
    Abstract: The relative importance of air pollution in the pathogenesis of bronchial asthma has been of interest for several decades. Numerous studies on the role of gaseous air pollution containing ozone, nitrogen dioxide, sulfur dioxide, and carbon monoxide have been published. Very little attention has been focused on the role of respirable particles in the causation of asthma. In this article we summarize some of our ongoing investigations into the sources and composition of airborne particles in the Los Angeles and Pasadena atmosphere, including the search for biologically active particles that may induce asthma attacks. It is found that the urban atmosphere contains not only combustion-derived particles from diesel engine exhaust and gasoline-powered motor vehicle exhaust, bur also particles formed from biological starting materials including plant debris, cigarette smoke, wood smoke, and meat smoke as well as tire debris containing some natural rubber and paved road dust. Paved road dust is a very complex mixture of particles including garden soil, tire dust, plant fragments, redeposited atmospheric particles of all types, and pollen fragments presumably ground up by passing traffic. We have shown previously that latex allergen can be extracted from tire dust, from roadside dust, and front respirable air samples taken at Los Angeles and Long Beach. At present, work is underway to identify the larger range of allergens that may be contributed by the entrainment of paved road dust into the atmosphere. The possible importance of pollen fragments present in paved rand dust in very small particle sizes is discussed as well as their potential relevance in asthma.
    BibTeX:
    @article{Glovsky1997,
      author = {Glovsky, MM and Miguel, AG and Cass, GR},
      title = {Particulate air pollution: Possible relevance in asthma},
      journal = {ALLERGY AND ASTHMA PROCEEDINGS},
      year = {1997},
      volume = {18},
      number = {3},
      pages = {163-166}
    }
    
    Golovin, A. & Henrick, K. MSDmotif: exploring protein sites and motifs {2008} BMC BIOINFORMATICS
    Vol. {9} 
    article DOI  
    Abstract: Background: Protein structures have conserved features - motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB) is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results: We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, phi/psi sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS) protocol. An additional entry point facilitates XML requests with XML responses. Conclusion: MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.
    BibTeX:
    @article{Golovin2008,
      author = {Golovin, Adel and Henrick, Kim},
      title = {MSDmotif: exploring protein sites and motifs},
      journal = {BMC BIOINFORMATICS},
      year = {2008},
      volume = {9},
      doi = {{10.1186/1471-2105-9-312}}
    }
    
    Goodrum, A. & Spink, A. Image searching on the Excite Web search engine {2001} INFORMATION PROCESSING & MANAGEMENT
    Vol. {37}({2}), pp. {295-311} 
    article  
    Abstract: A growing body of research is beginning to explore the information-seeking behavior of Web users. The vast majority of these studies have concentrated on the area of textual information retrieval (IR). Little research has examined how people search for non-textual information on the Internet, and few large-scale studies has investigated visual information-seeking behavior with general-purpose Web search engines. This study examined visual information needs as expressed in users' Web image queries. The data set examined consisted of 1,025,908 sequential queries from 211,058 users of Excite, a major Internet search service. Twenty-eight terms were used to identify queries for both still and moving images, resulting in a subset of 33,149 image queries by 9855 users. We provide data on: (1) image queries - the number of queries and the number of search terms per user, (2) image search sessions - the number of queries per user, modifications made to subsequent queries in a session, and (3) image terms - their rank/frequency distribution and the most highly used search terms. On average, there were 3.36 image queries per user containing an average of 3.74 terms per query. Image queries contained a large number of unique terms. The most frequently occurring image related terms appeared less than 10% of the time, with most terms occurring only once. We contrast this to earlier work by P.G.B. Enser, Journal of Documentation 51 (2) (1995) 126-170, who examined written queries for pictorial information in a non-digital environment. Implications for the development of models for visual information retrieval, and for the design of Web search engines are discussed. (C) 2001 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Goodrum2001,
      author = {Goodrum, A and Spink, A},
      title = {Image searching on the Excite Web search engine},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2001},
      volume = {37},
      number = {2},
      pages = {295-311}
    }
    
    Gordon, M. & Pathak, P. Finding information on the World Wide Web: the retrieval effectiveness of search engines {1999} INFORMATION PROCESSING & MANAGEMENT
    Vol. {35}({2}), pp. {141-180} 
    article  
    Abstract: Search engines are essential for finding information on the World Wide Web. We conducted a study to see how effective eight search engines are. Expert searchers sought information on the Web for users who had legitimate needs for information, and these users assessed the relevance of the information retrieved. We calculated traditional information retrieval measures of recall and precision at varying numbers of retrieved documents and used these as the bases for statistical comparisons of retrieval effectiveness among the eight search engines. We also calculated the likelihood that a document retrieved by one search engine was retrieved by other search engines as well. (C) 1999 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Gordon1999,
      author = {Gordon, M and Pathak, P},
      title = {Finding information on the World Wide Web: the retrieval effectiveness of search engines},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {1999},
      volume = {35},
      number = {2},
      pages = {141-180}
    }
    
    Graves, J. A survey of validated automated home blood pressure monitors available for the Internet shopper {2005} BLOOD PRESSURE MONITORING
    Vol. {10}({2}), pp. {103-107} 
    article  
    Abstract: Objective Self-measurement of blood pressure using an automated home blood pressure monitoring (AHBPM) is increasingly used in hypertension management. Internet commerce increases dramatically each year. This study looked to identify the availability of validity of AHBPM and the correct cuff size to go with the AHBPM. Methods and results Using the search engine `Google.com', the author identified 124 consecutive unique sites offering at least one AHBPM. Validated AHBPM were those devices that had published studies showing that they had passed a recognized validation protocol. Each site was evaluated for all forms of sphygmomanometer, number of AHBPM, manual blood pressure devices, all cuff sizes available, additional cost of large adult cuff, number of validated AHBPM offered, and whether the site mentioned device validation. Of the 124 sites, 109 (81 offered arm AHBPM and 66 (53 offered one or more (range, 1-11) validated AHBPM. Only six of the 66 (9 offering a validated AHBPM mentioned that fact; 58 of the 109 (53 sites offering arm AHBPM offered more than one size of cuff; and 46 of the 58 (80 charged extra for a large adult cuff (average 23.75, range, 4.80-98). Conclusions Validated AHBPMs are readily available on the Internet. Currently, these sites do little to aid the consumer in purchasing a validated AHBPM. Large adult cuffs, commonly needed by hypertensive patients, are not always available for purchase. Charging extra for large adult cuffs is a potential hindrance to consumers purchasing the correct cuff size for accurate blood pressure measurement and should be eliminated. Blood &COPY; 2005 Lippincott Williams & Wilkins.
    BibTeX:
    @article{Graves2005,
      author = {Graves, JW},
      title = {A survey of validated automated home blood pressure monitors available for the Internet shopper},
      journal = {BLOOD PRESSURE MONITORING},
      year = {2005},
      volume = {10},
      number = {2},
      pages = {103-107}
    }
    
    Greene, D., Appel, A., Reinert, S. & Palumbo, M. Lumbar disc herniation - Evaluation of information on the internet {2005} SPINE
    Vol. {30}({7}), pp. {826-829} 
    article  
    Abstract: Study Design. An original study was performed evaluating the information presented on existing web sites for the topic of lumbar disc herniation. Objectives. The purpose of this study was to evaluate the type and quality of internet information available to patients on the topic of lumbar disc herniation. Our secondary objectives were to rank the identified World Wide Web sites with respect to the caliber of relevant information and to determine the propensity for secondary commercial gain by the web site sponsors. Summary of Background Data. Two-thirds of the United States population ``surfs'' the internet. A substantial percentage of internet users search for medical information on the World Wide Web. Because no standards exist regarding the publication of medical literature on the internet, the relevant web sites vary dramatically in terms of content and quality. Misleading or inaccurate information poses a theoretical risk to patients seeking treatment for medical conditions. Methods. Five search terms ( lumbar disc herniation, herniated nucleus pulposus, herniated disc, slipped disc, and sciatica) were entered into 5 commonly used search engines. The first 25 links displayed by each engine were evaluated for a theoretical total of 625 web sites. Each site was evaluated in terms of content, authorship, and secondary commercial gain. An information quality score of 0 to 25 points was generated for each site; a score of 20 or greater was indicative of ``high-quality'' content. Results. Our search identified 169 unique web sites of which only 16 ( 9.5 scored >= 20 on the information quality score; 103 (60.9 scored <= 10. The overall mean information quality score was 9. Highest mean scores were noted for commercial corporate (13.1) and hospital-based sites (11.2). Overall, 34.3% of sites sought secondary commercial gain. Higher scoring sites were more likely to appear within the first 10 links identified by each search engine. Conclusions. The quality of internet information on lumbar disc herniation is variable. Less than 10% of relevant web sites were determined to be of high-quality. The vast majority of sites were of poor informational value and more than one-third sought secondary commercial-gain. The rank list of high quality sites generated from our informational quality score should prove useful to patients seeking information on the internet pertaining to lumbar disc herniation.
    BibTeX:
    @article{Greene2005,
      author = {Greene, DL and Appel, AJ and Reinert, SE and Palumbo, MA},
      title = {Lumbar disc herniation - Evaluation of information on the internet},
      journal = {SPINE},
      year = {2005},
      volume = {30},
      number = {7},
      pages = {826-829}
    }
    
    Griffiths, J. & Brophy, P. Student searching behavior and the web: Use of academic resources and google {2005} LIBRARY TRENDS
    Vol. {53}({4}), pp. {539-554} 
    article  
    Abstract: This article reports results of two user studies of search engine use conducted to evaluate the United Kingdom's national academic sector digital information services and projects. The results presented here focus on student searching behavior and show that commercial Internet search engines dominate students' information-seeking strategy. Forty-five percent of students use Google as their first port of call when locating information, with the university library catalogue used by 10 percent of the sample. Results of students' perceptions of ease of use, success, time taken to search, and reasons for stopping a search are also presented.
    BibTeX:
    @article{Griffiths2005,
      author = {Griffiths, JR and Brophy, P},
      title = {Student searching behavior and the web: Use of academic resources and google},
      journal = {LIBRARY TRENDS},
      year = {2005},
      volume = {53},
      number = {4},
      pages = {539-554}
    }
    
    Griffiths, K. & Christensen, H. The quality and accessibility of Australian depression sites on the World Wide Web {2002} MEDICAL JOURNAL OF AUSTRALIA
    Vol. {176}({Suppl. S}), pp. {S97-S104} 
    article  
    Abstract: Objectives: To provide information about Australian depression sites and the quality of their content; to identify possible indicators of the quality of site content; and determine the accessibility of Australian depression web sites. Design: Cross-sectional survey of 15 Australian depression web sites. Main outcome measures: (I) Quality of treatment content (concordance of site information with evidence-based guidelines, number of evidence-based treatments recommended, discussion of other relevant issues, subjective rating of treatment content); (ii) potential quality indicators (conformity with DISCERN criteria, citation of scientific evidence); (iii) accessibility (search engine rank). Results: Mean content quality scores were not high and site accessibility was poor. There was a consistent association between the quality-of-content measures and the DISCERN and scientific accountability scores. Search engine rank was not associated with content quality. Conclusions: The quality of information about depression on Australian websites could be improved. DISCERN may be a useful indicator of website quality, as may scientific accountability. The sites that received the highest quality-of-content ratings were beyondblue, BluePages, CRUfAD and InfraPsych.
    BibTeX:
    @article{Griffiths2002,
      author = {Griffiths, KM and Christensen, H},
      title = {The quality and accessibility of Australian depression sites on the World Wide Web},
      journal = {MEDICAL JOURNAL OF AUSTRALIA},
      year = {2002},
      volume = {176},
      number = {Suppl. S},
      pages = {S97-S104}
    }
    
    Grimmelmann, J. eThe structure of search engine law {2007} IOWA LAW REVIEW
    Vol. {93}({1}), pp. {1-63} 
    article  
    BibTeX:
    @article{Grimmelmann2007,
      author = {Grimmelmann, James},
      title = {eThe structure of search engine law},
      journal = {IOWA LAW REVIEW},
      year = {2007},
      volume = {93},
      number = {1},
      pages = {1-63}
    }
    
    GUNER, O., HENRY, D. & PEARLMAN, R. USE OF FLEXIBLE QUERIES FOR SEARCHING CONFORMATIONALLY FLEXIBLE MOLECULES IN DATABASES OF 3-DIMENSIONAL STRUCTURES {1992} JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
    Vol. {32}({1}), pp. {101-109} 
    article  
    Abstract: Searching for conformationally flexible molecules is currently a topic of widespread study. In general, this type of three-dimensional (3D) search can proceed by locating the flexibility information either in a database (by storing multiple conformers or conformational analysis results), or in a search engine (by implementing flexible fitting methods), or in a search query (by combining fixed and mobile query features). This paper describes the third approach, using a flexible pharmacophoric query for ACE inhibitors. 3D searches were performed using the MACCS-3D structural database system to search MDDR-3D, a database of about 17000 3D drug structures of current interest. The structures in the database were built using the CONCORD program. The paper describes a stepwise procedure for building the query, performing searches, and optimizing the query to obtain a high ratio of structures with the desired activity. The results offer a useful solution to the problem of searching conformationally flexible molecules in databases of 3D structures and illustrate how to introduce conformational flexibility in the domain of the search query.
    BibTeX:
    @article{GUNER1992,
      author = {GUNER, OF and HENRY, DR and PEARLMAN, RS},
      title = {USE OF FLEXIBLE QUERIES FOR SEARCHING CONFORMATIONALLY FLEXIBLE MOLECULES IN DATABASES OF 3-DIMENSIONAL STRUCTURES},
      journal = {JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES},
      year = {1992},
      volume = {32},
      number = {1},
      pages = {101-109}
    }
    
    Gutwin, C., Paynter, G., Witten, I., Nevill-Manning, C. & Frank, E. Improving browsing in digital libraries with keyphrase indexes {1999} DECISION SUPPORT SYSTEMS
    Vol. {27}({1-2}), pp. {81-104} 
    article  
    Abstract: Browsing accounts for much of people's interaction with digital libraries, but it is poorly supported by standard search engines. Conventional systems often operate at the wrong level, indexing words when people think in terms of topics, and returning documents when people want a broader view. As a result, users cannot easily determine what is in a collection, how well a particular topic is covered, or what kinds of queries will provide useful results. We have built a new kind of search engine, Keyphind, that is explicitly designed to support browsing. Automatically extracted keyphrases form the basic unit of both indexing and presentation, allowing users to interact with the collection at the level of topics and subjects rather than words and documents. The keyphrase index also provides a simple mechanism for clustering documents, refining queries, and previewing results. We compared Keyphind to a traditional query engine in a small usability study. Users reported that certain kinds of browsing tasks were much easier with the new interface, indicating that a keyphrase index would be a useful supplement to existing search tools. (C) 1999 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Gutwin1999,
      author = {Gutwin, C and Paynter, G and Witten, I and Nevill-Manning, C and Frank, E},
      title = {Improving browsing in digital libraries with keyphrase indexes},
      journal = {DECISION SUPPORT SYSTEMS},
      year = {1999},
      volume = {27},
      number = {1-2},
      pages = {81-104}
    }
    
    Haas, M. Improving the economics of biodiesel production through the use of low value lipids as feedstocks: vegetable oil soapstock {2005} FUEL PROCESSING TECHNOLOGY
    Vol. {86}({10}), pp. {1087-1096} 
    article DOI  
    Abstract: Semirefined and refined vegetable oils are the predominant feedstocks for the production of biodiesel. However, their relatively high costs render the resulting fuels unable to compete with petroleum-derived fuel. We have investigated the production of fatty acid methyl esters (FAME; biodiesel) from soapstock (SS), a byproduct of edible oil refining that is substantially less expensive than edible-grade refined oils. Multiple approaches were taken in search of a route to the production of fatty acid methyl esters from soybean soapstock. The most effective method involved the complete saponification of the soapstock followed by acidulation using methods similar to those presently employed in industry. This resulted in an acid oil with a free fatty acid (FFA) content greater than 90 These fatty acids were efficiently converted to methyl esters by acid-catalyzed esterification. The fatty acid composition of the resulting ester product reflected that of soy soapstock and was largely similar to that of soybean oil. Following a simple washing protocol, this preparation met the established specifications for biodiesel of the American Society for Testing and Materials. Engine emissions and performance during operation on soy soapstock biodiesel were comparable to those on biodiesel from soy oil. An economic analysis suggested that the production cost of soapstock biodiesel would be approximately US 0.41/1, a 25% reduction relative to the estimated cost of biodiesel produced from soy oil. Published by Elsevier B.V.
    BibTeX:
    @article{Haas2005,
      author = {Haas, MJ},
      title = {Improving the economics of biodiesel production through the use of low value lipids as feedstocks: vegetable oil soapstock},
      journal = {FUEL PROCESSING TECHNOLOGY},
      year = {2005},
      volume = {86},
      number = {10},
      pages = {1087-1096},
      doi = {{10.1016/j.fuproc.2004.11.004}}
    }
    
    Halcomb, E.J., Gholizadeh, L., DiGiacomo, M., Phillips, J. & Davidson, P.M. Literature review: considerations in undertaking focus group research with culturally and linguistically diverse groups {2007} JOURNAL OF CLINICAL NURSING
    Vol. {16}({6}), pp. {1000-1011} 
    article DOI  
    Abstract: Aims. This integrated literature review seeks to identify the key considerations in conducting focus groups and discusses the specific considerations for focus group research with culturally and linguistically diverse groups. Background. The focus group method is a technique of group interview that generates data through the opinions expressed by participants. Focus groups have become an increasingly popular method of data collection in health care research. Although focus groups have been used extensively with Western populations, they are a particularly useful tool for engaging culturally and linguistically diverse populations. The success of focus groups in this context is dependent upon the cultural competence of the research team and the research questions. Methods. The electronic databases Medline, CINAHL, Embase, Psychlit and the Internet using the Google Scholar search engine were explored using the search terms `focus group', `cultural sensitivity', `transcultural nursing', `transcultural care', `cultural diversity' and `ethnic groups'. Hand searching of reference lists and relevant journals was also undertaken. English language articles were selected for the review if they discussed the following issues: (i) methodological implications of the focus group method; (ii) strengths and limitations of the focus group method; (iii) recommendations for researchers and (iv) use of the focus group in culturally and linguistically diverse groups. Conclusions were drawn from each of the articles and consensus regarding a summary of recommendations was derived from a minimum of two authors. Results. Findings from this review revealed several key issues involving focus group implementation including recruitment, sample size, data collection, data analysis and use within multicultural populations. Strengths and limitations of the focus group method were also identified. Conclusions. Focus groups are a useful tool to expand existing knowledge about service provision and identify consumer needs that will assist in the development of future intervention programmes, particularly within multicultural populations. Careful planning related to methodological and pragmatic issues are critical in deriving effective data and protecting participants. Relevance to clinical practice. Focus groups can facilitate increased understanding of perspectives of culturally and linguistically diverse groups and thereby shape clinical practice to better meet the needs of these groups.
    BibTeX:
    @article{Halcomb2007,
      author = {Halcomb, Elizabeth J. and Gholizadeh, Leila and DiGiacomo, Michelle and Phillips, Jane and Davidson, Patricia M.},
      title = {Literature review: considerations in undertaking focus group research with culturally and linguistically diverse groups},
      journal = {JOURNAL OF CLINICAL NURSING},
      year = {2007},
      volume = {16},
      number = {6},
      pages = {1000-1011},
      doi = {{10.1111/j.1365-2702.2006.01760.x}}
    }
    
    Hammouda, K. & Kamel, M. Efficient phrase-based document indexing for web document clustering {2004} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {16}({10}), pp. {1279-1296} 
    article  
    Abstract: Document clustering techniques mostly rely on single term analysis of the document data set, such as the Vector Space Model. To achieve more accurate document clustering, more informative features including phrases and their weights are particularly important in such scenarios. Document clustering is particularly useful in many applications such as automatic categorization of documents, grouping search engine results, building a taxonomy of documents, and others. This paper presents two key parts of successful document clustering. The first part is a novel phrase-based document index model, the Document Index Graph, which allows for incremental construction of a phrase-based index of the document set with an emphasis on efficiency, rather than relying on single-term indexes only. It provides efficient phrase matching that is used to judge the similarity between documents. The model is flexible in that it could revert to a compact representation of the vector space model if we choose not to index phrases. The second part is an incremental document clustering algorithm based on maximizing the tightness of clusters by carefully watching the pair-wise document similarity distribution inside clusters. The combination of these two components creates an underlying model for robust and accurate document similarity calculation that leads to much improved results in Web document clustering over traditional methods.
    BibTeX:
    @article{Hammouda2004,
      author = {Hammouda, KM and Kamel, MS},
      title = {Efficient phrase-based document indexing for web document clustering},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2004},
      volume = {16},
      number = {10},
      pages = {1279-1296}
    }
    
    Hansen, D.L., Derry, H.A., Resnick, P.J. & Richardson, C.R. Adolescents Searching for Health Information on the Internet: An Observational Study {2003} JOURNAL OF MEDICAL INTERNET RESEARCH
    Vol. {5}({4}) 
    article DOI  
    Abstract: Background: Adolescents' access to health information on the Internet is partly a function of their ability to search for and find answers to their health-related questions. Adolescents may have unique health and computer literacy needs. Although many surveys, interviews, and focus groups have been utilized to understand the information-seeking and information-retrieval behavior of adolescents looking for health information online, we were unable to locate observations of individual adolescents that have been conducted in this context. Objective: This study was designed to understand how adolescents search for health information using the Internet and what implications this may have on access to health information. Methods: A convenience sample of 12 students (age 12-17 years) from 1 middle school and 2 high schools in southeast Michigan were provided with 6 health-related questions and asked to look for answers using the Internet. Researchers recorded 68 specific searches using software that captured screen images as well as synchronized audio recordings. Recordings were reviewed later and specific search techniques and strategies were coded. A qualitative review of the verbal communication was also performed. Results: Out of 68 observed searches, 47 (69 were successful in that the adolescent found a correct and useful answer to the health question. The majority of sites that students attempted to access were retrieved directly from search engine results (77 or a search engine's recommended links (10; only a small percentage were directly accessed (5 or linked from another site (7. The majority (83 of followed links from search engine results came from the first 9 results. Incorrect spelling (30 of 132 search terms), number of pages visited within a site (ranging from 1-15), and overall search strategy (eg, using a search engine versus directly accessing a site), were each important determinants of success. Qualitative analysis revealed that participants used a trial-and-error approach to formulate search strings, scanned pages randomly instead of systematically, and did not consider the source of the content when searching for health information. Conclusions: This study provides a useful snapshot of current adolescent searching patterns. The results have implications for constructing realistic simulations of adolescent search behavior, improving distribution and usefulness of Web sites with health information relevant to adolescents, and enhancing educators' knowledge of what specific pitfalls students are likely to encounter.
    BibTeX:
    @article{Hansen2003,
      author = {Hansen, Derek L. and Derry, Holly A. and Resnick, Paul J. and Richardson, Caroline R.},
      title = {Adolescents Searching for Health Information on the Internet: An Observational Study},
      journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
      year = {2003},
      volume = {5},
      number = {4},
      doi = {{10.2196/jmir.5.4.e25}}
    }
    
    Harter, S. & Ford, C. Web-based analyses of e-journal impact: Approaches, problems, and issues {2000} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE
    Vol. {51}({13}), pp. {1159-1176} 
    article  
    Abstract: This study(1) assesses the ways in which citation searching of scholarly print journals is and is not analogous to backlink searching of scholarly e-journal articles on the WWW, and identifies problems and issues related to conducting and interpreting such searches. Backlink searches are defined here as searches for Web pages that link to a given URL. Backlink searches were conducted on a sample of 39 scholarly electronic journals. Search results were processed to determine the number of backlinking pages, total backlinks, and external backlinks made to the e-journals and to their articles. The results were compared to findings from a citation study performed on the same e-journals in 1996. A content analysis of a sample of the files backlinked to e-journal articles was also undertaken. The authors identify a number of reliability issues associated with the use of ``raw'' search engine data to evaluate the impact of electronic journals and articles. No correlation was found between backlink measures and ISI citation measures of e-journal impact, suggesting that the two measures may be assessing something quite different. Major differences were found between the types of entities that cite, and those that backlink, e-journal articles, with scholarly works comprising a very small percentage of backlinking files. These findings call into question the legitimacy of using backlink searches to evaluate the scholarly impact of e-journals and e-journal articles (and by extension, e-journal authors).
    BibTeX:
    @article{Harter2000,
      author = {Harter, SP and Ford, CE},
      title = {Web-based analyses of e-journal impact: Approaches, problems, and issues},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE},
      year = {2000},
      volume = {51},
      number = {13},
      pages = {1159-1176}
    }
    
    Hasegawa, K. & Funatsu, K. Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships {2000} SAR AND QSAR IN ENVIRONMENTAL RESEARCH
    Vol. {11}({3-4}), pp. {189-209} 
    article  
    Abstract: Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.
    BibTeX:
    @article{Hasegawa2000,
      author = {Hasegawa, K and Funatsu, K},
      title = {Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships},
      journal = {SAR AND QSAR IN ENVIRONMENTAL RESEARCH},
      year = {2000},
      volume = {11},
      number = {3-4},
      pages = {189-209}
    }
    
    Hawking, D., Craswell, N., Bailey, P. & Griffihs, K. Measuring search engine quality {2001} INFORMATION RETRIEVAL
    Vol. {4}({1}), pp. {33-59} 
    article  
    Abstract: The effectiveness of twenty public search engines is evaluated using TREC-inspired methods and a set of 54 queries taken from real Web search logs. The World Wide Web is taken as the test collection and a combination of crawler and text retrieval system is evaluated. The engines are compared on a range of measures derivable from binary relevance judgments of the first seven live results returned. Statistical testing reveals a significant difference between engines and high intercorrelations between measures. Surprisingly, given the dynamic nature of the Web and the time elapsed, there is also a high correlation between results of this study and a previous study by Gordon and Pathak. For nearly all engines, there is a gradual decline in precision at increasing cutoff after some initial fluctuation. Performance of the engines as a group is found to be inferior to the group of participants in the TREC-8 Large Web task, although the best engines approach the median of those systems. Shortcomings of current Web search evaluation methodology are identified and recommendations are made for future improvements. In particular, the present study and its predecessors deal with queries which are assumed to derive from a need to find a selection of documents relevant to a topic. By contrast, real Web search reflects a range of other information need types which require different judging and different measures.
    BibTeX:
    @article{Hawking2001,
      author = {Hawking, D and Craswell, N and Bailey, P and Griffihs, K},
      title = {Measuring search engine quality},
      journal = {INFORMATION RETRIEVAL},
      year = {2001},
      volume = {4},
      number = {1},
      pages = {33-59}
    }
    
    Heery, R. Review of metadata formats {1996} PROGRAM-AUTOMATED LIBRARY AND INFORMATION SYSTEMS
    Vol. {30}({4}), pp. {345-373} 
    article  
    Abstract: Increasing use of the Internet has heightened awareness among the information community of the need to provide user friendly searching and navigation tools that lead to quality information. An essential part of gaining effective access to Internet resources is to provide an index of available items in order to save users time and network overload. Discussions on metadata are focused on the format of the record used as the basis for the index. Control of the vast number of resources of the Internet requires an appropriate record format (or formats) which will enable the resource to be adequately described and easily located; records must be compatible with an appropriate search engine which in turn would ideally be compatible with a search and retrieval Internet protocol and all components should conform to international standards. At present there are a number of formats which meet at least some of these criteria, each of which has its own strengths.
    BibTeX:
    @article{Heery1996,
      author = {Heery, R},
      title = {Review of metadata formats},
      journal = {PROGRAM-AUTOMATED LIBRARY AND INFORMATION SYSTEMS},
      year = {1996},
      volume = {30},
      number = {4},
      pages = {345-373}
    }
    
    Heinz, E. How Darkthought plays chess {1997} ICCA JOURNAL
    Vol. {20}({3}), pp. {166-176} 
    article  
    Abstract: DARKTHOUGHT is a bitboard-based chess program developed at the University of Karlsruhe. It has successfully participated in all World Championships since 1995. On a 500MHz DEC Alpha-21164a with 128MB RAM, DARKTHOUGHT routinely reaches speeds of 200K nps (nodes per second) in the middlegame while peaking at over 650K nps in the endgame. This note describes the design and inner structure of DARKTHOUGHT. To this end, it presents detailed accounts of the chess engine while elaborating on three of its innovations: rotated bitboards, versatile search parameterization, and a fully progammable leaf-node evaluation function.
    BibTeX:
    @article{Heinz1997,
      author = {Heinz, EA},
      title = {How Darkthought plays chess},
      journal = {ICCA JOURNAL},
      year = {1997},
      volume = {20},
      number = {3},
      pages = {166-176}
    }
    
    Hellawell, G., Turner, K., Le Monnier, K. & Brewster, S. Urology and the Internet: an evaluation of Internet use by urology patients and of information available on urological topics {2000} BJU INTERNATIONAL
    Vol. {86}({3}), pp. {191-194} 
    article  
    Abstract: Objective To determine the use of the Internet by urological patients for obtaining information about their disease, and to conduct an evaluation of urological websites to determine the quality of information available. Patients and methods Questionnaires about Internet use were completed by 180 patients attending a general urological outpatient clinic and by 143 patients attending a prostate cancer outpatient clinic, The Internet evaluation was conducted by reviewing 50 websites listed by the Hotbot(TM) search engine for two urological topics, prostate cancer and testicular cancer, and recording details such as authorship, information content, references and information scores, Results Of the patients actively seeking further information about their health, 19% of the general urological outpatient group and 24% of the prostate cancer group used the Internet to obtain this information. Most websites were either academic or biomedical (62, provided conventional information (95, and were not referenced (71. The information score (range 10-100) was 44.3 for testicular cancer and 50.7 for prostate cancer: the difference in scores was not significant. Conclusion The use of the Internet by patients is increasing, with >20% of urology patients using the Internet to obtain further information about their health. Most Internet websites for urological topics provide conventional and good quality information. Urologists should be aware of the need to familiarize themselves with urological websites. Patients can then be directed to high-quality sites to allow them to educate themselves and to help them avoid misleading or unconventional websites.
    BibTeX:
    @article{Hellawell2000,
      author = {Hellawell, GO and Turner, KJ and Le Monnier, KJ and Brewster, SF},
      title = {Urology and the Internet: an evaluation of Internet use by urology patients and of information available on urological topics},
      journal = {BJU INTERNATIONAL},
      year = {2000},
      volume = {86},
      number = {3},
      pages = {191-194}
    }
    
    Helsens, K., Martens, L., Vandekerckhove, J. & Gevaert, K. MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results {2007} PROTEOMICS
    Vol. {7}({3}), pp. {364-366} 
    article DOI  
    Abstract: MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible and fully functional object model (http://genesis.ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications.
    BibTeX:
    @article{Helsens2007,
      author = {Helsens, Kenny and Martens, Lennart and Vandekerckhove, Joel and Gevaert, Kris},
      title = {MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results},
      journal = {PROTEOMICS},
      year = {2007},
      volume = {7},
      number = {3},
      pages = {364-366},
      doi = {{10.1002/pmic.200600682}}
    }
    
    Henshaw, R. & Valauskas, E. Metadata as a catalyst: Experiments with metadata and search engines in the Internet journal, First Monday {2001} LIBRI
    Vol. {51}({2}), pp. {86-101} 
    article  
    Abstract: This study examines metadata as a means to enhance information retrieval in a suite of seven search engines, AltaVista, Excite, Google, HotBot, InfoSeek, Lycos, and Northern Light. Papers were selected from issues of the Internet-only journal First Monday, and examined by portions of author and title in seven search engines, without metadata. Metatags were then added to these papers and the searches were repeated five months later. Metadata alone did not play a significant role in increasing the likelihood of a given paper being indexed or highly ranked by any specific search engine.
    BibTeX:
    @article{Henshaw2001,
      author = {Henshaw, R and Valauskas, EJ},
      title = {Metadata as a catalyst: Experiments with metadata and search engines in the Internet journal, First Monday},
      journal = {LIBRI},
      year = {2001},
      volume = {51},
      number = {2},
      pages = {86-101}
    }
    
    Henzinger, M., Heydon, A., Mitzenmacher, M. & Najork, M. Measuring index quality using random walks on the Web {1999} PROCEEDINGS OF THE EIGHTH INTERNATIONAL WORLD WIDE WEB CONFERENCE, pp. {213-225}  inproceedings  
    Abstract: Recent research has studied how to measure the size of a search engine, in terms of the number of pages indexed. In this paper, we consider a different measure for search engines, namely the quality of the pages in a search engine index. We provide a simple, effective algorithm for approximating the quality of an index by performing a random walk on the Web, and we use this methodology to compare the index quality of several major search engines. (C) 1999 Published by Elsevier Science B.V. All rights reserved.
    BibTeX:
    @inproceedings{Henzinger1999a,
      author = {Henzinger, MR and Heydon, A and Mitzenmacher, M and Najork, M},
      title = {Measuring index quality using random walks on the Web},
      booktitle = {PROCEEDINGS OF THE EIGHTH INTERNATIONAL WORLD WIDE WEB CONFERENCE},
      year = {1999},
      pages = {213-225},
      note = {8th International World Wide Web Conference, TORONTO, CANADA, MAY 11-14, 1999}
    }
    
    Henzinger, M., Heydon, A., Mitzenmacher, M. & Najork, M. Measuring index quality using random walks on the Web {1999} COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING
    Vol. {31}({11-16}), pp. {1291-1303} 
    article  
    Abstract: Recent research has studied how to measure the size of a search engine, in terms of the number of pages indexed. In this paper, we consider a different measure for search engines, namely the quality of the pages in a search engine index. We provide a simple, effective algorithm for approximating the quality of an index by performing a random walk on the Web, and we use this methodology to compare the index quality of several major search engines. (C) 1999 Published by Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Henzinger1999,
      author = {Henzinger, MR and Heydon, A and Mitzenmacher, M and Najork, M},
      title = {Measuring index quality using random walks on the Web},
      journal = {COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING},
      year = {1999},
      volume = {31},
      number = {11-16},
      pages = {1291-1303}
    }
    
    Herskovic, J.R., Tantaka, L.Y., Hersh, W. & Bernstam, E.V. A day in the life of PubMed: Analysis of a typical day's query log {2007} JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
    Vol. {14}({2}), pp. {212-220} 
    article DOI  
    Abstract: Objective: To characterize PubMed usage over a typical day and compare it to previous studies of user behavior on Web search engines. Design: We performed a lexical and semantic analysis of 2,689,166 queries issued on PubMed over 24 consecutive hours on a typical day. Measurements: We measured the number of queries, number of distinct users, queries per user, terms per query, common terms, Boolean operator use, common phrases, result set size, MeSH categories, used semantic measurements to group queries into sessions, and studied the addition and removal of terms from consecutive queries to gauge search strategies. Results: The size of the result sets from a sample of queries showed a bimodal distribution, with peaks at approximately 3 and 100 results, suggesting that a large group of queries was tightly focused and another was broad. Like Web search engine sessions, most PubMed sessions consisted of a single query. However, PubMed queries contained more terms. Conclusion: PubMed's usage profile should be considered when educating users, building user interfaces, and developing future biomedical information retrieval systems.
    BibTeX:
    @article{Herskovic2007,
      author = {Herskovic, Jorge R. and Tantaka, Len Y. and Hersh, William and Bernstam, Elmer V.},
      title = {A day in the life of PubMed: Analysis of a typical day's query log},
      journal = {JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION},
      year = {2007},
      volume = {14},
      number = {2},
      pages = {212-220},
      doi = {{10.1197/jamia.M2191}}
    }
    
    Higgs, R.E., Knierman, M.D., Freeman, A.B., Gelbert, L.M., Patil, S.T. & Hale, J.E. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments {2007} JOURNAL OF PROTEOME RESEARCH
    Vol. {6}({5}), pp. {1758-1767} 
    article DOI  
    Abstract: We present a wrapper-based approach to estimate and control the false discovery rate for peptide identifications using the outputs from multiple commercially available MS/MS search engines. Features of the approach include the flexibility to combine output from multiple search engines with sequence and spectral derived features in a flexible classification model to produce a score associated with correct peptide identifications. This classification model score from a reversed database search is taken as the null distribution for estimating p-values and false discovery rates using a simple and established statistical procedure. Results from 10 analyses of rat sera on an LTQ-FT mass spectrometer indicate that the method is well calibrated for controlling the proportion of false positives in a set of reported peptide identifications while correctly identifying more peptides than rule-based methods using one search engine alone. Keywords: peptide identification center dot false discovery rate center dot Sequest center dot X! Tandem center dot statistical significance center dot proteomics
    BibTeX:
    @article{Higgs2007,
      author = {Higgs, Richard E. and Knierman, Michael D. and Freeman, Angela Bonner and Gelbert, Lawrence M. and Patil, Sandeep T. and Hale, John E.},
      title = {Estimating the statistical significance of peptide identifications from shotgun proteomics experiments},
      journal = {JOURNAL OF PROTEOME RESEARCH},
      year = {2007},
      volume = {6},
      number = {5},
      pages = {1758-1767},
      doi = {{10.1021/pr0605320}}
    }
    
    Hjaltason, G. & Samet, H. Distance browsing in spatial databases {1999} ACM TRANSACTIONS ON DATABASE SYSTEMS
    Vol. {24}({2}), pp. {265-318} 
    article  
    Abstract: We compare two different techniques for browsing through a collection of spatial objects stored in an R-tree spatial data structure on the basis of their distances from an arbitrary spatial query object. The conventional approach is one that makes use of a k-nearest neighbor algorithm where k is known prior to the invocation of the algorithm. Thus if m. k neighbors are needed, the k-nearest neighbor algorithm has to be reinvoked for m neighbors, thereby possibly performing some redundant computations. The second approach is incremental in the sense that having obtained the k nearest neighbors, the k + 1(st) neighbor can be obtained without having to calculate the k + 1 nearest neighbors from scratch. The incremental approach is useful when processing complex queries where one of the conditions involves spatial proximity (e.g., the nearest city to Chicago with population greater than a million), in which case a query engine can make use of a pipelined strategy. We present a general incremental nearest neighbor algorithm that is applicable to a large class of hierarchical spatial data structures. This algorithm is adapted to the R-tree and its performance is compared to an existing k-nearest neighbor algorithm for R-trees [Roussopoulos et al. 1995]. Experiments show that the incremental nearest neighbor algorithm significantly outperforms the k-nearest neighbor algorithm for distance browsing queries in a spatial database that uses the R-tree as a spatial index. Moreover, the incremental nearest neighbor algorithm usually outperforms the k-nearest neighbor algorithm when applied to the k-nearest neighbor problem for the R-tree, although the improvement is not nearly as large as for distance browsing queries. In fact, we prove informally that at any step in its execution the incremental nearest neighbor algorithm is optimal with respect to the spatial data structure that is employed. Furthermore, based on some simplifying assumptions, we prove that in two dimensions the number of distance computations and leaf nodes accesses made by the algorithm for finding k neighbors is O (k + k).
    BibTeX:
    @article{Hjaltason1999,
      author = {Hjaltason, GR and Samet, H},
      title = {Distance browsing in spatial databases},
      journal = {ACM TRANSACTIONS ON DATABASE SYSTEMS},
      year = {1999},
      volume = {24},
      number = {2},
      pages = {265-318}
    }
    
    Ho, L. LINERs as low-luminosity active galactic nuclei {1999}
    Vol. {23}({5/6})AGN/NORMAL GALAXY CONNECTION, pp. {813-822} 
    inproceedings  
    Abstract: Many nearby galaxies contain optical signatures of nuclear activity in the form of LINER nuclei. LINERs may be the weakest and most common manifestation of the quasar phenomenon. The physical origin of this class of objects, however, has been ambiguous. I draw upon a number of recent observations to argue that a significant fraction of LINERs are low-luminosity active galactic nuclei. The evidence in favor of this interpretation includes the similarity in the properties of the host galaxies of LINERs and Seyferts, the detection of broad-line regions, the detection of black holes in a handful of nearby galaxies that are spectroscopically recognized as LINERs, the presence of a compact nuclear source seen in the radio, ultraviolet, and X-rays, and the detection of nonthermal spectra in the hard X-ray band. The spectral energy distributions of LINERs differ dramatically from those of luminous AGNs, most notably in the absence of the ``big blue bump.'' This and other characteristics suggest that the central engine in LINERs is fed by a very low accretion rate. (C) 1999 COSPAR. Published by Elsevier Science Ltd.
    BibTeX:
    @inproceedings{Ho1999,
      author = {Ho, LC},
      title = {LINERs as low-luminosity active galactic nuclei},
      booktitle = {AGN/NORMAL GALAXY CONNECTION},
      year = {1999},
      volume = {23},
      number = {5/6},
      pages = {813-822},
      note = {E1 2 Symposium of COSPAR Scientific Commission E on the AGN/Normal Galaxy Connection, 32nd COSPAR Scientific Assembly, NAGOYA, JAPAN, JUL 12-19, 1998}
    }
    
    Ho, L. ``Low-State'' black hole accretion in nearby galaxies {2005} ASTROPHYSICS AND SPACE SCIENCE
    Vol. {300}({1-3}), pp. {219-225} 
    article DOI  
    Abstract: I summarize the main observational properties of low-luminosity AGNs in nearby galaxies to argue that they are the high-mass analogs of black hole X-ray binaries in the ``low/hard'' state. The principal characteristics of low-state AGNs can be accommodated with a scenario in which the central engine is comprised of three components: an optically thick, geometrically accretion disk with a truncated inner radius, a radiatively inefficient flow, and a compact jet.
    BibTeX:
    @article{Ho2005,
      author = {Ho, LC},
      title = {``Low-State'' black hole accretion in nearby galaxies},
      journal = {ASTROPHYSICS AND SPACE SCIENCE},
      year = {2005},
      volume = {300},
      number = {1-3},
      pages = {219-225},
      doi = {{10.1007/s10509-005-1198-3}}
    }
    
    Hodge, F., Kennedy, J. & Maines, L. Does search-facilitating technology improve the transparency of financial reporting? {2004} ACCOUNTING REVIEW
    Vol. {79}({3}), pp. {687-703} 
    article  
    Abstract: XBRL (eXtensible Business Reporting Language) is an emerging technology that facilitates directed searches and simultaneous presentation of related financial statement and footnote information. We investigate whether using an XBRL-enhanced search engine helps nonprofessional financial statement users acquire and integrate related financial information when making an investment decision. We conduct our investigation in the context of recognition versus disclosure of stock option compensation. Our results reveal that many users do not access the technology, but those who do use it are better able to acquire and integrate information. Specifically, we find that when stock option accounting varies between firms, the use of an XBRL-enhanced search engine increases the likelihood that individuals acquire information about stock option compensation disclosed in the footnotes. We also find that XBRL helps individuals integrate the implications of this information, resulting in different investment decisions between individuals who use and do not use the search engine. Our results suggest that search-facilitating technologies, such as XBRL, aid financial statement users by improving the transparency of firms' financial statement information and managers' choices for reporting that information. Our results also reveal that wide publicity about the benefits of using search-facilitating technology may be needed to induce financial statement users to access the technology.
    BibTeX:
    @article{Hodge2004,
      author = {Hodge, FD and Kennedy, JJ and Maines, LA},
      title = {Does search-facilitating technology improve the transparency of financial reporting?},
      journal = {ACCOUNTING REVIEW},
      year = {2004},
      volume = {79},
      number = {3},
      pages = {687-703}
    }
    
    Hoffman, J., Wu, H., Krajcik, J. & Soloway, E. The nature of middle school learners' science content understandings with the use of on-line resources {2003} JOURNAL OF RESEARCH IN SCIENCE TEACHING
    Vol. {40}({3}), pp. {323-346} 
    article DOI  
    Abstract: Early research on using the World Wide Web indicated that middle school students did not explore much and used Web tools naively. In response to these challenges, an on-line research engine, Artemis, was designed to provide a permanent workspace and allow students access to preselective on-line resources. This study investigated the depth and accuracy of sixth-grade students' content understandings as well as their use of search and assess strategies when they used on-line resources via Artemis. Eight student pairs from two science classes experienced support from teachers and used scaffolded curriculum materials while completing four on-line inquiry units during 9 months. Multiple sources of data were collected, including video recordings of students' computer activities and conversations, students' artifacts and - online postings, classroom and lab video recordings, and interview transcripts. Analyses of data showed that students constructed meaningful understandings through on-line inquiry, although the accuracy and depth of their understandings varied. The findings suggest that students might develop accurate and in-depth understandings if they use search and assess strategies appropriately, if resources are thoughtfully chosen, and if support from the learning environment is extensively provided. This research lends evidence to questions regarding the value of students engaging in on-line inquiry. (C) 2003 Wiley Periodicals, Inc.
    BibTeX:
    @article{Hoffman2003,
      author = {Hoffman, JL and Wu, HK and Krajcik, JS and Soloway, E},
      title = {The nature of middle school learners' science content understandings with the use of on-line resources},
      journal = {JOURNAL OF RESEARCH IN SCIENCE TEACHING},
      year = {2003},
      volume = {40},
      number = {3},
      pages = {323-346},
      doi = {{10.1002/tea.10079}}
    }
    
    Hoffman-Goetz, L. & Clarke, J. Quality of breast cancer sites on the World Wide Web {2000} CANADIAN JOURNAL OF PUBLIC HEALTH-REVUE CANADIENNE DE SANTE PUBLIQUE
    Vol. {91}({4}), pp. {281-284} 
    article  
    Abstract: The Internet is a powerful tool for accessing information about complex health topics. The purpose of this study was to evaluate breast cancer Internet sites using published criteria about website structure. Two searches were undertaken (November 1998 and lune 1999) using the Yahoo search engine, providing a sample of 136 unique addresses. The results showed 1) owner's credentials were identified in 31.6% of sites, 2) financial charges were stated in 10.3% of sites, 3) less than 14.0% identified site creation date, 4) 33.1% identified content posting update, 5) 30.1% identified content content posting update, 5) 30.1% information sources, and 6) just under 88% of sites provided e-mail interactivity. The results indicate variability in breast cancer Internet siteswith respect to framework criteria of accountability, We suggest that websites that lack fundamental indicators (such as dating and sources) do not provide the user with fundamental information that could enable informed decision making about site quality.
    BibTeX:
    @article{Hoffman-Goetz2000,
      author = {Hoffman-Goetz, L and Clarke, JN},
      title = {Quality of breast cancer sites on the World Wide Web},
      journal = {CANADIAN JOURNAL OF PUBLIC HEALTH-REVUE CANADIENNE DE SANTE PUBLIQUE},
      year = {2000},
      volume = {91},
      number = {4},
      pages = {281-284}
    }
    
    Hoffmann, F. & Nelles, O. Genetic programming for model selection of TSK-fuzzy systems {2001} INFORMATION SCIENCES
    Vol. {136}({1-4, Sp. Iss. SI}), pp. {7-28} 
    article  
    Abstract: This paper compares a genetic programming (GP) approach with a greedy partition algorithm (LOLIMOT) for structure identification of local linear neuro-fuzzy models. The crisp linear conclusion part of a Takagi-Sugeno-Kang (TSK) fuzzy rule describes the underlying model in the local region specified in the premise. The objective of structure identification is to identify an optimal partition of the input space into Gaussian, axis-orthogonal fuzzy sets. The linear parameters in the rule consequent are then estimated by means of a local weighted least-squares algorithm. LOLIMOT is an incremental tree-construction algorithm that partitions the input space by axis-orthogonal splits, In each iteration it greedily adds the new model that minimizes the classification error. GP performs a global search for the optimal partition tree and is therefore able to backtrack in case of sub-optimal intermediate split decisions. We compare the performance of both methods for function approximation of a highly nonlinear two-dimensional test function and an engine characteristic map. (C) 2001 Elsevier Science Inc, All rights reserved.
    BibTeX:
    @article{Hoffmann2001,
      author = {Hoffmann, F and Nelles, O},
      title = {Genetic programming for model selection of TSK-fuzzy systems},
      journal = {INFORMATION SCIENCES},
      year = {2001},
      volume = {136},
      number = {1-4, Sp. Iss. SI},
      pages = {7-28},
      note = {8th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2000), MADRID, SPAIN, JUL 03-07, 2000}
    }
    
    Holm, L. & Park, J. DaliLite workbench for protein structure comparison {2000} BIOINFORMATICS
    Vol. {16}({6}), pp. {566-567} 
    article  
    Abstract: DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.
    BibTeX:
    @article{Holm2000,
      author = {Holm, L and Park, J},
      title = {DaliLite workbench for protein structure comparison},
      journal = {BIOINFORMATICS},
      year = {2000},
      volume = {16},
      number = {6},
      pages = {566-567}
    }
    
    Howe, A. & Dreilinger, D. SAVVYSEARCH - A metasearch engine that learns which search engines to query {1997} AI MAGAZINE
    Vol. {18}({2}), pp. {19-25} 
    article  
    Abstract: Search engines are among the most successful applications on the web today So many search engines have been created that it is difficult for users to know where they are, how to use them, and what topics they best address. Metasearch engines reduce the user burden by dispatching queries to multiple search engines in parallel. The SAVVYSEARCH metasearch engine is designed to efficiently query other search engines by carefully selecting those search engines likely to return useful results and responding to fluctuating load demands on the web. SAVVYSEARCH learns to identify which search engines ale most appropriate for particular queries, reasons about resource demands, and represents an iterative parallel search strategy as a simple plan.
    BibTeX:
    @article{Howe1997,
      author = {Howe, AE and Dreilinger, D},
      title = {SAVVYSEARCH - A metasearch engine that learns which search engines to query},
      journal = {AI MAGAZINE},
      year = {1997},
      volume = {18},
      number = {2},
      pages = {19-25}
    }
    
    HU, X., FOLEY, H. & STILES, A. DESIGN OF ALCOHOL SYNTHESIS CATALYSTS ASSISTED BY A KNOWLEDGE-BASED EXPERT SYSTEM {1991} INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
    Vol. {30}({7}), pp. {1419-1427} 
    article  
    Abstract: A new knowledge-based, expert system approach is presented for the design of a family of heterogeneous catalysts for alcohol synthesis. The knowledge base for solving this problem is a hybrid consisting of numerical data, declarative facts, and heuristic rules. Design rules were derived from an integration of the information about the performance of the catalyst, reaction mechanism, and the nature of the active sites. An example for a specific case is constructed on the basis of compositional and kinetic data for mixed metal oxide catalysts used to reduce carbon monoxide with hydrogen to alcohols. An inference engine was constructed by simulating the kine of thinking that an experienced catalyst designer employs. By this method, an expert system can guide the search for an optimum catalyst formulation, its preparation procedure, and the best reaction conditions to achieve the specified selectivity of the desired product. In this way, the expert system can provide a path to the design of the catalyst through a systematic and logically structured database that is accessible and interactive.
    BibTeX:
    @article{HU1991,
      author = {HU, XD and FOLEY, HC and STILES, AB},
      title = {DESIGN OF ALCOHOL SYNTHESIS CATALYSTS ASSISTED BY A KNOWLEDGE-BASED EXPERT SYSTEM},
      journal = {INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH},
      year = {1991},
      volume = {30},
      number = {7},
      pages = {1419-1427}
    }
    
    Huang, C. & Cheng, K. Using word-level ATPG and modular arithmetic constraint-solving techniques for assertion property checking {2001} IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
    Vol. {20}({3}), pp. {381-391} 
    article  
    Abstract: We present a new approach to checking assertion properties for register-transfer level (RTL) design verification. Our approach combines structural word-level automatic test pattern generation (ATPG) and modular arithmetic constraint-solving techniques to solve the constraints imposed by the target assertion property, Our word-level ATPG and implication technique not only solves the constraints on the control logic, but also propagates the logic implications to the datapath, A novel arithmetic constraint solver based on modular number system is then employed to solve the remaining constraints in datapath, The advantages of the new method are threefold, First, the decision-making process of the word-level ATPG is confined to the selected control signals only, Therefore, the enumeration of enormous number of choices at the datapath signals is completely avoided. Second, our new implication translation techniques allow word-level logic implication being performed across the boundary of datapath and control logic and, therefore, efficiently cut down the ATPG search space. Third, our arithmetic constraint solver is based on modular instead of integral number system. It can thus avoid the false-negative effect resulting from the bit-vector value modulation A prototype system has been built that consists of an industrial front-end hardware description language (HDL) parser, a property-tu-constraint converter, and the ATPG/arithmetic constraint-solving engine. The experimental results on some public benchmark and industrial circuits demonstrate the efficiency of our approach and its applicability to large industrial designs.
    BibTeX:
    @article{Huang2001,
      author = {Huang, CY and Cheng, KT},
      title = {Using word-level ATPG and modular arithmetic constraint-solving techniques for assertion property checking},
      journal = {IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS},
      year = {2001},
      volume = {20},
      number = {3},
      pages = {381-391}
    }
    
    Huang, C., Chien, L. & Oyang, Y. Relevant term suggestion in interactive Web search based on contextual information in query session logs {2003} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {54}({7}), pp. {638-649} 
    article DOI  
    Abstract: This paper proposes an effective term suggestion approach to interactive Web search. Conventional approaches to making term suggestions involve extracting co-occurring keyterms from highly ranked retrieved documents. Such approaches must deal with term extraction difficulties and interference from irrelevant documents, and, more importantly, have difficulty extracting terms that are conceptually related but do not frequently co-occur in documents. In this paper, we present a new, effective log-based approach to relevant term extraction and term suggestion. Using this approach, the relevant terms suggested for a user query are those that co-occur in similar query sessions from search engine logs, rather than in the retrieved documents. In addition, the suggested terms in each interactive search step can be organized according to its relevance to the entire query session, rather than to the most recent single query as in conventional approaches. The proposed approach was tested using a proxy server log containing about two million query transactions submitted to search engines in Taiwan. The obtained experimental results show that the proposed approach can provide organized and highly relevant terms, and can exploit the contextual information in a user's query session to make more effective suggestions.
    BibTeX:
    @article{Huang2003,
      author = {Huang, CK and Chien, LF and Oyang, YJ},
      title = {Relevant term suggestion in interactive Web search based on contextual information in query session logs},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2003},
      volume = {54},
      number = {7},
      pages = {638-649},
      doi = {{10.1002/asi.10256}}
    }
    
    Huang, Y., Hsieh, B., Chen, T. & Chen, L. Analysis, fast algorithm, and VLSI architecture design for H.264/AVC intra frame coder {2005} IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
    Vol. {15}({3}), pp. {378-401} 
    article DOI  
    Abstract: Intra prediction with rate-distortion constrained mode decision is the most important technology in H.264/AVC intra frame coder, which is competitive with the latest image coding standard JPEG2000, in terms of both coding performance and computational complexity. The predictor generation engine for intra prediction and the transform engine for mode decision are critical because the operations require a lot of memory access and occupy 80% of the computation time of the entire intra compression process. A low cost general purpose processor cannot process these operations in real time. In this paper, we proposed two solutions for platform-based design of H.264/AVC intra frame coder. One solution is a software implementation targeted at low-end applications. Context-based decimation of unlikely candidates, subsampling of matching operations, bit-width truncation to reduce the computations, and interleaved full-search/partial-search strategy to stop the error propagation and to maintain the image quality, are proposed and combined as our fast algorithm. Experimental results show that our method can reduce 60% of the computation used for intra prediction and mode decision while keeping the peak signal-to-noise ratio degradation less than 0.3 dB. The other solution is a hardware accelerator targeted at high-end applications. After comprehensive analysis of instructions and exploration of parallelism, we proposed our system architecture with four-parallel intra prediction and mode decision to enhance the processing capability. Hadamard-based mode decision is modified as discrete cosine transform-based version to reduce 40% of memory access. Two-stage macroblock pipelining is also proposed to double the processing speed and hardware utilization. The other features of our design are reconfigurable predictor generator supporting all of the 13 intra prediction modes, parallel multitransform and inverse transform engine, and CAVLC bitstream engine. A prototype chip is fabricated with TSMC 0.25-mum CMOS 1P5M technology. Simulation results show that our implementation can process 16 mega-pixels (4096 x 4096) within 1 s, or namely 720 x 480 4:2:0 30 Hz video in real time, at the operating frequency of 54 MHz. The transistor count is 429 K, and the core size is only 1.855 x 1.885 mm(2).
    BibTeX:
    @article{Huang2005,
      author = {Huang, YW and Hsieh, BY and Chen, TC and Chen, LG},
      title = {Analysis, fast algorithm, and VLSI architecture design for H.264/AVC intra frame coder},
      journal = {IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY},
      year = {2005},
      volume = {15},
      number = {3},
      pages = {378-401},
      doi = {{10.1109/TCSVT.2004.842620}}
    }
    
    Hungerford, D. Minimally invasive total hip arthroplasty - In opposition {2004} JOURNAL OF ARTHROPLASTY
    Vol. {19}({4, Suppl. 1}), pp. {81-82} 
    article DOI  
    Abstract: At the Knee Society Winter Meeting in 2003, Seth Greenwald and I debated about whether there should be new standards (ie, regulations) applied to the release of information to the public on ``new developments.'' I argued for the public's ``right to know'' prior to the publication of peer-reviewed literature. He argued for regulatory constraint or ``proving by peer-reviewed publication'' before alerting the public. It is not a contradiction for me to Currently argue against the public advertising of minimally invasive (MIS) total hip arthroplasty as not yet being in the best interest of the public. It is hard to remember a concept that has so captured both the public's and the surgical community's fancy as MIS. Patients are ``demanding'' MIS without knowing why. Surgeons are offering it as the next best, greatest thing without having developed the skill and experience to avoid the surgery's risks. If you put ``minimally invasive hip replacement'' into the Google search engine (http:// www.google.com), you get 5,170 matches. If You put the same words in PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi), referencing the National Library of Medicine database, You get SEVENTEEN; none is really a peer-reviewed article. Most are I page papers in orthopedics front medical education meetings. Oil the other hand, there are over 6,000 peer-reviewed articles on total hip arthroplasty. Dr. Thomas Sculco, my couterpart in this debate, wrote an insightful editorial in the American Journal of Orthopedic Surgery in which lie stated: ``Although these procedures have generated incredible interest and enthusiasm, I am concerned that they may be performed to the detriment of our patients.'' I couldn't agree with him more. Smaller is not necessarily better and, when it is worse, it will be the `'smaller'' that is held accountable.
    BibTeX:
    @article{Hungerford2004,
      author = {Hungerford, DS},
      title = {Minimally invasive total hip arthroplasty - In opposition},
      journal = {JOURNAL OF ARTHROPLASTY},
      year = {2004},
      volume = {19},
      number = {4, Suppl. 1},
      pages = {81-82},
      note = {Meeting on Current Concepts in Joint Replacement, Las Vegas, NV, 2003},
      doi = {{10.1016/j.arth.2004.04.007}}
    }
    
    Ilic, D., Bessell, T., Silagy, C. & Green, S. Specialized medical search-engines are no better than general search-engines in sourcing consumer information about androgen deficiency {2003} HUMAN REPRODUCTION
    Vol. {18}({3}), pp. {557-561} 
    article DOI  
    Abstract: BACKGROUND: The Internet provides consumers with access to online health information; however, identifying relevant and valid information can be problematic. Our objectives were firstly to investigate the efficiency of search-engines, and then to assess the quality of online information pertaining to androgen deficiency in the ageing male (ADAM). METHODS: Keyword searches were performed on nine search-engines (four general and five medical) to identify website information regarding ADAM. Search-engine efficiency was compared by percentage of relevant websites obtained via each search-engine. The quality of information published on each website was assessed using the DISCERN rating tool. RESULTS: Of 4927 websites searched, 47 (1.44 and 10 (0.60 relevant websites were identified by general and medical search-engines respectively. The overall quality of online information on ADAM was poor. The quality of websites retrieved using medical search-engines did not differ significantly from those retrieved by general search-engines. CONCLUSION: Despite the poor quality of online information relating to ADAM, it is evident that medical search-engines are no better than general search-engines in sourcing consumer information relevant to ADAM.
    BibTeX:
    @article{Ilic2003,
      author = {Ilic, D and Bessell, TL and Silagy, CA and Green, S},
      title = {Specialized medical search-engines are no better than general search-engines in sourcing consumer information about androgen deficiency},
      journal = {HUMAN REPRODUCTION},
      year = {2003},
      volume = {18},
      number = {3},
      pages = {557-561},
      doi = {{10.1093/humrep/deg154}}
    }
    
    Iliyas, A., Zahedi-Niaki, M.H., Eic, M. & Kaliaguine, S. Control of hydrocarbon cold-start emissions: A search for potential adsorbents {2007} MICROPOROUS AND MESOPOROUS MATERIALS
    Vol. {102}({1-3}), pp. {171-177} 
    article DOI  
    Abstract: A principle of single-file diffusion has been successfully employed to control automotive hydrocarbon (HC) emissions particularly during the cold-start period. Temperature programmed desorption technique of toluene and ethylene, as probe sorbates, was employed to screen a series of as synthesized one-dimensional molecular sieves as potential HC traps. Ethylene was found to be trapped to varying degrees by the larger toluene molecules within the 1-D pores of the synthesized samples. In particular, ZSM-12 and SAPO-5 showed superior trapping performance for both sorbates. ZSM- 12 was selected as a better candidate because of its higher temperature of desorption maximum for ethylene (150 degrees C), which is comparable to the light-off temperature of automotive catalytic converter. It was also found that this adsorbent was stable up to the desired temperature of operation i.e., 800 degrees C, however with some reduction in ethylene trapping capacity. (C) 2007 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Iliyas2007,
      author = {Iliyas, A. and Zahedi-Niaki, M. H. and Eic, M. and Kaliaguine, S.},
      title = {Control of hydrocarbon cold-start emissions: A search for potential adsorbents},
      journal = {MICROPOROUS AND MESOPOROUS MATERIALS},
      year = {2007},
      volume = {102},
      number = {1-3},
      pages = {171-177},
      doi = {{10.1016/j.micromeso.2006.12.038}}
    }
    
    Imin, N., De Jong, F., Mathesius, U., van Noorden, G., Saeed, N., Wang, X., Rose, R. & Rolfe, B. Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts {2004} PROTEOMICS
    Vol. {4}({7}), pp. {1883-1896} 
    article DOI  
    Abstract: Using a combination of two-dimensional gel electrophoresis (2-DE) protein mapping and mass spectrometry (MS) analysis, we have established proteome reference maps of Medicago truncatula embryogenic tissue culture cells. The cultures were generated from single protoplasts, which provided a relatively homogenous cell population. We used these to analyze protein expression at the globular stages of somatic embryogenesis, which is the earliest morphogenetic embryonic stage. Over 3000 proteins could reproducibly be resolved over a p/range of 4-11. Three hundred and twelve protein spots were extracted from colloidal Coomassie Blue-stained 2-DE gels and analyzed by matrix-assisted laser desorption/ionization-time of flight MS analysis and tandem MS sequencing. This enabled the identification of 169 protein spots representing 128 unique gene products using a publicly available expressed sequence tag database and the MASCOT search engine. These reference maps will be valuable for the investigation of the molecular events which occur during somatic embryogenesis in M. truncatula. The proteome reference maps and supplementary materials will be available and updated for public access at http://semele.anu.edu.au/.
    BibTeX:
    @article{Imin2004,
      author = {Imin, N and De Jong, F and Mathesius, U and van Noorden, G and Saeed, NA and Wang, XD and Rose, RJ and Rolfe, BG},
      title = {Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts},
      journal = {PROTEOMICS},
      year = {2004},
      volume = {4},
      number = {7},
      pages = {1883-1896},
      note = {Meeting of the Australian-Electrophoresis-and-Proteomics-Society, Melbourne, AUSTRALIA, SEP 27-28, 2003},
      doi = {{10.1002/pmic.200300803}}
    }
    
    Imin, N., Nizamidin, M., Daniher, D., Nolan, K., Rose, R. & Rolfe, B. Proteomic analysis of somatic embryogenesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treatments {2005} PLANT PHYSIOLOGY
    Vol. {137}({4}), pp. {1250-1260} 
    article DOI  
    Abstract: The Medicago truncatula line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than wild-type Jemalong. We have compared proteomes of tissue cultures from leaf explants of these two lines. Both 2HA and Jemalong explants were grown on media containing the auxin 1-naphthaleneacetic acid and the cytokinin 6-benzylaminopurine. Proteins were extracted from the cultures at different time points (2, 5, and 8 weeks), separated by two-dimensional gel electrophoresis, and detected by silver staining. More than 2,000 proteins could be reproducibly resolved and detected on each gel. Statistical analysis showed that 54 protein spots were significantly (P < 0.05) changed in expression (accumulation) during the 8 weeks of culture, and most of these spots were extracted from colloidal Coomassie-stained two-dimensional gel electrophoresis gels and were subjected to matrix-assisted laser desorption ionization time-of-flight mass spectrometry or liquid chromatography-tandem mass spectrometry analysis. Using a publicly available expressed sequence tag database and the Mascot search engine, we were able to identify 16 differentially expressed proteins. More than 60% of the differentially expressed protein spots had very different patterns of gene expression between 2HA and Jernalong during the 8 weeks of culture.
    BibTeX:
    @article{Imin2005,
      author = {Imin, N and Nizamidin, M and Daniher, D and Nolan, KE and Rose, RJ and Rolfe, BG},
      title = {Proteomic analysis of somatic embryogenesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treatments},
      journal = {PLANT PHYSIOLOGY},
      year = {2005},
      volume = {137},
      number = {4},
      pages = {1250-1260},
      doi = {{10.1104/pp.104.055277}}
    }
    
    Ingwersen, P. The calculation of Web impact factors {1998} JOURNAL OF DOCUMENTATION
    Vol. {54}({2}), pp. {236-243} 
    article  
    Abstract: This case study reports the investigations into the feasibility and reliability of calculating impact factors for web sites, called Web Impact Factors (Web-IF). The study analyses a selection of seven small and medium scale national and four large web domains as well as six institutional web sites over a series of snapshots taken of the web during a month. The data isolation and calculation methods are described and the tests discussed. The results thus far demonstrate that Web-IFs are calculable with high confidence for national and sector domains whilst institutional Web-Ifs should be approached with caution. The data isolation method makes use of sets of inverted but logically identical Boolean set operations and their mean values in order to generate the impact factors associated with internal- (self-) link web pages and external-link web pages. Their logical sum is assumed to constitute the workable frequency of web pages linking up to the web location in question. The logical operations are necessary to overcome the variations in retrieval outcome produced by the AltaVista search engine.
    BibTeX:
    @article{Ingwersen1998,
      author = {Ingwersen, P},
      title = {The calculation of Web impact factors},
      journal = {JOURNAL OF DOCUMENTATION},
      year = {1998},
      volume = {54},
      number = {2},
      pages = {236-243}
    }
    
    Inoue, K., Yokomori, R., Yamamoto, T., Matsushita, M. & Kusumoto, S. Ranking significance of software components based on use relations {2005} IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
    Vol. {31}({3}), pp. {213-225} 
    article  
    Abstract: Collections of already developed programs are important resources for efficient development of reliable software systems. In this paper, we propose a novel graph-representation model of a software component library ( repository), called component rank model. This is based on analyzing actual usage relations of the components and propagating the significance through the usage relations. Using the component rank model, we have developed a Java class retrieval system named SPARS-J and applied SPARS-J to various collections of Java files. The result shows that SPARS-J gives a higher rank to components that are used more frequently. As a result, software engineers looking for a component have a better chance of finding it quickly. SPARS-J has been used by two companies, and has produced promising results.
    BibTeX:
    @article{Inoue2005,
      author = {Inoue, K and Yokomori, R and Yamamoto, T and Matsushita, M and Kusumoto, S},
      title = {Ranking significance of software components based on use relations},
      journal = {IEEE TRANSACTIONS ON SOFTWARE ENGINEERING},
      year = {2005},
      volume = {31},
      number = {3},
      pages = {213-225},
      note = {25th International Conference on Software Engineering (ICSE 2003), PORTLAND, OR, MAY 03-10, 2003}
    }
    
    Introna, L. & Nissenbaum, H. Defining the Web: The politics of search engines {2000} COMPUTER
    Vol. {33}({1}), pp. {54+} 
    article  
    Abstract: Although the Web itself might truthfully claim a sovereign disinterested and unbiased attitude toward the people who use it, the authors of this article claim that search engines, the tools that navigate the astronomical number of pages (800 million and counting), favor popular, wealthy, and powerful sites at the expense of others. Some researchers have estimated that, taken individually, none of the Web search engines studied indexes more than 16 percent of the total indexable Web. Combined, the results from all search engines they studied covered only about 42 percent of the Web. But what about those portions of the Web that remain hidden from view? This article looks at how search engine developers, designers, and producers grapple with the technical limits that restrict what their engines can find. The authors also examine influences that may determine systematic inclusion and extematic inclusion and exclusion of certain sites, and the factors that dictate systematic prominence for some sites while relegating others to systematic invisibility.
    BibTeX:
    @article{Introna2000,
      author = {Introna, L and Nissenbaum, H},
      title = {Defining the Web: The politics of search engines},
      journal = {COMPUTER},
      year = {2000},
      volume = {33},
      number = {1},
      pages = {54+}
    }
    
    Inza, I., Larranaga, P. & Sierra, B. Feature subset selection by Bayesian networks: a comparison with genetic and sequential algorithms {2001} INTERNATIONAL JOURNAL OF APPROXIMATE REASONING
    Vol. {27}({2}), pp. {143-164} 
    article  
    Abstract: In this paper we perform a comparison among FSS-EBNA, a randomized, population-based and evolutionary algorithm, and two genetic and other two sequential search approaches in the well-known feature subset selection (FSS) problem. In FSS-EBNA, the FSS problem, stated as a search problem, uses the estimation of Bayesian network algorithm (EBNA) search engine, an algorithm within the estimation of distribution algorithm (EDA) approach. The EDA paradigm is born from the roots of the genetic algorithm (GA) community in order to explicitly discover the relationships among the features of the problem and not disrupt them by genetic recombination operators. The EDA paradigm avoids the use of recombination operators and it guarantees the evolution of the population of solutions and the discovery of these relationships by the factorization of the probability distribution of best individuals in each generation of the search. In EBNA, this factorization is carried out by a Bayesian network induced by a cheap local search mechanism. FSS-EBNA can be seen as a hybrid Soft Computing system, a synergistic combination of probabilistic and evolutionary computing to solve the FSS task. Promising results on a set of real Data Mining domains are achieved by FSS-EBNA in the comparison respect to well-known genetic and sequential search algorithms. (C) 2001 Elsevier Science Inc. All rights reserved.
    BibTeX:
    @article{Inza2001,
      author = {Inza, I and Larranaga, P and Sierra, B},
      title = {Feature subset selection by Bayesian networks: a comparison with genetic and sequential algorithms},
      journal = {INTERNATIONAL JOURNAL OF APPROXIMATE REASONING},
      year = {2001},
      volume = {27},
      number = {2},
      pages = {143-164},
      note = {2nd Workshop on Casual Networks, from Inference to Data Mining (CaNew 2000), BERLIN, GERMANY, 2000}
    }
    
    Inza, I., Sierra, B. & Blanco, R. Gene selection by sequential search wrapper approaches in microarray cancer class prediction {2002} JOURNAL OF INTELLIGENT & FUZZY SYSTEMS
    Vol. {12}({1}), pp. {25-33} 
    article  
    Abstract: In the last years, there has been a large growth in gene expression profiling technologies, which are expected to provide insight into cancer related cellular processes. Machine Learning algorithms, which are extensively applied in many areas of the real world, are not still popular in the Bioinformatics community. We report on the successful application of four well known supervised Machine Learning methods (IB1, Naive-Bayes. C4.5 and CN2) to cancer class prediction problems in three DNA microarray datasets of huge dimensionality (Colon, Leukemia and NCI-60). The essential gene selection process in microarray domains is performed by a sequential search engine, evaluating the goodness of each gene subset by a wrapper approach which executes, by a leave-one-out process, the supervised algorithm to obtain its accuracy estimation. By the use of the gene selection procedure, the accuracy of supervised algorithms is significantly improved and the number of genes of the classification models is notably reduced for all datasets.
    BibTeX:
    @article{Inza2002,
      author = {Inza, I and Sierra, B and Blanco, R},
      title = {Gene selection by sequential search wrapper approaches in microarray cancer class prediction},
      journal = {JOURNAL OF INTELLIGENT & FUZZY SYSTEMS},
      year = {2002},
      volume = {12},
      number = {1},
      pages = {25-33}
    }
    
    Ipsen, I. & Kirkland, S. Convergence analysis of a PageRank updating algorithm by Langville and Meyer {2006} SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS
    Vol. {27}({4}), pp. {952-967} 
    article DOI  
    Abstract: The PageRank updating algorithm proposed by Langville and Meyer is a special case of an iterative aggregation/disaggregation (SIAD) method for computing stationary distributions of very large Markov chains. It is designed, in particular, to speed up the determination of PageRank, which is used by the search engine Google in the ranking of web pages. In this paper the convergence, in exact arithmetic, of the SIAD method is analyzed. The SIAD method is expressed as the power method preconditioned by a partial LU factorization. This leads to a simple derivation of the asymptotic convergence rate of the SIAD method. It is known that the power method applied to the Google matrix always converges, and we show that the asymptotic convergence rate of the SIAD method is at least as good as that of the power method. Furthermore, by exploiting the hyperlink structure of the web it can be shown that the asymptotic convergence rate of the SIAD method applied to the Google matrix can be made strictly faster than that of the power method.
    BibTeX:
    @article{Ipsen2006,
      author = {Ipsen, ICF and Kirkland, S},
      title = {Convergence analysis of a PageRank updating algorithm by Langville and Meyer},
      journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS},
      year = {2006},
      volume = {27},
      number = {4},
      pages = {952-967},
      doi = {{10.1137/S0895479804439808}}
    }
    
    Jacso, P. Google Scholar: the pros and the cons {2005} ONLINE INFORMATION REVIEW
    Vol. {29}({2}), pp. {208-214} 
    article DOI  
    Abstract: Purpose - To identify the pros and the cons of Google Scholar. Design/methodology/approach - Chronicles the recent history of the Google Scholar search engine from its inception in November 2004 and critiques it with regard to its merits and demerits. Findings - Feels that there are massive content omissions presently but that, with future changes in its structure, Google Scholar will become an excellent free tool for scholarly information discovery and retrieval. Originality/value - Presents a useful analysis for potential users of the Google Scholar site.
    BibTeX:
    @article{Jacso2005,
      author = {Jacso, P},
      title = {Google Scholar: the pros and the cons},
      journal = {ONLINE INFORMATION REVIEW},
      year = {2005},
      volume = {29},
      number = {2},
      pages = {208-214},
      doi = {{10.1108/14684520510598066}}
    }
    
    Jain, A. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine {2003} JOURNAL OF MEDICINAL CHEMISTRY
    Vol. {46}({4}), pp. {499-511} 
    article DOI  
    Abstract: Surflex is a fully automatic flexible molecular docking algorithm that combines the scoring function from the Hammerhead docking system with a search engine that relies on a surface-based molecular similarity method as a means to rapidly generate suitable putative poses for molecular fragments. Results are presented evaluating reliability and accuracy of dockings compared with crystallographic experimental results on 81 protein/ligand pairs of substantial structural diversity. In over 80% of the complexes, Surflex's highest scoring docked pose was within 2.5 Angstrom root-mean-square deviation (rmsd), with over 90% of the complexes having one of the top ranked poses within 2.5 Angstrom rmsd. Results are also presented assessing Surflex's utility as a screening tool on two protein targets (thymidine kinase and estrogen receptor) using data sets on which competing methods were run. Performance of Surflex was significantly better, with true positive rates of greater than 80% at false positive rates of less than 1 Docking time was roughly linear in number of rotatable bonds, beginning with a few seconds for rigid molecules and adding approximately 10 s per rotatable bond.
    BibTeX:
    @article{Jain2003,
      author = {Jain, AN},
      title = {Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine},
      journal = {JOURNAL OF MEDICINAL CHEMISTRY},
      year = {2003},
      volume = {46},
      number = {4},
      pages = {499-511},
      doi = {{10.1021/jm.020406h}}
    }
    
    Jain, A. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities {1996} JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
    Vol. {10}({5}), pp. {427-440} 
    article  
    Abstract: Exploitation of protein structures for potential drug leads by molecular docking is critically dependent on methods for scoring putative protein-ligand interactions. An ideal function for scoring must exhibit predictive accuracy and high computational speed, and must be tolerant of variations in the relative protein-ligand molecular alignment and conformation. This paper describes the development of an empirically derived scoring function, based on the binding affinities of protein-ligand complexes coupled with their crystallographically determined structures. The function's primary terms involve hydrophobic and polar complementarity, with additional terms for entropic and solvation effects. The issue of alignment/conformation dependence was solved by constructing a continuous differentiable nonlinear function with the requirement that maxima in ligand conformation/alignment space corresponded closely to crystallographically determined structures. The expected error in the predicted affinity based on cross-validation was 1.0 log unit, The function is sufficiently fast and accurate to serve as the objective function of a molecular-docking search engine. The function is particularly well suited to the docking problem, since it has spatially narrow maxima that are broadly accessible via gradient descent.
    BibTeX:
    @article{Jain1996,
      author = {Jain, AN},
      title = {Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities},
      journal = {JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN},
      year = {1996},
      volume = {10},
      number = {5},
      pages = {427-440}
    }
    
    Janket, S., Baird, A., Chuang, S. & Jones, J. Meta-analysis of periodontal disease and risk of coronary heart disease and stroke {2003} ORAL SURGERY ORAL MEDICINE ORAL PATHOLOGY ORAL RADIOLOGY AND ENDODONTICS
    Vol. {95}({5}), pp. {559-569} 
    article DOI  
    Abstract: Objective. The purpose of this study was to analyze published studies and abstracts in order to provide a quantitative summary of periodontal disease as a risk factor for cardiovascular disease and to explore the possible causes for conflicting results in the literature. Study design. We searched all published literature on the Medline literature search engine since 1980. An additional search was performed with bibliographic citations from each article. Nine cohort studies (8 prospective and I retrospective), in which relative risks (Us), Cls, and P values were reported or could be calculated were included. Four researchers independently extracted RRs, Cls, and P values from each study and evaluated the degree of confounding adjustment. The combined result was calculated with weighted average, and sources of disparity were tested with regression analyses. Results. The summary RR was 1.19 (95% Cl, 1.08 1.32), indicating a higher risk of future cardiovascular events in individuals with periodontal disease compared with those without. In an analysis stratified to individuals of less than or equal to65 years of age, the RR was 1.44 (95% Cl, 1.20 to 1.73). When the outcome was restricted to stroke only, the RR was 2.85 (95% Cl, 1.78 to 4.56). In the metaregression analysis, the effects of residual confounding caused an overestimate of the results by 12.9% and, with a proxy for periodontal disease, caused an underestimate of 29.7 Conclusion. Periodontal disease appears to be associated with a 19% increase in risk of future cardiovascular disease. This increase in RR is more prominent (44 in persons aged less than or equal to65 years. Although the increment of risk between subjects with or without periodontal disease in the general population is modest, at around 20% because nearly 40% of population has periodontal disease, this modest increase may have a profound public health impact.
    BibTeX:
    @article{Janket2003,
      author = {Janket, SJ and Baird, AE and Chuang, SK and Jones, JA},
      title = {Meta-analysis of periodontal disease and risk of coronary heart disease and stroke},
      journal = {ORAL SURGERY ORAL MEDICINE ORAL PATHOLOGY ORAL RADIOLOGY AND ENDODONTICS},
      year = {2003},
      volume = {95},
      number = {5},
      pages = {559-569},
      note = {79th General Session of the International-Association-for-Dental-Research, CHIBA, JAPAN, JUN 27-30, 2001},
      doi = {{10.1067/moe.2003.107}}
    }
    
    Jansen, B. & Molina, P. The effectiveness of Web search engines for retrieving relevant ecommerce links {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({4}), pp. {1075-1098} 
    article DOI  
    Abstract: Ecommerce is developing into a fast-growing channel for new business, so a strong presence in this domain could prove essential to the success of numerous commercial organizations. However, there is little research examining ecommerce at the individual customer level, particularly on the success of everyday ecommerce searches. This is critical for the continued success of online commerce. The purpose of this research is to evaluate the effectiveness of search engines in the retrieval of relevant ecommerce links. The study examines the effectiveness of five different types of search engines in response to ecommerce queries by comparing the engines' quality of ecommerce links using topical relevancy ratings. This research employs 100 ecommerce queries, five major search engines, and more than 3540 Web links. The findings indicate that links retrieved using an ecommerce search engine are significantly better than those obtained from most other engines types but do not significantly differ from links obtained from a Web directory service. We discuss the implications for Web system design and ecommerce marketing campaigns. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Jansen2006a,
      author = {Jansen, BJ and Molina, PR},
      title = {The effectiveness of Web search engines for retrieving relevant ecommerce links},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {4},
      pages = {1075-1098},
      doi = {{10.1016/j.ipm.2005.09.003}}
    }
    
    Jansen, B. & Spink, A. How are we searching the World Wide Web? A comparison of nine search engine transaction logs {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({1}), pp. {248-263} 
    article DOI  
    Abstract: The Web and especially major Web search engines are essential tools in the quest to locate online information for many people. This paper reports results from research that examines characteristics and changes in Web searching from nine studies of five Web search engines based in the US and Europe. We compare interactions occurring between users and Web search engines from the perspectives of session length, query length, query complexity, and content viewed among the Web search engines. The results of our research shows (1) users are viewing fewer result pages, (2) searchers on US-based Web search engines use more query operators than searchers on European-based search engines, (3) there are statistically significant differences in the use of Boolean operators and result pages viewed, and (4) one cannot necessary apply results from studies of one particular Web search engine to another Web search engine. The wide spread use of Web search engines, employment of simple queries, and decreased viewing of result pages may have resulted from algorithmic enhancements by Web search engine companies. We discuss the implications of the findings for the development of Web search engines and design of online content. (c) 2004 Published by Elsevier Ltd.
    BibTeX:
    @article{Jansen2006,
      author = {Jansen, BJ and Spink, A},
      title = {How are we searching the World Wide Web? A comparison of nine search engine transaction logs},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {1},
      pages = {248-263},
      doi = {{10.1016/j.ipm.2004.10.007}}
    }
    
    Jansen, B. & Spink, A. An analysis of Web searching by European AlltheWeb.com users {2005} INFORMATION PROCESSING & MANAGEMENT
    Vol. {41}({2}), pp. {361-381} 
    article DOI  
    Abstract: The Web has become a worldwide source of information and a mainstream business tool. It is changing the way people conduct the daily business of their lives. As these changes are occurring, we need to understand what Web searching trends are emerging within the various global regions. What are the regional differences and trends in Web searching, if any? What is the effectiveness of Web search engines as providers of information? As part of a body of research studying these questions, we have analyzed two data sets collected from queries by mainly European users submitted to AlltheWeb.com on 6 February 2001 and 28 May 2002. AlltheWeb.com is a major and highly rated European search engine. Each data set contains approximately a million queries submitted by over 200,000 users and spans a 24-h period. This longitudinal benchmark study shows that European Web searching is evolving in certain directions. There was some decline in query length, with extremely simple queries. European search topics are broadening, with a notable percentage decline in sexual and pornographic searching. The majority of Web searchers view fewer than five Web documents, spending only seconds on a Web document. Approximately 50% of the Web documents viewed by these European users were topically relevant. We discuss the implications for Web information systems and information content providers. (C) 2003 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Jansen2005,
      author = {Jansen, BJ and Spink, A},
      title = {An analysis of Web searching by European AlltheWeb.com users},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2005},
      volume = {41},
      number = {2},
      pages = {361-381},
      doi = {{10.1016/S0306-4573(03)00067-0}}
    }
    
    Jansen, B.J. Search log analysis: What it is, what's been done, how to do it {2006} LIBRARY & INFORMATION SCIENCE RESEARCH
    Vol. {28}({3}), pp. {407-432} 
    article DOI  
    Abstract: The use of data stored in transaction logs of Web search engines, Intranets, and Web sites can provide valuable insight into understanding the information-searching process of online searchers. This understanding can enlighten information system design, interface development, and devising the information architecture for content collections. This article presents a review and foundation for conducting Web search transaction log analysis. A methodology is outlined consisting of three stages, which are collection, preparation, and analysis. The three stages of the methodology are presented in detail with discussions of goals, metrics, and processes at each stage. Critical terms in transaction log analysis for Web searching are defined. The strengths and limitations of transaction log analysis as a research method are presented. An application to log client-side interactions that supplements transaction logs is reported on, and the application is made available for use by the research community. Suggestions are provided on ways to leverage the strengths of, while addressing the limitations of, transaction log analysis for Web-searching research. Finally, a complete flat text transaction log from a commercial search engine is available as supplementary material with this manuscript. (c) 2006 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Jansen2006b,
      author = {Jansen, Bemard J.},
      title = {Search log analysis: What it is, what's been done, how to do it},
      journal = {LIBRARY & INFORMATION SCIENCE RESEARCH},
      year = {2006},
      volume = {28},
      number = {3},
      pages = {407-432},
      doi = {{10.1016/j.lisr.2006.06.005}}
    }
    
    Jansen, B.J., Booth, D.L. & Spink, A. Determining the informational, navigational, and transactional intent of Web queries {2008} INFORMATION PROCESSING & MANAGEMENT
    Vol. {44}({3}), pp. {1251-1266} 
    article DOI  
    Abstract: In this paper, we define and present a comprehensive classification of user intent for Web searching. The classification consists of three hierarchical levels of informational, navigational, and transactional intent. After deriving attributes of each, we then developed a software application that automatically classified queries using a Web search engine log of over a million and a half queries submitted by several hundred thousand users. Our findings show that more than 80% of Web queries are informational in nature, with about 10% each being navigational and transactional. In order to validate the accuracy of our algorithm, we manually coded 400 queries and compared the results from this manual classification to the results determined by the automated method. This comparison showed that the automatic classification has an accuracy of 74 Of the remaining 25% of the queries, the user intent is vague or multi-faceted, pointing to the need for probabilistic classification. We discuss how search engines can use knowledge of user intent to provide more targeted and relevant results in Web searching. (C) 2007 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Jansen2008,
      author = {Jansen, Bernard J. and Booth, Danielle L. and Spink, Amanda},
      title = {Determining the informational, navigational, and transactional intent of Web queries},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2008},
      volume = {44},
      number = {3},
      pages = {1251-1266},
      doi = {{10.1016/j.ipm.2007.07.015}}
    }
    
    Jansen, B.J., Brown, A. & Resnick, M. Factors relating to the decision to click on a sponsored link {2007} DECISION SUPPORT SYSTEMS
    Vol. {44}({1}), pp. {46-59} 
    article DOI  
    Abstract: In this paper, we report results of an investigation into the factors influencing the selection of sponsored links by e-commerce Web searchers. In this research, 56 participants each engaged in six e-commerce Web searching tasks. We mined these tasks from the transaction log of a major Web search engine, so the tasks represent real e-commerce searching information needs. Using 60 organic and 30 sponsored Web links retrieved by submitting these queries to the Google search engine, we controlled the quality of the Web search engine listings by switching non-sponsored and sponsored links on half of the tasks for each participant. This approach allowed for both investigating the bias toward sponsored links while controlling for quality of content. Data included 2453 interactions with result page links, 961 utterances evaluating these links, and 102 results from a post-study survey. The results of the data analysis indicate that there is a statistically significant preference for non-sponsored links with searchers viewing these results first more than 82% of the time. Searchers view sponsored links primarily as advertisements, appreciate these links if they are relevant, and are unconcerned if the search engines disclose them as sponsored links. The implications for sponsored links as a long-term business model are discussed. (C) 2007 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Jansen2007,
      author = {Jansen, Bernard J. and Brown, Anna and Resnick, Marc},
      title = {Factors relating to the decision to click on a sponsored link},
      journal = {DECISION SUPPORT SYSTEMS},
      year = {2007},
      volume = {44},
      number = {1},
      pages = {46-59},
      doi = {{10.1016/j.dss.2007.02.009}}
    }
    
    Jayasinghe, S., Hristova, K. & White, S. MPtopo: A database of membrane protein topology {2001} PROTEIN SCIENCE
    Vol. {10}({2}), pp. {455-458} 
    article  
    Abstract: The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.
    BibTeX:
    @article{Jayasinghe2001,
      author = {Jayasinghe, S and Hristova, K and White, SH},
      title = {MPtopo: A database of membrane protein topology},
      journal = {PROTEIN SCIENCE},
      year = {2001},
      volume = {10},
      number = {2},
      pages = {455-458}
    }
    
    Jess, T., Gamborg, M., Matzen, P., Munkholm, P. & Sorensen, T. Increased risk of intestinal cancer in Crohn's disease: A meta-analysis of population-based cohort studies {2005} AMERICAN JOURNAL OF GASTROENTEROLOGY
    Vol. {100}({12}), pp. {2724-2729} 
    article DOI  
    Abstract: OBJECTIVES: The risk of intestinal malignancy in Crohn's disease (CD) remains uncertain since risk estimates vary worldwide. The global CD population is growing and there is a demand for better knowledge of prognosis of this disease. Hence, the aim of the present study was to conduct a meta-analysis of population-based data on intestinal cancer risk in CD. METHODS: The MEDLINE search engine and abstracts from international conferences were searched for the relevant literature by use of explicit search criteria. All papers fulfilling the strict inclusion criteria were scrutinized for data on population size, time of follow-up, and observed to expected cancer rates. STATA meta-analysis software was used to perform overall pooled risk estimates (standardized incidence ratio (SIR), observed/expected) and meta-regression analyses of the influence of specific variables on SIR. RESULTS: Six papers fulfilled the inclusion criteria and reported SIRs of colorectal cancer (CRC) in CD varying from 0.9 to 2.2. The pooled SIR for CRC was significantly increased (SIR, 1.9; 95% CI 1.4-2.5), as was the risk for colon cancer separately (SIR, 2.5; 95% CI 1.7-3.5). Regarding small bowel cancer, five studies reported SIRs ranging from 3.4 to 66.7, and the overall pooled estimate was 27.1 (95% CI 14.9-49.2). CONCLUSIONS: The present meta-analysis of intestinal cancer risk in CD, based on population-based studies only, revealed an overall increased risk of both CRC and small bowel cancer among patients with CD. However, some of the available data were several decades old, and future studies taking new treatment strategies into account are required.
    BibTeX:
    @article{Jess2005,
      author = {Jess, T and Gamborg, M and Matzen, P and Munkholm, P and Sorensen, TIA},
      title = {Increased risk of intestinal cancer in Crohn's disease: A meta-analysis of population-based cohort studies},
      journal = {AMERICAN JOURNAL OF GASTROENTEROLOGY},
      year = {2005},
      volume = {100},
      number = {12},
      pages = {2724-2729},
      doi = {{10.1111/j.1572-0241.2005.00287.x}}
    }
    
    Jess, T., Gamborg, M., Munkholm, P. & Srensen, T.I.A. Overall and cause-specific mortality in ulcerative colitis: Meta-analysis of population-based inception cohort studies {2007} AMERICAN JOURNAL OF GASTROENTEROLOGY
    Vol. {102}({3}), pp. {609-617} 
    article DOI  
    Abstract: OBJECTIVES: It remains debated whether patients with ulcerative colitis (UC) are at greater risk of dying and whether a possible alteration in mortality can be attributed to specific causes of death. We aimed to clarify this issue by conducting a meta-analysis of population-based inception cohort studies on overall and cause-specific mortality in patients with UC. METHODS: The MEDLINE search engine and abstracts from international conferences were searched for relevant literature by use of explicit search criteria. STATA meta-analysis software was used to calculate pooled risk estimates (SMR, standardized mortality ratio, observed/expected deaths) of overall mortality and specific causes of death and to conduct metaregression analyses of the influence of specific variables on SMR. RESULTS: Ten papers fulfilled the inclusion criteria, reporting SMRs varying from 0.7 to 1.4. The overall pooled estimate was 1.1 (95% confidence interval [CI] 0.9-1.2, P = 0.42). However, greater risk of dying was observed during the first years of follow-up, in patients with extensive colitis, and in patients from Scandinavia. Metaregression analysis showed an increase in SMR by increasing cohort size. UC-related mortality accounted for 17% of all deaths. Mortality from gastrointestinal diseases, nonalcoholic liver diseases, pulmonary embolisms, and respiratory diseases was increased whereas mortality from pulmonary cancer was reduced. CONCLUSIONS: The overall risk of dying in patients with UC did not differ from that of the background population, although subgroups of patients were at greater risk of dying. The cause-of-death distribution seemed to differ from that of the background population.
    BibTeX:
    @article{Jess2007,
      author = {Jess, Tine and Gamborg, Michael and Munkholm, Pia and Srensen, Thorkild I. A.},
      title = {Overall and cause-specific mortality in ulcerative colitis: Meta-analysis of population-based inception cohort studies},
      journal = {AMERICAN JOURNAL OF GASTROENTEROLOGY},
      year = {2007},
      volume = {102},
      number = {3},
      pages = {609-617},
      doi = {{10.1111/j.1572-0241.2006.0100.x}}
    }
    
    Jiang, S., Frazier, R., Yamaguchi, E., Blanco, M., Dasgupta, S., Zhou, Y., Cagin, T., Tang, Y. & Goddard, W. The SAM model for wear inhibitor performance of dithiophosphates on iron oxide {1997} JOURNAL OF PHYSICAL CHEMISTRY B
    Vol. {101}({39}), pp. {7702-7709} 
    article  
    Abstract: Zinc dithiophosphate (DTP) molecules have long been used as wear inhibitor oil additives for automotive engines. In order to obtain an atomistic understanding of the mechanism by which these molecules inhibit wear, we examined the geometries, energetics, and vibrations of an oxidized iron surface [(001) surface of alpha-Fe2O3] using the MSX force field (FF) based on ab initio quantum chemistry (QC) calculations, The DTP molecules studied include (RO)(2)PS2 with R = methyl, isobutyl, isopropyl, and phenyl. The alpha-Fe2O3 surface is described using the generalized valence bond (GVB) model of bonding. The geometries, binding energies, and vibrational frequencies from ab initio calculations on simple clusters art used with the biased Hessian method to develop the MSX FF suitable for describing the binding of DTP molecules to the surfaces. We find that the cohesive energies for the self-assembled monolayers (SAM) of the DTP molecules on the Fe2O3 surface correlate with the antiwear performance observed in experimental engine tests. This suggests that the search for more effective and environmentally benign wear inhibitors can use the cohesive energies for SAM formation as a criterion in selecting and prioritizing compounds for experimental testing.
    BibTeX:
    @article{Jiang1997,
      author = {Jiang, SY and Frazier, R and Yamaguchi, ES and Blanco, M and Dasgupta, S and Zhou, YH and Cagin, T and Tang, YC and Goddard, WA},
      title = {The SAM model for wear inhibitor performance of dithiophosphates on iron oxide},
      journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
      year = {1997},
      volume = {101},
      number = {39},
      pages = {7702-7709}
    }
    
    Jing, Y. & Baluja, S. VisualRank: Applying PageRank to large-scale image search {2008} IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
    Vol. {30}({11}), pp. {1877-1890} 
    article DOI  
    Abstract: Because of the relative ease in understanding and processing text, commercial image-search systems often rely on techniques that are largely indistinguishable from text search. Recently, academic studies have demonstrated the effectiveness of employing image-based features to provide either alternative or additional signals to use in this process. However, it remains uncertain whether such techniques will generalize to a large number of popular Web queries and whether the potential improvement to search quality warrants the additional computational cost. In this work, we cast the image-ranking problem into the task of identifying ``authority'' nodes on an inferred visual similarity graph and propose VisualRank to analyze the visual link structures among images. The images found to be ``authorities'' are chosen as those that answer the image-queries well. To understand the performance of such an approach in a real system, we conducted a series of large-scale experiments based on the task of retrieving images for 2,000 of the most popular products queries. Our experimental results show significant improvement, in terms of user satisfaction and relevancy, in comparison to the most recent Google Image Search results. Maintaining modest computational cost is vital to ensuring that this procedure can be used in practice; we describe the techniques required to make this system practical for large-scale deployment in commercial search engines.
    BibTeX:
    @article{Jing2008,
      author = {Jing, Yushi and Baluja, Shumeet},
      title = {VisualRank: Applying PageRank to large-scale image search},
      journal = {IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE},
      year = {2008},
      volume = {30},
      number = {11},
      pages = {1877-1890},
      doi = {{10.1109/TPAMI.2008.121}}
    }
    
    Jones, C., Abdelmoty, A., Finch, D., Fu, G. & Vaid, S. The SPIRIT spatial search engine: Architecture, ontologies and spatial indexing {2004}
    Vol. {3234}GEOGRAPHIC INFORMATION SCIENCE, PROCEEDINGS, pp. {125-139} 
    inproceedings  
    Abstract: The SPIRIT search engine provides a test bed for the development of web search technology that is specialised for access to geographical information. Major components include the user interface, a geographical ontology, maintenance and retrieval functions for a test collection of web documents, textual and spatial indexes, relevance ranking and metadata extraction. Here we summarise the functionality and interaction between these components before focusing on the design of the geo-ontology and the development of spatio-textual indexing methods. The geo-ontology supports functionality for disambiguation, query expansion, relevance ranking and metadata extraction. Geographical place names are accompanied by multiple geometric footprints and qualitative spatial relationships. Spatial indexing of documents has been integrated with text indexing through the use of spatio-textual keys in which terms are concatenated with spatial cells to which they relate. Preliminary experiments demonstrate considerable performance benefits when compared with pure text indexing and with text indexing followed by a spatial filtering stage.
    BibTeX:
    @inproceedings{Jones2004,
      author = {Jones, CB and Abdelmoty, AI and Finch, D and Fu, GH and Vaid, S},
      title = {The SPIRIT spatial search engine: Architecture, ontologies and spatial indexing},
      booktitle = {GEOGRAPHIC INFORMATION SCIENCE, PROCEEDINGS},
      year = {2004},
      volume = {3234},
      pages = {125-139},
      note = {3rd International Conference on Geographic Information Science, Adelphi, MD, OCT 20-23, 2004}
    }
    
    Jones, C., Abdelmoty, A. & Fu, G. Maintaining ontologies for geographical information retrieval on the web {2003}
    Vol. {2888}ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS 2003: COOPIS, DOA, AND ODBASE, pp. {934-951} 
    inproceedings  
    Abstract: A geo-ontology has a key role to play in the development of a spatially-aware search engine, with regard to providing support for query disambiguation, query term expansion, relevance ranking and web resource annotation. This paper reviews these functions, discusses the user requirements which influence the design of the ontology, with regard to different types of query and fundamental spatial concepts, before presenting a base model for a geographical ontology which will provide a foundation for subsequent implementation as well as experimentation with alternative ontology models. The report also reviews various ontology languages available for expressing ontologies and give examples for encoding the geo-ontology in them.
    BibTeX:
    @inproceedings{Jones2003,
      author = {Jones, CB and Abdelmoty, AI and Fu, GH},
      title = {Maintaining ontologies for geographical information retrieval on the web},
      booktitle = {ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS 2003: COOPIS, DOA, AND ODBASE},
      year = {2003},
      volume = {2888},
      pages = {934-951},
      note = {OTM Confederated International Conference CoopIS, DOA and ODBASE, CATANIA, ITALY, NOV 03-07, 2003}
    }
    
    Juidette, H. & Youlal, H. Fuzzy dynamic path planning using genetic algorithms {2000} ELECTRONICS LETTERS
    Vol. {36}({4}), pp. {374-376} 
    article  
    Abstract: Fuzzy control concepts are useful in bath global and local path planning tasks for autonomous mobile objects. The search for an optimal decision table to be used as the inference engine in fuzzy-based planning and navigation algorithms is highly important. The authors address the problem using genetic algorithms as a scarch and optimisation tool. The approach fields better planned paths compared to those obtained from random decision tables generated using rules of thumb.
    BibTeX:
    @article{Juidette2000,
      author = {Juidette, H and Youlal, H},
      title = {Fuzzy dynamic path planning using genetic algorithms},
      journal = {ELECTRONICS LETTERS},
      year = {2000},
      volume = {36},
      number = {4},
      pages = {374-376}
    }
    
    Kahn, Jr., C.E. & Thao, C. GoldMiner: A radiology image search engine {2007} AMERICAN JOURNAL OF ROENTGENOLOGY
    Vol. {188}({6}), pp. {1475-1478} 
    article DOI  
    BibTeX:
    @article{Kahn2007,
      author = {Kahn, Jr., Charles E. and Thao, Cheng},
      title = {GoldMiner: A radiology image search engine},
      journal = {AMERICAN JOURNAL OF ROENTGENOLOGY},
      year = {2007},
      volume = {188},
      number = {6},
      pages = {1475-1478},
      doi = {{10.2214/AJR.06.1740}}
    }
    
    Kalemci, E., Boggs, S.E., Kouveliotou, C., Finger, M. & Baring, M.G. Search for polarization from the prompt gamma-ray emission of GRB 041219a with SPI on INTEGRAL {2007} ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES
    Vol. {169}({1}), pp. {75-82} 
    article  
    Abstract: Measuring the polarization of the prompt gamma-ray emission from gamma-ray bursts (GRBs) can significantly improve our understanding of both the GRB emission mechanisms as well as the underlying engine driving the explosion. We searched for polarization in the prompt gamma-ray emission of GRB 041219a with the SPI instrument on INTEGRAL. Using multiple-detector coincidence events in the 100 - 350 keV energy band, our analysis yields a polarization fraction from this GRB of 98% +/- 33 Statistically, we cannot claim a polarization detection from this source. Moreover, different event selection criteria lead to even less significant polarization fractions, e. g., lower polarization fractions are obtained when higher energies are included in the analysis. We cannot strongly rule out the possibility that the measured modulation is dominated by instrumental systematics. Therefore, SPI observations of GRB 041219a do not significantly constrain GRB models. However, this measurement demonstrates the capability of SPI to measure polarization, as well as the techniques developed for this analysis.
    BibTeX:
    @article{Kalemci2007,
      author = {Kalemci, E. and Boggs, S. E. and Kouveliotou, C. and Finger, M. and Baring, M. G.},
      title = {Search for polarization from the prompt gamma-ray emission of GRB 041219a with SPI on INTEGRAL},
      journal = {ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES},
      year = {2007},
      volume = {169},
      number = {1},
      pages = {75-82}
    }
    
    Kay, S. & Hoyle, S. Mail order, the Internet, and invasive aquatic weeds {2001} JOURNAL OF AQUATIC PLANT MANAGEMENT
    Vol. {39}, pp. {88-91} 
    article  
    Abstract: Aquatic and wetland weeds pose serious threats to the freshwater resources of the United States. Essentially unregulated sale of plants for aquarium and ornamental pool use has resulted in the recent introduction and spread of several highly invasive weeds, including giant salvinia. This problem has been exacerbated during the past few years by mail-order and e-commerce. The objective of this study was to examine mail order and the internet as sources for sale of invasive aquatic weeds, with primary emphasis on the Internet. An online search was conducted using the search engine Yahoo(TM). Data were collected on twelve of the most common and highly invasive weeds sold by the industry. The data from the first 100 hits were grouped into regulatory, educational, commercial, hobbyist, and foreign sites. Essentially every aquatic or wetland plant listed in the United States as either a Federal Noxious Weed or as a noxious weed in one or more states was found. Twelve highly invasive plants intentionally sold by the wetland nurseries and water garden dealerships were found listed for sale by sites throughout tire United States and internationally. This study shows that stronger enforcement of laws and regulations and an intensive education and outreach effort are needed to prevent further introductions of invasive weeds through the aquatic and wetland plant industry.
    BibTeX:
    @article{Kay2001,
      author = {Kay, SH and Hoyle, ST},
      title = {Mail order, the Internet, and invasive aquatic weeds},
      journal = {JOURNAL OF AQUATIC PLANT MANAGEMENT},
      year = {2001},
      volume = {39},
      pages = {88-91},
      note = {40th Annual Meeting of the Aquatic-Plant-Management-Society, SAN DIEGO, CALIFORNIA, JUL 16-20, 2000}
    }
    
    Kegl, B. Numerical analysis of injection characteristics using biodiesel fuel {2006} FUEL
    Vol. {85}({17-18}), pp. {2377-2387} 
    article DOI  
    Abstract: This paper deals with numerical analysis of injection process using biodiesel/mineral diesel fuel blends with the aim to search for the potentials to reduce engine harmful emissions. The considered fuels are neat biodiesel from rapeseed oil and its blends with mineral diesel D2. For the numerical analysis a one-dimensional mathematical model is employed. In order to model accurately the investigated fuels, the employed empirical expressions for their properties are determined by experiments. To verify the mathematical model and the empirical expressions, experiments and numerical simulation are run on a mechanical control diesel fuel injection M system at several operating regimes. Injection process at many different operating regimes and using several fuel blends are then investigated numerically. Attention is focused on the injection characteristics, especially on fuelling, fuelling at some stage of injection, mean injection rate, mean injection pressure, injection delay and injection timing, which influence the most important engine characteristics. The analysis of the obtained results reveals that, while keeping engine performance within acceptable limits, harmful emissions can be reduced by adjusting appropriately pump injection timing in dependence on the biodiesel content. This prediction is also confirmed experimentally. (c) 2006 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Kegl2006,
      author = {Kegl, Breda},
      title = {Numerical analysis of injection characteristics using biodiesel fuel},
      journal = {FUEL},
      year = {2006},
      volume = {85},
      number = {17-18},
      pages = {2377-2387},
      doi = {{10.1016/j.fuel.2006.05.009}}
    }
    
    Kellar, M., Watters, C. & Shepherd, M. A field study characterizing Web-based information-seeking tasks {2007} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {58}({7}), pp. {999-1018} 
    article DOI  
    Abstract: Previous studies have examined various aspects of user behavior on the Web, including general information-seeking patterns, search engine use, and revisitation habits. Little research has been conducted to study how users navigate and interact with their Web browser across different information-seeking tasks. We have conducted a field study of 21 participants, in which we logged detailed Web usage and asked participants to provide task categorizations of their Web usage based on the following categories: Fact Finding, Information Gathering, Browsing, and Transactions. We used implicit measures logged during each task session to provide usage measures such as dwell time, number of pages viewed, and the use of specific browser navigation mechanisms. We also report on differences in how participants interacted with their Web browser across the range of information-seeking tasks. Within each type of task, we found several distinguishing characteristics. In particular, Information Gathering tasks were the most complex; participants spent more time completing this task, viewed more pages, and used the Web browser functions most heavily during this task. The results of this analysis have been used to provide implications for future support of information seeking on the Web as well as direction for future research in this area.
    BibTeX:
    @article{Kellar2007,
      author = {Kellar, Melanie and Watters, Carolyn and Shepherd, Michael},
      title = {A field study characterizing Web-based information-seeking tasks},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2007},
      volume = {58},
      number = {7},
      pages = {999-1018},
      doi = {{10.1002/asi.20590}}
    }
    
    Keller, F. & Lapata, M. Using the Web to obtain frequencies for unseen bigrams {2003} COMPUTATIONAL LINGUISTICS
    Vol. {29}({3}), pp. {459-484} 
    article  
    Abstract: This article shows that the Web can be employed to obtain frequencies for bigrams that are unseen in a given corpus. We describe a method for retrieving counts for adjective-noun, noun-noun, and verb-object bigrams from the Web by querying a search engine. We evaluate this method by demonstrating: (a) a high correlation between Web frequencies and corpus frequencies; (b) a reliable correlation between Web frequencies and plausibility judgments; (c) a reliable correlation between Web frequencies and frequencies recreated using class-based smoothing, (d) a good performance of Web frequencies in a pseudodisambiguation task.
    BibTeX:
    @article{Keller2003,
      author = {Keller, F and Lapata, M},
      title = {Using the Web to obtain frequencies for unseen bigrams},
      journal = {COMPUTATIONAL LINGUISTICS},
      year = {2003},
      volume = {29},
      number = {3},
      pages = {459-484}
    }
    
    Keller, F., Lapata, M. & Ourioupina, O. Using the Web to overcome data sparseness {2002} PROCEEDINGS OF THE 2002 CONFERENCE ON EMPIRICAL METHODS IN NATURAL LANGUAGE PROCESSING, pp. {230-237}  inproceedings  
    Abstract: This paper shows that the web can be employed to obtain frequencies for bigrams that are unseen in a given corpus. We describe a method for retrieving counts for adjective-noun, noun-noun, and verb-object bigrams from the web by querying a search engine. We evaluate this method by demonstrating that web frequencies and correlate with frequencies obtained from a carefully edited, balanced corpus. We also perform a task-based evaluation, showing that web frequencies can reliably predict human plausibility judgments.
    BibTeX:
    @inproceedings{Keller2002,
      author = {Keller, F and Lapata, M and Ourioupina, O},
      title = {Using the Web to overcome data sparseness},
      booktitle = {PROCEEDINGS OF THE 2002 CONFERENCE ON EMPIRICAL METHODS IN NATURAL LANGUAGE PROCESSING},
      year = {2002},
      pages = {230-237},
      note = {Conference on Empirical Methods in Natural Language Processing, Philadelphia, PA, JUL 06-07, 2002}
    }
    
    Kerlavage, A., Bonazzi, V., di Tommaso, M., Lawrence, C., Li, P., Mayberry, F., Mural, R., Nodell, M., Yandell, M., Zhang, J. & Thomas, P. The Celera Discovery System (TM) {2002} NUCLEIC ACIDS RESEARCH
    Vol. {30}({1}), pp. {129-136} 
    article  
    Abstract: The Celera Discovery System(TM) (CDS) is a web-accessible research workbench for mining genomic and related biological information. Users have access to the human and mouse genome sequences with annotation presented in summary form in BioMolecule Reports for genes, transcripts and proteins. Over 40 additional databases are available, including sequence, mapping, mutation, genetic variation, mRNA expression, protein structure, motif and classification data. Data are accessible by browsing reports, through a variety of interactive graphical viewers, and by advanced query capability provided by the LION SRS(TM) search engine. A growing number of sequence analysis tools are available, including sequence similarity, pattern searching, multiple sequence alignment and Hidden Markov Model search. A user workspace keeps track of queries and analyses. CDS is widely used by the academic research community and requires a subscription for access. The system and academic pricing information are available at http://cds.celera.com.
    BibTeX:
    @article{Kerlavage2002,
      author = {Kerlavage, A and Bonazzi, V and di Tommaso, M and Lawrence, C and Li, P and Mayberry, F and Mural, R and Nodell, M and Yandell, M and Zhang, JH and Thomas, P},
      title = {The Celera Discovery System (TM)},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2002},
      volume = {30},
      number = {1},
      pages = {129-136}
    }
    
    Kherfi, M., Ziou, D. & Bernardi, A. Image retrieval from the World Wide Web: Issues, techniques, and systems {2004} ACM COMPUTING SURVEYS
    Vol. {36}({1}), pp. {35-67} 
    article  
    Abstract: With the explosive growth of the World Wide Web, the public is gaining access to massive amounts of information. However, locating needed and relevant information remains a difficult task, whether the information is textual or visual. Text search engines have existed for some years now and have achieved a certain degree of success. However, despite the large number of images available on the Web, image search engines are still rare. In this article, we show that in order to allow people to profit from all this visual information, there is a need to develop tools that help them to locate the needed images with good precision in a reasonable time, and that such tools are useful for many applications and purposes. The article surveys the main characteristics of the existing systems most often cited in the literature, such as ImageRover, WebSeek, Diogenes, and Atlas WISE. It then examines the various issues related to the design and implementation of a Web image search engine, such as data gathering and digestion, indexing, query specification, retrieval and similarity, Web coverage, and performance evaluation. A general discussion is given for each of these issues, with examples of the ways they are addressed by existing engines, and 130 related references are given. Some concluding remarks and directions for future research are also presented.
    BibTeX:
    @article{Kherfi2004,
      author = {Kherfi, ML and Ziou, D and Bernardi, A},
      title = {Image retrieval from the World Wide Web: Issues, techniques, and systems},
      journal = {ACM COMPUTING SURVEYS},
      year = {2004},
      volume = {36},
      number = {1},
      pages = {35-67}
    }
    
    Khoo, L., Ang, C. & Zhang, J. A fuzzy-based genetic approach to the diagnosis of manufacturing systems {2000} ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
    Vol. {13}({3}), pp. {303-310} 
    article  
    Abstract: This paper describes the development of a hybrid approach that integrates graph theory, fuzzy sets and genetic algorithms for the diagnosis of manufacturing systems. The approach enables the modelling of causal relations of system components in manufacturing systems. Based on the model thus established, a worst-first search technique has been proposed and developed for the identification of probable fault-propagation paths. As manufacturing diagnosis often involves the interpretation of uncertainty, fuzzy-set theory is employed for this purpose. Unlike conventional diagnostic systems which assume that all the system components or nodes of a manufacturing system model are measurable, the genetic-algorithm-based search engine developed in this work is able to deal with nodes that cannot be, or are not, measured. Details of the hybrid approach, the worst-first search technique and the genetic-algorithms-based search engine are discussed. The framework of a prototype fuzzy-based genetic diagnostic system is described. Details of the system validation are also presented. (C) 2000 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Khoo2000,
      author = {Khoo, LP and Ang, CL and Zhang, J},
      title = {A fuzzy-based genetic approach to the diagnosis of manufacturing systems},
      journal = {ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE},
      year = {2000},
      volume = {13},
      number = {3},
      pages = {303-310}
    }
    
    Kibbe, W.A. OligoCalc: an online oligonucleotide properties calculator {2007} NUCLEIC ACIDS RESEARCH
    Vol. {35}({Suppl. S}), pp. {W43-W46} 
    article DOI  
    Abstract: We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intramolecular hairpin loop formation. OligoCalc has a familiar `calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900 000 accesses of OligoCalc from nearly 200 000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.north western. edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.
    BibTeX:
    @article{Kibbe2007,
      author = {Kibbe, Warren A.},
      title = {OligoCalc: an online oligonucleotide properties calculator},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2007},
      volume = {35},
      number = {Suppl. S},
      pages = {W43-W46},
      doi = {{10.1093/nar/gkm234}}
    }
    
    KISHIMOTO, M., MOOYOUNG, M. & ALLSOP, P. A FUZZY EXPERT SYSTEM FOR THE OPTIMIZATION OF GLUTAMIC-ACID PRODUCTION {1991} BIOPROCESS ENGINEERING
    Vol. {6}({4}), pp. {163-172} 
    article  
    Abstract: A ``fuzzy'' expert system was developed to allow the effective use of semi-quantitative or imprecise information in the determination of the optimal operating conditions of a fermentation process. The system incorporated fuzzy relations representing both the trends of experimental data and semi-quantitative information obtained from the literature. The inference method used consisted primarily of search and reasoning based on fuzzy set theory. The resulting expert system incorporated a generalized inference engine designed to deal with various types of fermentation processes, it only being necessary to alter the knowledge database in order to adapt the system to process modifications. The construction of the knowledge database from experimental data or semi-quantitative information was designed to be carried out semi-automatically using a graphic computer tool. The expert system was applied to the optimization of glutamic acid production by fermentation. The optimal conditions predicted by the expert system were found experimentally to give maximum production.
    BibTeX:
    @article{KISHIMOTO1991,
      author = {KISHIMOTO, M and MOOYOUNG, M and ALLSOP, P},
      title = {A FUZZY EXPERT SYSTEM FOR THE OPTIMIZATION OF GLUTAMIC-ACID PRODUCTION},
      journal = {BIOPROCESS ENGINEERING},
      year = {1991},
      volume = {6},
      number = {4},
      pages = {163-172}
    }
    
    Kobayashi, M. & Takeda, K. Information retrieval on the Web {2000} ACM COMPUTING SURVEYS
    Vol. {32}({2}), pp. {144-173} 
    article  
    Abstract: In this paper we review studies of the growth of the Internet and technologies that are useful for information search and retrieval on the Web. We present data an the Internet from several different sources, e.g., current as well as projected number of users, hosts, and Web sites. Although numerical figures vary, overall trends cited by the sources are consistent and point to exponential growth in the past and in the coming decade. Hence it is not surprising that about 85% of Internet users surveyed claim using search engines and search services to find specific information. The same surveys show, however, that users are not satisfied with the performance of the current generation of search engines; the slow retrieval speed, communication delays, and poor quality of retrieved results (e.g., noise and broken links) are commonly cited problems. We discuss the development of new techniques targeted to resolve some of the problems associated with Web-based information retrieval,and speculate an future trends.
    BibTeX:
    @article{Kobayashi2000,
      author = {Kobayashi, M and Takeda, K},
      title = {Information retrieval on the Web},
      journal = {ACM COMPUTING SURVEYS},
      year = {2000},
      volume = {32},
      number = {2},
      pages = {144-173}
    }
    
    Koehler, J., Philippi, S., Specht, M. & Rueegg, A. Ontology based text indexing and querying for the semantic web {2006} KNOWLEDGE-BASED SYSTEMS
    Vol. {19}({8}), pp. {744-754} 
    article DOI  
    Abstract: This publication shows how the gap between the HTML based internet and the RDF based vision of the semantic web might be bridged, by linking words in texts to concepts of ontologies. Most current search engines use indexes that are built at the syntactical level and return hits based on simple string comparisons. However, the indexes do not contain synonyms, cannot differentiate between homonyms ('mouse' as a pointing vs. `mouse' as an animal) and users receive different search results when they use different conjugation forms of the same word. In this publication, we present a system that uses ontologies and Natural Language Processing techniques to index texts, and thus supports word sense disambiguation and the retrieval of texts that contain equivalent words, by indexing them to concepts of ontologies. For this purpose, we developed fully automated methods for mapping equivalent concepts of imported RDF ontologies (for this prototype WordNet, SUMO and OpenCyc). These methods will thus allow the seamless integration of domain specific ontologies for concept based information retrieval in different domains. To demonstrate the practical workability of this approach, a set of web pages that contain synonyms and homonyms were indexed and can be queried via a search engine like query frontend. However, the ontology based indexing approach can also be used for other data mining applications such text clustering, relation mining and for searching free text fields in biological databases. The ontology alignment methods and some of the text mining principles described in this publication are now incorporated into the ONDEX system http://ondex.sourceforge.net/. (c) 2006 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Koehler2006,
      author = {Koehler, Jacob and Philippi, Stephan and Specht, Michael and Rueegg, Alexander},
      title = {Ontology based text indexing and querying for the semantic web},
      journal = {KNOWLEDGE-BASED SYSTEMS},
      year = {2006},
      volume = {19},
      number = {8},
      pages = {744-754},
      doi = {{10.1016/j.knosys.2006.04.015}}
    }
    
    KOEKEMOER, A., HENKEL, C., GREENHILL, L., DEY, A., VANBREUGEL, W., ANTONUCCI, R. & CODELLA, C. A WATER-VAPOR GIGA-MASER IN THE ACTIVE GALAXY TXFS2226-184 {1995} NATURE
    Vol. {378}({6558}), pp. {697-699} 
    article  
    Abstract: ACTIVE galactic nuclei are thought to be powered by gas falling into a massive black hole; the different types of active galaxy mag arise because we view them through a thick torus of molecular gas at varying angles of inclination(1). One way to determine whether the black hole is surrounded by a torus, which would obscure the accretion disk around the black hole along certain lines of sight, is to search for water masers, as these exist only in regions with plentiful molecular gas. Since the first detection(2) of an extragalactic water maser in 1979, they have come to be associated primarily with active galaxies, and have even been used to probe the mass of the central engine(3). Here we report the detection of a water giga-maser in the radio galaxy TXFS2226-184. The strength of the emission supports a recently proposed theory of maser pumping(4) that allows for even more powerful masers, which might be detectable at cosmological distances. Water masers may accordingly provide a may to determine distances to galaxies outside the usual distance ladder, providing an independent calibration of the Hubble constant(3,5).
    BibTeX:
    @article{KOEKEMOER1995,
      author = {KOEKEMOER, AM and HENKEL, C and GREENHILL, LJ and DEY, A and VANBREUGEL, W and ANTONUCCI, R and CODELLA, C},
      title = {A WATER-VAPOR GIGA-MASER IN THE ACTIVE GALAXY TXFS2226-184},
      journal = {NATURE},
      year = {1995},
      volume = {378},
      number = {6558},
      pages = {697-699}
    }
    
    Kohli, E., Gaspari, M., Raj, H., Parmar, V., Sharma, S., van der Greef, J., Kumari, R., Gupta, G., Seema, Khurana, P., Tyagi, Y., Watterson, A. & Olsen, C. Acetoxy drug: protein transacetylase of buffalo liver-characterization and mass spectrometry of the acetylated protein product {2004} BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
    Vol. {1698}({1}), pp. {55-66} 
    article DOI  
    Abstract: The purification and characterization of the buffalo liver microsomal transacetylase (TAase) catalyzing the transfer of acetyl groups from a model acetoxy drug: 7,8-diacetoxy-4-methylcoumarin (DAMC) to GST3-3 has been described here. The enzyme was routinely assayed using DAMC and cytosolic GST as the substrates and was partially purified from microsomes of the buffalo liver. The enzyme was found to have approximate molecular weight of 65 kDa. The action of TAase and DAMC on liver cytosolic GST resulted in the formation of monoacetoxymonohydroxy-4-methylcoumarin (MAMHC) and 7,8-dihydroxy-4-methylcoumarin (DHMC), although the former was the major metabolite. The buffalo liver microsomal TAase exhibited hyperbolic kinetics and yielded K-m (1667 muM) and V-max (192 units) when the concentration of DAMC was varied keeping the concentration of GST constant. After having characterized the nature of the substrates and a product of the TAase-catalyzed reaction, we set out to identify the acetylated protein which is another product of the reaction. GST3-3 was used as a model protein substrate for the action of TAase using DAMC as the acetyl donor. The subunit of control and modified GST3-3 were separated by SDS-polyacrylamide gel electrophoresis (PAGE) and digested with trypsin. The tryptic peptides were extracted from the gel pieces and analyzed by matrix assisted laser desorption/ionization- time of flight-mass spectrometry (MALDI-TOFMS). The data search for calibrated and labeled mass peaks of peptides was performed on the Matrix Science Server using the search engine Mascot. The peptide maps so obtained covered 97% of the GST3-3 sequence. On comparison of MALDI peptide maps of modified and control GST, seven new peaks were recognized corresponding to the potentially acetylated peptides in peptide map. The mass value of each of them was 42 Da higher than the theoretical mass of a non-modified GST3-3 tryptic peptide, strongly suggesting acetylation. By examining the fragmentation patterns and by comparing experimental and predicted values for MS/MS daughter ions, the identity of the seven acetylated GST tryptic peptides could be confirmed by the application of LC/MS/MS. In the modified GST, N-terminal proline and six lysines (Lys(51), Lys(82), Lys(123), Lsy(181), Lys(191), and Lys(210)) were found to be acetylated. The structure of acetylated GST revealed that the lysines that underwent acetylation were peripheral in positions. (C) 2003 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Kohli2004,
      author = {Kohli, E and Gaspari, M and Raj, HG and Parmar, VS and Sharma, SK and van der Greef, J and Kumari, R and Gupta, G and Seema and Khurana, P and Tyagi, YK and Watterson, AC and Olsen, CE},
      title = {Acetoxy drug: protein transacetylase of buffalo liver-characterization and mass spectrometry of the acetylated protein product},
      journal = {BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS},
      year = {2004},
      volume = {1698},
      number = {1},
      pages = {55-66},
      doi = {{10.1016/j.bbapap.2003.10.004}}
    }
    
    Koshman, S., Spink, A. & Jansen, B.J. Web searching on the vivisimo search engine {2006} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {57}({14}), pp. {1875-1887} 
    article DOI  
    Abstract: The application of clustering to Web search engine technology is a novel approach that offers structure to the information deluge often faced by Web searchers. Clustering methods have been well studied in research labs; however, real user searching with clustering systems in operational Web environments is not well understood. This article reports on results from a transaction log analysis of Vivisimo.com, which is a Web meta-search engine that dynamically clusters users' search results. A transaction log analysis was conducted on 2-week's worth of data collected from March 28 to April 4 and April 25 to May 2, 2004, representing 100% of site traffic during these periods and 2,029,734 queries overall. The results show that the highest percentage of queries contained two terms. The highest percentage of search sessions contained one query and was less than 1 minute in duration. Almost half of user interactions with clusters consisted of displaying a cluster's result set, and a small percentage of interactions showed cluster tree expansion. Findings show that 11.1 % of search sessions were multitasking searches, and there are a broad variety of search topics in multitasking search sessions. Other searching interactions and statistics on repeat users of the search engine are reported. These results provide insights into search characteristics with a cluster-based Web search engine and extend research into Web searching trends.
    BibTeX:
    @article{Koshman2006,
      author = {Koshman, Sherry and Spink, Amanda and Jansen, Bernard J.},
      title = {Web searching on the vivisimo search engine},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2006},
      volume = {57},
      number = {14},
      pages = {1875-1887},
      doi = {{10.1002/asi.20408}}
    }
    
    Kouris, I., Makris, C. & Tsakalidis, A. Using information retrieval techniques for supporting data mining {2005} DATA & KNOWLEDGE ENGINEERING
    Vol. {52}({3}), pp. {353-383} 
    article DOI  
    Abstract: The classic two-stepped approach of the Apriori algorithm and its descendants, which consisted of finding all large itemsets and then using these itemsets to generate all association rules has worked well for certain categories of data. Nevertheless for many other data types this approach shows highly degraded performance and proves rather inefficient. We argue that we need to search all the search space of candidate itemsets but rather let the database unveil its secrets as the customers use it. We propose a system that does not merely scan all possible combinations of the itemsets, but rather acts like a search engine specifically implemented for making recommendations to the customers using techniques borrowed from Information Retrieval. (C) 2004 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Kouris2005,
      author = {Kouris, IN and Makris, CH and Tsakalidis, AK},
      title = {Using information retrieval techniques for supporting data mining},
      journal = {DATA & KNOWLEDGE ENGINEERING},
      year = {2005},
      volume = {52},
      number = {3},
      pages = {353-383},
      doi = {{10.1016/j.datak.2004.07.004}}
    }
    
    Kristensen, D., Brond, J., Nielsen, P., Andersen, J., Sorensen, O., Jorgensen, V., Budin, K., Matthiesen, J., Veno, P., Jespersen, H., Ahrens, C., Schandorff, S., Ruhoff, P., Wisniewski, J., Bennett, K. & Podtelejnikov, A. Experimental Peptide Identification Repository (EPIR) - An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data {2004} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {3}({10}), pp. {1023-1038} 
    article DOI  
    Abstract: LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine ( e. g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.
    BibTeX:
    @article{Kristensen2004,
      author = {Kristensen, DB and Brond, JC and Nielsen, PA and Andersen, JR and Sorensen, OT and Jorgensen, V and Budin, K and Matthiesen, J and Veno, P and Jespersen, HM and Ahrens, CH and Schandorff, S and Ruhoff, PT and Wisniewski, JR and Bennett, KL and Podtelejnikov, AV},
      title = {Experimental Peptide Identification Repository (EPIR) - An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2004},
      volume = {3},
      number = {10},
      pages = {1023-1038},
      doi = {{10.1074/mcp.T400004-MCP200}}
    }
    
    Kuchcinski, K. Constraints-driven scheduling and resource assignment {2003} ACM TRANSACTIONS ON DESIGN AUTOMATION OF ELECTRONIC SYSTEMS
    Vol. {8}({3}), pp. {355-383} 
    article  
    Abstract: This paper describes a new method for modeling and solving different scheduling and resource assignment problems that are common in high-level synthesis (HLS) and system-level synthesis. It addresses assignment of resources for operations and tasks as well as their static, off-line scheduling. Different heterogeneous constraints are considered for these problems. These constraints can be grouped into two classes: problem-specific constraints and design-oriented constraints. They are uniformly modeled, in our approach, by finite domain (FD) constraints and solved using related constrained programming (CP) techniques. This provides a way to improve quality of final solutions. We have developed in Java a constraint solver engine, JaCoP ( Java Constraint Programming), to evaluate this approach. This solver and a related framework make it possible to model different resource assignment and scheduling problems, and handle them uniformly. The JaCoP prototype system has been extensively evaluated on a number of HLS and system-level synthesis benchmarks. We have been able to obtain optimal results together with related proofs of optimality for all HLS scheduling benchmarks and for all explored design styles ( except one functional pipeline design). Many system-level benchmarks can also be solved optimally. For large randomly generated task graphs, we have used heuristic search methods and obtained results that are 1 - 3% worse than lower bounds or optimal results. These experiments have proved the feasibility of the presented approach.
    BibTeX:
    @article{Kuchcinski2003,
      author = {Kuchcinski, K},
      title = {Constraints-driven scheduling and resource assignment},
      journal = {ACM TRANSACTIONS ON DESIGN AUTOMATION OF ELECTRONIC SYSTEMS},
      year = {2003},
      volume = {8},
      number = {3},
      pages = {355-383}
    }
    
    Kunachak, S., Kunachakr, S., Sirikulchayanonta, V. & Leelaudomniti, P. Dermabrasion is an effective treatment for acquired bilateral nevus of Ota-like macules {1996} DERMATOLOGIC SURGERY
    Vol. {22}({6}), pp. {559-562} 
    article  
    Abstract: BACKGROUND. Dermal pigmented lesion, or acquired bilateral nevus of Ota-like macules, is a common entity in Asian skin. There are no established data supporting the safety, effectiveness, and cosmesis of its treatment. The lesions do not respond to bleaching or peeling agents. OBJECTIVE. To search for a means of treatment that is cost effective, safe, and yields a good cosmetic result. If possible, these requirement should be accomplished within one session. METHODS. Three hundred and twenty patients who presented themselves with acquired bilateral nevus of Ota-like macules were included in the study. Area dermabrasion using a hand engine with a coarse diamond fraise was performed in every case. RESULTS. Three hundred and twenty patients (97 achieved 100% clearance of the pigment. In the remaining 10 patients (3 there was 5% residual pigment. The wound healed with excellent cosmesis, and without changing skirt texture. CONCLUSION. Dermabrasion is an excellent modality for the treatment of acquired nevus of Ota-like macules.
    BibTeX:
    @article{Kunachak1996,
      author = {Kunachak, S and Kunachakr, S and Sirikulchayanonta, V and Leelaudomniti, P},
      title = {Dermabrasion is an effective treatment for acquired bilateral nevus of Ota-like macules},
      journal = {DERMATOLOGIC SURGERY},
      year = {1996},
      volume = {22},
      number = {6},
      pages = {559-562}
    }
    
    Kurshan, R., Levin, V., Minea, M., Peled, D. & Yenigun, H. Static partial order reduction {1998}
    Vol. {1384}TOOLS AND ALGORITHMS FOR THE CONSTRUCTION AND ANALYSIS OF SYSTEMS, pp. {345-357} 
    inproceedings  
    Abstract: The state space explosion problem is central to automatic verification algorithms. One of the successful techniques to abate this problem is called `partial order reduction'. It is based on the observation that in many cases the specification of concurrent programs does not depend on the order in which concurrently executed events are interleaved. In this paper we present a new version of partial order reduction that allows all of the reduction to be set up at the time of compiling the system description. Normally, partial order reduction requires developing specialized verification algorithms, which in the course of a state space search, select a subset of the possible transitions from each reached global state. In our approach, the set of atomic transitions obtained from the system description after our special compilation, already generates a smaller number of choices from each state. Thus, rather than conducting a modified search of the state space generated by the original state transition relation, our approach involves an ordinary search of the reachable state space generated by a modified state transition relation. Among the advantages of this technique over other versions of the reduction is that it can be directly implemented using existing verification tools, as it requires no change of the verification engine: the entire reduction mechanism is set up at compile time. One major application is the use of this reduction technique together with symbolic model checking and localization reduction, obtaining a combined reduction. We discuss an implementation and experimental results for SDL programs translated into COSPAN notation by applying our reduction techniques. This is part of a hardware-software co-verification project.
    BibTeX:
    @inproceedings{Kurshan1998,
      author = {Kurshan, R and Levin, V and Minea, M and Peled, D and Yenigun, H},
      title = {Static partial order reduction},
      booktitle = {TOOLS AND ALGORITHMS FOR THE CONSTRUCTION AND ANALYSIS OF SYSTEMS},
      year = {1998},
      volume = {1384},
      pages = {345-357},
      note = {4th International Conference on Tool and Algorithms for the Construction and Analysis of Systems (TACAS'98) at the Joint ETAPS'98, LISBON, PORTUGAL, MAR 28-APR 04, 1998}
    }
    
    Kwok, C., Etzioni, O. & Weld, D. Scaling question answering to the Web {2001} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {19}({3}), pp. {242-262} 
    article  
    Abstract: The wealth of information on the web makes it an attractive resource for seeking quick answers to simple, factual questions such as ``who was the first American in space?'' or ``what is the second tallest mountain in the world?'' Yet today's most advanced web search services (e.g., Google and AskJeeves) make it surprisingly tedious to locate answers to such questions, In this paper, we extend question-answering techniques, first studied in the information retrieval literature, to the web and experimentally evaluate their performance, First we introduce MULDER, which we believe to be the first general-purpose, fully-automated question-answering system available on the web. Second, we describe MULDER's architecture, which relies on multiple search-engine queries, natural-language parsing, and a novel voting procedure to yield reliable answers coupled with high recall. Finally, we compare MULDER's performance to that of Google and AskJeeves on questions drawn from the TREC-8 question answering track. We find that MULDER's recall is more than a factor of three higher than that of AskJeeves, In addition, we find that Google requires 6.6 times as much user effort to achieve the same level of recall as MULDER.
    BibTeX:
    @article{Kwok2001,
      author = {Kwok, C and Etzioni, O and Weld, D},
      title = {Scaling question answering to the Web},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2001},
      volume = {19},
      number = {3},
      pages = {242-262}
    }
    
    Lacroix, Z. Biological data integration: Wrapping data and tools {2002} IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE
    Vol. {6}({2}), pp. {123-128} 
    article  
    Abstract: Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat riles, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an extensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.
    BibTeX:
    @article{Lacroix2002,
      author = {Lacroix, Z},
      title = {Biological data integration: Wrapping data and tools},
      journal = {IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE},
      year = {2002},
      volume = {6},
      number = {2},
      pages = {123-128}
    }
    
    Lahanas, M., Baltas, D. & Zamboglou, N. Anatomy-based three-dimensional dose optimization in brachytherapy using multiobjective genetic algorithms {1999} MEDICAL PHYSICS
    Vol. {26}({9}), pp. {1904-1918} 
    article  
    Abstract: In conventional dose optimization algorithms, in brachytherapy, multiple objectives are expressed in terms of an aggregating function which combines individual objective values into a single utility value, making the problem single objective, prior to optimization. A multiobjective genetic algorithm (MOGA) was developed for dose optimization based on an a posteriori approach, leaving the decision-making process to a planner and offering a representative trade-off surface of the various objectives. The MOGA provides a flexible search engine which provides the maximum of information for a decision maker. Tests performed with various treatment plans in brachytherapy have shown that MOGA gives solutions which are superior to those of traditional dose optimization algorithms. Objectives were proposed in terms of the COW distribution and differential volume histograms, taking into account patient anatomy in the optimization process. (C) 1999 American Association of Physicists in Medicine. [S0094-2405(99)00309-0].
    BibTeX:
    @article{Lahanas1999,
      author = {Lahanas, M and Baltas, D and Zamboglou, N},
      title = {Anatomy-based three-dimensional dose optimization in brachytherapy using multiobjective genetic algorithms},
      journal = {MEDICAL PHYSICS},
      year = {1999},
      volume = {26},
      number = {9},
      pages = {1904-1918}
    }
    
    Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., King, N., Stein, S.E. & Aebersold, R. Development and validation of a spectral library searching method for peptide identification from MS/MS {2007} PROTEOMICS
    Vol. {7}({5}), pp. {655-667} 
    article  
    Abstract: A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high-quality spectral library was constructed by combining the high-confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerewsiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteornic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.
    BibTeX:
    @article{Lam2007,
      author = {Lam, Henry and Deutsch, Eric W. and Eddes, James S. and Eng, Jimmy K. and King, Nichole and Stein, Stephen E. and Aebersold, Ruedi},
      title = {Development and validation of a spectral library searching method for peptide identification from MS/MS},
      journal = {PROTEOMICS},
      year = {2007},
      volume = {7},
      number = {5},
      pages = {655-667}
    }
    
    Lamb, J. Innovation - The Connectivity Map: a new tool for biomedical research {2007} NATURE REVIEWS CANCER
    Vol. {7}({1}), pp. {54-60} 
    article DOI  
    Abstract: The ultimate objective of biomedical research is to connect human diseases with the genes that underlie them and drugs that treat them. But this remains a daunting task, and even the most inspired researchers still have to resort to laborious screens of genetic or chemical libraries. What if at least some parts of this screening process could be systematized and centralized? And hits found and hypotheses generated with something resembling an internet search engine? These are the questions the Connectivity Map project set out to answer.
    BibTeX:
    @article{Lamb2007,
      author = {Lamb, Justin},
      title = {Innovation - The Connectivity Map: a new tool for biomedical research},
      journal = {NATURE REVIEWS CANCER},
      year = {2007},
      volume = {7},
      number = {1},
      pages = {54-60},
      doi = {{10.1038/nrc2044}}
    }
    
    LaPelle, N., Luckmann, R., Simpson, E. & Martin, E. Identifying strategies to improve access to credible and relevant information for public health professionals: a qualitative study {2006} BMC PUBLIC HEALTH
    Vol. {6} 
    article DOI  
    Abstract: Background: Movement towards evidence-based practices in many fields suggests that public health (PH) challenges may be better addressed if credible information about health risks and effective PH practices is readily available. However, research has shown that many PH information needs are unmet. In addition to reviewing relevant literature, this study performed a comprehensive review of existing information resources and collected data from two representative PH groups, focusing on identifying current practices, expressed information needs, and ideal systems for information access. Methods: Nineteen individual interviews were conducted among employees of two domains in a state health department - communicable disease control and community health promotion. Subsequent focus groups gathered additional data on preferences for methods of information access and delivery as well as information format and content. Qualitative methods were used to identify themes in the interview and focus group transcripts. Results: Informants expressed similar needs for improved information access including single portal access with a good search engine; automatic notification regarding newly available information; access to best practice information in many areas of interest that extend beyond biomedical subject matter; improved access to grey literature as well as to more systematic reviews, summaries, and full-text articles; better methods for indexing, filtering, and searching for information; and effective ways to archive information accessed. Informants expressed a preference for improving systems with which they were already familiar such as PubMed and listservs rather than introducing new systems of information organization and delivery. A hypothetical ideal model for information organization and delivery was developed based on informants' stated information needs and preferred means of delivery. Features of the model were endorsed by the subjects who reviewed it. Conclusion: Many critical information needs of PH practitioners are not being met efficiently or at all. We propose a dual strategy of: 1) promoting incremental improvements in existing information delivery systems based on the expressed preferences of the PH users of the systems and 2) the concurrent development and rigorous evaluation of new models of information organization and delivery that draw on successful resources already operating to deliver information to clinical medical practitioners.
    BibTeX:
    @article{LaPelle2006,
      author = {LaPelle, NR and Luckmann, R and Simpson, EH and Martin, ER},
      title = {Identifying strategies to improve access to credible and relevant information for public health professionals: a qualitative study},
      journal = {BMC PUBLIC HEALTH},
      year = {2006},
      volume = {6},
      doi = {{10.1186/1471-2458-6-89}}
    }
    
    Laperriere, L. & ElMaraghy, H. GAPP: A generative assembly process planner {1996} JOURNAL OF MANUFACTURING SYSTEMS
    Vol. {15}({4}), pp. {282-293} 
    article  
    Abstract: This paper presents results of exhaustive research in automated assembly planning. A generative assembly process planner (GAPP) has been developed that takes as input a solid model of the product to be assembled and outputs its feasible assembly sequences. Once the product has been modeled as a solid using a commercial solid modeler, the resulting solid model's boundary representation (B-Rep) file is interpreted by the GAPP to generate mating information among parts in the form of a relational graph. This graph becomes the input of a search graph process whose constrained expansion reveals all feasible assembly sequences from a geometric, stability, and accessibility point of view. The relative goodness of different feasible assembly sequences can be determined using pertinent criteria such as the number of reorientations involved or the clustering of similar assembly operations into successive ones. The expansion engine is very flexible and enables many different types of assembly problems to be handled uniformly, for example, finding disassembly repair sequences not requiring complete product disassembly or generating assembly sequences that force the building of predefined subassemblies. Examples with real industrial products are provided to illustrate the potential of using this tool.
    BibTeX:
    @article{Laperriere1996,
      author = {Laperriere, L and ElMaraghy, HA},
      title = {GAPP: A generative assembly process planner},
      journal = {JOURNAL OF MANUFACTURING SYSTEMS},
      year = {1996},
      volume = {15},
      number = {4},
      pages = {282-293}
    }
    
    Lapuerta, M., Hernandez, J., Ballesteros, R. & Duran, A. Composition and size of diesel particulate emissions from a commercial European engine tested with present and future fuels {2003} PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART D-JOURNAL OF AUTOMOBILE ENGINEERING
    Vol. {217}({D10}), pp. {907-919} 
    article  
    Abstract: The search for alternative fuels, such as methyl ester from vegetable oils or water-oil emulsions, has become even more pertinent in the current context of fossil fuel shortage, the diesel vehicle population explosion and the new environmental policies. In this paper, the results of experimental research on particulate emissions from a typical indirect injection (IDI) diesel engine running under five different operating conditions and tested with fourteen types of conventional and alternative fuel are reported. The chemical analysis of the emitted particulate matter showed, for example, that the total mass of particulate emissions decreases when using biofuels owing to a reduction in their insoluble fraction. Moreover, composition analysis made it possible to identify the hydrocarbons adsorbed on the soot surface, to quantify their proportion with respect to the total particulate mass and to distinguish between their origins. The results of surface analysis using scanning electron microscopy showed for all the fuels that the number of particles detected per filter surface increased with load. This analysis also showed the effect of some fuel specifications (aromatic and sulphur content) on certain parameters related to the particle size distribution obtained from the filter images.
    BibTeX:
    @article{Lapuerta2003,
      author = {Lapuerta, M and Hernandez, JJ and Ballesteros, R and Duran, A},
      title = {Composition and size of diesel particulate emissions from a commercial European engine tested with present and future fuels},
      journal = {PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART D-JOURNAL OF AUTOMOBILE ENGINEERING},
      year = {2003},
      volume = {217},
      number = {D10},
      pages = {907-919}
    }
    
    Larson, R., McDonough, J., OLeary, P., Kuntz, L. & Moon, R. Cheshire II: Designing a next-generation online catalog {1996} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE
    Vol. {47}({7}), pp. {555-567} 
    article  
    Abstract: The Cheshire II online catalog system was designed to provide a bridge between the realms of purely bibliographical information and the rapidly expanding full-text and multimedia collections available online. It is based on a number of national and international standards for data description, communication, and interface technology. The system uses a client-server architecture with X window client communication with an SGML-based probabilistic search engine using the Z39.50 information retrieval protocol.
    BibTeX:
    @article{Larson1996,
      author = {Larson, RR and McDonough, J and OLeary, P and Kuntz, L and Moon, R},
      title = {Cheshire II: Designing a next-generation online catalog},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE},
      year = {1996},
      volume = {47},
      number = {7},
      pages = {555-567}
    }
    
    Lawrence, S. & Giles, C. Searching the World Wide Web {1998} SCIENCE
    Vol. {280}({5360}), pp. {98-100} 
    article  
    Abstract: The coverage and recency of the major World Wide Web search engines was analyzed, yielding some surprising results. The coverage of any one engine is significantly limited: No single engine indexes more than about one-third of the ``indexable Web,'' the coverage of the six engines investigated varies by an order of magnitude, and combining the results of the six engines yields about 3.5 times as many documents on average as compared with the results from only one engine. Analysis of the overlap between pairs of engines gives an estimated lower bound on the size of the indexable Web of 320 million pages.
    BibTeX:
    @article{Lawrence1998,
      author = {Lawrence, S and Giles, CL},
      title = {Searching the World Wide Web},
      journal = {SCIENCE},
      year = {1998},
      volume = {280},
      number = {5360},
      pages = {98-100}
    }
    
    Lazzari, B., Caprera, A., Vecchietti, A., Stella, A., Milanesi, L. & Pozzi, C. ESTree db: a tool for peach functional genomics {2005} BMC BIOINFORMATICS
    Vol. {6}({Suppl. 4}) 
    article DOI  
    Abstract: Background: The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results: The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion: The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.
    BibTeX:
    @article{Lazzari2005,
      author = {Lazzari, B and Caprera, A and Vecchietti, A and Stella, A and Milanesi, L and Pozzi, C},
      title = {ESTree db: a tool for peach functional genomics},
      journal = {BMC BIOINFORMATICS},
      year = {2005},
      volume = {6},
      number = {Suppl. 4},
      note = {Annual Meeting of the Italian-Society-of-Bioinformatics, Milan, ITALY, MAR 17-19, 2005},
      doi = {{10.1186/1471-2105-6-S4-S16}}
    }
    
    Lee, Z.M.-P., Bussema, III, C. & Schmidt, T.M. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea {2009} NUCLEIC ACIDS RESEARCH
    Vol. {37}({Sp. Iss. SI}), pp. {D489-D493} 
    article DOI  
    Abstract: A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1-15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16Sr RNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.
    BibTeX:
    @article{Lee2009,
      author = {Lee, Zarraz May-Ping and Bussema, III, Carl and Schmidt, Thomas M.},
      title = {rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2009},
      volume = {37},
      number = {Sp. Iss. SI},
      pages = {D489-D493},
      doi = {{10.1093/nar/gkn689}}
    }
    
    Lei, Z., Elmer, A., Watson, B., Dixon, R., Mendes, P. & Sumner, L. A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula {2005} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {4}({11}), pp. {1812-1825} 
    article DOI  
    Abstract: The proteome of a Medicago truncatula cell suspension culture was analyzed using two-dimensional electrophoresis and nanoscale HPLC coupled to a tandem Q-TOF mass spectrometer (QSTAR Pulsar i) to yield an extensive protein reference map. Coomassie Brilliant Blue R-250 was used to visualize more than 1661 proteins, which were excised, subjected to in-gel trypsin digestion, and analyzed using nanoscale HPLC/MS/MS. The resulting spectral data were queried against a custom legume protein database using the MASCOT search engine. A total of 1367 of the 1661 proteins were identified with high rigor, yielding an identification success rate of 83% and 907 unique protein accession numbers. Functional annotation of the M. truncatula suspension cell proteins revealed a complete tricarboxylic acid cycle, a nearly complete glycolytic pathway, a significant portion of the ubiquitin pathway with the associated proteolytic and regulatory complexes, and many enzymes involved in secondary metabolism such as flavonoid/isoflavonoid, chalcone, and lignin biosynthesis. Proteins were also identified from most other functional classes including primary metabolism, energy production, disease/defense, protein destination/storage, protein synthesis, transcription, cell growth/division, and signal transduction. This work represents the most extensive proteomic description of M. truncatula suspension cells to date and provides a reference map for future comparative proteomic and functional genomic studies of the response of these cells to biotic and abiotic stress.
    BibTeX:
    @article{Lei2005,
      author = {Lei, Z and Elmer, AM and Watson, BS and Dixon, RA and Mendes, PJ and Sumner, LW},
      title = {A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2005},
      volume = {4},
      number = {11},
      pages = {1812-1825},
      doi = {{10.1074/mcp.D500005-MCP200}}
    }
    
    Leifman, G., Meir, R. & Tal, A. Semantic-oriented 3d shape retrieval using relevance feedback {2005} VISUAL COMPUTER
    Vol. {21}({8-10, Sp. Iss. SI}), pp. {865-875} 
    article DOI  
    Abstract: Shape-based retrieval of 3D models has become an important challenge in computer graphics. Object similarity, however, is a subjective matter, dependent on the human viewer, since objects have semantics and are not mere geometric entities. Relevance feedback aims at addressing the subjectivity of similarity. This paper presents a novel relevance feedback algorithm that is based on supervised as well as unsupervised feature extraction techniques. It also proposes a novel signature for 3D models, the sphere projection. A Web search engine that realizes the signature and the relevance feedback algorithm is presented. We show that the proposed approach produces good results and outperforms previous techniques.
    BibTeX:
    @article{Leifman2005,
      author = {Leifman, G and Meir, R and Tal, A},
      title = {Semantic-oriented 3d shape retrieval using relevance feedback},
      journal = {VISUAL COMPUTER},
      year = {2005},
      volume = {21},
      number = {8-10, Sp. Iss. SI},
      pages = {865-875},
      note = {13th Pacific Conference on Computer Graphics and Applications, Macao, PEOPLES R CHINA, OCT 12-14, 2005},
      doi = {{10.1007/s00371-005-0341-z}}
    }
    
    Lemkin, P. The 2DWG meta-database of two-dimensional electrophoretic gel images on the Internet {1997} ELECTROPHORESIS
    Vol. {18}({15}), pp. {2759-2773} 
    article  
    Abstract: The 2DWG meta-database is a searchable database of two-dimensional (2-D) electrophoretic gel images found on the Internet. A meta-database contains information about locating data in other databases - but not that data itself. This database was constructed because of a need for an enriched set of World Wide Web (WWW) locations (URLs) of 2-D gel images on the Internet. These gel images are used in conjunction with the National Cancer Institute (NCI) Flicker Server to manipulate and visually compare 2-D gel images across the Internet. User's gels may also be compared with those in the database. The 2DWG is organized as a spreadsheet table with each gel image being represented by a row sorted by tissue type. Data for each gel includes tissue type, species, cell-line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists, etc. The 2DWG may be searched to find relevant subsets of gels. Searching is done using the dbEngine - a WWW database search engine which accesses selected rows of gels from the full 2DWG table. The 2DWG meta-database is accessible on the WWW at http://www-lecb.ncifcrf.gov/2dwgDB/ and the NCI Flicker server at http://wwwlecb.ncifcrf.gov/flicker/.
    BibTeX:
    @article{Lemkin1997,
      author = {Lemkin, PF},
      title = {The 2DWG meta-database of two-dimensional electrophoretic gel images on the Internet},
      journal = {ELECTROPHORESIS},
      year = {1997},
      volume = {18},
      number = {15},
      pages = {2759-2773}
    }
    
    Lempel, R. & Moran, S. SALSA: The stochastic approach for link-structure analysis {2001} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {19}({2}), pp. {131-160} 
    article  
    Abstract: Today, when searching for information on the WWW, one usually performs a query through a term-based search engine. These engines return, as the query's result, a list of Web pages whose contents matches the query. For broad-topic queries, such searches often result in a huge set of retrieved documents, many of which are irrelevant to the user. However, much information is contained in the link-structure of the WWW. Information such as which pages are linked to others can be used to augment search algorithms. In this context, Jon Kleinberg introduced the notion of two distinct types of Web pages: hubs and authorities. Kleinberg argued that hubs and authorities exhibit a mutually reinforcing relationship: a good hub will point to many authorities, and a good authority will be pointed at by many hubs. In light of this, he devised an algorithm aimed at finding authoritative pages. We present SALSA, a new stochastic approach for link-structure analysis, which examines random walks on graphs derived from the link-structure. We show that both SALSA and Kleinberg's Mutual Reinforcement approach employ the same metaalgorithm. We then prove that SALSA is equivalent to a weighted in-degree analysis of the link-structure of WWW subgraphs, making it computationally more efficient than the Mutual Reinforcement approach. We compare the results of applying SALSA to the results derived through Kleinberg's approach. These comparisons reveal a topological phenomenon called the TKC Effect which, in certain cases, prevents the Mutual Reinforcement approach from identifying meaningful authorities.
    BibTeX:
    @article{Lempel2001,
      author = {Lempel, R and Moran, S},
      title = {SALSA: The stochastic approach for link-structure analysis},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2001},
      volume = {19},
      number = {2},
      pages = {131-160}
    }
    
    Lempel, R. & Moran, S. The stochastic approach for link-structure analysis (SALSA) and the TKC effect {2000} COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING
    Vol. {33}({1-6}), pp. {387-401} 
    article  
    Abstract: Today, when searching for information on the World Wide Web, one usually performs a query through a term-based search engine. These engines return, as the query's result, a list of Web sites whose contents match the query. For broad topic queries, such searches often result in a huge set of retrieved documents, many of which are irrelevant to the user. However, much information is contained in the link-structure of the World Wide Web. Information such as which pages are linked to others can be used to augment search algorithms. In this context, Jon Kleinberg introduced the notion of two distinct types of Web sites: hubs and authorities. Kleinberg argued that hubs and authorities exhibit a mutually reinforcing relationship: a good hub will point to many authorities, and a good authority will be pointed at by many hubs. In light of this, he devised an algorithm aimed at finding authoritative sites. We present SALSA, a new stochastic approach for link structure analysis, which examines random walks on graphs derived from the link structure. We show that both SALSA and Kleinberg's mutual reinforcement approach employ the same meta-algorithm. We then prove that SALSA is equivalent to a weighted in-degree analysis of the link-structure of World Wide Web subgraphs, making it computationally more efficient than the mutual reinforcement approach. We compare the results of applying SALSA to the results derived through kleinberg's approach. These comparisons reveal a topological phenomenon called the TKC effect (Tightly Knit Community) which, in certain cases, prevents the mutual reinforcement approach from identifying meaningful authorities. (C) 2000 Published by Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Lempel2000,
      author = {Lempel, R and Moran, S},
      title = {The stochastic approach for link-structure analysis (SALSA) and the TKC effect},
      journal = {COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING},
      year = {2000},
      volume = {33},
      number = {1-6},
      pages = {387-401},
      note = {9th International World Wide Web Conference (WWW9), AMSTERDAM, NETHERLANDS, MAY 15-19, 2000}
    }
    
    Leroy, G., Lally, A. & Chen, H. The use of dynamic contexts to improve casual Internet searching {2003} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {21}({3}), pp. {229-253} 
    article  
    Abstract: Research has shown that most users' online information searches are suboptimal. Query optimization based on a relevance feedback or genetic algorithm using dynamic query contexts can help casual users search the Internet. These algorithms can draw on implicit user feedback based on the surrounding links and text in a search engine result set to expand user queries with a variable number of keywords in two manners. Positive expansion adds terms to a user's keywords with a Boolean ``and,'' negative expansion adds terms to the user's keywords with a Boolean ``not.'' Each algorithm was examined for three user groups, high, middle, and low achievers, who were classified according to their overall performance. The interactions of users with different levels of expertise with different expansion types or algorithms were evaluated. The genetic algorithm with negative expansion tripled recall and doubled precision for low achievers, but high achievers displayed an opposed trend and seemed to be hindered in this condition. The effect of other conditions was less substantial.
    BibTeX:
    @article{Leroy2003,
      author = {Leroy, G and Lally, AM and Chen, H},
      title = {The use of dynamic contexts to improve casual Internet searching},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2003},
      volume = {21},
      number = {3},
      pages = {229-253}
    }
    
    Levitin, G. & Lisnianski, A. A new approach to solving problems of multi-state system reliability optimization {2001} QUALITY AND RELIABILITY ENGINEERING INTERNATIONAL
    Vol. {17}({2}), pp. {93-104} 
    article  
    Abstract: Usually engineers try to achieve the required reliability level with minimal cost. The problem of total investment cost minimization, subject to reliability constraints, is well known as the reliability optimization problem. When applied to multi-state systems (MSS), the system has many performance levels, and reliability is considered as a measure of the ability of the system to meet the demand (required performance). In this case, the outage effect will be essentially different for units with different performance rate. Therefore, the performance of system components, as well as the demand, should be taken into account. In this paper, we present a technique for solving a family of MSS reliability optimization problems, such as structure optimization, optimal expansion, maintenance optimization and optimal multistage modernization. This technique combines a universal generating function (UGF) method used for fast reliability estimation of R-ISS and a genetic algorithm (GA) used as an optimization engine. The UGF method provides the ability to estimate relatively quickly different MSS reliability indices for series-parallel and bridge structures. It can be applied to MSS with different physical nature of system performance measure. The GA is a robust, universal optimization tool that uses only estimates of solution quality to determine the direction of search. Copyright (C) 2001 John Wiley & Sons, Ltd.
    BibTeX:
    @article{Levitin2001,
      author = {Levitin, G and Lisnianski, A},
      title = {A new approach to solving problems of multi-state system reliability optimization},
      journal = {QUALITY AND RELIABILITY ENGINEERING INTERNATIONAL},
      year = {2001},
      volume = {17},
      number = {2},
      pages = {93-104}
    }
    
    Lew, M.S., Sebe, N., Djeraba, C. & Jain, R. Content-based multimedia information retrieval: State of the art and challenges {2006} ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS
    Vol. {2}({1}), pp. {1-19} 
    article  
    Abstract: Extending beyond the boundaries of science, art, and culture, content-based multimedia information retrieval provides new paradigms and methods for searching through the myriad variety of media all over the world. This survey reviews 100+ recent articles on content-based multimedia information retrieval and discusses their role in current research directions which include browsing and search paradigms, user studies, affective computing, learning, semantic queries, new features and media types, high performance indexing, and evaluation techniques. Based on the current state of the art, we discuss the major challenges for the future.
    BibTeX:
    @article{Lew2006,
      author = {Lew, Michael S. and Sebe, Nicu and Djeraba, Chabane and Jain, Ramesh},
      title = {Content-based multimedia information retrieval: State of the art and challenges},
      journal = {ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS},
      year = {2006},
      volume = {2},
      number = {1},
      pages = {1-19}
    }
    
    Lewandowski, D., Wahlig, H. & Meyer-Bautor, G. The freshness of web search engine databases {2006} JOURNAL OF INFORMATION SCIENCE
    Vol. {32}({2}), pp. {131-148} 
    article DOI  
    Abstract: This study measures the frequency with which search engines update their indices. Therefore, 38 websites that are updated on a daily basis were analysed within a time-span of six weeks. The analysed search engines were Google, Yahoo and MSN. We find that Google performs best overall with the most pages updated on a daily basis, but only MSN is able to update all pages within a time-span of less than 20 days. Both other engines have outliers that are older. In terms of indexing patterns, we find different approaches at the different engines. While MSN shows clear update patterns, Google shows some outliers and the update process of the Yahoo index seems to be quite chaotic. Implications are that the quality of different search engine indices varies and more than one engine should be used when searching for current content.
    BibTeX:
    @article{Lewandowski2006,
      author = {Lewandowski, D and Wahlig, H and Meyer-Bautor, G},
      title = {The freshness of web search engine databases},
      journal = {JOURNAL OF INFORMATION SCIENCE},
      year = {2006},
      volume = {32},
      number = {2},
      pages = {131-148},
      doi = {{10.1177/0165551506062326}}
    }
    
    Leydesdorff, L. & Vaughan, L. Co-occurrence matrices and their applications in information science: Extending ACA to the Web environment {2006} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {57}({12}), pp. {1616-1628} 
    article DOI  
    Abstract: Co-occurrence matrices, such as cocitation, coword, and colink matrices, have been used widely in the information sciences. However, confusion and controversy have hindered the proper statistical analysis of these data. The underlying problem, in our opinion, involved understanding the nature of various types of matrices. This article discusses the difference between a symmetrical cocitation matrix and an asymmetrical citation matrix as well as the appropriate statistical techniques that can be applied to each of these matrices, respectively. Similarity measures (such as the Pearson correlation coefficient or the cosine) should not be applied to the symmetrical cocitation matrix but can be applied to the asymmetrical citation matrix to derive the proximity matrix. The argument is illustrated with examples. The study then extends the application of co-occurrence matrices to the Web environment, in which the nature of the available data and thus data collection methods are different from those of traditional databases such as the Science Citation Index. A set of data collected with the Google Scholar search engine is analyzed by using both the traditional methods of multivariate analysis and the new visualization software Pajek, which is based on social network analysis and graph theory.
    BibTeX:
    @article{Leydesdorff2006,
      author = {Leydesdorff, Loet and Vaughan, Liwen},
      title = {Co-occurrence matrices and their applications in information science: Extending ACA to the Web environment},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2006},
      volume = {57},
      number = {12},
      pages = {1616-1628},
      doi = {{10.1002/asi.20335}}
    }
    
    Li, W., Filippenko, A., Treffers, R., Friedman, A., Halderson, E., Johnson, R., King, J., Modjaz, M., Papenkova, M., Sato, Y. & Shefler, T. The Lick Observatory Supernova Search {2000}
    Vol. {522}COSMIC EXPLOSIONS, pp. {103-106} 
    inproceedings  
    Abstract: We report here the current status of the Lick Observatory Supernova Search (LOSS) with the Katzman Automatic Imaging Telescope (KAIT). The progress on both the hardware and the software of the system is described, and we present a list of recent discoveries. LOSS is the world's most successful search engine for nearby supernovae.
    BibTeX:
    @inproceedings{Li2000,
      author = {Li, WD and Filippenko, AV and Treffers, RR and Friedman, A and Halderson, E and Johnson, RA and King, JY and Modjaz, M and Papenkova, M and Sato, Y and Shefler, T},
      title = {The Lick Observatory Supernova Search},
      booktitle = {COSMIC EXPLOSIONS},
      year = {2000},
      volume = {522},
      pages = {103-106},
      note = {10th Annual Astrophysics Conference on Cosmic Explosions, COLLEGE PK, MD, OCT 11-13, 1999}
    }
    
    Li, X. A review of the development and application of the Web impact factor {2003} ONLINE INFORMATION REVIEW
    Vol. {27}({6}), pp. {407-417} 
    article DOI  
    Abstract: Since 1996, hyperlinks have been studied extensively by applying existing bibliometric methods. The Web impact factor (WIF), for example, is the online counterpart of the journal impact factor. This paper reviews how this link-based metric has been developed, enhanced and applied. Not only has the metric itself undergone improvement but also the relevant data collection techniques have been enhanced. WIFs have also been validated by significant correlations with traditional research measures. Bibliometric techniques have been further applied to the Web and patterns that might have otherwise been ignored have been found from hyperlinks. This paper concludes with some suggestions for future research.
    BibTeX:
    @article{Li2003,
      author = {Li, XM},
      title = {A review of the development and application of the Web impact factor},
      journal = {ONLINE INFORMATION REVIEW},
      year = {2003},
      volume = {27},
      number = {6},
      pages = {407-417},
      doi = {{10.1108/14684520310510046}}
    }
    
    Li, Y. Toward a qualitative search engine {1998} IEEE INTERNET COMPUTING
    Vol. {2}({4}), pp. {24-29} 
    article  
    BibTeX:
    @article{Li1998,
      author = {Li, YH},
      title = {Toward a qualitative search engine},
      journal = {IEEE INTERNET COMPUTING},
      year = {1998},
      volume = {2},
      number = {4},
      pages = {24-29}
    }
    
    Liaw, S. & Huang, H. An investigation of user attitudes toward search engines as an information retrieval tool {2003} COMPUTERS IN HUMAN BEHAVIOR
    Vol. {19}({6}), pp. {751-765} 
    article DOI  
    Abstract: After the Internet has gained great popularity at homes and schools, there is much information on the Web. Today, one of the primary uses of the Internet is information retrieval from search engines. The main purpose of the current study is to develop and examine an individual attitude model towards search engines as a tool for retrieving information. This model integrates individual computer experience with perceptions. In addition, it also combines perception theories, such as technology acceptance model (TAM) and motivation, in order to understand individual attitudes toward search engines. The results show that individual computer experience, quality of search systems, motivation, and perceptions of technology acceptance are all key factors that affect individual feelings to use search engines as an information retrieval tool. (C) 2003 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Liaw2003,
      author = {Liaw, SS and Huang, HM},
      title = {An investigation of user attitudes toward search engines as an information retrieval tool},
      journal = {COMPUTERS IN HUMAN BEHAVIOR},
      year = {2003},
      volume = {19},
      number = {6},
      pages = {751-765},
      doi = {{10.1016/S0747-5632(03)00009-8}}
    }
    
    Liebel, U., Kindler, B. & Pepperkok, R. `Harvester': a fast meta search engine of human protein resources {2004} BIOINFORMATICS
    Vol. {20}({12}), pp. {1962-1963} 
    article DOI  
    Abstract: We have developed a Web-based tool named `Harvester' that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every single protein is assembled on a single HTML page as a combination of database screen-shots and plain text. A full text meta search engine, similar to Google(TM), allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. A feedback forum allows users to comment on Harvester and to report database inconsistencies.
    BibTeX:
    @article{Liebel2004,
      author = {Liebel, U and Kindler, B and Pepperkok, R},
      title = {`Harvester': a fast meta search engine of human protein resources},
      journal = {BIOINFORMATICS},
      year = {2004},
      volume = {20},
      number = {12},
      pages = {1962-1963},
      doi = {{10.1093/bioinformatics/bth146}}
    }
    
    Lim, C., Lee, K. & Kim, G. Multiple sets of features for automatic genre classification of web documents {2005} INFORMATION PROCESSING & MANAGEMENT
    Vol. {41}({5}), pp. {1263-1276} 
    article DOI  
    Abstract: With the increase of information on the Web, it is difficult to find desired information quickly out of the documents retrieved by a search engine. One way to solve this problem is to classify web documents according to various criteria. Most document classification has been focused on a subject or a topic of a document. A genre or a style is another view of a document different from a subject or a topic. The genre is also a criterion to classify documents. In this paper, we suggest multiple sets of features to classify genres of web documents. The basic set of features, which have been proposed in the previous studies, is acquired from the textual properties of documents, such as the number of sentences, the number of a certain word, etc. However, web documents are different from textual documents in that they contain URL and HTML tags within the pages. We introduce new sets of features specific to web documents, which are extracted from URL and HTML tags. The present work is an attempt to evaluate the performance of the proposed sets of features, and to discuss their characteristics. Finally, we conclude which is an appropriate set of features in automatic genre classification of web documents. (c) 2004 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Lim2005,
      author = {Lim, CS and Lee, KJ and Kim, GC},
      title = {Multiple sets of features for automatic genre classification of web documents},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2005},
      volume = {41},
      number = {5},
      pages = {1263-1276},
      doi = {{10.1016/j.ipm.2004.06.004}}
    }
    
    Lin, C., Lin, G. & Lue, T. Cyclic nucleotide signaling in cavernous smooth muscle {2005} JOURNAL OF SEXUAL MEDICINE
    Vol. {2}({4}), pp. {478-491} 
    article DOI  
    Abstract: Introduction. Penile erection depends on cavernous smooth muscle relaxation that is principally regulated by cyclic nucleotide signaling. It is hoped that a comprehensive review of publications relevant to this subject will be helpful to both scientists and clinicians who are interested in the sciences of erectile function/dysfunction. Aims. To review the roles of extracellular signaling molecules, their receptors, intracellular effectors, and phosphodiesterases in cyclic nucleotide signaling that leads to cavernous smooth muscle relaxation. The involvement of these molecules in the development of erectile dysfunction and the possibility of using them as therapeutic agents or targets are also discussed. Methods. Entrez, the search engine for life sciences, was used to search for publications relevant to the topics of this review. Keywords used in the searches included vascular, cavernous, penis, smooth muscle, signaling molecules (adenosine, nitric oxide, etc.), and key elements in the cyclic nucleotide signaling pathways (cAMP, cGMP, cyclases, PKG, PKA, etc.). Articles that are dedicated to the study of erectile function/dysfunction were prioritized for citation. Results. More than 1,000 articles were identified, many of which are studies of the vascular system and are therefore reviewed but not cited. Studies on erectile function have identified both cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) signaling pathways in cavernous smooth muscle. Many signaling molecules of these two pathways have been shown capable of inducing erection when administered intracavernously However, for sexually induced erection, nitric oxide (NO) is the responsible signaling molecule and it passes on the signal through soluble guanyl cyclase (sGC), cGMP, and protein kinase G (PKG). Conclusions. The NO/sGC/cGMP/PKG pathway is principally responsible for sexually stimulated erection. Detu-mescence is mainly carried out by the degradation of cGMP by phosphodiesterase 5. Both cAMP and cGMP signaling pathways are susceptible to genetic and biochemical alterations in association with erectile dysfunction. Several key elements along these pathways are potential therapeutic targets.
    BibTeX:
    @article{Lin2005,
      author = {Lin, CS and Lin, G and Lue, TF},
      title = {Cyclic nucleotide signaling in cavernous smooth muscle},
      journal = {JOURNAL OF SEXUAL MEDICINE},
      year = {2005},
      volume = {2},
      number = {4},
      pages = {478-491},
      doi = {{10.1111/j.1743-6109.2005.00080.x}}
    }
    
    Lin, S. & Chen, Y. Design of self-learning fuzzy sliding mode controllers based on genetic algorithms {1997} FUZZY SETS AND SYSTEMS
    Vol. {86}({2}), pp. {139-153} 
    article  
    Abstract: In this paper, genetic algorithms were applied to search a sub-optimal fuzzy rule-base for a fuzzy sliding mode controller. Two types of fuzzy sliding mode controllers based on genetic algorithms were proposed. The fitness functions were defined so that the controllers which can drive and keep the state on the user-defined sliding surface would be assigned a higher fitness value. The sliding surface plays a very important role in the design of a fuzzy sliding mode controller. It can dominate the dynamic behaviors of the control system as well as reduce the size of the fuzzy rule-base. In conventional fuzzy logic control, an increase in either input variables or the associated linguistic labels would lead to the exponential growth of the number of rules. The number of parameters or the equivalent length of strings used in the computations of genetic algorithms for a fuzzy logic controller are usually quite extensive. As a result, the considerable computation load prevents the use of genetic operations in the tuning of membership functions in a fuzzy rule-base. This paper shows that the number of rules in a fuzzy sliding mode controller is a linear function of the number of input variables. The computation load of the inference engine in a fuzzy sliding mode controller is thus smaller than that in a fuzzy logic controller. Moreover, the string length of parameters is shorter in a fuzzy sliding mode controller than in a fuzzy logic controller when the parameters are searched by genetic algorithms. The simulation results showed the efficiency of the proposed approach and demonstrated the applicability of the genetic algorithm in the fuzzy sliding mode controller design. (C) 1997 Elsevier Science B.V.
    BibTeX:
    @article{Lin1997,
      author = {Lin, SC and Chen, YY},
      title = {Design of self-learning fuzzy sliding mode controllers based on genetic algorithms},
      journal = {FUZZY SETS AND SYSTEMS},
      year = {1997},
      volume = {86},
      number = {2},
      pages = {139-153}
    }
    
    Lissman, T. & Boehnlein, J. A critical review of Internet information about depression {2001} PSYCHIATRIC SERVICES
    Vol. {52}({8}), pp. {1046-1050} 
    article  
    Abstract: Objective: The source and quality of information about depression available on the Internet were examined. Methods. Online searches using the phrase ``depression and treatment'' were conducted on ten major Internet search engines. The first 20 sites generated by each engine were examined. The Web sites and the individual Web pages they contained were categorized by source, target audience, and affiliation with either a for-profit or a not-for-profit organization. Each site was rated by whether it mentioned the nine symptoms and five major criteria of a major depressive episode and whether it made any of three basic treatment recommendations. Ratings were compared to determine whether treatment differences between the sites could be attributed to the site's source. Results: The search generated a total of 178 active sites. Overall, the quality of information was poor. Only half of the sites mentioned any DSM-IV diagnostic symptom or criteria. in their descriptions of depression, and only a quarter listed 11 to 14 symptoms or criteria. Almost half of the sites made no mention of medications, psychotherapy, or professional consultation as suggested treatments for depression. Almost two-thirds of the pages were found on for-profit sites. Documents from these sites scored lower on diagnostic accuracy and treatment recommendations than those from not-for-profit sites. Conclusions: The quality of information on the Internet produced by the search was quite low. For-profit Web sites appeared much more frequently than not-for-profit sites among the first 20 sites generated by each search engine, and they contained poorer information.
    BibTeX:
    @article{Lissman2001,
      author = {Lissman, TL and Boehnlein, JK},
      title = {A critical review of Internet information about depression},
      journal = {PSYCHIATRIC SERVICES},
      year = {2001},
      volume = {52},
      number = {8},
      pages = {1046-1050}
    }
    
    Liu, B. & Ling, S. On the selection of informative wavelets for machinery diagnosis {1999} MECHANICAL SYSTEMS AND SIGNAL PROCESSING
    Vol. {13}({1}), pp. {145-162} 
    article  
    Abstract: A new method of machinery fault diagnosis based on wavelet analysis is presented. We introduce an extension to Mallat and Zhang's matching pursuit for machinery diagnosis is presented. Instead of the `best matching' criterion, a mutual information measure is used to search a redundant wavelet dictionary for a small set of wavelets that carry meaningful information about machinery faults. With these informative wavelets treated as feature extractors, this approach effectively facilitates the diagnosis of machinery faults of a non-stationary nature. This method has been applied to the detection of diesel engine malfunctions. The results show that both the sensitivity and the reliability of this approach are good. (C) 1999 Academic Press.
    BibTeX:
    @article{Liu1999,
      author = {Liu, B and Ling, SF},
      title = {On the selection of informative wavelets for machinery diagnosis},
      journal = {MECHANICAL SYSTEMS AND SIGNAL PROCESSING},
      year = {1999},
      volume = {13},
      number = {1},
      pages = {145-162}
    }
    
    Liu, F., Yu, C. & Meng, W. Personalized web search for improving retrieval effectiveness {2004} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {16}({1}), pp. {28-40} 
    article  
    Abstract: Current Web search engines are built to serve all users, independent of the special needs of any individual user. Personalization of Web search is to carry out retrieval for each user incorporating his/her interests. We propose a novel technique to learn user profiles from users' search histories. The user profiles are then used to improve retrieval effectiveness in Web search. A user profile and a general profile are learned from the user's search history and a category hierarchy, respectively. These two profiles are combined to map a user query into a set of categories which represent the user's search intention and serve as a context to disambiguate the words in the user's query. Web search is conducted based on both the user query and the set of categories. Several profile learning and category mapping algorithms and a fusion algorithm are provided and evaluated. Experimental results indicate that our technique to personalize Web search is both effective and efficient.
    BibTeX:
    @article{Liu2004,
      author = {Liu, F and Yu, C and Meng, WY},
      title = {Personalized web search for improving retrieval effectiveness},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2004},
      volume = {16},
      number = {1},
      pages = {28-40}
    }
    
    Liu, M. & Frangopol, D. Multiobjective maintenance planning optimization for deteriorating bridges considering condition, safety, and life-cycle cost {2005} JOURNAL OF STRUCTURAL ENGINEERING-ASCE
    Vol. {131}({5}), pp. {833-842} 
    article DOI  
    Abstract: Many of the currently available bridge management system tools focus on minimizing life-cycle maintenance cost of deteriorating bridges while imposing constraints on structural performance. The computed single optimal maintenance planning solution, however, may not necessarily meet a bridge manager's specific requirements on lifetime bridge performance. In this paper the life-cycle maintenance planning of deteriorating bridges is formulated as a multiobjective optimization problem that treats the lifetime condition and safety levels as well as life-cycle maintenance cost as separate objective functions. A multiobjective genetic algorithm is used as the search engine to automatically locate a large pool of different maintenance scenarios that exhibits an optimized tradeoff among conflicting objectives. This tradeoff provides improved opportunity for bridge managers to actively select the final maintenance scenario that most desirably balances life-cycle maintenance cost, condition, and safety levels of deteriorating bridges.
    BibTeX:
    @article{Liu2005,
      author = {Liu, M and Frangopol, DM},
      title = {Multiobjective maintenance planning optimization for deteriorating bridges considering condition, safety, and life-cycle cost},
      journal = {JOURNAL OF STRUCTURAL ENGINEERING-ASCE},
      year = {2005},
      volume = {131},
      number = {5},
      pages = {833-842},
      doi = {{10.1061/(ASCE)0733-9445(2005)131:5(833)}}
    }
    
    Lo Conte, L., Brenner, S., Hubbard, T., Chothia, C. & Murzin, A. SCOP database in 2002: refinements accommodate structural genomics {2002} NUCLEIC ACIDS RESEARCH
    Vol. {30}({1}), pp. {264-267} 
    article  
    Abstract: The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are grouped into species and hierarchically classified into families, superfamilies, folds and classes. Recently, we introduced a new set of features with the aim of standardizing access to the database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects. These features include: a new set of identifiers, which uniquely identify each entry in the hierarchy; a compact representation of protein domain classification; a new set of parseable files, which fully describe all domains in SCOP and the hierarchy itself. These new features are reflected in the ASTRAL compendium. The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
    BibTeX:
    @article{LoConte2002,
      author = {Lo Conte, L and Brenner, SE and Hubbard, TJP and Chothia, C and Murzin, AG},
      title = {SCOP database in 2002: refinements accommodate structural genomics},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2002},
      volume = {30},
      number = {1},
      pages = {264-267}
    }
    
    Loia, V., Pedrycz, W. & Senatore, S. P-FCM: a proximity-based fuzzy clustering for user-centered web applications {2003} INTERNATIONAL JOURNAL OF APPROXIMATE REASONING
    Vol. {34}({2-3}), pp. {121-144} 
    article DOI  
    Abstract: In last years, the Internet and the web have been evolved in an astonishing way. Standard web search services play an important role as useful tools for the Internet community even though they suffer from a certain difficulty. The web continues its growth, making the reliability of Internet-based information and retrieval systems more complex. Nevertheless there has been a substantial analysis of the gap between the expected information and the returned information, the work of web search engine is still very hard. There are different problems concerning web searching activity, one among these falls in the query phase. Each engine provide an interface which the user is forced to learn. Often, the searching process returns a huge list of answers that are irrelevant, unavailable, or outdated. The tediosity of querying, due to the fact the queries are too weak to cope with the user's expressiveness, has stimulated the designers to enrich the human-system interaction with new searching metaphors. One of these is the searching of ``similar'' pages, as offered by Google, Yahoo and others. The idea is very good, since the similarity gives an easy and intuitive mechanism to express a complex relation. We believe that this approach could become more effective if the user can rely on major flexibility in expressing the similarity dependencies with respect the current and available possibilities. In this paper we introduce a novel method for considering and processing the user-driven similarity during web navigation. We define an extension of fuzzy C-means algorithm, namely proximity fuzzy C-means (P-FCM) incorporating a measure of similarity or dissimilarity as user's feedback on the clusters. We present the theoretical framework of this extension and then we observe, through a suite of web-based experiments, how significant is the impact of user's feedback during P-FCM functioning. These observations suggest that the P-FCM approach can offer a relatively simple way of improving the web page classification according with the user interaction with the search engine. (C) 2003 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Loia2003,
      author = {Loia, V and Pedrycz, W and Senatore, S},
      title = {P-FCM: a proximity-based fuzzy clustering for user-centered web applications},
      journal = {INTERNATIONAL JOURNAL OF APPROXIMATE REASONING},
      year = {2003},
      volume = {34},
      number = {2-3},
      pages = {121-144},
      doi = {{10.1016/j.ijar.2003.07.004}}
    }
    
    Lokeshwar, V., Habuchi, T., Grossman, H., Murphy, W., Hautmann, S., Hemstreet, G., Bono, A., Getzenberg, R., Goebell, P., Schmitz-Drager, B., Schalken, J., Fradet, Y., Marberger, M., Messing, E. & Droller, M. Bladder tumor markers beyond cytology: International consensus panel on bladder tumor markers {2005} UROLOGY
    Vol. {66}({6A, Suppl. S}), pp. {35-63} 
    article DOI  
    Abstract: This is the first of 2 articles that summarize the findings of the International Consensus Panel on cytology and bladder tumor markers. The objectives of our panel were to reach a consensus on the areas where markers are needed, to define the attributes of an ideal tumor marker, and to identify which marker(s) would be suitable for diagnosis and/or surveillance of bladder cancer. Our panel consisted of urologists and researchers from Europe, Asia, and the United States who reviewed original articles, reviews, and book chapters on individual bladder tumor markers published in the English language mainly using the PubMed search engine. Panel members also met during 3 international meetings to write recommendations regarding bladder tumor markers. The panel found that the most practical use of noninvasive tests is to monitor bladder cancer recurrence, thereby reducing the number of surveillance cystoscopies performed each year. Markers also may be useful in the screening of high-risk individuals for early detection of bladder cancer. However, more prospective studies are needed to strengthen this argument. Case-control and cohort studies show that several markers have a higher sensitivity to detect bladder cancer. However, cytology is the superior marker in terms of specificity, although some markers in limited numbers of studies have shown specificity equivalent to that of cytology. Our panel believes that several bladder tumor markers are more accurate in detecting bladder cancer than prostate-specific antigen (PSA) is in detecting prostate cancer. However, bladder tumor markers are held to a higher standard than PSA. Therefore, use of bladder tumor markers in the management of patients with bladder cancer will require the willingness of both urologists and clinicians to accept them.
    BibTeX:
    @article{Lokeshwar2005,
      author = {Lokeshwar, VB and Habuchi, T and Grossman, HB and Murphy, WM and Hautmann, SH and Hemstreet, GP and Bono, AV and Getzenberg, RH and Goebell, P and Schmitz-Drager, BJ and Schalken, JA and Fradet, Y and Marberger, M and Messing, E and Droller, MJ},
      title = {Bladder tumor markers beyond cytology: International consensus panel on bladder tumor markers},
      journal = {UROLOGY},
      year = {2005},
      volume = {66},
      number = {6A, Suppl. S},
      pages = {35-63},
      note = {27th Congress of the Societe-Internationale-Urologie (SIU), Honolulu, HI, OCT 03-07, 2004},
      doi = {{10.1016/j.urology.2005.08.064}}
    }
    
    Lorigo, L., Pan, B., Hernbrooke, H., Joachims, T., Granka, L. & Gay, G. The influence fo task and gender on search and evaluation behavior using Google {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({4}), pp. {1123-1131} 
    article DOI  
    Abstract: To improve search engine effectiveness, we have observed an increased interest in gathering additional feedback about users' information needs that goes beyond the queries they type in. Adaptive search engines use explicit and implicit feedback indicators to model users or search tasks. In order to create appropriate models, it is essential to understand how users interact with search engines, including the determining factors of their actions. Using eye tracking, we extend this understanding by analyzing the sequences and patterns with which users evaluate query result returned to them when using Google. We find that the query result abstracts are viewed in the order of their ranking in only about one fifth of the cases, and only an average of about three abstracts per result page are viewed at all. We also compare search behavior variability with respect to different classes of users and different classes of search tasks to reveal whether user models or task models may be greater predictors of behavior. We discover that gender and task significantly influence different kinds of search behaviors discussed here. The results are suggestive of improvements to query-based search interface designs with respect to both their use of space and workflow. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Lorigo2006,
      author = {Lorigo, L and Pan, B and Hernbrooke, H and Joachims, T and Granka, L and Gay, G},
      title = {The influence fo task and gender on search and evaluation behavior using Google},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {4},
      pages = {1123-1131},
      doi = {{10.1016/j.ipm.2005.10.001}}
    }
    
    Lu, P. & Hsu, T. Application of autoassociative neural network on gas-path sensor data validation {2002} JOURNAL OF PROPULSION AND POWER
    Vol. {18}({4}), pp. {879-888} 
    article  
    Abstract: Gas-path analysis holds a central position in the engine condition monitoring and fault diagnostics technique. The success of gas-path analysis, as concluded from previous investigations, depends mainly on the quality of the measurements obtained. For approaches using either a classical Kalman filter method or a contemporary artificial neural network approach, a high success rate of diagnosis can only be guaranteed when a correct set of measurement deltas is available. The objective of the present work is to design a genetic autoassociative neural network algorithm that can perform offline sensor data validation simultaneously for noise filtering and bias detection and correction. The neural network-based sensor validation procedure usually suffers from the slow convergence in network training. In addition, the trained network often fails to provide an accurate accommodation when bias error is detected. To remedy these network training and bias accommodation problems, a two-step approach is proposed. The first step is the construction of a noise-filtering and a self-mapping autoassociative neural network based on the backpropagation algorithm. The second step uses an optimization procedure built on top of these noise-filtering and self-mapping nets to perform bias detection and correction. A nongradient genetic algorithm search is employed as the optimization method. It is shown in the present work that effective sensor data validation can be achieved for noise filtering, bias correction, and missing sensor data replacement incurred in the gas-path analysis. This newly developed algorithm can also serve as an intelligent trend detector. A true performance delta and trend change can be identified with no delay, to assure a timely and high-quality engine fault diagnosis.
    BibTeX:
    @article{Lu2002,
      author = {Lu, PJ and Hsu, TC},
      title = {Application of autoassociative neural network on gas-path sensor data validation},
      journal = {JOURNAL OF PROPULSION AND POWER},
      year = {2002},
      volume = {18},
      number = {4},
      pages = {879-888}
    }
    
    Lubbecke, M. & Zimmermann, U. Engine routing and scheduling at industrial in-plant railroads {2003} TRANSPORTATION SCIENCE
    Vol. {37}({2}), pp. {183-197} 
    article  
    Abstract: In-plant railroad engine scheduling involves routing and scheduling decisions for a heterogeneous fleet of switching engines to serve a set of time-window- and capacity-constrained transportation requests. Despite an ever-increasing competition, the current planning is purely by pencil and paper. Our paper describes the mathematical and algorithmic developments for addressing in-plant railroad decision support for scheduling and routing. The problem discussed in our work is related to the multiple-vehicle pickup and delivery problem. Exploiting the structure of admissible schedules of our particular railroad situation, we introduce two formulations of the problem as mixed integer and set partitioning programs. We propose solving the linear programming relaxation of the set partition model by column generation. We focus on the pricing problem stated in the form of a constrained shortest path problem, which is NP complete in the strong sense. A new exact label correcting algorithm is developed that prunes the search space in a novel manner. Heuristically obtained integer solutions of a practical quality are proposed as well. All the claims are demonstrated by computational experiments on both artificial and real-life data. We discuss implementation details as well.
    BibTeX:
    @article{Lubbecke2003,
      author = {Lubbecke, ME and Zimmermann, UT},
      title = {Engine routing and scheduling at industrial in-plant railroads},
      journal = {TRANSPORTATION SCIENCE},
      year = {2003},
      volume = {37},
      number = {2},
      pages = {183-197}
    }
    
    Lucas, W. & Topi, H. Form and function: The impact of query term and operator usage on Web search results {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({2}), pp. {95-108} 
    article  
    Abstract: Conventional wisdom holds that queries to information retrieval systems will yield more relevant results if they contain multiple topic-related terms and use Boolean and phrase operators to enhance interpretation. Although studies have shown that the users of Web-based search engines typically enter short, term-based queries and rarely use search operators, little information exists concerning the effects of term and operator usage on the relevancy of search results. In this study, search engine users formulated queries on eight search topics. Each query was submitted to the user-specified search engine, and relevancy ratings for the retrieved pages were assigned. Expert-formulated queries were also submitted and provided a basis for comparing relevancy ratings across search engines. Data analysis based on our research model of the term and operator factors affecting relevancy was then conducted. The results show that the difference in the number of terms between expert and nonexpert searches, the percentage of matching terms between those searches, and the erroneous use of nonsupported operators in nonexpert searches explain most of the variation in the relevancy of search results. These findings highlight the need for designing search engine interfaces that provide greater support in the areas of term selection and operator usage.
    BibTeX:
    @article{Lucas2002,
      author = {Lucas, W and Topi, H},
      title = {Form and function: The impact of query term and operator usage on Web search results},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {2},
      pages = {95-108}
    }
    
    MacLean, B., Eng, J.K., Beavis, R.C. & McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine {2006} BIOINFORMATICS
    Vol. {22}({22}), pp. {2830-2832} 
    article DOI  
    Abstract: Motivation: Tandem mass spectrometry (MS/MS) identifies protein sequences using database search engines, at the core of which is a score that measures the similarity between peptide MS/MS spectra and a protein sequence database. The TANDEM application was developed as a freely available database search engine for the proteomics research community. To extend TANDEM as a platform for further research on developing improved database scoring methods, we modified the software to allow users to redefine the scoring function and replace the native TANDEM scoring function while leaving the remaining core application intact. Redefinition is performed at run time so multiple scoring functions are available to be selected and applied from a single search engine binary. We introduce the implementation of the pluggable scoring algorithm and also provide implementations of two TANDEM compatible scoring functions, one previously described scoring function compatible with PeptideProphet and one very simple scoring function that quantitative researchers may use to begin their development. This extension builds on the open-source TANDEM project and will facilitate research into and dissemination of novel algorithms for matching MS/MS spectra to peptide sequences. The pluggable scoring schema is also compatible with related search applications P3 and Hunter, which are part of the X! suite of database matching algorithms. The pluggable scores and the X! suite of applications are all written in C++.
    BibTeX:
    @article{MacLean2006,
      author = {MacLean, Brendan and Eng, Jimmy K. and Beavis, Ronald C. and McIntosh, Martin},
      title = {General framework for developing and evaluating database scoring algorithms using the TANDEM search engine},
      journal = {BIOINFORMATICS},
      year = {2006},
      volume = {22},
      number = {22},
      pages = {2830-2832},
      doi = {{10.1093/bioinformatics/btl379}}
    }
    
    MacLean, H. & Lave, L. Evaluating automobile fuel/propulsion system technologies {2003} PROGRESS IN ENERGY AND COMBUSTION SCIENCE
    Vol. {29}({1}), pp. {1-69} 
    article  
    Abstract: We examine the life cycle implications of a wide range of fuels and propulsion systems that could power cars and light trucks in the US and Canada over the next two to three decades ((1) reformulated gasoline and diesel, (2) compressed natural gas, (3) methanol and ethanol, (4) liquid petroleum gas, (5) liquefied natural gas, (6) Fischer-Tropsch liquids from natural gas, (7) hydrogen, and (8) electricity; (a) spark ignition port injection engines, (b) spark ignition direct injection engines, (c) compression ignition engines, (d) electric motors with battery power, (e) hybrid electric propulsion options, and (f) fuel cells). We review recent studies to evaluate the environmental, performance, and cost characteristics of fuel/propulsion technology combinations that are currently available or will be available in the next few decades. Only options that could power a significant proportion of the personal transportation fleet are investigated. Contradictions among the goals of customers, manufacturers, and society have led society to assert control through extensive regulation of fuel composition, vehicle emissions, and fuel economy. Changes in social goals, fuel-engine-emissions technologies, fuel availability, and customer desires require a rethinking of current regulations as well as the design of vehicles and fuels that will appeal to consumers over the next decades. The almost 250 million light-duty vehicles (LDV; cars and light trucks) in the US and Canada are responsible for about 14% of the economic activity in these countries for the year 2002. These vehicles are among our most important personal assets and liabilities, since they are generally the second most expensive asset we own, costing almost 100 000 over the lifetime of a vehicle. While an essential part of our lifestyles and economies, in the US, for example, the light-duty fleet is also responsible for 42 000 highways deaths, and four million injuries each year, consumes almost half of the petroleum used, and causes large amounts of illness and premature death due to the emissions of air pollutants (e.g. nitrogen oxides, carbon monoxide, hydrocarbons and particles). The search for new technologies and fuels has been driven by regulators, not the marketplace. Absent regulation, most consumers would demand larger, more powerful vehicles, ignoring fuel economy and emissions of pollutants and greenhouse gases; the vehicles that get more than 35 mpg make up less than 1% of new car sales. Federal regulators require increased vehicle safety, decreased pollution emissions, and better fuel economy. In addition, California and Canadian regulators are concerned about lowering greenhouse gas emissions. Many people worry about the US dependence on imported petroleum, and people in both countries desire a switch from petroleum to a more sustainable fuel. The fuel-technology combinations and vehicle attributes of concern to drivers and regulators are examined along with our final evaluation of the alternatives compared to a conventional gasoline-fueled spark ignition port injection automobile. When the US Congress passed laws intended to increase safety, decrease emissions, and increase fuel economy, they did not realize that these goals were contradictory. For example, increasing safety requires increasing weight, which lowers fuel economy; decreasing emissions generally decreases engine efficiency. By spending more money or by reducing the performance of the vehicle, most of the attributes can be improved without harming others. For example, spending more money can lighten the vehicle (as with an aluminum frame with greater energy absorbing capacity), improving performance and safety; a smaller engine can increase fuel economy without diminishing safety or increasing pollution emissions, but performance -- We discuss methods needed to evaluate the attractiveness of vehicles employing alternative fuels and propulsion systems including: 1. Predicting the vehicle attributes and tradeoffs among these attributes that consumers will find appealing; 2. assessing current and near term technologies to predict the primary attributes of each fuel and propulsion system as well as its externalities and secondary effects; 3. applying a life cycle assessment approach; 4. completing a benefit-cost analysis to quantify the net social benefit of each alternative system; 5. assessing the comparative advantages of centralized command and control regulation versus the use of market incentives; 6. characterizing and quantifying uncertainty. An especially important feature of the analysis is ensuring that vehicles to be compared are similar on the basis of size, safety, acceleration, range; fuel economy, emissions and other vehicle attributes. Since it is nearly impossible to find two vehicles that are identical, we use the criterion of asking whether consumers (and regulators) consider them to be comparable. Comparability has proven to be a difficult task for analysts. No one has managed a fully satisfactory method for adjustment, although some have made progress. Absurd comparisons, such as comparing the fuel economy of a Metro to that of an Expedition, have not been made because of the good sense of analysts. However, steps should be taken to achieve further progress in developing methods to address this issue. Comparing fuels and propulsion systems require a comprehensive, quantitative, life cycle approach to the analysis. It must be more encompassing than `well-to-wheels' analysis. Well-to-wheels is comprised of two components, the `well-to-tank' (all activities involved in producing the fuel) and `tank-to-wheel' (the operation/driving of the vehicle). The analyses must include the extraction of all raw materials, fuel production, infrastructure requirements, component manufacture, vehicle manufacture, use, and end-of-life phases of the vehicle. Focusing on a portion of the system can be misleading. The analysis must be quantitative and include the array of environmental discharges, as well as life cycle cost information, since each fuel and propulsion system has its comparative advantages. Comparing systems requires knowing how much better each alternative is with respect to some dimensions and how much worse it is with respect to others. Since focusing on a single stage or attribute of a system can be misleading, e.g. only tailpipe emissions, we explore the life cycle implications of each fuel and propulsion technology. For example, the California Air Resources Board focused on tailpipe emissions in requiring zero emissions vehicles, neglecting the other attributes of battery-powered cars, such as other environmental discharges, cost, consumer acceptance and performance. The necessity of examining the whole life cycle and all the attributes is demonstrated by the fact that CARB had to rescind its requirement that 2% of new vehicles sold in 1998 and 10% sold in 2003 be zero emissions vehicles. No one fuel/propulsion system dominates the others on all the dimensions in Table 8. This means that society must decide which attributes are more important, as well as the tradeoffs among attributes. For example, higher manufacturing cost could be offset by lower fuel costs over the life of the vehicle. Changes in social goals, technology, fuel options, customer desires, and public policy since 1970 have changed vehicle design, fuel production, manufacturing plants, and infrastructure. In particular, gasoline or diesel in an internal combustion engine (ICE) is currently the cheapest system and is likely to continue to be the cheapest system through 2020. These vehicles will continue to evolve with improvements in performance; safety, fuel economy, and lower pollution emissions. However, if society desires a more sustainable system or one that emits significantly less greenhouse gases, consumers will have to pay more for an alternative fuel or propulsion system. We review a dozen life cycle studies that have examined LDV, comparing different fuels and/or propulsion systems. The studies are summarized in Tables 4 and 5. The studies vary in the fuel/propulsion options they consider, the environmental burdens they report, and the assumptions they employ, making it difficult to compare results. However, all of the studies include the `well-to-tank' and `tank-to-wheel' activities and the majority of the studies include a measure of efficiency and greenhouse gas emissions associated with these activities. We limit our comparison to these activities and measures. The life cycle studies match most closely for the well-to-tank portion and for conventional fossil fuels. See Table 6 for a summary of the ranges of efficiency and greenhouse gas emissions reported in the studies for the well-to-tank portion for the various options. For the well-to-tank portion for the production of electricity, renewable fuels, and hydrogen, differing, fuel production pathways are most important. Due to the range of different production options for these fuels (as well as other issues such as study assumptions), results are much more variable. In addition, there is less experience with producing these fuels, resulting in more uncertainty. It is important to distinguish between total and fossil energy required for production when comparing efficiencies among the fuels. Petroleum-based fuels have the highest efficiency for the well-to-tank portion when;total energy is considered. However, if only fossil energy is considered, biomass-based fuels such as ethanol become more attractive. The tank-to-wheel portions are more difficult to compare. Each study uses its selected vehicle (e.g. conventional sedans, light-weight sedans, pickup trucks); many present assumptions regarding the vehicle efficiencies. However, the studies do not generally report the range of assumptions or test conditions. The well-to-wheel results (the sum of the well-to-tank and tank-to-wheel activities) of the studies are still more difficult to compare. The baseline vehicle (with a few exceptions) is a current gasoline fueled ICE port fuel injection vehicle; it combines an efficient well-to-tank portion with a relatively inefficient tank-to-wheel portion. A direct injection diesel vehicle is considerably more efficient and therefore results in lower emissions of carbon dioxide even though the carbon content in the diesel is higher than that in gasoline. Fuel cell vehicles have a high theoretical efficiency but generally a low efficiency well-to-tank portion, which offsets some of the vehicle efficiency, benefits. Table 7 shows the ranges of values reported in the life cycle studies for the well-to-wheel greenhouse gas emissions. All of the fossil fuel options result in emissions of large amounts of greenhouse gases. Ethanol and hydrogen have the potential to reduce greenhouse gas emissions significantly. However, this is highly dependent on the pathways for ethanol and hydrogen production, especially the amount of fossil fuel inputs during production. Some of the hydrogen options result in higher greenhouse gas emissions than those of a gasoline ICE vehicle. Results for hybrid electric vehicles (HEVs) are dependent on the efficiency improvements over conventional vehicles that are assumed. As noted above, Table 8 summarizes our best judgment as to how each fuel/propulsion system combination would be evaluated on each attribute desired by consumers or society. No one system beats the alternatives on all dimensions. The most desirable system is defined by the properties that the evaluator thinks are most important. Despite the many difficulties and complexities, there are some broad conclusions regarding LDV for the next two to three decades. The vehicle options likely to be competitive during the next two decades are those using improved ICES, including HEVs burning `clean' gasoline or diesel. An extensive infrastructure has been developed to locate, extract, transport, refine, and retail gasoline and diesel. Any alternative to petroleum would require a new infrastructure with attendant disruption and costs running to trillions of dollars. The current infrastructure is a major reason for continuing to use gasoline and diesel fuels. Absent a breakthrough in electrochemistry, battery-powered vehicles will remain expensive and have an unattractive range. The failure to produce a breakthrough despite considerable research does not give much hope that vastly superior, inexpensive batteries will be produced within our time frame. Fuel cell propulsion systems are unlikely to be competitive before 2020, if they are ever competitive. Although, fuel cells have high theoretical efficiencies, and do not need a tailpipe and therefore have vehicle emissions benefits over conventional vehicles, generating the hydrogen and getting it to the vehicle requires large amounts of energy. The current well-to-wheel analyses show that using a liquid fuel and onboard reforming produces a system inferior to gasoline powered ICEs on the basis of efficiency and environmental discharges. Storage of the hydrogen onboard the vehicle is another challenge. Fischer-Tropsch liquids from natural gas and ethanol from biomass may become widespread. The Fischer-Tropsch liquids will penetrate if there are large amounts of stranded natural gas selling for very low prices at the same time that petroleum is expensive or extremely low sulfur is required in diesel fuel. Ethanol could become the dominant fuel if energy independence, sustainability, or very low carbon dioxide emissions become important-or if petroleum prices double. Absent major technology breakthroughs, a doubling of petroleum prices, or stringent regulation of fuel economy or greenhouse gas emissions, the 2030 LDV will be powered by a gasoline ICE. The continuing progress in increasing engine efficiency, lowering emissions, and supplying inexpensive gasoline makes it extremely difficult for any of the alternative fuels or propulsion technologies to displace the gasoline (diesel) fueled ICE. This conclusion should not be interpreted as one of despair or pessimism. Rather, the progress in improving the ICE and providing gasoline/diesel at low price has obviated the need for alternative technologies. Many of the technologies that we examine, such as cellulosic ethanol or Fishcher-Tropsch fuels from natural gas or HEVs are attractive. If there were no further progress in improving the gasoline/diesel fuel ICE or the fuel became more expensive, one or more of these options would take over the market. Thus, the fact that the current fuel and technology is so hard to displace means that society is getting what it wants at low cost. Extensive progress has been made by analysts in examining the life cycles of a range of fuels and propulsion systems for personal transportation vehicles. The most important contribution of these methods and studies is getting decision-makers to focus on the important attributes and to avoid looking only at one aspect of the fuel cycle or propulsion system or at only one media for environmental burdens. The current state of knowledge should avoid the recurrence of the fiasco of requiring battery-powered cars on the grounds that they are good for the environment and will appeal to consumers. (C) 2003 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{MacLean2003,
      author = {MacLean, HL and Lave, LB},
      title = {Evaluating automobile fuel/propulsion system technologies},
      journal = {PROGRESS IN ENERGY AND COMBUSTION SCIENCE},
      year = {2003},
      volume = {29},
      number = {1},
      pages = {1-69}
    }
    
    Malamateniou, F., Vassilacopoulos, G. & Mantas, J. A search engine for virtual patient records {1999} INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
    Vol. {55}({2}), pp. {103-115} 
    article  
    Abstract: Virtual patient records provide a means for integrated access to patient information that may be scattered around different healthcare settings. Within the boundaries of a health district providing all levels of care, this concept can be implemented in an Intranet environment to support longitudinal patient care activities across the participating healthcare providers. Since medical information is stored on multiple Intranet sites in various forms (e.g. codified data, transcribed documents, and images), a suite of appropriate tools is needed to enable access to such information in combined form. In most cases, however, access to medical information should be restricted to authorized users. To serve this purpose, a prototype search engine incorporating an authorization and access control functionality has been developed and presented in this paper. The system is based on the signature file access method and an experimental implementation written in JAVA is also described. (C) 1999 Elsevier Science Ireland Ltd. All rights reserved.
    BibTeX:
    @article{Malamateniou1999,
      author = {Malamateniou, F and Vassilacopoulos, G and Mantas, J},
      title = {A search engine for virtual patient records},
      journal = {INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS},
      year = {1999},
      volume = {55},
      number = {2},
      pages = {103-115}
    }
    
    Maloney, S., Ilic, D. & Green, S. Accessibility, nature and quality of health information on the Internet: a survey on osteoarthritis {2005} RHEUMATOLOGY
    Vol. {44}({3}), pp. {382-385} 
    article DOI  
    Abstract: Objectives. This study aims to determine the quality and validity of information available on the Internet about osteoarthritis and to investigate the best way of sourcing this information. Methods. Keywords relevant to osteoarthritis were searched across 15 search engines representing medical, general and meta-search engines. Search engine efficiency was defined as the percentage of unique and relevant websites from all websites returned by each search engine. The quality of relevant information was appraised using the DISCERN tool and the concordance of the information offered by the website with the available evidence about osteoarthritis determined. Results. A total of 3443 websites were retrieved, of which 344 were identified as unique and providing information relevant to osteoarthritis. The overall quality of website information was poor. There was no significant difference between types of search engine in sourcing relevant information; however, the information retrieved from medical search engines was of a higher quality. Fewer than a third of the websites identified as offering relevant information cited evidence to support their recommendations. Conclusions. Although the overall quality of website information about osteoarthritis was poor, medical search engines may provide consumers with the opportunity to source high-quality health information on the Internet. In the era of evidence-based medicine, one of the main obstacles to the Internet reaching its potential as a medical resource is the failure of websites to incorporate and attribute evidence-based information.
    BibTeX:
    @article{Maloney2005,
      author = {Maloney, S and Ilic, D and Green, S},
      title = {Accessibility, nature and quality of health information on the Internet: a survey on osteoarthritis},
      journal = {RHEUMATOLOGY},
      year = {2005},
      volume = {44},
      number = {3},
      pages = {382-385},
      doi = {{10.1093/rheumatology/keh498}}
    }
    
    Mamoulis, N. & Papadias, D. Multiway spatial joins {2001} ACM TRANSACTIONS ON DATABASE SYSTEMS
    Vol. {26}({4}), pp. {424-475} 
    article  
    Abstract: Due to the evolution of Geographical Information Systems, large collections of spatial data having various thematic contents are currently available. As a result, the interest of users is not limited to simple spatial selections and joins, but complex query types that implicate numerous spatial inputs become more common. Although several algorithms have been proposed for computing the result of pairwise spatial joins, limited work exists on processing and optimization of multiway spatial joins. In this article, we review pairwise spatial join algorithms and show how they can be combined for multiple inputs. In addition, we explore the application of synchronous traversal (ST), a methodology that processes synchronously all inputs without producing intermediate results. Then, we integrate the two approaches in an engine that includes ST and pairwise algorithms, using dynamic programming to determine the optimal execution plan. The results show that, in most cases, multiway spatial joins are best processed by combining ST with pairwise methods. Finally, we study the optimization of very large queries by employing randomized search algorithms.
    BibTeX:
    @article{Mamoulis2001,
      author = {Mamoulis, N and Papadias, D},
      title = {Multiway spatial joins},
      journal = {ACM TRANSACTIONS ON DATABASE SYSTEMS},
      year = {2001},
      volume = {26},
      number = {4},
      pages = {424-475}
    }
    
    Mansfield, J., McIntosh, L., Crowson, A., Mantsch, H. & Jackson, M. LDA-guided search engine for the nonsubjective analysis of infrared microscopic maps {1999} APPLIED SPECTROSCOPY
    Vol. {53}({11}), pp. {1323-1330} 
    article  
    Abstract: Acquisition of large data sets from human tissues by infrared (IR) microscopy is now routine. However, processing such large data sets, which may contain more than 10 000 spectra, provides an enormous challenge. Overcoming this challenge and developing nonsubjective methods for the analysis of IR microscopic results remain the major hurdle to developing clinically useful applications. A three-step pattern recognition strategy based upon linear discriminant analysis has been developed for use as a search engine for tissue characterization. The three-step strategy includes a genetic algorithm-guided data reduction step, a classification step based upon linear discriminant analysis, and a final step in which the discriminant coefficients are converted into a visually appealing, nonsubjective representation of the distribution of each class throughout the tissue section. The application of this search engine in the characterization of tumor-bearing skin is demonstrated.
    BibTeX:
    @article{Mansfield1999,
      author = {Mansfield, JR and McIntosh, LM and Crowson, AN and Mantsch, HH and Jackson, M},
      title = {LDA-guided search engine for the nonsubjective analysis of infrared microscopic maps},
      journal = {APPLIED SPECTROSCOPY},
      year = {1999},
      volume = {53},
      number = {11},
      pages = {1323-1330}
    }
    
    Marchler-Bauer, A., Addess, K., Chappey, C., Geer, L., Madej, T., Matsuo, Y., Wang, Y. & Bryant, S. MMDB: Entrez's 3D structure database {1999} NUCLEIC ACIDS RESEARCH
    Vol. {27}({1}), pp. {240-243} 
    article  
    Abstract: The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The goal of Entrez's 3D-structure database is to make this information accessible and usable by molecular biologists (http://www.ncbi.nlm.nih.gov/Entrez). To this end Entrez provides two major analysis tools, a search engine based on sequence and structure `neighboring' and an integrated visualization system for sequence and structure alignments. From a protein's sequence `neighbors' one may rapidly identify other members of a protein family, including those where 3D structure is known. By comparing aligned sequences and/or structures in detail, using the visualization system, one may identify conserved features and perhaps infer functional properties. Here we describe how these analysis tools may be used to investigate the structure and function of newly discovered proteins, using the PTEN gene product as an example.
    BibTeX:
    @article{Marchler-Bauer1999,
      author = {Marchler-Bauer, A and Addess, KJ and Chappey, C and Geer, L and Madej, T and Matsuo, Y and Wang, Y and Bryant, SH},
      title = {MMDB: Entrez's 3D structure database},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {1999},
      volume = {27},
      number = {1},
      pages = {240-243}
    }
    
    Marian, A., Bruno, N. & Gravano, L. Evaluating top-k queries over web-accessible databases {2004} ACM TRANSACTIONS ON DATABASE SYSTEMS
    Vol. {29}({2}), pp. {319-362} 
    article  
    Abstract: A query to a web search engine usually consists of a list of keywords, to which the search engine responds with the best or ``top'' k pages for the query. This top-k query model is prevalent over multimedia collections in general, but also over plain relational data for certain applications. For example, consider a relation with information on available restaurants, including their location, price range for one diner, and overall food rating. A user who queries such a relation might simply specify the user's location and target price range, and expect in return the best 10 restaurants in terms of some combination of proximity to the user, closeness of match to the target price range, and overall food rating. Processing top-k queries efficiently is challenging for a number of reasons. One critical such reason is that, in many web applications, the relation attributes might not be available other than through external web-accessible form interfaces, which we will have to query repeatedly for a potentially large set of candidate objects. In this article, we study how to process top-k queries efficiently in this setting, where the attributes for which users specify target values might be handled by external, autonomous sources with a variety of access interfaces. We present a sequential algorithm for processing such queries, but observe that any sequential top-k query processing strategy is bound to require unnecessarily long query processing times, since web accesses exhibit high and variable latency. Fortunately, web sources can be probed in parallel, and each source can typically process concurrent requests, although sources may impose some restrictions on the type and number of probes that they are willing to accept. We adapt our sequential query processing technique and introduce an efficient algorithm that maximizes source-access parallelism to minimize query response time, while satisfying source-access constraints. We evaluate our techniques experimentally using both synthetic and real web-accessible data and show that parallel algorithms can be significantly more efficient than their sequential counterparts.
    BibTeX:
    @article{Marian2004,
      author = {Marian, A and Bruno, N and Gravano, L},
      title = {Evaluating top-k queries over web-accessible databases},
      journal = {ACM TRANSACTIONS ON DATABASE SYSTEMS},
      year = {2004},
      volume = {29},
      number = {2},
      pages = {319-362}
    }
    
    Marinescu, V., Kohane, I. & Riva, A. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes {2005} BMC BIOINFORMATICS
    Vol. {6} 
    article DOI  
    Abstract: Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. Results: We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method. Conclusion: The search engine, available at http://mapper.chip.org,allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.
    BibTeX:
    @article{Marinescu2005,
      author = {Marinescu, VD and Kohane, IS and Riva, A},
      title = {MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes},
      journal = {BMC BIOINFORMATICS},
      year = {2005},
      volume = {6},
      doi = {{10.1186/1471-2105-6-79}}
    }
    
    Markatos, E. On caching search engine query results {2001} COMPUTER COMMUNICATIONS
    Vol. {24}({2}), pp. {137-143} 
    article  
    Abstract: In this paper we explore the problem of Caching of Search Engine Query Results in order to reduce the computing and I/O requirements needed to support the functionality of a search engine of the World Wide Web. We study query traces from the EXCITE search engine and show that they have a significant amount of temporal locality that is, a significant percentage of the queries have been submitted more than once by the same or a different user. Using trace-driven simulation we demonstrate that medium-size caches can hold the results of most of the frequently submitted queries. Finally, we compare the effectiveness of static and dynamic caching and conclude that although dynamic caching can use large caches more effectively, static caching can perform better for (very) small caches. (C) 2001 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Markatos2001,
      author = {Markatos, EP},
      title = {On caching search engine query results},
      journal = {COMPUTER COMMUNICATIONS},
      year = {2001},
      volume = {24},
      number = {2},
      pages = {137-143},
      note = {5th International Web Caching and Content Delivery Workshop, LISBON, PORTUGAL, MAY 22-24, 2000}
    }
    
    Marko, K., Schulz, S. & Hahn, U. MorphoSaurus - Design and evaluation of an interlingua-based, cross-language document retrieval engine for the medical domain {2005} METHODS OF INFORMATION IN MEDICINE
    Vol. {44}({4}), pp. {537-545} 
    article  
    Abstract: Objectives: We propose an interlingua-bosed indexing approach to account for the particular challenges that arise in the design and implementation of cross-language document retrieval systems for the medical domain. Methods: Documents, as well as queries, are mapped to a language-independent conceptual layer on which retrieval operations are performed. We contrast this approach with the direct translation of German queries to English ones which, subsequently, are matched against English documents. Results: We evaluate both approaches, interlingua-based and direct translation, on a large medical document collection, the OHSUMED corpus. A substantial benefit for interlingua-bosed document retrieval using German queries on English texts is found, which amounts to 93% of the (monolingual) English baseline. Conclusions: Most state-of-the-art cross-language information retrieval systems translate user queries to the language(s) of the target documents. In contradistinction to this approach, translating both documents and user queries into a language-independent concept-like representation format is more beneficial to enhance cross-language retrieval performance.
    BibTeX:
    @article{Marko2005,
      author = {Marko, K and Schulz, S and Hahn, U},
      title = {MorphoSaurus - Design and evaluation of an interlingua-based, cross-language document retrieval engine for the medical domain},
      journal = {METHODS OF INFORMATION IN MEDICINE},
      year = {2005},
      volume = {44},
      number = {4},
      pages = {537-545},
      note = {49th Annual Conference of the German-Society-for-Medical-Informatics-Biometry-and-Epidemiology, Innsbruck, AUSTRIA, SEP 26-30, 2004}
    }
    
    Mathur, S., Shanti, N., Brkaric, M., Sood, V., Kubeck, J., Paulino, C. & Merola, A. Surfing for scoliosis: The quality of information available on the Internet {2005} SPINE
    Vol. {30}({23}), pp. {2695-2700} 
    article  
    Abstract: Study Design. A cross section of Web sites accessible to the general public was surveyed. Objective. To evaluate the quality and accuracy of information on scoliosis that a patient might access on the Internet. Summary of Background Data. The Internet is a rapidly expanding communications network with an estimated 765 million users worldwide by the year 2005. Medical information is one of the most common sources of inquires on the Web. More than 100 million Americans accessed the Internet for medical information in the year 2000. Undoubtedly, the use of the Internet for patient information needs will continue to expand as Internet access becomes more readily available. This expansion combined with the Internet's poorly regulated format can lead to problems in the quality of information available. Since the Internet operates on a global scale, implementing and enforcing standards have been difficult. The largely uncontrolled information can potentially negatively influence consumer health outcomes. Methods. To identify potential sites, five search engines were selected and the word ``scoliosis'' was entered into each search engine. A total of 50 Web sites were chosen for review. Each Web site was evaluated according to the type of Web site, quality content, and informational accuracy by three board-certified academic orthopedic surgeons, fellowship trained in spinal surgery, who each has been in practice for a minimum of 8 years. Each Web site was categorized as academic, commercial, physician, nonphysician health professional, and unidentified. In addition, each Web site was evaluated according to scoliosis-specific content using a point value system of 32 disease-specific key words pertinent to the care of scoliosis on an ordinal scale. A list of these words is given. Point values were given for the use of key words related to disease summary, classifications, treatment options, and complications. The accuracy of the individual Web site was evaluated by each spine surgeon using a scale of 1 to 4. A score of 1 represents that the examiner agreed with less than 25% of the information while a score of 4 represents greater than 75% agreement. Results. Of the total 50 Web sites evaluated, 44% were academic, 18% were physician based, 16% were commercial, 12% were unidentified, and 10% were nonphysician health professionals. The quality content score (maximum, 32 points) for academic sites was 12.6 +/- 3.8, physician sites 11.3 +/- 4.0, commercial sites 11 +/- 4.2, unidentified 7.6 +/- 3.9, and nonphysician health professional site 7.0 +/- 1.8. The accuracy score (maximum, 12 points) was 6.6 +/- 2.4 for academic sites, 6.3 +/- 3.0 for physician-professional sites, 6.0 +/- 2.7 for unidentified sites, 5.5 +/- 3.8 for nonphysician professional sites, and 5.0 +/- 1.5 for commercial Web sites. The academic Web sites had the highest mean scores in both quality and accuracy content scores. Conclusion. The information about scoliosis on the Internet is of limited quality and poor information value. Although the majority of the Web sites were academic, the content quality and accuracy scores were still poor. The lowest scoring Web sites were the nonphysician professionals and the unidentified sites, which were often message boards. Overall, the highest scoring Web site related to both quality and accuracy of information was www.srs.org. This Web site was designed by the Scoliosis Research Society. The public and the medical communities need to be aware of these existing limitations of the Internet. Based on our review, the physician must assume primary responsibility of educating and counseling their patients.
    BibTeX:
    @article{Mathur2005,
      author = {Mathur, S and Shanti, N and Brkaric, M and Sood, V and Kubeck, J and Paulino, C and Merola, AA},
      title = {Surfing for scoliosis: The quality of information available on the Internet},
      journal = {SPINE},
      year = {2005},
      volume = {30},
      number = {23},
      pages = {2695-2700}
    }
    
    Mattie, M., Staib, L., Stratmann, E., Tagare, H., Duncan, J. & Miller, P. PathMaster: Content-based cell image retrieval using automated feature extraction {2000} JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
    Vol. {7}({4}), pp. {404-415} 
    article  
    Abstract: Objective: Currently, when cytopathology images are archived, they are typically stored with a limited text-based description of their content. Such a description inherently fails to quantify the properties of an image and refers to an extremely small fraction of its information content. This paper describes a method for automatically indexing images of individual cells and their associated diagnoses by computationally derived cell descriptors. This methodology may serve to better index data contained in digital image databases, thereby enabling cytologists and pathologists to cross-reference cells of unknown etiology or nature. Design: The indexing method, implemented in a program called PathMaster, uses a series of computer-based feature extraction routines. Descriptors of individual cell characteristics generated by these routines are employed as indexes of cell morphology, texture, color, and spatial orientation. Measurements: The indexing fidelity of the program was tested after populating its database with images of 152 lymphocytes/lymphoma cells captured from lymph node touch preparations stained with hematoxylin and eosin. Images of ``unknown'' lymphoid cells, previously unprocessed, were then submitted for feature extraction and diagnostic cross-referencing analysis. Results: PathMaster listed the correct diagnosis as its first differential in 94 percent of recognition trials. In the remaining 6 percent of trials, PathMaster listed the correct diagnosis within the first three ``differentials.'' Conclusion: PathMaster is a pilot cell image indexing program/search engine that creates an indexed reference of images. Use of such a reference may provide assistance in the diagnostic/prognostic process by furnishing a prioritized list of possible identifications for a cell of uncertain etiology.
    BibTeX:
    @article{Mattie2000,
      author = {Mattie, ME and Staib, L and Stratmann, E and Tagare, HD and Duncan, J and Miller, PL},
      title = {PathMaster: Content-based cell image retrieval using automated feature extraction},
      journal = {JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION},
      year = {2000},
      volume = {7},
      number = {4},
      pages = {404-415}
    }
    
    Mattioni, B., Kauffman, G., Jurs, P., Custer, L., Durham, S. & Pearl, G. Predicting the genotoxicity of secondary and aromatic amines using data subsetting to generate a model ensemble {2003} JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
    Vol. {43}({3}), pp. {949-963} 
    article DOI  
    Abstract: Binary quantitative structure-activity relationship (QSAR) models are developed to classify a data set of 334 aromatic and secondary amine compounds as genotoxic or nongenotoxic based on information calculated solely from chemical structure. Genotoxic endpoints for each compound were determined using the SOS Chromotest in both the presence and absence of an S9 rat liver homogenate. Compounds were considered genotoxic if assay results indicated a positive genotoxicity hit for either the S9 inactivated or S9 activated assay. Each compound in the data set was encoded through the calculation of numerical descriptors that describe various aspects of chemical structure (e.g. topological, geometric, electronic, polar surface area). Furthermore, five additional descriptors that focused on the secondary and aromatic nitrogen atoms in each molecule were calculated specifically for this study. Descriptor subsets were examined using a genetic algorithm search engine interfaced with a k-Nearest Neighbor fitness evaluator to find the most information-rich subsets, which ultimately served as the final predictive models. Models were chosen for their ability to minimize the total number of misclassifications, with special attention given to those models that possessed fewer occurrences of positive toxicity hits being misclassified as nontoxic (false negatives). In addition, a subsetting procedure was used to form an ensemble of models using different combinations of compounds in the training and prediction sets. This was done to ensure that consistent results could be obtained regardless of training set composition. The procedure also allowed for each compound to be externally validated three times by different training set data with the resultant predictions being used in a ``majority rules'' voting scheme to produce a consensus prediction for each member of the data set. The individual models produced an average training set classification rate of 71.6% and an average prediction set classification rate of 67.7 However, the model ensemble was able to correctly classify the genotoxicity of 72.2% of all prediction set compounds.
    BibTeX:
    @article{Mattioni2003,
      author = {Mattioni, BE and Kauffman, GW and Jurs, PC and Custer, LL and Durham, SK and Pearl, GM},
      title = {Predicting the genotoxicity of secondary and aromatic amines using data subsetting to generate a model ensemble},
      journal = {JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES},
      year = {2003},
      volume = {43},
      number = {3},
      pages = {949-963},
      doi = {{10.1021/ci034013i}}
    }
    
    Melis, E., Goguadze, G., Homik, M., Libbrecht, P., Ullrich, C. & Winterstein, S. Semantic-aware components and services of ActiveMath {2006} BRITISH JOURNAL OF EDUCATIONAL TECHNOLOGY
    Vol. {37}({3}), pp. {405-423} 
    article  
    Abstract: ActiveMath is a complex web-based adaptive learning environment with a number of components and interactive learning tools. The basis for handling semantics of learning content is provided by its semantic (mathematics) content markup, which is additionally annotated with educational metadata. Several components, tools and external services can make use of that content markup, eg, a course generator, a semantic search engine and user input evaluation services. The components and services have to communicate, pass content and state changes, actions, etc including mathematical semantics and educational markup. The novel event infrastructure supports this communication. This paper focuses on the usage of the content's semantics by selected novel components and sketches the communication.
    BibTeX:
    @article{Melis2006,
      author = {Melis, E and Goguadze, G and Homik, M and Libbrecht, P and Ullrich, C and Winterstein, S},
      title = {Semantic-aware components and services of ActiveMath},
      journal = {BRITISH JOURNAL OF EDUCATIONAL TECHNOLOGY},
      year = {2006},
      volume = {37},
      number = {3},
      pages = {405-423}
    }
    
    Menczer, F. Complementing search engines with online web mining agents {2003} DECISION SUPPORT SYSTEMS
    Vol. {35}({2}), pp. {195-212} 
    article  
    Abstract: While search engines have become the major decision support tools for the Internet, there is a growing disparity between the image of the World Wide Web stored in search engine repositories and the actual dynamic, distributed nature of Web data. We propose to attack this problem using an adaptive population of intelligent agents mining the Web online at query time. We discuss the benefits and shortcomings of using dynamic search strategies versus the traditional static methods in which search and retrieval are disjoint. This paper presents a public Web intelligence tool called MySpiders, a threaded multiagent system designed for information discovery. The performance of the system is evaluated by comparing its effectiveness in locating recent, relevant documents with that of search engines. We present results suggesting that augmenting search engines with adaptive populations of intelligent search agents can lead to a significant competitive advantage. We also discuss some of the challenges of evaluating such a system on current Web data, introduce three novel metrics for this purpose, and outline some of the lessons learned in the process. (C) 2002 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Menczer2003,
      author = {Menczer, F},
      title = {Complementing search engines with online web mining agents},
      journal = {DECISION SUPPORT SYSTEMS},
      year = {2003},
      volume = {35},
      number = {2},
      pages = {195-212}
    }
    
    Mendes, E., Mosley, N. & Counsell, S. Investigating Web size metrics for early Web cost estimation {2005} JOURNAL OF SYSTEMS AND SOFTWARE
    Vol. {77}({2}), pp. {157-172} 
    article DOI  
    Abstract: This paper's aim is to bring light to this issue by identifying size metrics and cost drivers for early Web cost estimation based on current practices of several Web Companies worldwide. This is achieved using two surveys and a case study. The first survey (SI) used a search engine to obtain Web project quote forms employed by Web companies worldwide to provide initial quotes on Web development projects. The 133 Web project quote forms gathered data on size metrics, cost factors, contingency and possibly profit metrics. These metrics were organised into categories and ranked. Results indicated that the two most common size metrics used for Web cost estimation were ``total number of Web pages'' (70 and ``which features/functionality to be provided by the application'' (66. The results of S1 were then validated by a mature Web company that has more than 12years of experience in Web development and a portfolio of more than 50 Web applications. The analysis was conducted using an interview. Finally. once the case Study was finished, a second validation was conducted using a survey (S2) involving local New Zealand Web companies. The results of both validations were used to prepare Web project data entry forms to gather data on Web projects worldwide. After gathering data on 67 real Web projects worldwide, multivariate regression applied to the data confirmed that the number of Web pages and features/functionality provided by the application to be developed were the two most influential effort predictors. (c) 2004 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Mendes2005,
      author = {Mendes, E and Mosley, N and Counsell, S},
      title = {Investigating Web size metrics for early Web cost estimation},
      journal = {JOURNAL OF SYSTEMS AND SOFTWARE},
      year = {2005},
      volume = {77},
      number = {2},
      pages = {157-172},
      doi = {{10.1016/j.jss.2004.08.034}}
    }
    
    Meng, F., Du, Y., Miller, L., Patrie, S., Robinson, D. & Kelleher, N. Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics {2004} ANALYTICAL CHEMISTRY
    Vol. {76}({10}), pp. {2852-2858} 
    article  
    Abstract: For improved detection of diverse posttranslational modifications (PTMs), direct fragmentation of protein ions by top down mass spectrometry holds promise but has yet to be achieved on a large scale. Using lysate from Saccharomyces cerevisiae, 117 gene products were identified with 100% sequence coverage revealing 26 acetylations, 1 N-terminal dimethylation, 1 phosphorylation, 18 duplicate genes, and 44 proteolytic fragments. The platform for this study combined continuous-elution gel electrophoresis, reversed-phase liquid chromatography, automated nanospray coupled with a quadrupole-FT hybrid mass spectrometer, and a new search engine for querying a custom database. The proteins identified required no manual validation, ranged from 5 to 39 kDa, had codon biases from 0.93 to 0.083, and were primarily associated with glycolysis and protein synthesis. Illustrations of gene-specific identifications, PTM detection and subsequent PTM localization (using either electron capture dissociation or known PTM data stored in a database) show how larger scale proteome projects incorporating top down may proceed in the future using commercial Q-FT instruments.
    BibTeX:
    @article{Meng2004,
      author = {Meng, FY and Du, Y and Miller, LM and Patrie, SM and Robinson, DE and Kelleher, NL},
      title = {Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics},
      journal = {ANALYTICAL CHEMISTRY},
      year = {2004},
      volume = {76},
      number = {10},
      pages = {2852-2858}
    }
    
    Meng, W., Yu, C. & Liu, K. Building efficient and effective metasearch engines {2002} ACM COMPUTING SURVEYS
    Vol. {34}({1}), pp. {48-89} 
    article  
    Abstract: Frequently a user's information needs are stored in the databases of multiple search engines. It is inconvenient and inefficient for an ordinary user to invoke multiple search engines and identify useful documents from the returned results. To support unified access to multiple search engines, a metasearch engine can be constructed. When a metasearch engine receives a query from a user, it invokes the underlying search engines to retrieve useful information for the user. Metasearch engines have other benefits as a search tool such as increasing the search coverage of the Web and improving the scalability of the search. In this article, we survey techniques that have been proposed to tackle several underlying challenges for building a good metasearch engine. Among the main challenges, the database selection problem is to identify search engines that are likely to return useful documents to a given query. The document selection problem is to determine what documents to retrieve from each identified search engine. The result merging problem is to combine the documents returned from multiple search engines. We will also point out some problems that need to be further researched.
    BibTeX:
    @article{Meng2002,
      author = {Meng, WY and Yu, C and Liu, KL},
      title = {Building efficient and effective metasearch engines},
      journal = {ACM COMPUTING SURVEYS},
      year = {2002},
      volume = {34},
      number = {1},
      pages = {48-89}
    }
    
    Meric, F., Bernstam, E., Mirza, N., Hunt, K., Ames, F., Ross, M., Kuerer, H., Pollock, R., Musen, M. & Singletary, S. Breast cancer on the world wide web: cross sectional survey of quality of information and popularity of websites {2002} BRITISH MEDICAL JOURNAL
    Vol. {324}({7337}), pp. {577-581} 
    article  
    Abstract: Objectives To determine the characteristics of popular breast cancer related websites and whether more popular sites are of higher quality. Design The search engine Google was used to generate a list of websites about breast cancer. Google ranks search results by measures of link popularity-the number of links to a site from other sites. The top 200 sites returned in response to the query ``breast cancer'' were divided into ``more popular'' and ``less popular'' subgroups by three different measures of link popularity: Google rank and number of links reported independently by Google and by AltaVista (another search engine). Main outcome measures Type and quality of content Results More popular sites according to Google rank were more likely than less popular ones to contain information on ongoing clinical trials (27% v 12 P=0.01), results of trials (12% v 3 P=0.02), and opportunities for psychosocial adjustment (48% v 23 P < 0.01). These characteristics were also associated with higher number of links as reported by Google and AltaVista. More popular sites by number of linking sites were also more likely to provide updates on other breast cancer research, information on legislation and advocacy, and a message board service. Measures of quality such as display of authorship, attribution or references, currency of information, and disclosure did not differ between groups. Conclusions Popularity of websites is associated with type rather than quality of content Sites that include content correlated with popularity may best meet the public's desire for information about breast cancer.
    BibTeX:
    @article{Meric2002,
      author = {Meric, F and Bernstam, EV and Mirza, NQ and Hunt, KK and Ames, FC and Ross, MI and Kuerer, HM and Pollock, RE and Musen, MA and Singletary, SE},
      title = {Breast cancer on the world wide web: cross sectional survey of quality of information and popularity of websites},
      journal = {BRITISH MEDICAL JOURNAL},
      year = {2002},
      volume = {324},
      number = {7337},
      pages = {577-581}
    }
    
    Mettrop, W. & Nieuwenhuysen, P. Internet search engines - Fluctuations in document accessibility {2001} JOURNAL OF DOCUMENTATION
    Vol. {57}({5}), pp. {623-651} 
    article  
    Abstract: An empirical investigation of the consistency of retrieval through Internet search engines is reported. Thirteen engines are evaluated: AltaVista, EuroFerret, Excite, HotBot, InfoSeek, Lycos, MSN, NorthernLight, Snap, WebCrawler and three national Dutch engines: Ilse, Search.nl and Vindex. The focus is on a characteristic related to size: the degree of consistency to which an engine retrieves documents. Does an engine always present the same relevant documents that are, or were, available in its database? We observed and identified three types of fluctuations in the result sets of several kinds of searches, many of them significant. These should be taken into account by users who apply an Internet search engine, for instance to retrieve as many relevant documents as possible, or to retrieve a document that was already found in a previous search, or to perform scientometric/bibliometric measurements. The fluctuations should also be considered as a complication of other research on the behaviour and performance of Internet search engines. In conclusion: in view of the increasing importance of the Internet as a publication/communication medium, the fluctuations in the result sets of Internet search engines can no longer be neglected.
    BibTeX:
    @article{Mettrop2001,
      author = {Mettrop, W and Nieuwenhuysen, P},
      title = {Internet search engines - Fluctuations in document accessibility},
      journal = {JOURNAL OF DOCUMENTATION},
      year = {2001},
      volume = {57},
      number = {5},
      pages = {623-651}
    }
    
    Metzler, D. & Croft, W. Combining the language model and inference network approaches to retrieval {2004} INFORMATION PROCESSING & MANAGEMENT
    Vol. {40}({5}), pp. {735-750} 
    article DOI  
    Abstract: The inference network retrieval model, as implemented in the InQuery search engine, allows for richly structured queries. However, it incorporates a form of ad hoc tf.idf estimates for word probabilities. Language modeling offers more formal estimation techniques. In this paper we combine the language modeling and inference network approaches into a single framework. The resulting model allows structured queries to be evaluated using language modeling estimates. We explore the issues involved, such as combining beliefs and smoothing of proximity nodes. Experimental results are presented comparing the query likelihood model, the InQuery system, and our new model. The results reaffirm that high quality structured queries outperform unstructured queries and show that our system consistently achieves higher average precision than InQuery. (C) 2004 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Metzler2004,
      author = {Metzler, D and Croft, WB},
      title = {Combining the language model and inference network approaches to retrieval},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2004},
      volume = {40},
      number = {5},
      pages = {735-750},
      doi = {{10.1016/j.ipm.2004.05.001}}
    }
    
    Meyer, D. Sophisticated quantum search without entanglement {2000} PHYSICAL REVIEW LETTERS
    Vol. {85}({9}), pp. {2014-2017} 
    article  
    Abstract: Grover's quantum search algorithm has recently been implemented without entanglement, by replacing multiple particles with a single particle having exponentially many states. We recall that all physical resources must be accounted for to quantify algorithm complexity, and that this scheme typically incurs exponential costs in some other resource(s). In particular, we demonstrate that a recent experimental realization requires exponentially increasing precision. There is, however, a quantum algorithm which searches a ``sophisticated'' database (not unlike a Web search engine) with a single query, but which we show does not require entanglement even for multiparticle implementations.
    BibTeX:
    @article{Meyer2000,
      author = {Meyer, DA},
      title = {Sophisticated quantum search without entanglement},
      journal = {PHYSICAL REVIEW LETTERS},
      year = {2000},
      volume = {85},
      number = {9},
      pages = {2014-2017}
    }
    
    Micarelli, A. & Sciarrone, F. Anatomy and empirical evaluation of an adaptive Web-based information filtering system {2004} USER MODELING AND USER-ADAPTED INTERACTION
    Vol. {14}({2-3}), pp. {159-200} 
    article  
    Abstract: A case study in adaptive information filtering systems for the Web is presented. The described system comprises two main modules, named HUMOS and WIFS. HUMOS is a user modeling system based on stereotypes. It builds and maintains long term models of individual Internet users, representing their information needs. The user model is structured as a frame containing informative words, enhanced with semantic networks. The proposed machine learning approach for the user modeling process is based on the use of an artificial neural network for stereotype assignments. WIFS is a content-based information filtering module, capable of selecting html/text documents on computer science collected from the Web according to the interests of the user. It has been created for the very purpose of the structure of the user model utilized by HUMOS. Currently, this system acts as an adaptive interface to the Web search engine ALTA VISTA(TM). An empirical evaluation of the system has been made in experimental settings. The experiments focused on the evaluation, by means of a non-parametric statistics approach, of the added value in terms of system performance given by the user modeling component; it also focused on the evaluation of the usability and user acceptance of the system. The results of the experiments are satisfactory and support the choice of a user model-based approach to information filtering on the Web.
    BibTeX:
    @article{Micarelli2004,
      author = {Micarelli, A and Sciarrone, F},
      title = {Anatomy and empirical evaluation of an adaptive Web-based information filtering system},
      journal = {USER MODELING AND USER-ADAPTED INTERACTION},
      year = {2004},
      volume = {14},
      number = {2-3},
      pages = {159-200}
    }
    
    Michelena, N., Scheffer, C., Fellini, R. & Papalambros, P. CORBA-based object-oriented framework for distributed system design {1999} MECHANICS OF STRUCTURES AND MACHINES
    Vol. {27}({4}), pp. {365-392} 
    article  
    Abstract: A generic framework for designing large, complicated systems is formulated, implemented, and used in the design of mechanical systems, including a pressure vessel, an: automotive hybrid powertrain, and a tracked vehicle. The framework supports: simulation-based design, distributed and heterogeneous computing resources, custom and legacy simulation and analysis codes, reconfigurability of the design problem, and security of operation across untrusted networks. The framework also facilitates the implementation of methodologies for system design that employ design model partitioning and coordination, as well as a variety of models and search algorithms. Common Object Request Broker Architecture (CORBA) middleware for distributed, object-oriented applications was selected to develop and implement the framework. Framework components include subsystem model, design model, search engine, design model partitioning, design coordination, and user interface.
    BibTeX:
    @article{Michelena1999,
      author = {Michelena, N and Scheffer, C and Fellini, R and Papalambros, P},
      title = {CORBA-based object-oriented framework for distributed system design},
      journal = {MECHANICS OF STRUCTURES AND MACHINES},
      year = {1999},
      volume = {27},
      number = {4},
      pages = {365-392}
    }
    
    Mirabal, N., Halpern, J., Eracleous, M. & Becker, R. Search for the identification of 3EG J1835+5918: Evidence for a new type of high-energy gamma-ray source {2000} ASTROPHYSICAL JOURNAL
    Vol. {541}({1, Part 1}), pp. {180-193} 
    article  
    Abstract: The EGRET source 3EG J1835 + 5918 is the brightest and most accurately positioned of the as-yet unidentified high-energy gamma-ray sources at high Galactic latitude (l, b = 89 degrees, 25 degrees). We present a multiwavelength study of the region around it, including X-ray, radio, and optical imaging surveys, as well as optical spectroscopic classification of most of the active objects in this area. Identifications are made of all but one of the ROSAT and ASCA sources in this region to a flux limit of approximately 5 x 10(-14) ergs cm(-2) s(-1), which is 10(-4) of the gamma-ray flux. The identified X-ray sources in or near the EGRET error ellipse are radio-quiet QSOs, a galaxy cluster, and coronal emitting stars. We also find nine quasars using purely optical color selection, and we have monitored the entire field for variable optical objects on short and long timescales without any notable discoveries. The radio sources inside the error ellipse are all fainter than 4 mJy at 1.4 GHz. There are no fiat-spectrum radio sources in the vicinity; the brightest neighboring radio sources are steep-spectrum radio galaxies or quasars. Since no blazar-like or pulsar-like candidate has been found as a result of these searches, 3EG J1835 + 5918 must be lacking one or more of the physically essential attributes of these known classes of gamma-ray emitters. If it is an AGN it lacks the beamed emission radio of blazars by at least a factor of 100 relative to identified EGRET blazars. If it is an isolated neutron star, it lacks the steady thermal X-rays from a cooling surface and the magnetospheric nonthermal X-ray emission that is characteristic of all EGRET pulsars. If a pulsar, 3EG J1835 + 5918 must be either older or more distant than Geminga, and probably an even more efficient or beamed gamma-ray engine. One intermittent ROSAT source falls on a blank optical field to a limit of B > 23.4, V > 25.2, and R > 24.5. In view of this conspicuous absence, RX J1836.2 + 5925 should be examined further as a candidate for identification with 3EG J1835 + 5918 and possibly the prototype of a new class of high-energy gamma-ray source.
    BibTeX:
    @article{Mirabal2000,
      author = {Mirabal, N and Halpern, JP and Eracleous, M and Becker, RH},
      title = {Search for the identification of 3EG J1835+5918: Evidence for a new type of high-energy gamma-ray source},
      journal = {ASTROPHYSICAL JOURNAL},
      year = {2000},
      volume = {541},
      number = {1, Part 1},
      pages = {180-193}
    }
    
    Mishne, G. & de Rijke, M. A study of blog search {2006}
    Vol. {3936}ADVANCES IN INFORMATION RETRIEVAL, pp. {289-301} 
    inproceedings  
    Abstract: We present an analysis of a large blog search engine query log, exploring a number of angles such as query intent, query topics, and user sessions. Our results show that, blog searches have different intents than general web searches, suggesting that the primary targets of blog searchers are tracking references to named entities, and locating blogs by theme. In terms of interest areas, flog searchers are, on average, more engaged in technology, entertainment, and politics than web searchers, with a particular interest in current, events. The user behavior observed is similar to that in general web search: short sessions with an interest in the first few results only.
    BibTeX:
    @inproceedings{Mishne2006,
      author = {Mishne, Gilad and de Rijke, Maarten},
      title = {A study of blog search},
      booktitle = {ADVANCES IN INFORMATION RETRIEVAL},
      year = {2006},
      volume = {3936},
      pages = {289-301},
      note = {28th European Conference on Information Retrieval (ECIR 2006), London, ENGLAND, APR 10, 2005-APR 12, 2006}
    }
    
    Misra, A., Khurana, L., Vikram, N.K., Goel, A. & Wasir, J.S. Metabolic syndrome in children: Current issues and South Asian perspective {2007} NUTRITION
    Vol. {23}({11-12}), pp. {895-910} 
    article DOI  
    Abstract: Objective: The objective of this review is to discuss definition, determinants, and management issues of the metabolic syndrome in children with a focus on South Asians. Methods: The literature search was done using the PubMed search engine (National Library of Medicine, Bethesda, MD, USA). Manual searches for other important references and medical databases were also done. Results: There is a need for an integrated definition of the metabolic syndrome in children and adolescents, taking cognizance of the ethnic-specific variations. Obesity and body fat patterning are important determinants of insulin resistance and the metabolic syndrome in children and ethnic variations in these parameters are seen. Excess body fat and thicker truncal subcutaneous fat are important predisposing factors for development of insulin resistance in South Asian children. Because the metabolic syndrome tracks into adulthood, its manifestations need to be recognized early for prevention of diabetes and coronary heart disease. Therapeutic lifestyle changes, maintenance of high levels of physical activity and normal weight are most important strategies; pharmacologic therapy for individual components of the metabolic syndrome is occasionally needed. Conclusion: The metabolic syndrome in children is an important clinical marker of diabetes and coronary heart disease in adults. In view of the rapid increase in the metabolic syndrome in most populations, high-risk screening and effective public-intervention educational programs are urgently needed. (C) 2007 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Misra2007,
      author = {Misra, Anoop and Khurana, Lokesh and Vikram, Naval K. and Goel, Ashish and Wasir, Jasjeet S.},
      title = {Metabolic syndrome in children: Current issues and South Asian perspective},
      journal = {NUTRITION},
      year = {2007},
      volume = {23},
      number = {11-12},
      pages = {895-910},
      doi = {{10.1016/j.nut.2007.08.018}}
    }
    
    Miyamoto, S. Information clustering based on fuzzy multisets {2003} INFORMATION PROCESSING & MANAGEMENT
    Vol. {39}({2}), pp. {195-213} 
    article  
    Abstract: A fuzzy multiset model for information clustering is proposed with application to information retrieval on the World Wide Web. Noting that a search engine retrieves multiple occurrences of the same subjects with possibly different degrees of relevance, we observe that fuzzy multisets provide an appropriate model of information retrieval on the WWW. Information clustering which means both term clustering and document clustering is considered. Three methods of the hard c-means, fuzzy c-means, and an agglomerative method using cluster centers are proposed. Two distances between fuzzy multisets and algorithms for calculating cluster centers are defined. Theoretical properties concerning the clustering algorithms are studied. Illustrative examples are given to show how the algorithms work. (C) 2002 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Miyamoto2003,
      author = {Miyamoto, S},
      title = {Information clustering based on fuzzy multisets},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2003},
      volume = {39},
      number = {2},
      pages = {195-213}
    }
    
    Mojon-Azzi, S., Jiang, X., Wagner, U. & Mojon, D. Redundant publications in scientific ophthalmologic journals - The tip of the iceberg? {2004} OPHTHALMOLOGY
    Vol. {111}({5}), pp. {863-866} 
    article DOI  
    Abstract: Objective: The number of scientific publications is often used to measure scientific achievement. This practice can motivate unethical conduct, such as redundant or duplicate publications, defined as publication of the same scientific contents in more than 1 journal. The aim of this study was to estimate the amount of redundant publications in ophthalmologic journals. Design: Retrospective analysis of published literature. Methods: We developed an electronic search engine for redundancies to estimate the amount of duplicate publications in scientific journals. When redundancies reached a given degree (matching score), the articles were screened manually based on authors, titles, and abstracts. We applied this method to the 22 433 articles that were published between 1997 and 2000 in 70 ophthalmologic journals indexed by MEDLINE. Main Outcome Measures: The number of duplicate publications with a matching score of 0.6 or more, the number of involved journals, and the number of authors. Results: Redundancies reached a matching score of 0.6 or more in 13 967 pairs of articles. Out of them, a sample of 2210 was reviewed manually. We found 60 redundant articles and estimated that 1.39% of the publications were redundant. Thirty-two journals and an estimate of 1092 authors were involved. In 5% of cases, the scientific conclusions were modified. Conclusions: Because of the restrictive selection process, the impracticability of detecting all redundant publications, and the estimated amount of duplicates increases with lower matching scores, we regard our estimate to be the tip of the iceberg. Duplicate publications have several negative impacts, but neither peer reviewers nor editors can protect their journal from them completely. Several deterrents for duplicate publications are possible, but as long as publications remain the central requirement for academic advancement, a solution seems unlikely. Nevertheless, it is the responsibility of all those who care about objective research and evidence-based medicine to address this problem-not only in ophthalmology. Ophthalmology 2004;111: 863-866 (C) 2004 by the American Academy of Ophthalmology.
    BibTeX:
    @article{Mojon-Azzi2004,
      author = {Mojon-Azzi, SM and Jiang, XY and Wagner, U and Mojon, DS},
      title = {Redundant publications in scientific ophthalmologic journals - The tip of the iceberg?},
      journal = {OPHTHALMOLOGY},
      year = {2004},
      volume = {111},
      number = {5},
      pages = {863-866},
      doi = {{10.1016/j.ophtha.2003.09.029}}
    }
    
    Mojsilovic, A., Gomes, J. & Rogowitz, B. Semantic-friendly indexing and quering of images based on the extraction of the objective semantic cues {2004} INTERNATIONAL JOURNAL OF COMPUTER VISION
    Vol. {56}({1-2, Sp. Iss. SI}), pp. {79-107} 
    article  
    Abstract: bstract image semantics resists all forms of modeling, very much like any kind of intelligence does. However, in order to develop more satisfying image navigation systems, we need tools to construct a semantic bridge between the user and the database. In this paper we present an image indexing scheme and a query language, which allow the user to introduce cognitive dimension to the search. At an abstract level, this approach consists of: (1) learning the ``natural language'' that humans speak to communicate their semantic experience of images, (2) understanding the relationships between this language and objective measurable image attributes, and then (3) developing corresponding feature extraction schemes. More precisely, we have conducted a number of subjective experiments in which we asked human subjects to group images, and then explain verbally why they did so. The results of this study indicated that a part of the abstraction involved in image interpretation is often driven by semantic categories, which can be broken into more tangible semantic entities, i.e. objective semantic indicators. By analyzing our experimental data, we have identified some candidate semantic categories (i.e. portraits, people, crowds, cityscapes, landscapes, etc.) and their underlying semantic indicators (i.e. skin, sky, water, object, etc.). These experiments also helped us derive important low-level image descriptors, accounting for our perception of these indicators. We have then used these findings to develop an image feature extraction and indexing scheme. In particular, our feature set has been carefully designed to match the way humans communicate image meaning. This led us to the development of a ``semantic-friendly'' query language for browsing and searching diverse collections of images. We have implemented our approach into an Internet search engine, and tested it on a large number of images. The results we obtained are very promising.
    BibTeX:
    @article{Mojsilovic2004,
      author = {Mojsilovic, A and Gomes, J and Rogowitz, B},
      title = {Semantic-friendly indexing and quering of images based on the extraction of the objective semantic cues},
      journal = {INTERNATIONAL JOURNAL OF COMPUTER VISION},
      year = {2004},
      volume = {56},
      number = {1-2, Sp. Iss. SI},
      pages = {79-107}
    }
    
    Molloy, R. & Parasuraman, R. Monitoring an automated system for a single failure: Vigilance and task complexity effects {1996} HUMAN FACTORS
    Vol. {38}({2}), pp. {311-322} 
    article  
    Abstract: The present study examined the effects of task complexity and time on task on the monitoring of a single automation failure during performance of a complex flight simulation task involving tracking, fuel management, and engine-status monitoring. Two groups of participants performed either all three flight simulation tasks simultaneously (multicomplex task) or the monitoring task alone (single-complex task); a third group performed a simple visual vigilance task (simple task). For the multicomplex task, monitoring for a single failure of automation control was poorer than when participants monitored engine malfunctions under manual control. Furthermore, more participants detected the automation failure in the first 10 min of a 30-min session than in the last 10 min of the session, for both the simple and the multicomplex task. Participants in the single-complex condition detected the automation failure equally well in both periods. The results support previous findings of inefficiency in monitoring automation and show that automation-related monitoring inefficiency occurs even when there is a single automation failure. Implications for theories of vigilance and automation design are discussed.
    BibTeX:
    @article{Molloy1996,
      author = {Molloy, R and Parasuraman, R},
      title = {Monitoring an automated system for a single failure: Vigilance and task complexity effects},
      journal = {HUMAN FACTORS},
      year = {1996},
      volume = {38},
      number = {2},
      pages = {311-322}
    }
    
    Morand, J., Macri, J. & Adeli, K. Proteomic profiling of hepatic endoplasmic reticulum-associated proteins in an animal model of insulin resistance and metabolic dyslipidemia {2005} JOURNAL OF BIOLOGICAL CHEMISTRY
    Vol. {280}({18}), pp. {17626-17633} 
    article DOI  
    Abstract: Hepatic insulin resistance and lipoprotein overproduction are common features of the metabolic syndrome and insulin-resistant states. A fructose-fed, insulin-resistant hamster model was recently developed to investigate mechanisms linking the development of hepatic insulin resistance and overproduction of atherogenic lipoproteins. Here we report a systematic analysis of protein expression profiles in the endoplasmic reticulum (ER) fractions isolated from livers of fructose-fed hamsters with the intention of identifying new candidate proteins involved in hepatic complications of insulin resistance and lipoprotein dysregulation. We have profiled hepatic ER-associated proteins from chow-fed (control) and fructose-fed (insulin-resistant) hamsters using two-dimensional gel electrophoresis and mass spectrometry. A total of 26 large scale two-dimensional gels of hepatic ER were used to identify 34 differentially expressed hepatic ER protein spots observed to be at least 2-fold differentially expressed with fructose feeding and the onset of insulin resistance. Differentially expressed proteins were identified by matrix-assisted laser desorption ionization-quadrupole time of flight (MALDI-Q-TOF), MALDI-TOF-postsource decay, and database mining using ProteinProspector MS-fit and MS-tag or the PROWL ProFound search engine using a focused rodent or mammalian search. Hepatic ER proteins ER60, ERp46, ERp29, glutamate dehydrogenase, and TAP1 were shown to be more than 2-fold downregulated, whereas alpha-glucosidase, P-glycoprotein, fibrinogen, protein disulfide isomerase, GRP94, and apolipoprotein E were all found to be up-regulated in the hepatic ER of the fructose-fed hamster. Seven isoforms of ER60 in the hepatic ER were all shown to be downregulated at least 2-fold in hepatocytes from fructose-fed/insulin-resistant hamsters. Implications of the differential expression of positively identified protein factors in the development of hepatic insulin resistance and lipoprotein abnormalities are discussed.
    BibTeX:
    @article{Morand2005,
      author = {Morand, JPF and Macri, J and Adeli, K},
      title = {Proteomic profiling of hepatic endoplasmic reticulum-associated proteins in an animal model of insulin resistance and metabolic dyslipidemia},
      journal = {JOURNAL OF BIOLOGICAL CHEMISTRY},
      year = {2005},
      volume = {280},
      number = {18},
      pages = {17626-17633},
      doi = {{10.1074/jbc.M413343200}}
    }
    
    Morison, I., Paton, C. & Cleverley, S. The imprinted gene and parent-of-origin effect database {2001} NUCLEIC ACIDS RESEARCH
    Vol. {29}({1}), pp. {275-276} 
    article  
    Abstract: The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals. in addition a wide variety of other parent-of-origin effects, such as transmission of human disease phenotypes, transmission of QTLs, uniparental disomies and interspecies crosses are recorded. Data are accessed through a search engine and references are hyperlinked to PubMed.
    BibTeX:
    @article{Morison2001,
      author = {Morison, IM and Paton, CJ and Cleverley, SD},
      title = {The imprinted gene and parent-of-origin effect database},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2001},
      volume = {29},
      number = {1},
      pages = {275-276}
    }
    
    Morris, R., MacNeela, P., Scott, A., Treacy, P. & Hyde, A. Reconsidering the conceptualization of nursing workload: literature review {2007} JOURNAL OF ADVANCED NURSING
    Vol. {57}({5}), pp. {463-471} 
    article DOI  
    Abstract: Aim: This paper reports a literature review that aimed to analyse the way in which nursing intensity and patient dependency have been considered to be conceptually similar to nursing workload, and to propose a model to show how these concepts actually differ in both theoretical and practical terms. Background: The literature on nursing workload considers the concepts of patient `dependency' and nursing `intensity' in the realm of nursing workload. These concepts differ by definition but are used to measure the same phenomenon, i.e. nursing workload. Methods: The literature search was undertaken in 2004 using electronic databases, reference lists and other available literature. Papers were sourced from the Medline, Psychlit, CINAHL and Cochrane databases and through the general search engine Google. The keywords focussed on nursing workload, nursing intensity and patient dependency. Findings: Nursing work and workload concepts and labels are defined and measured in different and often contradictory ways. It is vitally important to understand these differences when using such conceptualizations to measure nursing workload. A preliminary model is put forward to clarify the relationships between nursing workload concepts. Conclusions: In presenting a preliminary model of nursing workload, it is hoped that nursing workload might be better understood so that it becomes more visible and recognizable. Increasing the visibility of nursing workload should have a positive impact on nursing workload management and on the provision of patient care.
    BibTeX:
    @article{Morris2007,
      author = {Morris, Roisin and MacNeela, Padraig and Scott, Anne and Treacy, Pearl and Hyde, Abbey},
      title = {Reconsidering the conceptualization of nursing workload: literature review},
      journal = {JOURNAL OF ADVANCED NURSING},
      year = {2007},
      volume = {57},
      number = {5},
      pages = {463-471},
      doi = {{10.1111/j.1365-2648.2006.04134.x}}
    }
    
    Morrison, J., Breitling, R., Higham, D. & Gilbert, D. GeneRank: Using search engine technology for the analysis of microarray experiments {2005} BMC BIOINFORMATICS
    Vol. {6} 
    article DOI  
    Abstract: Background: Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a ``treated'' sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method - based on the PageRank algorithm employed by the popular search engine Google - that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. Results: GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion: Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.
    BibTeX:
    @article{Morrison2005,
      author = {Morrison, JL and Breitling, R and Higham, DJ and Gilbert, DR},
      title = {GeneRank: Using search engine technology for the analysis of microarray experiments},
      journal = {BMC BIOINFORMATICS},
      year = {2005},
      volume = {6},
      doi = {{10.1186/1471-2105-6-233}}
    }
    
    Moukdad, H. & Large, A. Users' perceptions of the Web as revealed by transaction log analysis {2001} ONLINE INFORMATION REVIEW
    Vol. {25}({6}), pp. {349-358} 
    article  
    Abstract: When information seekers use an information retrieval system their strategy is based, at least in part, on the perceptions they have formed about that environment. A random sample was gathered of more than 2,000 actual search queries submitted by users to one Web search engine, WebCrawler, in two separate capture sessions. The results suggest that a high proportion of users do not employ advanced search features, and those who do frequently misunderstand them. Furthermore, many users seem to have formed a model of the Web that imbues it with the intelligence found in a reference librarian, for example, but not a retrieval system. The linguistic structure of many queries resembles a typical human,human communication model that is unlikely to produce satisfactory results in a human-computer communication environment such as that offered currently by the Web. Design of more intuitive systems is dependent upon a more complete understanding of user behaviour at the intellectual and emotional as well as the technical levels.
    BibTeX:
    @article{Moukdad2001,
      author = {Moukdad, H and Large, A},
      title = {Users' perceptions of the Web as revealed by transaction log analysis},
      journal = {ONLINE INFORMATION REVIEW},
      year = {2001},
      volume = {25},
      number = {6},
      pages = {349-358}
    }
    
    Mowshowitz, A. & Kawaguchi, A. Assessing bias in search engines {2002} INFORMATION PROCESSING & MANAGEMENT
    Vol. {38}({1}), pp. {141-156} 
    article  
    Abstract: This paper deals with the measurement of bias in search engines on the World Wide Web. Bias is taken to mean the balance and representativeness of items in a collection retrieved from a database for a set of queries. This calls for assessing the degree to which the distribution of items in a collection deviates from the ideal. Ascertaining this ideal poses problems similar to those associated with determining relevance in the measurement of recall and precision. Instead of enlisting subject experts or users to determine such an ideal, a family of comparable search engines is used to approximate it for a set of queries. The distribution is obtained by computing the frequencies of occurrence of the uniform resource locators (URLs) in the collection retrieved by several search engines for the given queries. Bias is assessed by measuring the deviation from the ideal of the distribution produced by a particular search engine. (C) 2001 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Mowshowitz2002,
      author = {Mowshowitz, A and Kawaguchi, A},
      title = {Assessing bias in search engines},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2002},
      volume = {38},
      number = {1},
      pages = {141-156}
    }
    
    Mukherjee, B. BONDI-97: A novel neutron energy spectrum unfolding tool using a genetic algorithm {1999} NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT
    Vol. {432}({2-3}), pp. {305-312} 
    article  
    Abstract: The neutron spectrum unfolding procedure using the count rate data obtained from a set of Bonner sphere neutron detectors requires the solution of the Fredholm integral equation of the first kind by using complex mathematical methods. This paper reports a new approach for the unfolding of neutron spectra using the Genetic Algorithm tool BONDI-97 (BOnner sphere Neutron DIfferentiation). The BONDI-97 was used as the input for Genetic Algorithm engine EVOLVER to search for a globally optimised solution vector from a population of randomly generated solutions. This solution vector corresponds to the unfolded neutron energy spectrum. The Genetic Algorithm engine emulates the Darwinian ``Survival of the Fittest'' strategy, the key ingredient of the ``Theory of Evolution''. The spectra of Am-241/Be (alpha,n) and Pu-239/Be (alpha,n) neutron sources were unfolded using the BONDI-97 tool. (C) 1999 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Mukherjee1999,
      author = {Mukherjee, B},
      title = {BONDI-97: A novel neutron energy spectrum unfolding tool using a genetic algorithm},
      journal = {NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT},
      year = {1999},
      volume = {432},
      number = {2-3},
      pages = {305-312}
    }
    
    Mukherjee, D., Delfosse, E., Kim, J. & Wang, Y. Optimal adaptation decision-taking for terminal and network quality-of-service {2005} IEEE TRANSACTIONS ON MULTIMEDIA
    Vol. {7}({3}), pp. {454-462} 
    article DOI  
    Abstract: In order to cater to the diversity of terminals and networks, efficient, and flexible adaptation of multimedia content in the delivery path to end consumers is required. To this end, it is necessary to associate the content with metadata that provides the relationship between feasible adaptation choices and various media characteristics obtained as a function of these choices. Furthermore, adaptation is driven by specification of terminal, network, user preference or rights based constraints on media characteristics that are to be satisfied by the adaptation process. Using the metadata and the constraint specification, an adaptation engine can take an appropriate decision for adaptation, efficiently and flexibly. MPEG-21 Part 7 entitled Digital Item Adaptation standardizes among other things the metadata and constraint specifications that act as interfaces to the decision-taking component of an adaptation engine. This paper presents the concepts behind these tools in the standard, shows universal methods based on pattern search to process the information in the tools to make decisions, and presents some adaptation use cases where these tools can be used.
    BibTeX:
    @article{Mukherjee2005,
      author = {Mukherjee, D and Delfosse, E and Kim, JG and Wang, Y},
      title = {Optimal adaptation decision-taking for terminal and network quality-of-service},
      journal = {IEEE TRANSACTIONS ON MULTIMEDIA},
      year = {2005},
      volume = {7},
      number = {3},
      pages = {454-462},
      doi = {{10.1109/TMM.2005.846798}}
    }
    
    Muller, H., Kenny, E. & Sternberg, P. Textpresso: An ontology-based information retrieval and extraction system for biological literature {2004} PLOS BIOLOGY
    Vol. {2}({11}), pp. {1984-1998} 
    article DOI  
    Abstract: We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95 Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org.
    BibTeX:
    @article{Muller2004,
      author = {Muller, HM and Kenny, EE and Sternberg, PW},
      title = {Textpresso: An ontology-based information retrieval and extraction system for biological literature},
      journal = {PLOS BIOLOGY},
      year = {2004},
      volume = {2},
      number = {11},
      pages = {1984-1998},
      doi = {{10.1371/journal.pbio.0020309}}
    }
    
    Musaad, S. & Haynes, E.N. Biomarkers of obesity and subsequent cardiovascular events {2007} EPIDEMIOLOGIC REVIEWS
    Vol. {29}, pp. {98-114} 
    article DOI  
    Abstract: Obesity is a major risk factor for cardiovascular diseases, but the mechanisms for increased cardiovascular risk in obesity are still unclear. Inflammation and increased oxidative stress are two potential mechanisms proposed to play a major role in the morbidity associated with obesity. Studies that investigate these mechanisms rely on biomarkers, but validated biomarkers for obesity-related cardiovascular outcomes are lacking. By finding optimal biomarkers, diagnostic criteria for cardiovascular diseases can be refined in the obese beyond ``traditional'' risk factors to identify early pathologic processes. The objective of this review is to identify potential early biomarkers resulting from obesity and associated with cardiovascular disease. Studies were initially identified through the search engine PubMed by using the keywords ``obesity'' and ``biomarker.'' Subsequently, combinations of the keywords ``obesity,'' ``biomarker,'' ``cardiovascular risk,'' ``adipose tissue,'' ``adipokine,'' ``adipocytokine,'' and ``oxidative stress'' were used. The SOURCE database and Online Mendelian Inheritance in Man (OMIM) were used to obtain more information on the biomarkers. Results of the searches yielded a large number of potential biomarkers that occur in obesity and which either correlate with traditional cardiovascular risk factors or predict subsequent cardiovascular events. Several biomarkers are promising regarding their biologic properties, but they require further validation in humans.
    BibTeX:
    @article{Musaad2007,
      author = {Musaad, Salma and Haynes, Erin N.},
      title = {Biomarkers of obesity and subsequent cardiovascular events},
      journal = {EPIDEMIOLOGIC REVIEWS},
      year = {2007},
      volume = {29},
      pages = {98-114},
      doi = {{10.1093/epirev/mxm005}}
    }
    
    Nahum, G.G., Uhl, K. & Kennedy, D.L. Antibiotic use in pregnancy and lactation - What is and is not known about teratogenic and toxic risks {2006} OBSTETRICS AND GYNECOLOGY
    Vol. {107}({5}), pp. {1120-1138} 
    article  
    Abstract: OBJECTIVE: Over ten million women are either pregnant or lactating in the United States at any time. The risks of medication use for these women are unique. In addition to normal physiologic changes that alter the pharmacokinetics of drugs, there is the concern of possible teratogenic and toxic effects on the developing fetus and newborn. This article reviews the risks and pharmacokinetic considerations for 11 broad-spectrum antibiotics that can be used to treat routine and life-threatening infections during pregnancy and lactation. DATA SOURCES: Information from the U.S. Food and Drug Administration (FDA) product labels, the Teratogen Information Service, REPROTOX, Shepard's Catalog of Teratogenic Agents, Clinical Pharmacology, and the peer-reviewed medical literature was reviewed concerning the use of 11 antibiotics in pregnant and lactating women. The PubMed search engine was used with the search terms ``[antibiotic name] and pregnancy,'' ``[antibiotic name] and lactation,'' and ``[antibiotic name] and breastfeeding'' from January 1940 to November 2005, as well as standard reference tracing. METHODS OF STUDY SELECTION: One hundred twenty-four references had sufficient information concerning numbers of subjects, methods, and findings to be included. TABULATION, INTEGRATION, AND RESULTS: The teratogenic potential in humans ranged from ``none'' (penicillin G and VK) to ``unlikely'' (amoxicillin, chloramphenicol, ciprofloxacin, doxycycline, levofloxacin, and rifampin) to ``undetermined'' (clindamycin, gentamicin, and vancomycin). Assessments were based on ``good data'' (penicillin G and VK), ``fair data'' (amoxicillin, chloramphenicol, ciprofloxacin, doxycycline, levofloxacin, and rifampin), ``limited data'' (clindamycin and gentamicin), and ``very limited data'' (vancomycin). Significant pharmacokinetic changes occurred during pregnancy for the penicillins, fluoroquinolones and gentamicin, indicating that dosage adjustments for these drugs may be necessary. With the exception of chloramphenicol, all of these antibiotics are considered compatible with breastfeeding. CONCLUSION: Health care professionals should consider the teratogenic and toxic risk profiles of antibiotics to assist in making prescribing decisions for pregnant and lactating women. These may become especially important if anti-infective countermeasures are required to protect the health, safety, and survival of individuals exposed to pathogenic bacteriologic agents that may occur from bioterrorist acts.
    BibTeX:
    @article{Nahum2006,
      author = {Nahum, Gerard G. and Uhl, Kathleen and Kennedy, Dianne L.},
      title = {Antibiotic use in pregnancy and lactation - What is and is not known about teratogenic and toxic risks},
      journal = {OBSTETRICS AND GYNECOLOGY},
      year = {2006},
      volume = {107},
      number = {5},
      pages = {1120-1138},
      note = {11th Annual FDA Science Forum, Washington, DC, APR 27-28, 2005}
    }
    
    Nelson, C.J., Huttlin, E.L., Hegeman, A.D., Harms, A.C. & Sussman, M.R. Implications of N-15-metabolic labeling for automated peptide identification in Arabidopsis thaliana {2007} PROTEOMICS
    Vol. {7}({8}), pp. {1279-1292} 
    article DOI  
    Abstract: We report the first metabolic labeling of Arabidopsis thaliana for proteomic investigation, demonstrating efficient and complete labeling of intact plants. Using a reversed-database strategy, we evaluate the performance of the MASCOT search engine in the analysis of combined natural abundance and N-15-labeled samples. We find that N-15-metabolic labeling appears to increase the ambiguity associated with peptide identifications due in part to changes in the number of isobaric amino acids when the isotopic label is introduced. This is reflected by changes in the distributions of false positive identifications with respect to MASCOT score. However, by determining the nitrogen count from each pair of labeled and unlabeled peptides we may improve our confidence in both heavy and light identifications.
    BibTeX:
    @article{Nelson2007,
      author = {Nelson, Clark J. and Huttlin, Edward L. and Hegeman, Adrian D. and Harms, Amy C. and Sussman, Michael R.},
      title = {Implications of N-15-metabolic labeling for automated peptide identification in Arabidopsis thaliana},
      journal = {PROTEOMICS},
      year = {2007},
      volume = {7},
      number = {8},
      pages = {1279-1292},
      doi = {{10.1002/pmic.200600832}}
    }
    
    Nemeth-Cawley, J. & Rouse, J. Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry {2002} JOURNAL OF MASS SPECTROMETRY
    Vol. {37}({3}), pp. {270-282} 
    article DOI  
    Abstract: Identifying unknown proteins has become a central focal point for proteomic and biopharmaceutical development laboratories. Our laboratory investigated using quadrupole time-of-flight mass spectrometry (Qq/TOFMS) for the analysis of intact proteins for the purpose of identifying unknowns while limiting the number of sample-handling steps between protein extraction and identification. Eight standard proteins, both unmodified and disulfide-bonded and ranging in mass from 5 to 66 kDa, were analyzed using nanoelectrospray and collision-induced dissociation to generate peptide sequence tags. An MS analysis, followed by MS/MS analyses on two to five individual protein charge states, were obtained to make an identification. Peptide sequence tags were extracted from the MS/MS data and used, in conjunction with molecular mass and source origin, to obtain protein identifications using the web-based search engine ProteinInfo (www.proteometrics.com). All of the proteins were unambiguously identified from the input data, after which, all of the major product ions were identified for structural information. In most cases, N- and/or C-terminal ions, and also stretches of consecutive product ions from the protein interior, were observed. This method was applied to the analysis and identification of an unknown detected via reversed-phase high-performance liquid chromatography. Copyright (C) 2002 John Wiley Sons, Ltd.
    BibTeX:
    @article{Nemeth-Cawley2002,
      author = {Nemeth-Cawley, JF and Rouse, JC},
      title = {Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry},
      journal = {JOURNAL OF MASS SPECTROMETRY},
      year = {2002},
      volume = {37},
      number = {3},
      pages = {270-282},
      doi = {{10.1002/jms.281}}
    }
    
    Nene, S. & Nayar, S. A simple algorithm for nearest neighbor search in high dimensions {1997} IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
    Vol. {19}({9}), pp. {989-1003} 
    article  
    Abstract: The problem of finding the closest point in high-dimensional spaces is common in pattern recognition. Unfortunately, the complexity of most existing search algorithms, such as k-d tree and R-tree, grows exponentially with dimension, making them impractical for dimensionality above 15. In nearly all applications, the closest point is of interest only if it lies within a user-specified distance E. We present a simple and practical algorithm to efficiently search for the nearest neighbor within Euclidean distance E. The use of projection search combined with a novel data structure dramatically improves performance in high dimensions. A complexity analysis is presented which helps to automatically determine epsilon in structured problems. A comprehensive set of benchmarks clearly shows the superiority of the proposed algorithm for a Variety of structured and unstructured search problems. Object recognition is demonstrated as an example application. The simplicity of the algorithm makes it possible to construct an inexpensive hardware search engine which can be 100 times faster than its software equivalent. A C++ implementation of our algorithm is available upon request to search@cs.columbia.edu/CAVE/.
    BibTeX:
    @article{Nene1997,
      author = {Nene, SA and Nayar, SK},
      title = {A simple algorithm for nearest neighbor search in high dimensions},
      journal = {IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE},
      year = {1997},
      volume = {19},
      number = {9},
      pages = {989-1003}
    }
    
    Nielsen, M., Savitski, M. & Zubarev, R. Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry {2005} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {4}({6}), pp. {835-845} 
    article DOI  
    Abstract: Identification of proteins by MS/MS is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein data base. The search engine assigns each spectrum a score indicating how well the experimental data complies with the expected one; a higher score means increased confidence in the identification. One problem is the false-positive identifications, which arise from incomplete data as well as from the presence of misleading ions in experimental mass spectra due to gas-phase reactions, stray ions, contaminants, and electronic noise. We employed a novel technique of reduction of false positives that is based on a combined use of orthogonal fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation ( CAD). Since ECD and CAD exhibit many complementary properties, their combined use greatly increased the analysis specificity, which was further strengthened by the high mass accuracy ( approximate to 1 ppm) afforded by Fourier transform mass spectrometry. The utility of this approach is demonstrated on a whole cell lysate from Escherichia coli. Analysis was made using the data-dependent acquisition mode. Extraction of complementary sequence information was performed prior to data base search using in-house written software. Only masses involved in complementary pairs in the MS/MS spectrum from the same or orthogonal fragmentation techniques were submitted to the data base search. ECD/ CAD identified twice as many proteins at a fixed statistically significant confidence level with on average a 64% higher Mascot score. The confidence in protein identification was hereby increased by more than 1 order of magnitude. The combined ECD/ CAD searches were on average 20% faster than CAD-only searches. A specially developed test with scrambled MS/MS data revealed that the amount of false-positive identifications was dramatically reduced by the combined use of CAD and ECD.
    BibTeX:
    @article{Nielsen2005,
      author = {Nielsen, ML and Savitski, MM and Zubarev, RA},
      title = {Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2005},
      volume = {4},
      number = {6},
      pages = {835-845},
      doi = {{10.1074/mcp.T400022-MCP200}}
    }
    
    Nieuwoudt, A. & Massoud, Y. Variability-aware multilevel integrated spiral inductor synthesis {2006} IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
    Vol. {25}({12}), pp. {2613-2625} 
    article DOI  
    Abstract: To successfully design spiral inductors in increasingly complex and integrated mixed-signal systems, effective design automation techniques must be created. In this paper, the authors develop an automated synthesis methodology for integrated spiral inductors to efficiently generate Pareto-optimal designs based on application requirements. At its core, the synthesis approach employs a scalable multilevel single-objective optimization,engine that integrates the flexibility of deterministic pattern search optimization with the rapid convergence of local nonlinear convex optimization. Multiobjective optimization techniques and surrogate functions are utilized to approximate Pareto surfaces in the design space to locate Pareto-optimal spiral inductor designs. Using the synthesis methodology, the authors also demonstrate how to reduce the impact of process variation and other sources of modeling error on spiral inductors. The results indicate that the multilevel single-objective optimization engine locates near-optimal spiral inductor geometries with significantly fewer function evaluations than current techniques, whereas the overall synthesis methodology efficiently optimizes inductor designs with an improvement of up to 51% in key design constraints while reducing the impact of process variation and modeling error.
    BibTeX:
    @article{Nieuwoudt2006,
      author = {Nieuwoudt, Arthur and Massoud, Yehia},
      title = {Variability-aware multilevel integrated spiral inductor synthesis},
      journal = {IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS},
      year = {2006},
      volume = {25},
      number = {12},
      pages = {2613-2625},
      doi = {{10.1109/TCAD.2006.882475}}
    }
    
    Nordhoff, E., Egelhofer, V., Giavalisco, P., Eickhoff, H., Horn, M., Przewieslik, T., Theiss, D., Schneider, U., Lehrach, H. & Gobom, J. Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: An analytical challenge for studying complex protein mixtures {2001} ELECTROPHORESIS
    Vol. {22}({14}), pp. {2844-2855} 
    article  
    Abstract: The large-gel two-dimensional electrophoresis (2-DE) technique, developed by Klose and co-workers over the past 25 years, provides the resolving power necessary to separate crude proteome extracts of higher eukaryotes. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) provides the sample throughput necessary to identify thousands of different protein species in an adequate time period. Spot excision, in situ proteolysis, and extraction of the cleavage products from the gel matrix, peptide purification and concentration as well as the mass spectrometric sample preparation are the crucial steps that interface the two analytical techniques. Today, these routines and not the mass spectrometric instrumentation determine how many protein digests can be analyzed per day per instrument. The present paper focuses on this analytical interface and reports on an integrated protocol and technology developed in our laboratory. Automated identification of proteins in sequence databases by mass spectrometric peptide mapping requires a powerful search engine that makes full use of the information contained in the experimental data, and scores the search results accordingly. This challenge is heading a second part of the paper.
    BibTeX:
    @article{Nordhoff2001,
      author = {Nordhoff, E and Egelhofer, V and Giavalisco, P and Eickhoff, H and Horn, M and Przewieslik, T and Theiss, D and Schneider, U and Lehrach, H and Gobom, J},
      title = {Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: An analytical challenge for studying complex protein mixtures},
      journal = {ELECTROPHORESIS},
      year = {2001},
      volume = {22},
      number = {14},
      pages = {2844-2855}
    }
    
    Nowacki, P., Byck, S., Prevost, L. & Scriver, C. PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases {1998} NUCLEIC ACIDS RESEARCH
    Vol. {26}({1}), pp. {220-225} 
    article  
    Abstract: PAHdb (http://www.mcgill.ca/pahdb) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897), Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without apparent effect on phenotype, PAHdb modules contain mutations, polymorphic haplotypes, genotype-phenotype correlations, expression analysis, sources of information and the reference sequence; the database also contains pages of clinical information and data on three ENU mouse orthologues of human HPA. Only six different mutations account for 60% of human HPA chromosomes worldwide, mutations stratify by population and geographic region, and the Oriental and Caucasian mutation sets are different (Fig. 3). PAHdb provides curated electronic publication and one third of its incoming reports are direct submissions, Each different mutation receives a systematic (nucleotide) name and a unique identifier (UID), Data are accessed both by a Newsletter and a search engine on the website; integrity of the database is ensured by keeping the curated template offline. There have been >6500 online interrogations of the website.
    BibTeX:
    @article{Nowacki1998,
      author = {Nowacki, PM and Byck, S and Prevost, L and Scriver, CR},
      title = {PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {1998},
      volume = {26},
      number = {1},
      pages = {220-225}
    }
    
    Obremskey, W., Bhandari, M., Dirsehl, D. & Shemitsch, E. Internal fixation versus arthroplasty of comminuted fractures of the distal humerus {2003} JOURNAL OF ORTHOPAEDIC TRAUMA
    Vol. {17}({6}), pp. {463-465} 
    article  
    Abstract: Background: A comminuted distal humerus fracture in an older patient is a difficult clinical problem. Open reduction internal fixation (ORIF) carries the risks of nonunion, loss of fixation, infection, and stiffness. Arthroplasty carries the risks of loosening, infection, and periprosthetic fracture. Both procedures are technically challenging, and complications following these procedures are frequent. Objective: To evaluate best available evidence to assist in guiding clinical decision making for ORIF versus arthroplasty of intraarticular distal humeral fractures in elderly patients. Highest Available Evidence: 1. Case series of internal fixation or arthroplasty of acute interarticular distal humerus fractures in the elderly (level IV). 2. Review of expert opinion without explicit critical appraisal or controlled research (level V). Study Identification: 1. Computerized data search 1969-2003 Cochrane Database OVID Search Engine 2. Reviews of bibliographies of selected articles.
    BibTeX:
    @article{Obremskey2003,
      author = {Obremskey, WT and Bhandari, M and Dirsehl, DR and Shemitsch, E},
      title = {Internal fixation versus arthroplasty of comminuted fractures of the distal humerus},
      journal = {JOURNAL OF ORTHOPAEDIC TRAUMA},
      year = {2003},
      volume = {17},
      number = {6},
      pages = {463-465}
    }
    
    Oh, H., Rizo, C., Enkin, M. & Jadad, A. What is eHealth (3): A systematic review of published definitions {2005} JOURNAL OF MEDICAL INTERNET RESEARCH
    Vol. {7}({1}) 
    article  
    Abstract: Context: The term eHealth is widely used by many individuals, academic institutions, professional bodies, and funding organizations. It has become an accepted neologism despite the lack of an agreed-upon clear or precise definition. We believe that communication among the many individuals and organizations that use the term could be improved by comprehensive data about the range of meanings encompassed by the term. Objective: To report the results of a systematic review of published, suggested, or proposed definitions of eHealth. Data Sources: Using the search query string ``eHealth'' OR ``e-Health'' OR ``electronic health'', we searched the following databases: Medline and Premedline (1966-June 2004), EMBASE (1980-May 2004), International Pharmaceutical Abstracts (1970-May 2004), Web of Science (all years), Information Sciences Abstracts (1966-May 2004), Library Information Sciences Abstracts (1969-May 2004), and Wilson Business Abstracts (1982-March 2004). In addition, we searched dictionaries and an Internet search engine. Study Selection: We included any source published in either print format or on the Internet, available in English, and containing text that defines or attempts to define eHealth in explicit terms. Two of us independently reviewed titles and abstracts of citations identified in the bibliographic databases and Internet search, reaching consensus on relevance by discussion. Data Extraction: We retrieved relevant reports, articles, references, letters, and websites containing definitions of eHealth. Two of us qualitatively analyzed the definitions and coded them for content, emerging themes, patterns, and novel ideas. Data Synthesis: The 51 unique definitions that we retrieved showed a wide range of themes, but no clear consensus about the meaning of the term eHealth. We identified 2 universal themes (health and technology) and 6 less general (commerce, activities, stakeholders, outcomes, place, and perspectives). Conclusions: The widespread use of the term eHealth suggests that it is an important concept, and that there is a tacit understanding of its meaning. This compendium of proposed definitions may improve communication among the many individuals and organizations that use the term.
    BibTeX:
    @article{Oh2005,
      author = {Oh, H and Rizo, C and Enkin, M and Jadad, A},
      title = {What is eHealth (3): A systematic review of published definitions},
      journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
      year = {2005},
      volume = {7},
      number = {1}
    }
    
    Ohm, J., Bunjamin, F., Liebsch, W., Makai, B., Muller, K., Smolic, A. & Zier, D. A set of visual feature descriptors and their combination in a low-level description scheme {2000} SIGNAL PROCESSING-IMAGE COMMUNICATION
    Vol. {16}({1-2}), pp. {157-179} 
    article  
    Abstract: This paper reports about descriptors for basic visual information features, which have been developed in the context of the forthcoming MPEG-7 standard. The four basic features supported are color, texture, shape and motion. A search engine system has been developed which supports combinations of basic feature descriptors in a low-level description scheme for similarity-based retrieval of visual (image and video) data. All basic descriptors have been developed so that invariance against common transformations of visual material, e.g. filtering, contrast/color manipulation, resizing, etc., is achieved, and that they are fitted to human perception properties. Furthermore, descriptors have been designed to allow fast, coarse-to-fine search procedures. Elements described in this contribution have been proposed for the MPEG-7 standard. They are currently either included in the MPEG-7 Experimentation Model (XM) or investigated within core experiments, which are performed during the standard's development. (C) 2000 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Ohm2000,
      author = {Ohm, JR and Bunjamin, F and Liebsch, W and Makai, B and Muller, K and Smolic, A and Zier, D},
      title = {A set of visual feature descriptors and their combination in a low-level description scheme},
      journal = {SIGNAL PROCESSING-IMAGE COMMUNICATION},
      year = {2000},
      volume = {16},
      number = {1-2},
      pages = {157-179}
    }
    
    Olah, M., Bologa, C. & Oprea, T. An automated PLS search for biologically relevant QSAR descriptors {2004} JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
    Vol. {18}({7-9}), pp. {437-449} 
    article DOI  
    Abstract: An automated PLS engine, WB- PLS, was applied to 1632 QSAR series with at least 25 compounds per series extracted from WOMBAT ( WOrld of Molecular BioAcTivity). WB- PLS extracts a single Y variable per series, as well as pre-computed X variables from a table. The table contained 2D descriptors, the drug-like MDL 320 keys as implemented in the Mesa A& C Fingerprint module, and inhouse generated topological-pharmacophore SMARTS counts and fingerprints. Each descriptor type was treated as a block, with or without scaling. Cross-validation, variable importance on projections ( VIP) above 0.8 and q(2) greater than or equal to 0.3 were applied for model significance. Among cross-validation methods, leave-one-in-seven-out (CV7) is a better measure of model significance, compared to leave-one-out ( measuring redundancy) and leave-half-out ( too restrictive). SMARTS counts overlap with 2D descriptors ( having a more quantitative nature), whereas MDL keys overlap with in-house. ngerprints ( both are more qualitative). The SMARTS counts is the most effective descriptor system, when compared to the other three. At the individual level, size-related descriptors and topological indices ( in the 2D property space), and branched SMARTS, aromatic and ring atom types and halogens are found to be most relevant according to the VIP criterion.
    BibTeX:
    @article{Olah2004,
      author = {Olah, M and Bologa, C and Oprea, TI},
      title = {An automated PLS search for biologically relevant QSAR descriptors},
      journal = {JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN},
      year = {2004},
      volume = {18},
      number = {7-9},
      pages = {437-449},
      doi = {{10.1007/s10822-004-4060-8}}
    }
    
    Omenn, G., States, D., Adamski, M., Blackwell, T., Menon, R., Hermjakob, H., Apweiler, R., Haab, B., Simpson, R., Eddes, J., Kapp, E., Moritz, R., Chan, D., Rai, A., Admon, A., Aebersold, R., Eng, J., Hancock, W., Hefta, S., Meyer, H., Paik, Y., Yoo, J., Ping, P., Pounds, J., Adkins, J., Qian, X., Wang, R., Wasinger, V., Wu, C., Zhao, X., Zeng, R., Archakov, A., Tsugita, A., Beer, I., Pandey, A., Pisano, M., Andrews, P., Tammen, H., Speicher, D. & Hanash, S. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database {2005} PROTEOMICS
    Vol. {5}({13}), pp. {3226-3245} 
    article DOI  
    Abstract: HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.
    BibTeX:
    @article{Omenn2005,
      author = {Omenn, GS and States, DJ and Adamski, M and Blackwell, TW and Menon, R and Hermjakob, H and Apweiler, R and Haab, BB and Simpson, RJ and Eddes, JS and Kapp, EA and Moritz, RL and Chan, DW and Rai, AJ and Admon, A and Aebersold, R and Eng, J and Hancock, WS and Hefta, SA and Meyer, H and Paik, YK and Yoo, JS and Ping, PP and Pounds, J and Adkins, J and Qian, XH and Wang, R and Wasinger, V and Wu, CY and Zhao, XH and Zeng, R and Archakov, A and Tsugita, A and Beer, I and Pandey, A and Pisano, M and Andrews, P and Tammen, H and Speicher, DW and Hanash, SM},
      title = {Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database},
      journal = {PROTEOMICS},
      year = {2005},
      volume = {5},
      number = {13},
      pages = {3226-3245},
      doi = {{10.1002/pmic.200500358}}
    }
    
    Oosterlinck, W., Solsona, E., Akaza, H., Busch, C., Goebell, P., Malmstrom, P., Ozen, H. & Sved, P. Low-grade Ta (noninvasive) urothelial carcinoma of the bladder {2005} UROLOGY
    Vol. {66}({6A, Suppl. S}), pp. {75-89} 
    article DOI  
    Abstract: This article discusses the development of international guidelines for the diagnosis, treatment, follow-up, and prevention of low-grade Ta urothelial carcinoma of the bladder. The authors, who are experts in this field from 3 continents and 7 countries, reviewed the English language literature through September 2004. The results of the authors' deliberations are presented here as a consensus document. The objective of this study was to determine the optimal diagnostic workup, treatment, follow-up, and prevention of low-grade, Ta urothelial carcinoma of the bladder. A consensus conference convened by the World Health Organization (WHO) and the Societe Internationale d'Urologie (SIU) met to critically review the literature on the diagnosis and treatment of low-grade Ta urothelial carcinoma of the bladder. Research was conducted using Medline; this search engine also was used to identify additional works not detected at the initial search. Evidence-based recommendations for diagnosis and management of the disease were made with reference to a 4-point scale. Low-grade Ta urothelial carcinoma of the bladder is a well-studied subject with many level I and 2 evidence references that support clinical practice. Findings from 135 reviewed citations are summarized. Many grade A and B recommendations on the diagnostic workup and management of this disease can be given with level 1 and 2 evidence based on prospective randomized clinical trials of sufficient statistical power. This should improve the quality of the treatment of this disease.
    BibTeX:
    @article{Oosterlinck2005,
      author = {Oosterlinck, W and Solsona, E and Akaza, H and Busch, C and Goebell, PJ and Malmstrom, PU and Ozen, H and Sved, P},
      title = {Low-grade Ta (noninvasive) urothelial carcinoma of the bladder},
      journal = {UROLOGY},
      year = {2005},
      volume = {66},
      number = {6A, Suppl. S},
      pages = {75-89},
      note = {27th Congress of the Societe-Internationale-Urologie (SIU), Honolulu, HI, OCT 03-07, 2004},
      doi = {{10.1016/j.urolog.2005.07.063}}
    }
    
    Oppenheim, C., Morris, A., McKnight, C. & Lowley, S. The evaluation of WWW search engines {2000} JOURNAL OF DOCUMENTATION
    Vol. {56}({2}), pp. {190-211} 
    article  
    Abstract: The literature of the evaluation of Internet search engines is reviewed. Although there have been many studies, there has been little consistency in the way such studies have been carried out. This problem is exacerbated by the fact that recall is virtually impossible to calculate in the fast changing Internet environment, and therefore the traditional Cranfield type of evaluation is not usually possible. A variety of alternative evaluation methods has been suggested to overcome this difficulty. The authors recommend that a standardised set of tools is developed for the evaluation of web search engines so that, in future, comparisons can be made between search engines more effectively, and that variations in performance of any given search engine over time can be tracked. The paper itself does not provide such a standard set of tools, but it investigates the issues and makes preliminary recommendations of the types of tools needed.
    BibTeX:
    @article{Oppenheim2000,
      author = {Oppenheim, C and Morris, A and McKnight, C and Lowley, S},
      title = {The evaluation of WWW search engines},
      journal = {JOURNAL OF DOCUMENTATION},
      year = {2000},
      volume = {56},
      number = {2},
      pages = {190-211}
    }
    
    Oyama, S., Kokubo, T. & Ishida, T. Domain-specific web search with keyword spices {2004} IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
    Vol. {16}({1}), pp. {17-27} 
    article  
    Abstract: Domain-specific Web search engines are effective tools for reducing the difficulty experienced when acquiring information from the Web. Existing methods for building domain-specific Web search engines require human expertise or specific facilities. However, we can build a domain-specific search engine simply by adding domain-specific keywords, called ``keyword spices,'' to the user's input query and forwarding it to a general-purpose Web search engine. Keyword spices can be effectively discovered from Web documents using machine learning technologies. This paper will describe domain-specific Web search engines that use keyword spices for locating recipes, restaurants, and used cars.
    BibTeX:
    @article{Oyama2004,
      author = {Oyama, S and Kokubo, T and Ishida, T},
      title = {Domain-specific web search with keyword spices},
      journal = {IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING},
      year = {2004},
      volume = {16},
      number = {1},
      pages = {17-27}
    }
    
    Ozmutlu, H. & Cavdur, F. Application of automatic topic identification on Excite Web search engine data logs {2005} INFORMATION PROCESSING & MANAGEMENT
    Vol. {41}({5}), pp. {1243-1262} 
    article DOI  
    Abstract: The analysis of contextual information in search engine query logs enhances the understanding of Web users' search patterns. Obtaining contextual information on Web search engine logs is a difficult task, since users submit few number of queries, and search multiple topics. Identification of topic changes within a search session is an important branch of search engine user behavior analysis. The purpose of this study is to investigate the properties of a specific topic identification methodology in detail, and to test its validity. The topic identification algorithm's performance becomes doubtful in various cases. These cases are explored and the reasons underlying the inconsistent performance of automatic topic identification are investigated with statistical analysis and experimental design techniques. (c) 2004 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Ozmutlu2005,
      author = {Ozmutlu, HC and Cavdur, F},
      title = {Application of automatic topic identification on Excite Web search engine data logs},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2005},
      volume = {41},
      number = {5},
      pages = {1243-1262},
      doi = {{10.1016/j.ipm.2004.04.018}}
    }
    
    Ozmutlu, H., Spink, A. & Ozmutla, S. Analysis of large data logs: an application of Poisson sampling on excite web queries {2002} INFORMATION PROCESSING & MANAGEMENT
    Vol. {38}({4}), pp. {473-490} 
    article  
    Abstract: Search engines are the gateway for users to retrieve information from the Web. There is a crucial need for tools that allow effective analysis of search engine queries to provide a greater understanding of Web users' information seeking behavior. The objective of the study is to develop an effective strategy for the selection of samples from large-scale data sets. Millions of queries are submitted to Web search engines daily and new sampling techniques are required to bring these databases to a manageable size, while preserving the statistically representative characteristics or the entire data set. This paper reports results from a study using data logs from the Excite Web search engine, We use Poisson sampling to develop a sampling strategy. and show how sample sets selected by Poisson sampling statistically effectively represent the characteristics of the entire dataset. In addition, this paper discusses the use of Poisson sampling in continuous monitoring of stochastic processes, such as Web site dynamics. (C) 2002 Published by Elsevier Science Ltd.
    BibTeX:
    @article{Ozmutlu2002,
      author = {Ozmutlu, HC and Spink, A and Ozmutla, S},
      title = {Analysis of large data logs: an application of Poisson sampling on excite web queries},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2002},
      volume = {38},
      number = {4},
      pages = {473-490}
    }
    
    Paquet, E. & Rioux, M. Nefertiti: a query by content system for three-dimensional model and image databases management {1999} IMAGE AND VISION COMPUTING
    Vol. {17}({2}), pp. {157-166} 
    article  
    Abstract: This paper presents a new approach for the classification and retrieval of three-dimensional images and models from databases. A set of retrieval algorithms is introduced. These algorithms are content-based, meaning that the input is not made out of keywords but of three-dimensional models. Tensors of inertia, distribution of normals, distribution of cords and multiresolution analysis are used to describe each model. The database can be searched by scale, shape or color or any combination of these parameters. A user-friendly interface makes the retrieval operation simple and intuitive and makes it possible to edit reference models according to the specifications of the user. Experimental results using a database of more than 400 range images and 1000 VRML models are presented (C) 1999 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Paquet1999,
      author = {Paquet, E and Rioux, M},
      title = {Nefertiti: a query by content system for three-dimensional model and image databases management},
      journal = {IMAGE AND VISION COMPUTING},
      year = {1999},
      volume = {17},
      number = {2},
      pages = {157-166},
      note = {International Conference on Recent Advances in 3-D Digital Imaging and Modeling, OTTAWA, CANADA, MAY 12-15, 1997}
    }
    
    Park, S., Lee, J. & Bae, H. End user searching: A Web log analysis of NAVER, a Korean Web search engine {2005} LIBRARY & INFORMATION SCIENCE RESEARCH
    Vol. {27}({2}), pp. {203-221} 
    article DOI  
    Abstract: Transaction logs of NAVER, a major Korean Web search engine, were analyzed to track the information-seeking behavior of Korean Web users. These transaction logs include more than 40 million queries collected over 1 week. This study examines current transaction log analysis methodologies and proposes a method for log cleaning, session definition, and query classification. A term definition method which is necessary for Korean transaction log analysis is also discussed. The results of this study show that users behave in a simple way: they type in short queries with a few query terms, seldom use advanced features, and view few results' pages. Users also behave in a passive way: they seldom change search environments set by the system. It is of interest that users tend to change their queries totally rather than adding or deleting terms to modify the previous queries. The results of this study might contribute to the development of more efficient and effective Web search engines and services. (c) 2005 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Park2005,
      author = {Park, S and Lee, JH and Bae, HJ},
      title = {End user searching: A Web log analysis of NAVER, a Korean Web search engine},
      journal = {LIBRARY & INFORMATION SCIENCE RESEARCH},
      year = {2005},
      volume = {27},
      number = {2},
      pages = {203-221},
      doi = {{10.1016/j.lisr.2005.01.013}}
    }
    
    Patwardhan, B., Vaidya, A. & Chorghade, M. Ayurveda and natural products drug discovery {2004} CURRENT SCIENCE
    Vol. {86}({6}), pp. {789-799} 
    article  
    Abstract: This review attempts to portray the discovery and development of medicine from galenical to genomical, with a focus on the potential and role of ayurveda. Natural products, including plants, animals and minerals have been the basis of treatment of human diseases. Indigenous people derived therapeutic materials from thousands of plants; however discovering medicines or poisons remains a vital question. Ayurveda is a traditional Indian medicinal system being practised for thousands of years. Considerable research on pharmacognosy, chemistry, pharmacology and clinical therapeutics has been carried out on ayurvedic medicinal plants. Many of the major pharmaceutical corporations have renewed their strategies in favour of natural products drug discovery and it is important to follow systems biology applications to facilitate the process. Numerous drugs have entered the international pharmacopoeia through the study of ethnopharmacology and traditional medicine. For ayurveda and other traditional medicines newer guidelines of standardization, manufacture and quality control are required. Employing a unique holistic approach, ayurvedic medicines are usually customized to an individual constitution. Traditional knowledge-driven drug development can follow a reverse pharmacology path and reduce time and cost of development. New approaches to improve and accelerate the joint drug discovery and development process are expected to take place mainly from innovation in drug target elucidation and lead structure discovery. Powerful new technologies such as automated separation techniques, high-throughput screening and combinatorial chemistry are revolutionizing drug discovery. Traditional knowledge will serve as a powerful search engine and most importantly, will greatly facilitate intentional, focused and safe natural products research to rediscover the drug discovery process.
    BibTeX:
    @article{Patwardhan2004,
      author = {Patwardhan, B and Vaidya, ADB and Chorghade, M},
      title = {Ayurveda and natural products drug discovery},
      journal = {CURRENT SCIENCE},
      year = {2004},
      volume = {86},
      number = {6},
      pages = {789-799}
    }
    
    Perriere, G., Combet, C., Penel, S., Blanchet, C., Thioulouse, J., Geourjon, C., Grassot, J., Charavay, C., Gouy, M., Duret, L. & Deleage, G. Integrated databanks access and sequence/structure analysis services at the PBIL {2003} NUCLEIC ACIDS RESEARCH
    Vol. {31}({13}), pp. {3393-3399} 
    article DOI  
    Abstract: The World Wide Web server of the PBIL (Pole Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.
    BibTeX:
    @article{Perriere2003,
      author = {Perriere, G and Combet, C and Penel, S and Blanchet, C and Thioulouse, J and Geourjon, C and Grassot, J and Charavay, C and Gouy, M and Duret, L and Deleage, G},
      title = {Integrated databanks access and sequence/structure analysis services at the PBIL},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2003},
      volume = {31},
      number = {13},
      pages = {3393-3399},
      doi = {{10.1093/nar/gkg530}}
    }
    
    Petersen, J. My favorite search engine {1998} INTERNET WORLD
    Vol. {9}({2}), pp. {12} 
    article  
    BibTeX:
    @article{Petersen1998,
      author = {Petersen, J},
      title = {My favorite search engine},
      journal = {INTERNET WORLD},
      year = {1998},
      volume = {9},
      number = {2},
      pages = {12}
    }
    
    Peterson, G., Aslani, P. & Williams, K.A. How do Consumers Search for and Appraise Information on Medicines on the Internet? A Qualitative Study Using Focus Groups {2003} JOURNAL OF MEDICAL INTERNET RESEARCH
    Vol. {5}({4}) 
    article DOI  
    Abstract: Background: Many consumers use the Internet to find information about their medicines. It is widely acknowledged that health information on the Internet is of variable quality and therefore the search and appraisal skills of consumers are important for selecting and assessing this information. The way consumers choose and evaluate information on medicines on the Internet is important because it has been shown that written information on medicines can influence consumer attitudes to and use of medicines. Objective: To explore consumer experiences in searching for and appraising Internet-based information on medicines. Methods: Six focus groups (N = 46 participants) were conducted in metropolitan Sydney, Australia from March to May 2003 with consumers who had used the Internet for information on medicines. Verbatim transcripts of the group discussions were analyzed using a grounded theory approach. Results: All participants reported using a search engine to find information on medicines. Choice of search engine was determined by factors such as the workplace or educational environments, or suggestions by family or friends. Some participants found information solely by typing the medicine name (drug or brand name) into the search engine, while others searched using broader terms. Search skills ranged widely from more-advanced (using quotation marks and phrases) to less-than-optimal (such as typing in questions and full sentences). Many participants selected information from the first page of search results by looking for keywords and descriptions in the search results, and by looking for the source of the information as apparent in the URL. Opinions on credible sources of information on medicines varied with some participants regarding information by pharmaceutical companies as the ``official'' information on a medicine, and others preferring what they considered to be impartial sources such as governments, organizations, and educational institutions. It was clear that although most participants were skeptical of trusting information on the Internet, they had not paid conscious attention to how they selected information on medicines. Despite this, it was evident that participants viewed the Internet as an important source for information on medicines. Conclusions: The results showed that there was a range of search and appraisal skills among participants, with many reporting a limited awareness of how they found and evaluated Internet-based information on medicines. Poor interpretation of written information on medicines has been shown to lead to anxiety and poor compliance to therapy. This issue is more important for Internet-based information since it is not subject to quality control and standardization as is written information on medicines. Therefore, there is a need for promoting consumer search and appraisal skills when using this information. Educating consumers in how to find and interpret Internet-based information on medicines may help them use their medicines in a safer and more-effective way.
    BibTeX:
    @article{Peterson2003,
      author = {Peterson, Geraldine and Aslani, Parisa and Williams, Kylie A.},
      title = {How do Consumers Search for and Appraise Information on Medicines on the Internet? A Qualitative Study Using Focus Groups},
      journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
      year = {2003},
      volume = {5},
      number = {4},
      doi = {{10.2196/jmir.5.4.e33}}
    }
    
    PINKAS, G. REASONING, NONMONOTONICITY AND LEARNING IN CONNECTIONIST NETWORKS THAT CAPTURE PROPOSITIONAL KNOWLEDGE {1995} ARTIFICIAL INTELLIGENCE
    Vol. {77}({2}), pp. {203-247} 
    article  
    Abstract: The paper presents a connectionist framework that is capable of representing and learning propositional knowledge. An extended version of propositional calculus is developed and is demonstrated to be useful for nonmonotonic reasoning, dealing with conflicting beliefs and for coping with inconsistency generated by unreliable knowledge sources, Formulas of the extended calculus are proved to be equivalent in a very strong sense to symmetric networks (like Hopfield networks and Boltzmann machines), and efficient algorithms are given for translating back and forth between the two forms of knowledge representation, A fast learning procedure is presented that allows symmetric networks to learn representations of unknown logic formulas by looking at examples, A connectionist inference engine is then sketched whose knowledge is either compiled from a symbolic representation or learned inductively from training examples. Experiments with large scale randomly generated formulas suggest that the parallel local search that is executed by the networks is extremely fast on average. Finally, it is shown that the extended logic can be used as a high-level specification language for connectionist networks, into which several recent symbolic systems may be mapped, The paper demonstrates how a rigorous bridge can be constructed that ties together the (sometimes opposing) connectionist and symbolic approaches.
    BibTeX:
    @article{PINKAS1995,
      author = {PINKAS, G},
      title = {REASONING, NONMONOTONICITY AND LEARNING IN CONNECTIONIST NETWORKS THAT CAPTURE PROPOSITIONAL KNOWLEDGE},
      journal = {ARTIFICIAL INTELLIGENCE},
      year = {1995},
      volume = {77},
      number = {2},
      pages = {203-247}
    }
    
    Pinzi, S., Garcia, I.L., Lopez-Gimenez, F.J., Luque de Castro, M.D., Dorado, G. & Dorado, M.P. The Ideal Vegetable Oil-based Biodiesel Composition: A Review of Social, Economical and Technical Implications {2009} ENERGY & FUELS
    Vol. {23}, pp. {2325-2341} 
    article DOI  
    Abstract: Though a considerable number of publications about biodiesel can be found in literature, several problems remain unsolved, encompassing economical, social, and technical issues. Thus, the biodiesel industry has come under attack by some environmental associations, and subsidies for biofuel production have been condemned by some governments. Yet, biodiesel may represent a truly competitive alternative to diesel fuel, for which fuel tax exemption and subsidies to energetic crops are needed. Biodiesel must increase its popularity among social movements and governments to constitute a valid alternative of energy source. In this sense, the use of nonedible oils to produce biodiesel is proposed in the present review. Moreover, the compromise of noninterference between land for energetic and food purposes must be addressed. Concerning technical issues, it is important to consider a transesterification optimization, which is missing or incomplete for too many vegetable oils already tested. In most cases, a common recipe to produce biodiesel from any raw material has been adopted, which may not represent the best approach. Such strategy may fit multifeedstock biodiesel plant needs but cannot be accepted for oils converted individually into biodiesel, because biodiesel yield will most likely fail, increasing costs. Transesterification optimization results depend on the chemical composition of vegetable oils and fats. Considering ``sustainable'' vegetable oils, biodiesel from Calophyllum inophyllum, Azadirachta indica, Terminalia catappa, Madhuca indica, Pongamia pinnata, and Jatropha curcas oils fits both current biodiesel standards: European EN 14214 and US ASTM D 6751 02. However, none of them can be considered to be the ``ideal'' alternative that matches all the main important fuel properties that ensure the best diesel engine behavior. In search of the ideal biodiesel composition, high presence of monounsaturated fatty acids (as oleic and palmitoleic acids), reduced presence of polyunsaturated acids, and controlled saturated acids content are recommended. In this sense, C 18: 1 and C 16:1 are the best-fitting acids in terms of oxidative stability and cold weather behavior, among many other properties. Furthermore, genetic engineering is an invaluable tool to design oils presenting the most suitable fatty acid profile to provide high quality biodiesel. Finally, most published research related to engine performance and emissions fails in using a standard methodology, which should be implemented to allow the comparison between tests and biofuels from different origin. In conclusion, a compromise between social, economical, and technical agents must be reached.
    BibTeX:
    @article{Pinzi2009,
      author = {Pinzi, S. and Garcia, I. L. and Lopez-Gimenez, F. J. and Luque de Castro, M. D. and Dorado, G. and Dorado, M. P.},
      title = {The Ideal Vegetable Oil-based Biodiesel Composition: A Review of Social, Economical and Technical Implications},
      journal = {ENERGY & FUELS},
      year = {2009},
      volume = {23},
      pages = {2325-2341},
      doi = {{10.1021/ef801098a}}
    }
    
    Piran, T. Gamma-ray bursts and the fireball model {1999} PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
    Vol. {314}({6}), pp. {575-667} 
    article  
    Abstract: Gamma-ray bursts (GRBs) have puzzled astronomers since their accidental discovery in the late 1960s. The BATSE detector on the COMPTON-GRO satellite has been detecting one burst per day for the last six years. Its findings have revolutionized our ideas about the nature of these objects. They have shown that GRBs are at cosmological distances. This idea was accepted with difficulties at first. The recent discovery of an X-ray afterglow by the Italian/Dutch satellite BeppoSAX has led to a detection of high red-shift absorption lines in the optical afterglow of GRB970508 and in several other bursts and to the identification of host galaxies to others. This has confirmed the cosmological origin. Cosmological GRBs release similar to 10(51)-10(53),erg in a few seconds making them the most (electromagnetically) luminous objects in the Universe. The simplest, most conventional, and practically inevitable, interpretation of these observations is that GRBs result from the conversion of the kinetic energy of ultra-relativistic particles or possibly the electromagnetic energy of a Poynting flux to radiation in an optically thin region. This generic ``fireball'' model has also been confirmed by the afterglow observations. The ``inner engine'' that accelerates the relativistic flow is hidden from direct observations. Consequently, it is difficult to infer its structure directly from current observations. Recent studies show, however, that this ``inner engine'' is responsible for the complicated temporal structure observed in GRBs. This temporal structure and energy considerations indicates that the ``inner engine'' is associated with the formation of a compact object - most likely a black hole. (C) 1999 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Piran1999,
      author = {Piran, T},
      title = {Gamma-ray bursts and the fireball model},
      journal = {PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS},
      year = {1999},
      volume = {314},
      number = {6},
      pages = {575-667}
    }
    
    Pitrelli, J., Bakis, R., Eide, E., Fernandez, R., Hamza, W. & Picheny, M. The IBM expressive text-to-speech synthesis system for American English {2006} IEEE TRANSACTIONS ON AUDIO SPEECH AND LANGUAGE PROCESSING
    Vol. {14}({4}), pp. {1099-1108} 
    article DOI  
    Abstract: Expressive text-to-speech (TTS) synthesis should contribute to the pleasantness, intelligibility, and speed of speech-based human-machine interactions which use TTS. We describe a TTS engine which can be directed, via text markup, to use a variety of expressive styles, here, questioning, contrastive emphasis, and conveying good and bad news. Differences in these styles lead us to investigate two approaches for expressive TTS, a ``corpus-driven'' and a ``prosodic-phonology'' approach. Each speaker records 11 h (excluding silences) of ``neutral'' sentences. In the corpus-driven approach, the speaker also records 1-h corpora in each-expressive style; these segments are tagged by style for use during search, and decision trees for determining f(0) contours and timing are trained separately for each of the neutral and expressive corpora. In the prosodic-phonology approach, rules translating certain expressive markup elements to tones and break indices (ToBI) are manually determined, and the ToBI elements are used in single f(0) and duration trees for all expressions. Tests show that listeners identify synthesis in particular styles ranging from 70% correctly for ``conveying bad news'' to 85% for ``yes-no questions:'' Further improvements are demonstrated through the use of speaker-pooled f(0) and duration models.
    BibTeX:
    @article{Pitrelli2006,
      author = {Pitrelli, JF and Bakis, R and Eide, EM and Fernandez, R and Hamza, W and Picheny, MA},
      title = {The IBM expressive text-to-speech synthesis system for American English},
      journal = {IEEE TRANSACTIONS ON AUDIO SPEECH AND LANGUAGE PROCESSING},
      year = {2006},
      volume = {14},
      number = {4},
      pages = {1099-1108},
      doi = {{10.1109/TASL.2006.876123}}
    }
    
    Polgreen, P.M., Chen, Y., Pennock, D.M. & Nelson, F.D. Using Internet Searches for Influenza Surveillance {2008} CLINICAL INFECTIOUS DISEASES
    Vol. {47}({11}), pp. {1443-1448} 
    article DOI  
    Abstract: The Internet is an important source of health information. Thus, the frequency of Internet searches may provide information regarding infectious disease activity. As an example, we examined the relationship between searches for influenza and actual influenza occurrence. Using search queries from the Yahoo! search engine (http://search.yahoo.com) from March 2004 through May 2008, we counted daily unique queries originating in the United States that contained influenza-related search terms. Counts were divided by the total number of searches, and the resulting daily fraction of searches was averaged over the week. We estimated linear models, using searches with 1-10-week lead times as explanatory variables to predict the percentage of cultures positive for influenza and deaths attributable to pneumonia and influenza in the United States. With use of the frequency of searches, our models predicted an increase in cultures positive for influenza 1-3 weeks in advance of when they occurred (P < .001), and similar models predicted an increase in mortality attributable to pneumonia and influenza up to 5 P < .001 weeks in advance (P < .001). Search-term surveillance may provide an additional tool for disease surveillance.
    BibTeX:
    @article{Polgreen2008,
      author = {Polgreen, Philip M. and Chen, Yiling and Pennock, David M. and Nelson, Forrest D.},
      title = {Using Internet Searches for Influenza Surveillance},
      journal = {CLINICAL INFECTIOUS DISEASES},
      year = {2008},
      volume = {47},
      number = {11},
      pages = {1443-1448},
      doi = {{10.1086/593098}}
    }
    
    Pondman, K.M., Futterer, J.J., ten Haken, B., Kool, L.J.S., Witjes, J.A., Hambrock, T., Macura, K.J. & Barentsz, J.O. MR-guided biopsy of the prostate: An overview of techniques and a systematic review {2008} EUROPEAN UROLOGY
    Vol. {54}({3}), pp. {517-527} 
    article DOI  
    Abstract: Context: Systematic transrectal ultrasound-guided biopsy (TRUSBx) is the gold standard for detecting prostate cancer. This systematic approach is characterized by low sensitivity (39-52 and high specificity (81-82. Magnetic resonance (MR)-guided biopsy techniques are becoming more and more available, but there is no current consensus on the optimal technique. Objective: This review presents an overview of MR-guided biopsy techniques for prostate cancer detection. Evidence acquisition: Current literature was reviewed regarding MR-guided biopsy for prostate cancer detection. A literature search was performed using the commercially available MedLine online search engine. Combinations of the following search and Medical Subject Headings terms were applied to retrieve relevant articles: ``magnetic resonance,'' ``prostatic neoplasms,'' and ``biopsy.'' Review articles and studies describing techniques other than MR-guided biopsy were excluded. Evidence synthesis: Biopsy of the prostate is an essential procedure for determining optimal treatment. Systematic TRUSBx is the gold standard, but it fails to detect numerous tumors. Diagnostic MR imaging provides more accurate selection of regions in which tumors are suspected. Using these diagnostic images during an MR-directed biopsy procedure improves quality of the biopsy. In open MR scanners, the prebiopsy images often must be registered to the real-time biopsy images because open MR scanners do not provide optimal tissue contrast; thus, the patient must first be examined in a closed MR scanner and then biopsied in an open scanner. The advantage of open MR over closed MR is that the physician has easy patient access. With special equipment, prostate MR-guided biopsy is also possible in a closed system. Closed MR scanners can be used for the prebiopsy scan as well as for the biopsy procedure. Conclusions: The combination of a diagnostic MR examination and MR-guided biopsy is a promising tool and may be used in patients with previous negative TRUSBx. (C) 2008 European Association of Urology. Published by Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Pondman2008,
      author = {Pondman, Kirsten M. and Futterer, Jurgen J. and ten Haken, Bennie and Kool, Leo J. Schultze and Witjes, J. Alfred and Hambrock, Thomas and Macura, Katarzyna J. and Barentsz, Jelle O.},
      title = {MR-guided biopsy of the prostate: An overview of techniques and a systematic review},
      journal = {EUROPEAN UROLOGY},
      year = {2008},
      volume = {54},
      number = {3},
      pages = {517-527},
      doi = {{10.1016/j.eururo.2008.06.001}}
    }
    
    Porter, A., Kongthon, A. & Lui, J. Research profiling: Improving the literature review {2002} SCIENTOMETRICS
    Vol. {53}({3}), pp. {351-370} 
    article  
    Abstract: We propose enhancing the traditional literature review through ``research profiling''. This broad scan of contextual literature can extend the span of science by better linking efforts across research domains. Topical relationships, research trends, and complementary capabilities can be discovered, thereby facilitating research projects. Modem search engine and text mining tools enable research profiling by exploiting the wealth of accessible information in electronic abstract databases such as MEDLINE and Science Citation Index. We illustrate the potential by showing sixteen ways that ``research profiling'' can augment a traditional literature review on the topic of data mining.
    BibTeX:
    @article{Porter2002,
      author = {Porter, AL and Kongthon, A and Lui, JC},
      title = {Research profiling: Improving the literature review},
      journal = {SCIENTOMETRICS},
      year = {2002},
      volume = {53},
      number = {3},
      pages = {351-370}
    }
    
    Prasad, C., Krishna, M., Reddy, C. & Mohan, K. Performance evaluation of non-edible vegetable oils as substitute fuels in low heat rejection diesel engines {2000} PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART D-JOURNAL OF AUTOMOBILE ENGINEERING
    Vol. {214}({D2}), pp. {181-187} 
    article  
    Abstract: Search for renewable fuels such as vegetable oils, in particular non-edible vegetable oils, has become more pertinent in the context of the fossil fuel crisis and vehicle population explosion. The drawbacks associated with vegetable oils for use in diesel engines call for a hot combustion chamber. The concept of the low heat rejection diesel engine is gaining prominence for adopting vegetable oils as substitute fuels for conventional diesel fuel. Non-edible vegetable oils such as Pongamia oil and Jatropha curcas oil are found to be effective substitute fuels in the low heat rejection diesel engine. Esterification, preheating and increase in injection pressures have been tried for effective utilization of the vegetable oils. Performance parameters such as the brake specific energy consumption (b.s.e.c.) and exhaust gas temperature (EGT) have been reported for varying magnitudes of brake mean effective pressure (b.m.e.p.) with different non-edible vegetable oils as substitute fuels. The pollution levels of black smoke and NO, have been recorded. Combustion diagnosis is also carried out with the: aid of a miniature piezoelectric pressure transducer and TDC (top dead centre) encoder.
    BibTeX:
    @article{Prasad2000,
      author = {Prasad, CMV and Krishna, MVSM and Reddy, CP and Mohan, KR},
      title = {Performance evaluation of non-edible vegetable oils as substitute fuels in low heat rejection diesel engines},
      journal = {PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART D-JOURNAL OF AUTOMOBILE ENGINEERING},
      year = {2000},
      volume = {214},
      number = {D2},
      pages = {181-187}
    }
    
    Pu, H., Chuang, S. & Yang, C. Subject categorization of query terms for exploring Web users' search interests {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({8}), pp. {617-630} 
    article DOI  
    Abstract: Subject content analysis of Web query terms is essential to understand Web searching interests. Such analysis includes exploring search topics and observing changes in their frequency distributions with time. To provide a basis for in-depth analysis of users' search interests on a larger scale, this article presents a query categorization approach to automatically classifying Web query terms into broad subject categories. Because a query is short in length and simple in structure, its intended subject(s) of search is difficult to judge. Our approach, therefore, combines the search processes of real-world search engines to obtain highly ranked Web documents based on each unknown query term. These documents are used to extract cooccurring terms and to create a feature set. An effective ranking function has also been developed to find the most appropriate categories. Three search engine logs in Taiwan were collected and tested. They contained over 5 million queries from different periods of time. The achieved performance is quite encouraging compared with that of human categorization. The experimental results demonstrate that the approach is efficient in dealing with large numbers of queries and adaptable to the dynamic Web environment. Through good integration of human and machine efforts, the frequency distributions of subject categories in response to changes in users' search interests can be systematically observed in real time. The approach has also shown potential for use in various information retrieval applications, and provides a basis for further Web searching studies.
    BibTeX:
    @article{Pu2002,
      author = {Pu, HT and Chuang, SL and Yang, C},
      title = {Subject categorization of query terms for exploring Web users' search interests},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {8},
      pages = {617-630},
      doi = {{10.1002/asi.10071}}
    }
    
    Puhan, S., Vedaraman, N., Ram, B., Sankarnarayanan, G. & Jeychandran, K. Mahua oil (Madhuca Indica seed oil) methyl ester as biodiesel-preparation and emission characterstics {2005} BIOMASS & BIOENERGY
    Vol. {28}({1}), pp. {87-93} 
    article DOI  
    Abstract: There is an increasing interest in many countries to search for suitable alternative fuels that are environment friendly. Although straight vegetable oils can be used in diesel engines, their high viscosities, low volatilities and poor cold flow properties have led to the investigation of various derivatives. Biodiesel is a fatty acid alkyl ester, which can be derived from any vegetable oil by transesterification. Biodiesel is a renewable, biodegradable and non-toxic fuel. In this study, Mahua oil (Madhuca indica seed oil) was transesterified with methanol using sodium hydroxide as catalyst to obtain mahua oil methyl ester. This biodiesel was tested in a single cylinder, four stroke, direct injection, constant speed, compression ignition diesel engine (Kirloskar) to evaluate the performance and emissions. (C) 2004 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Puhan2005,
      author = {Puhan, S and Vedaraman, N and Ram, BVB and Sankarnarayanan, G and Jeychandran, K},
      title = {Mahua oil (Madhuca Indica seed oil) methyl ester as biodiesel-preparation and emission characterstics},
      journal = {BIOMASS & BIOENERGY},
      year = {2005},
      volume = {28},
      number = {1},
      pages = {87-93},
      doi = {{10.1016/j.biombioe.2004.06.002}}
    }
    
    Qiao, X., Hou, T., Zhang, W., Guo, S. & Xu, S. A 3D structure database of components from Chinese traditional medicinal herbs {2002} JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
    Vol. {42}({3}), pp. {481-489} 
    article DOI  
    Abstract: This article described a 3D structure database of components extracted from Chinese Traditional Medicinal (CTM) herbs. It offers, not only basic molecular properties and optimized 3D structure of the compounds but also detailed information on their herbal origin, including basic herbal category (e.g. English name, Latin name. and family), effective parts, and clinical effects. An easy to use, interactive GUI browser allows users to perform various searches via complex logical query builder. Combined with the latest network database engine (MySQL.), it can achieve excellent performance under both a local network and an Internet environment. We have tested it on the design of inhibitors of NS3-NS4A protease. Results show that the structure database of component,, extracted from Chinese medicinal herbs can be a rich source in searching the lead compound.
    BibTeX:
    @article{Qiao2002,
      author = {Qiao, XB and Hou, TJ and Zhang, W and Guo, SL and Xu, SJ},
      title = {A 3D structure database of components from Chinese traditional medicinal herbs},
      journal = {JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES},
      year = {2002},
      volume = {42},
      number = {3},
      pages = {481-489},
      doi = {{10.1021/ci010113h}}
    }
    
    Rahimi, R., Nikfar, S. & Abdollahi, M. Increased morbidity and mortality in acute human organophosphate-poisoned patients treated by oximes: a meta-analysis of clinical trials {2006} HUMAN & EXPERIMENTAL TOXICOLOGY
    Vol. {25}({3}), pp. {157-162} 
    article DOI  
    Abstract: Organophosphates are one of the most common causes of poisoning, especially in the Third world, with high morbidity and mortality. The treatment of this type of poisoning involves the use of atropine and oximes. Atropine has been used successfully in large doses to counteract the muscarinic effects of organophosphate poisoning, but the efficacy of oximes in the management of this poisoning remains under question. In this study, we undertook a meta-analysis by reviewing all clinical trials to evaluate the efficacy of oximes in the management of organophosphate poisoning. The databases of PUBMED, EMBASE, Cochrane, SCOPUS, and the search engine of Google were searched for all clinical trials on the use of oximes in organophosphate poisoning. The inclusion criteria were death, development of intermediate syndrome, and need for ventilation. Six clinical trials met the inclusion criteria and were included in the metaanalysis. The x 2 tests for heterogeneity (P = 0.25, 0.16, and 0.33, respectively) indicated that the included studies were not significantly heterogeneous and could be combined. A significant relative risk ( P = 0.0017) for death among oxime-exposed was 2.17 ( 95% CI of 1.34 - 3.51). The need for ventilation' in patients who received oxime was higher ( P = 0.03) than those who did not receive oxime with a relative risk of 1.53 (1.16 - 2.02). The incidence of ` intermediate syndrome' for oxime-exposed patients was significantly higher ( P = 0.01) than oxime non-exposed patients with a relative risk of 1.57 (95% CI 1.11 - 2.11). It can be concluded that oximes are not effective in the management of organophosphate-poisoned patients and, surprisingly, they can be dangerous and worsen the patient's clinical situation.
    BibTeX:
    @article{Rahimi2006,
      author = {Rahimi, R and Nikfar, S and Abdollahi, M},
      title = {Increased morbidity and mortality in acute human organophosphate-poisoned patients treated by oximes: a meta-analysis of clinical trials},
      journal = {HUMAN & EXPERIMENTAL TOXICOLOGY},
      year = {2006},
      volume = {25},
      number = {3},
      pages = {157-162},
      doi = {{10.1191/0960327106ht602oa}}
    }
    
    Rai, M. & Madavan, N. Aerodynamic design using neural networks {2000} AIAA JOURNAL
    Vol. {38}({1}), pp. {173-182} 
    article  
    Abstract: An aerodynamic design procedure that incorporates the advantages of both traditional response surface methodology and neural networks is described. The procedure employs a strategy called parameter-based partitioning of the design space and uses a sequence of response surfaces based on both neural networks and polynomial fits to traverse the design space in search of the optimal solution. This approach results in response surfaces that have both the power of neural networks and the economy of low-order polynomials (in terms of number of simulations needed and network training requirements). Such an approach can handle design problems with many more parameters than would be possible using neural networks alone. The design procedure has been applied to the redesign of a turbine airfoil from a modern jet engine. This redesign involved the use of 15 design variables. The results obtained are closer to the target design than those obtained using an earlier method with only three design variables. The capability of the method in transforming generic shapes, such as simple curved plates, into optimal airfoils is also demonstrated.
    BibTeX:
    @article{Rai2000,
      author = {Rai, MM and Madavan, NK},
      title = {Aerodynamic design using neural networks},
      journal = {AIAA JOURNAL},
      year = {2000},
      volume = {38},
      number = {1},
      pages = {173-182},
      note = {7th AIAA/USAF/NASA/ISSMO Symposium on Multidisciplinary Analysis and Optimization, ST LOUIS, MISSOURI, SEP 02-04, 1998}
    }
    
    Rampitsch, C., Bykova, N., McCallum, B., Beimcik, E. & Ens, W. Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction {2006} PROTEOMICS
    Vol. {6}({6}), pp. {1897-1907} 
    article DOI  
    Abstract: Wheat leaf rust is caused by the fungus Puccinia triticina. The genetics of resistance follows the gene-for-gene hypothesis, and thus the presence or absence of a single host resistance gene renders a plant resistant or susceptible to a leaf rust race bearing the corresponding avirulence gene. To investigate some of the changes in the proteomes of both host and pathogen during disease development, a susceptible line of wheat infected with a virulent race of leaf rust were compared to mock-inoculated wheat using 2-DE (with IEF pH 4-8) and MS. Up-regulated protein spots were excised and analyzed by MALDI-QqTOF MS/MS, followed by cross-species protein identification. Where possible MS/MS spectra were matched to homologous proteins in the NCBI database or to fungal ESTs encoding putative proteins. Searching was done using the MASCOT search engine. Remaining unmatched spectra were then sequenced de novo and queried against the NCBInr database using the BLAST and MS BLAST tools. A total of 32 consistently up-regulated proteins were examined from the gels representing the 9-day post-infection proteome in susceptible plants. of these 7 are host proteins, 22 are fungal proteins of known or hypothetical function and 3 are unknown proteins of putative fungal origin.
    BibTeX:
    @article{Rampitsch2006,
      author = {Rampitsch, C and Bykova, NV and McCallum, B and Beimcik, E and Ens, W},
      title = {Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction},
      journal = {PROTEOMICS},
      year = {2006},
      volume = {6},
      number = {6},
      pages = {1897-1907},
      doi = {{10.1002/pmic.200500351}}
    }
    
    Raskin, R. & Pan, M. Knowledge representation in the semantic web for Earth and environmental terminology (SWEET) {2005} COMPUTERS & GEOSCIENCES
    Vol. {31}({9}), pp. {1119-1125} 
    article DOI  
    Abstract: The semantic web for Earth and environmental terminology (SWEET) is an investigation in improving discovery and use of Earth science data, through software understanding of the semantics of web resources. Semantic understanding is enabled through the use of ontologics, or formal representations of technical concepts and their interrelations in a form that supports domain knowledge. The ultimate vision of the semantic web consists of web pages with XML namespace tags around terms, enabling search tools to ascertain their meanings by following the link to the defining ontologies. Such a scenario both reduces the number of false hits (where a search returns alternative, unintended meanings of a term) and increases the number of successful hits (where searcher and information provider have a syntax mismatch of the same concept). For SWEET, we developed a collection of ontologies using the web ontology language (OWL) that include both orthogonal concepts (space, time, Earth realms, physical quantities, etc.) and integrative science knowledge concepts (phenomena, events, etc.). This paper describes the development of a knowledge space for Earth system science and related concepts (such as data properties). Some of the ontology contents are ``virtual'' by means of an OWL wrapper associated with terms in large external databases (including gazetteers and Earthquake databases). We developed a search tool that finds alternative search terms (based on the semantics) and redirects the expanded set of terms to a search engine. (C) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Raskin2005,
      author = {Raskin, RG and Pan, MJ},
      title = {Knowledge representation in the semantic web for Earth and environmental terminology (SWEET)},
      journal = {COMPUTERS & GEOSCIENCES},
      year = {2005},
      volume = {31},
      number = {9},
      pages = {1119-1125},
      doi = {{10.1016/j.cageo.2004.12.004}}
    }
    
    Ratha, N., Karu, K., Chen, S. & Jain, A. Real-time matching system for large fingerprint databases {1996} IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
    Vol. {18}({8}), pp. {799-813} 
    article  
    Abstract: With the current rapid growth in multimedia technology, there is an imminent need for efficient techniques to search and query large image databases. Because of their unique and peculiar needs, image databases cannot be treated in a similar fashion to other types of digital libraries. The contextual dependencies present in images, and the complex nature of two-dimensional image data make the representation issues more difficult for image databases. An invariant representation of an image is still an open research issue. For these reasons, it is difficult to find a universal content-based retrieval technique. Current approaches based on shape, texture, and color for indexing image databases have met with limited success. Further, these techniques have not been adequately tested in the presence of noise and distortions. A given application domain offers stronger constraints for improving the retrieval performance. Fingerprint databases are characterized by their large size as well as noisy and distorted query images. Distortions are very common in fingerprint images due to elasticity of the skin. In this paper, a method of indexing large fingerprint image databases is presented. The approach integrates a number of domain-specific high-level features such as pattern class and ridge density at higher levels of the search. At the lowest level, it incorporates elastic structural feature-based matching for indexing the database. With a multilevel indexing approach, we have been able to reduce the search space. The search engine has also been implemented on Splash 2-a field programmable gate array (FPGA)-based array processor to obtain near-ASIC level speed of matching. Our approach has been tested on a locally collected test data and on NIST-9, a large fingerprint database available in the public domain.
    BibTeX:
    @article{Ratha1996,
      author = {Ratha, NK and Karu, K and Chen, SY and Jain, AK},
      title = {Real-time matching system for large fingerprint databases},
      journal = {IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE},
      year = {1996},
      volume = {18},
      number = {8},
      pages = {799-813}
    }
    
    Rey, S., Acab, M., Gardy, J., Laird, M., DeFays, K., Lambert, C. & Brinkman, F. PSORTdb: a protein subcellular localization database for bacteria {2005} NUCLEIC ACIDS RESEARCH
    Vol. {33}({Sp. Iss. SI}), pp. {D164-D168} 
    article DOI  
    Abstract: Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets. PSORTdb (http://db.psort.org/) is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (similar to2000 proteins) was manually curated by us and represents the largest dataset of its kind. Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins. Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats. Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources. PSORTdb is freely available under GNU General Public License.
    BibTeX:
    @article{Rey2005,
      author = {Rey, S and Acab, M and Gardy, JL and Laird, MR and DeFays, K and Lambert, C and Brinkman, FSL},
      title = {PSORTdb: a protein subcellular localization database for bacteria},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2005},
      volume = {33},
      number = {Sp. Iss. SI},
      pages = {D164-D168},
      doi = {{10.1093/nar/gki027}}
    }
    
    Reynolds, P. & Vahdat, A. Efficient Peer-to-Peer keyword searching {2003}
    Vol. {2672}MIDDLEWARE 2003, PROCEEDINGS, pp. {21-40} 
    inproceedings  
    Abstract: The recent file storage applications built on top of peer-to-peer distributed hash tables lack search capabilities. We believe that search is an important part of any document publication system. To that end, we have designed and analyzed a distributed search engine based on a distributed hash table. Our simulation results predict that our search engine can answer an average query in under one second, using under one kilobyte of bandwidth.
    BibTeX:
    @inproceedings{Reynolds2003,
      author = {Reynolds, P and Vahdat, A},
      title = {Efficient Peer-to-Peer keyword searching},
      booktitle = {MIDDLEWARE 2003, PROCEEDINGS},
      year = {2003},
      volume = {2672},
      pages = {21-40},
      note = {ACM/IFIP/UNSENIX International Middeware Conference, RIO DE JANEIRO, BRAZIL, JUN 15-20, 2003}
    }
    
    Richardson, M. & Domingos, P. The intelligent surfer: Probabilistic combination of link and content information in PageRank {2002}
    Vol. {14}ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 14, VOLS 1 AND 2, pp. {1441-1448} 
    inproceedings  
    Abstract: The PageRank algorithm, used in the Google search engine, greatly improves the results of Web search by taking into account the link structure of the Web. PageRank assigns to a page a score proportional to the number of times a random surfer would visit that page, if it surfed indefinitely from page to page, following all outlinks from a page with equal probability. We propose to improve PageRank by using a more intelligent surfer, one that is guided by a probabilistic model of the relevance of a page to a query. Efficient execution of our algorithm at query time is made possible by precomputing at crawl time (and thus once for all queries) the necessary terms. Experiments on two large subsets of the Web indicate that our algorithm significantly outperforms PageRank in the (human-rated) quality of the pages returned, while remaining efficient enough to be used in today's large search engines.
    BibTeX:
    @inproceedings{Richardson2002,
      author = {Richardson, M and Domingos, P},
      title = {The intelligent surfer: Probabilistic combination of link and content information in PageRank},
      booktitle = {ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 14, VOLS 1 AND 2},
      year = {2002},
      volume = {14},
      pages = {1441-1448},
      note = {15th Annual Conference on Neural Information Processing Systems (NIPS), VANCOUVER, CANADA, DEC 03-08, 2001}
    }
    
    Riegman, P.H.J., Dinjens, W.N.M., Oomen, M.H.A., Spatz, A., Ratcliffe, C., Knoxc, K., Mager, R., Kerr, D., Pezzella, F., van Damme, B., van de Vijver, M., van Boven, H., Morents, M.M., Alonso, S., Kerjaschki, D., Pammer, J., Lopez-Guerrero, J.A., Bosch, A.L., Carbone, A., Gloghini, A., Teodorovic, I., Isabelle, M., Jamine, D., Passioukov, A., Lejeune, S., Therasse, P., van Veen, E.B., Lam, K.H. & Oosterhuis, J.W. TVBaFrost 1: Uniting local Frozen Tumour Banks into a European Network: an overview {2006} EUROPEAN JOURNAL OF CANCER
    Vol. {42}({16}), pp. {2678-2683} 
    article DOI  
    Abstract: TuBaFrost is the consortium responsible for the creation of a virtual European human frozen tumour tissue bank: a collection of high quality frozen residual, accurately classified tumour tissue samples, which are stored in European cancer centres and universities. This virtual tissue bank, searchable on the internet, has rules for access and use, and a code of conduct to comply with the various legal and ethical regulations in European countries. The easy accessibility and the European scale of the bank will result in the availability of a large number of samples even of rarer tumour types. Standardisation of collection, storage and quality control throughout the network is achieved minimising inter-institutional variability. A website providing access to upload, search and request samples is a key tool of the tissue bank. The search engine makes use of virtual microscopy. An overview of the development of the European virtual frozen tissue bank infrastructure is described in this paper. The various key aspects are described in more detail in a series of articles to appear in this journal. (c) 2006 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Riegman2006,
      author = {Riegman, P. H. J. and Dinjens, W. N. M. and Oomen, M. H. A. and Spatz, A. and Ratcliffe, C. and Knoxc, K. and Mager, R. and Kerr, D. and Pezzella, F. and van Damme, B. and van de Vijver, M. and van Boven, H. and Morents, M. M. and Alonso, S. and Kerjaschki, D. and Pammer, J. and Lopez-Guerrero, J. A. and Bosch, A. Llombart and Carbone, A. and Gloghini, A. and Teodorovic, I. and Isabelle, M. and Jamine, D. and Passioukov, A. and Lejeune, S. and Therasse, P. and van Veen, E. B. and Lam, K. H. and Oosterhuis, J. W.},
      title = {TVBaFrost 1: Uniting local Frozen Tumour Banks into a European Network: an overview},
      journal = {EUROPEAN JOURNAL OF CANCER},
      year = {2006},
      volume = {42},
      number = {16},
      pages = {2678-2683},
      doi = {{10.1016/j.ejca.2006.04.031}}
    }
    
    Rieh, S. & Xie, H. Analysis of multiple query reformulations on the web: The interactive information retrieval context {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({3}), pp. {751-768} 
    article DOI  
    Abstract: This study examines the facets and patterns of multiple Web query reformulations with a focus on reformulation sequences. Based on IR interaction models, it was presumed that query reformulation is the product of the interaction between the user and the IR system. Query reformulation also reflects the interplay between the surface and deeper levels of user interaction. Query logs were collected from a Web search engine through the selection of search sessions in which users submitted six or more unique queries per session. The final data set was composed of 313 search sessions. Three facets of query reformulation (content, format, and resource) as well as nine sub-facets were derived from the data. In addition, analysis of modification sequences identified eight distinct patterns: specified, generalized, parallel, building-block, dynamic, multitasking, recurrent, and format reformulation. Adapting Saracevic's stratified model, the authors develop a model of Web query reformulation based on the results of the study. The implications for Web search engine design are finally discussed and the functions of an interactive reformulation tool are suggested. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Rieh2006,
      author = {Rieh, SY and Xie, H},
      title = {Analysis of multiple query reformulations on the web: The interactive information retrieval context},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {3},
      pages = {751-768},
      doi = {{10.1016/j.ipm.2005.05.005}}
    }
    
    Rigoutsos, I., Riek, P., Graham, R. & Novotny, J. Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors {2003} NUCLEIC ACIDS RESEARCH
    Vol. {31}({15}), pp. {4625-4631} 
    article DOI  
    Abstract: One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular alpha-helical character (i.e. pi-helices, 3(10)-helices and kinks). A `search engine' derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above `non-canonical' helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from alpha-helicity are encoded locally in sequence patterns only about 7-9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure-function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.
    BibTeX:
    @article{Rigoutsos2003,
      author = {Rigoutsos, I and Riek, P and Graham, RM and Novotny, J},
      title = {Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2003},
      volume = {31},
      number = {15},
      pages = {4625-4631},
      doi = {{10.1093/nar/gkg639}}
    }
    
    Rinner, O., Seebacher, J., Walzthoeni, T., Mueller, L., Beck, M., Schmidt, A., Mueller, M. & Aebersold, R. Identification of cross-linked peptides from large sequence databases {2008} NATURE METHODS
    Vol. {5}({4}), pp. {315-318} 
    article DOI  
    Abstract: We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.
    BibTeX:
    @article{Rinner2008,
      author = {Rinner, Oliver and Seebacher, Jan and Walzthoeni, Thomas and Mueller, Lukas and Beck, Martin and Schmidt, Alexander and Mueller, Markus and Aebersold, Ruedi},
      title = {Identification of cross-linked peptides from large sequence databases},
      journal = {NATURE METHODS},
      year = {2008},
      volume = {5},
      number = {4},
      pages = {315-318},
      doi = {{10.1038/NMETH.1192}}
    }
    
    Risvik, K. & Michelsen, R. Search engines and Web dynamics {2002} COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING
    Vol. {39}({3}), pp. {289-302} 
    article  
    Abstract: In this paper we study several dimensions of Web dynamics in the context of large-scale Internet search engines. Both growth and update dynamics clearly represent big challenges for search engines. We show how the problems arise in all components of a reference search engine model. Furthermore, we use the FAST Search Engine architecture as a case study for showing some possible solutions for Web dynamics and search engines. The focus is to demonstrate solutions that work in practice for real systems. The service is running live at www.alltheweb.com and major portals worldwide with more than 30 million queries a day, about 700 million full-text documents, a crawl base of 1.8 billion documents, updated every I I days, at a rate of 400 documents/second. We discuss future evolution of the Web, and some important issues for search engines will be scheduling and query execution as well as increasingly heterogeneous architectures to handle the dynamic Web. (C) 2002 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Risvik2002,
      author = {Risvik, KM and Michelsen, R},
      title = {Search engines and Web dynamics},
      journal = {COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING},
      year = {2002},
      volume = {39},
      number = {3},
      pages = {289-302},
      note = {International Workshop on Web Dynamics in conjunction with the 8th International Conference on Database Theory, LONDON, ENGLAND, JAN, 2001}
    }
    
    Rocha, R., Silva, F. & Costa, V. On applying or-parallelism and tabling to logic programs {2005} THEORY AND PRACTICE OF LOGIC PROGRAMMING
    Vol. {5}({Part 1-2}), pp. {161-205} 
    article DOI  
    Abstract: Logic programming languages, such as Prolog, provide a high-level, declarative approach to programming. Logic Programming offers great potential for implicit parallelism, thus allowing parallel systems to often reduce a program's execution time without programmer intervention. We believe that for complex applications that take several hours, if not days, to return an answer, even limited speedups from parallel execution can directly translate to very significant productivity gains. It has been argued that Prolog's evaluation strategy - SLD resolution often limits the potential of the logic programming paradigm. The past years have therefore seen widening efforts at increasing Prolog's declarativeness and expressiveness. Tabling has proved to be a viable technique to efficiently overcome SLD's susceptibility to infinite loops and redundant subcomputations. Our research demonstrates that implicit or-parallelism is a natural fit for logic programs with tabling. To substantiate this belief, we have designed and implemented an or-parallel tabling engine - OPTYap - and we used a shared-memory parallel machine to evaluate its performance. To the best of our knowledge, OPTYap is the first implementation of a parallel tabling engine for logic programming systems. OPTYap builds on Yap's efficient sequential Prolog engine. Its execution model is based on the SLG-WAM for tabling, and on the environment copying for or-parallelism. Preliminary results indicate that the mechanisms proposed to parallelize search in the context of SLD resolution can indeed be effectively and naturally generalized to parallelize tabled computations, and that the resulting systems can achieve good performance on shared-memory parallel machines. More importantly, it emphasizes our belief that through applying or-parallelism and tabling to logic programs the range of applications for Logic Programming can be increased.
    BibTeX:
    @article{Rocha2005,
      author = {Rocha, R and Silva, F and Costa, VS},
      title = {On applying or-parallelism and tabling to logic programs},
      journal = {THEORY AND PRACTICE OF LOGIC PROGRAMMING},
      year = {2005},
      volume = {5},
      number = {Part 1-2},
      pages = {161-205},
      doi = {{10.1017/S1471068404002030}}
    }
    
    Rogers, S.N., Ahad, S.A. & Murphy, A.P. A structured review and theme analysis of papers published on `quality of life' in head and neck cancer: 2000-2005 {2007} ORAL ONCOLOGY
    Vol. {43}({9}), pp. {843-868} 
    article DOI  
    Abstract: Over the past 10 years, quality of life (QOL) has been increasingly recognised as an important outcome parameter in head and neck cancer. Validated questionnaires have emerged and there has been an increase in the number of papers published each year. The aim of this article is to review the literature over the past five years (2000-2005 inclusive), to identify papers reporting outcomes using patient self-competed questionnaires and group these into themes. The tabulated summary allows for the areas of health related quality of life research to be identified and to explore issues that are perhaps deficit in the literature. The three authors independently searched the literature published in the English language using the ISI search engine with cross-reference using Pub Med and Ovid. The search terms were; quality of life, questionnaire, and head and neck cancer. Studies were placed in to one of five themes. There were 165 studies identified. The numbers in each theme were predictors of QOL [Hassanein KA, Musgrove BT, Bradbury E. Functional status of patients with oral cancer and its relation to style of coping, social support and psychological status. Br J Oral Maxillofac Surg 2001;39:340-5.], functional outcome [Klug C, Neuburg J, Glaser C, Schwarz B, Kermer C, Millesi W. Quality of life 2-10 years after combined treatment for advanced oral and oropharyngeal cancer. Int J Oral Maxillofac Surg 2002;31:664-9.], questionnaire development [Hanna E, Sherman A, Cash D, Adams D, Vural E, Fan CY, et at. Quality of life for patients following total laryngectomy vs chemoradiation for laryngeal preservation. Arch Otolaryngol Head Neck Surg 2004;130:875-9.], randomised clinical trials [Kanatas AN, Rogers SN. A national survey of health-related quality of life questionnaires in head and neck oncology. Ann R Coll Surg Engl reviews [Kanatas AN, Rogers SN. A national survey of health-related quality of life questionnaires in head and neck oncology. Ann R Coll Surg Engl 2004;86:6-10.]. Although many facets of HRQOL following head and neck cancer have been explored over the last five years the paper identifies issues where research is still lacking. (c) 2007 Published by Elsevier Ltd.
    BibTeX:
    @article{Rogers2007,
      author = {Rogers, S. N. and Ahad, S. A. and Murphy, A. P.},
      title = {A structured review and theme analysis of papers published on `quality of life' in head and neck cancer: 2000-2005},
      journal = {ORAL ONCOLOGY},
      year = {2007},
      volume = {43},
      number = {9},
      pages = {843-868},
      doi = {{10.1016/j.oratoncotogy.2007.02.006}}
    }
    
    Rosenthal, E., Masdon, J., Buckman, C. & Hawn, M. Duplicate publications in the otolaryngology literature {2003} LARYNGOSCOPE
    Vol. {113}({5}), pp. {772-774} 
    article  
    Abstract: Objective/Hypothesis: A duplicate publication duplicates other published work by the same author(s). The purpose of the study was to define the extent of this problem within the otolaryngology literature. Study Design: Retrospective review of the literature. Methods: Original articles published in Archives of Otolaryngology-Head and Neck Surgery and Laryngoscope in 1999 were reviewed using the OVID search engine. Titles and abstracts from English articles written by the same first, second, or last author were analyzed, and suspected publications were evaluated. Duplicate publications were classified as dual (identical data set and conclusions) or suspected dual (nearly identical data set and conclusions) publications. Results: Of the 492 articles evaluated, 40 index articles were identified. These led to a total of 42 (8.5 duplicate articles of which 27 were classified as dual and 15 as suspected dual publications. Approximately half of the duplicate publications were published by authors in the United States (55. Duplicate articles usually appeared within 12 months of the each other (74 and failed to cross-reference the earlier publication (83. Conclusions: Journal editors have become aware of an increase in the number of duplicate publications in the medical literature. The incidence of duplicate publications in the otolaryngology literature appears to be similar to that in other specialties.
    BibTeX:
    @article{Rosenthal2003,
      author = {Rosenthal, EL and Masdon, JL and Buckman, C and Hawn, M},
      title = {Duplicate publications in the otolaryngology literature},
      journal = {LARYNGOSCOPE},
      year = {2003},
      volume = {113},
      number = {5},
      pages = {772-774},
      note = {105th Annual Meeting of the Triological-Society, BOCA RATON, FLORIDA, MAY 12-14, 2002}
    }
    
    Ross, N. & Wolfram, D. End user searching on the Internet: An analysis of term pair topics submitted to the Excite search engine {2000} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE
    Vol. {51}({10}), pp. {949-958} 
    article  
    Abstract: Queries submitted to the Excite search engine were analyzed for subject content based on the cooccurrence of terms within multiterm queries. More than 1000 of the most frequently cooccurring term pairs were categorized into one or more of 30 developed subject areas. Subject area frequencies and their cooccurrences with one another were tallied and analyzed using hierarchical cluster analysis and multidimensional scaling. The cluster analyses revealed several anticipated and a few unanticipated groupings of subjects, resulting in several well-defined high-level clusters of broad subject areas. Multidimensional scaling of subject cooccurrences revealed similar relationships among the different subject categories. Applications that arise from a better understanding of the topics users search and their relationships are discussed.
    BibTeX:
    @article{Ross2000,
      author = {Ross, NCM and Wolfram, D},
      title = {End user searching on the Internet: An analysis of term pair topics submitted to the Excite search engine},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE},
      year = {2000},
      volume = {51},
      number = {10},
      pages = {949-958}
    }
    
    Roussinov, D. & Chen, H. Information navigation on the web by clustering and summarizing query results {2001} INFORMATION PROCESSING & MANAGEMENT
    Vol. {37}({6}), pp. {789-816} 
    article  
    Abstract: We report our experience with a novel approach to interactive information seeking that is grounded in the idea of summarizing query results through automated document clustering. We went through a complete system development and evaluation cycle: designing the algorithms and interface for our prototype, implementing them and testing with human users. Our prototype acted as an intermediate layer between the user and a commercial Internet search engine (AltaVista), thus allowing searches of the significant portion of World Wide Web. In our final evaluation, we processed data from 36 users and concluded that our prototype improved search performance over using the same search engine (AltaVista) directly. We also analyzed effects of various related demographic and task related parameters. (C) 2001 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Roussinov2001,
      author = {Roussinov, DG and Chen, HC},
      title = {Information navigation on the web by clustering and summarizing query results},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2001},
      volume = {37},
      number = {6},
      pages = {789-816}
    }
    
    ROY, I. & EVERSMAN, W. IMPROVED FINITE-ELEMENT MODELING OF THE TURBOFAN ENGINE INLET RADIATION PROBLEM {1995} JOURNAL OF VIBRATION AND ACOUSTICS-TRANSACTIONS OF THE ASME
    Vol. {117}({1}), pp. {109-115} 
    article  
    Abstract: Improvements have been made in the finite element model of the acoustic radiated field from a turbofan engine inlet in the presence of a mean flow. The problem of acoustic radiation from a turbofan engine inlet is difficult to model numerically because of the large domain and high frequencies involved. A numerical model with conventional finite elements in the nearfield and wave envelope elements in the far field has been constructed. By employing an irrotational mean flow assumption, both the mean flow and the acoustic perturbation problem have been posed in an axisymmetric formulation in terms of the velocity potential, thereby minimizing computer storage and time requirements. The finite element mesh has been altered in search of an improved solution. The mean flow problem has been reformulated with new boundary conditions to make it theoretically rigorous. The sound source at the fan face has been modeled as a combination of positive and negative propagating duct eigenfunctions. Therefore, a finite element duct eigenvalue problem has been solved on the fan face and the resulting modal matrix has been used to implement a source boundary condition on the fan face in the acoustic radiation problem. In the post processing of the solution, the acoustic pressure has been evaluated at Gauss points inside the elements and the nodal pressure values have been interpolated from them. This has significantly improved the results. The effect of the geometric position of the transition circle between conventional finite elements and wave envelope elements has been studied and it has been found that the transition can be made nearer to the inlet than previously assumed.
    BibTeX:
    @article{ROY1995,
      author = {ROY, ID and EVERSMAN, W},
      title = {IMPROVED FINITE-ELEMENT MODELING OF THE TURBOFAN ENGINE INLET RADIATION PROBLEM},
      journal = {JOURNAL OF VIBRATION AND ACOUSTICS-TRANSACTIONS OF THE ASME},
      year = {1995},
      volume = {117},
      number = {1},
      pages = {109-115}
    }
    
    Sacchetti, P., Zvara, P. & Plante, M. The Internet and patient education - Resources and their reliability: Focus on a select urologic topic {1999} UROLOGY
    Vol. {53}({6}), pp. {1117-1120} 
    article  
    Abstract: Objectives. The information revolution triggered by the rapid growth of the Internet has allowed healthcare providers and patients to access a rapidly expanding volume of information. To address the quality of this information, a survey of the data on a single urology-related topic available on the Internet was performed. Methods. The search on the World Wide Web (Web) was performed using the search engine HotBot and search directory Yahoo. The Web pages were assessed according to their relevancy to the topic chosen. Relevance rates were derived from the number of relevant sites divided by the total number of sites found. Relevant sites were subsequently ranked for quality on the basis of their accuracy, comprehensiveness, and objectivity. HotBot was then subsequently divided by domain, with each assessed separately. Yahoo was analyzed in its entirety. The resources were then compared for relevance and quality of information. Results. When using the keyword ``Viagra,'' HotBot responded with 15,109 hits. Yahoo presented 51 hits under the category, ``Health: Pharmacy: Drugs and Medications: Specific Drugs and Medications: Viagra (Sildenafil).'' The relevance rate for the first 50 hits in the search engine HotBot was 0.08. The relevance rates for the edu and org domains found by HotBot were 0.22 and 0.24, respectively; those for com and net were both 0.10. The relevance rate for the search directory Yahoo was 0.20. For relevant sites, the quality of the information presented was significantly higher in the Yahoo and in the HotBot domains hosted by nonprofit organizations when compared with HotBot in general and with its commercially oriented domains. HotBot overall was found to contain seven excellent sites, of which only three were found within Yahoo. Conclusions. Although the medical information available on the Web has proliferated at a remarkable rate, the number of Web sites providing complete, nonbiased information continues to represent only a small portion of the total. We have shown that the search directory Yahoo reduced the number of irrelevant sites significantly, but at the same time, some very valuable information available in HotBot was missing. At present, it may be useful to conduct searches within Yahoo followed by a review of both the edu and org HotBot domains. UROLOGY 53: 1117-1120, 1999. (C) 1999, Elsevier Science Inc. All rights reserved.
    BibTeX:
    @article{Sacchetti1999,
      author = {Sacchetti, P and Zvara, P and Plante, MK},
      title = {The Internet and patient education - Resources and their reliability: Focus on a select urologic topic},
      journal = {UROLOGY},
      year = {1999},
      volume = {53},
      number = {6},
      pages = {1117-1120}
    }
    
    Saha, S.K., Das, A.K. & Chanda, B. Image retrieval based on indexing and relevance feedback {2007} PATTERN RECOGNITION LETTERS
    Vol. {28}({3}), pp. {357-366} 
    article DOI  
    Abstract: In content based image retrieval (CBIR) system, search engine retrieves the images similar to the query image according to a similarity measure. It should be fast enough and must have a high precision of retrieval. Indexing scheme is used to achieve a fast response and relevance feedback helps in improving the retrieval precision. In this paper, a human perception based similarity measure is presented and based on it a simple yet novel indexing scheme with relevance feedback is discussed. The indexing scheme is designed based on the primary and secondary keys which are selected by analysing the entropy of features. A relevance feedback method is proposed based on Mann-Whitney test. The test is used to identify the discriminating features from the relevant and irrelevant images in a retrieved set. Then emphasis of the discriminating features are updated to improve the retrieval performance. The relevance feedback scheme is implemented for two different similarity measure (Euclidean distance based and human perception based). The experiment justifies the effectiveness of the proposed methodologies. Finally, the indexing scheme and relevance feedback mechanism are combined to build up the search engine. (c) 2006 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Saha2007,
      author = {Saha, Sanjoy K. and Das, Amit K. and Chanda, Bhabatosh},
      title = {Image retrieval based on indexing and relevance feedback},
      journal = {PATTERN RECOGNITION LETTERS},
      year = {2007},
      volume = {28},
      number = {3},
      pages = {357-366},
      note = {4th Indian Conference on Computer Vision, Graphics and Image Processing, Kolkata, INDIA, DEC, 2004},
      doi = {{10.1016/j.patrec.2006.04.005}}
    }
    
    Sangireddy, R. & Somani, A. High-speed IP routing with binary decision diagrams based hardware address lookup engine {2003} IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS
    Vol. {21}({4}), pp. {513-521} 
    article DOI  
    Abstract: With a rapid increase in the data transmission link rates and an immense continuous growth in the Internet traffic, the demand for routers that perform Internet protocol packet forwarding at high speed and throughput is ever increasing. The key issue in the router performance is the IP address lookup mechanism based on the longest prefix matching scheme. Earlier work on fast Internet Protocol Version 4 (IPv4) routing table lookup includes, software mechanisms based on tree traversal or binary search methods, and hardware schemes based on content addressable memory (CAM), memory lookups and the CPU caching. These schemes depend on the memory access technology which limits their performance. The paper presents a binary decision diagrams (BDDs) based optimized combinational logic for an efficient implementation of fast address lookup scheme in reconfigurable hardware. The results show that the BDD hardware engine gives a throughput of up to 175.7 million lookups per second (Ml/s) for a large AADS routing table with 33 796 prefixes, a throughput of up to 168.6 Ml/s for an MAE-West routing table With 29 487 prefixes, and a throughput of up to 229.3 Ml/s for the Pacbell routing table with 6822 prefixes. Besides the performance of the scheme, routing table update and the scalability to Internet Protocol Version 6 (IPv6) issues are discussed.(1).
    BibTeX:
    @article{Sangireddy2003,
      author = {Sangireddy, R and Somani, AK},
      title = {High-speed IP routing with binary decision diagrams based hardware address lookup engine},
      journal = {IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS},
      year = {2003},
      volume = {21},
      number = {4},
      pages = {513-521},
      doi = {{10.1109/JSAC.2003.810516}}
    }
    
    Saponara, S., Casula, M., Rovati, F., Alfonso, D. & Fanucci, L. Dynamic control of motion estimation search parameters for low complex H.264 video coding {2006} IEEE TRANSACTIONS ON CONSUMER ELECTRONICS
    Vol. {52}({1}), pp. {232-239} 
    article  
    Abstract: This paper presents a novel technique to reduce the motion estimation (ME) complexity in H.264/AVC video coding. A low complexity context-aware controller is added to a basic search engine; at coding time the controller extracts from the search engine partial results information on the input signal statistics, using them to dynamically configure the ME search parameters, such as number of reference frames, valid block modes and search area. Unnecessary computations and memory accesses can be avoided, decreasing ME complexity while keeping unaltered coding efficieney for a wide range of applications: bit-rates from tens of kbits/s to tens of Mbits/s and video formats from QCIF to CCIR. The context-aware control can be used with any ME search engine and in the paper is successfully applied to Full Search and fast ME, as EPZS and UMHS, in the JM10 software model of H264/AVC.(1)
    BibTeX:
    @article{Saponara2006,
      author = {Saponara, S and Casula, M and Rovati, F and Alfonso, D and Fanucci, L},
      title = {Dynamic control of motion estimation search parameters for low complex H.264 video coding},
      journal = {IEEE TRANSACTIONS ON CONSUMER ELECTRONICS},
      year = {2006},
      volume = {52},
      number = {1},
      pages = {232-239}
    }
    
    Saravanan, C., Shao, Y., Baer, R., Ross, P. & Head-Gordon, M. Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks {2003} JOURNAL OF COMPUTATIONAL CHEMISTRY
    Vol. {24}({5}), pp. {618-622} 
    article DOI  
    Abstract: A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package. (C) 2003 Wiley Periodicals, Inc.
    BibTeX:
    @article{Saravanan2003,
      author = {Saravanan, C and Shao, Y and Baer, R and Ross, PN and Head-Gordon, M},
      title = {Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks},
      journal = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
      year = {2003},
      volume = {24},
      number = {5},
      pages = {618-622},
      doi = {{10.1002/jcc.10224}}
    }
    
    Savage, S., Burrows, M., Nelson, G., Sobalvarro, P. & Anderson, T. Eraser: A dynamic data race detector for multithreaded programs {1997} ACM TRANSACTIONS ON COMPUTER SYSTEMS
    Vol. {15}({4}), pp. {391-411} 
    article  
    Abstract: Multithreaded programming is difficult and error prone. It is easy to make a mistake in synchronization that produces a data race, yet it can be extremely hard to locate this mistake during debugging. This article describes a new tool, called Eraser, for dynamically detecting data races in lock-based multithreaded programs. Eraser uses binary rewriting techniques to monitor every shared-memory reference and verify that consistent locking behavior is observed. We present several case studies, including undergraduate coursework and a multithreaded Web search engine, that demonstrate the effectiveness of this approach.
    BibTeX:
    @article{Savage1997,
      author = {Savage, S and Burrows, M and Nelson, G and Sobalvarro, P and Anderson, T},
      title = {Eraser: A dynamic data race detector for multithreaded programs},
      journal = {ACM TRANSACTIONS ON COMPUTER SYSTEMS},
      year = {1997},
      volume = {15},
      number = {4},
      pages = {391-411},
      note = {16th ACM Symposium on Operating System Principles (SOSP), ST MALO, FRANCE, OCT, 1997}
    }
    
    Schein, M. & Paladugu, R. Redundant surgical publications: Tip of the iceberg? {2001} SURGERY
    Vol. {129}({6}), pp. {655-661} 
    article DOI  
    Abstract: Background. A redundant publication is one which duplicates previous simultaneous, or future publication by the same author or group or, alternatively, could have been combine with the latter into one paper. As there is no information about the extent of this problem in the surgical literature, we set out to assess the incidence, spectrum, and salient characteristics of redundant publications in 3 leading surgical journals. Methods. Original articles (excluding reviews, editorials, abstracts, and letters) published during 1998 in the journals of Surgery, The British Journal of Surgery and Archives of Surgery were searched by using the on-line search engine PUBMED. Each original article was scrutinized to identify redundancy by combining the names of the first, second, and last authors with a few key words from the title. Papers were defined as ``suspected'' redundant publications if they were found to address the same topic as the ``index'' article and shared some or most of the elements of methodology, results, or conclusions. The full versions of all suspected papers were retrieved and compared with the index articles. A grading system was developed to define several types of redundant publications: A. ``dual'' B. ``potentially dual''; C. ``Salami-slicing. `` Results. A total of 660 articles were screened. There were 92 index articles (14 leading to 147 suspected papers found in other journals, representing some potential form of a redundant publication. The vast majority of suspected papers were published within approximately a year of the index paper and were not cited by the latter. Most (69 of the suspected papers were also published in surgical journals. Only 12 (8.1 appeared in, or originated from, a ``local-foreign'' journal. Twenty (13.6 of the suspected papers met the criteria for dual publications, 50 (34 for potentially dual publications, and 77 (52.4 were considering products of salami-slicing. Conclusions. Almost 1 in every 6 original articles published in leading surgical journals represents some form of redundancy. Current on-line search technology provides an effective tool for identifying and tracing such publications, but it is not used routinely as part of the peer review process. Redundancies occur in sever well-defined patterns; the phenomenon is widespread, and it cuts across the entire spectrum of surgeons in the United States and abroad. Redundant publication must be recognized not as a mere nuisance but a real threat to the quality and intellectual impact of surgical publishing.
    BibTeX:
    @article{Schein2001,
      author = {Schein, M and Paladugu, R},
      title = {Redundant surgical publications: Tip of the iceberg?},
      journal = {SURGERY},
      year = {2001},
      volume = {129},
      number = {6},
      pages = {655-661},
      doi = {{10.1067/msy.2001.114549}}
    }
    
    Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G. & Schomburg, D. BRENDA, the enzyme database: updates and major new developments {2004} NUCLEIC ACIDS RESEARCH
    Vol. {32}({Sp. Iss. SI}), pp. {D431-D433} 
    article DOI  
    Abstract: BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83 000 different enzymes from 9800 different organisms, classified in similar to 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from similar to 46 000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.
    BibTeX:
    @article{Schomburg2004,
      author = {Schomburg, I and Chang, A and Ebeling, C and Gremse, M and Heldt, C and Huhn, G and Schomburg, D},
      title = {BRENDA, the enzyme database: updates and major new developments},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2004},
      volume = {32},
      number = {Sp. Iss. SI},
      pages = {D431-D433},
      doi = {{10.1093/nar/gkh081}}
    }
    
    Schulz, S. E - a brainiac theorem prover {2002} AI COMMUNICATIONS
    Vol. {15}({2-3}), pp. {111-126} 
    article  
    Abstract: We describe the superposition-based theorem prover E. E is a sound and complete prover for clausal first order logic with equality. Important properties of the prover include strong redundancy elimination criteria, the DISCOUNT loop proof procedure, a very flexible interface for specifying search control heuristics, and an efficient inference engine. We also discuss strength and weaknesses of the system.
    BibTeX:
    @article{Schulz2002,
      author = {Schulz, S},
      title = {E - a brainiac theorem prover},
      journal = {AI COMMUNICATIONS},
      year = {2002},
      volume = {15},
      number = {2-3},
      pages = {111-126}
    }
    
    Schutte, B., Mitros, J., Bartlettt, J., Walters, J., Jia, H., Welsh, M., Casavant, T. & McCray, P. Discovery of five conserved beta-defensin gene clusters using a computational search strategy {2002} PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
    Vol. {99}({4}), pp. {2129-2133} 
    article DOI  
    Abstract: The innate immune system includes antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. beta-Defensins comprise one important family of mammalian antimicrobial peptides. The annotation of the human genome fails to reveal the expected diversity, and a recent query of the draft sequence with the BLAST search engine found only one new beta-defensin gene (DEF83). To define better the G-defensin gene family, we adopted a genomics approach that uses HMMER, a computational search tool based on hidden Markov models, in combination With BLAST. This strategy identified 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting each cluster pair arose from a common ancestor and was retained because of conserved functions. Preliminary analysis indicates that at least 26 of the predicted genes are transcribed. These results demonstrate the value of a genomewide search strategy to identify genes with conserved structural motifs. Discovery of these genes represents a new starting point for exploring the role of beta-defensins in innate immunity.
    BibTeX:
    @article{Schutte2002,
      author = {Schutte, BC and Mitros, JP and Bartlettt, JA and Walters, JD and Jia, HP and Welsh, MJ and Casavant, TL and McCray, PB},
      title = {Discovery of five conserved beta-defensin gene clusters using a computational search strategy},
      journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
      year = {2002},
      volume = {99},
      number = {4},
      pages = {2129-2133},
      doi = {{10.1073/pnas.042692699}}
    }
    
    Schwartz, C. Web search engines {1998} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE
    Vol. {49}({11}), pp. {973-982} 
    article  
    Abstract: This review looks briefly at the history of World Wide Web search engine development, considers the current state of affairs, and reflects on the future. Networked discovery tools have evolved along with Internet resource availability. World Wide Web search engines display some complexity in their variety, content, resource acquisition strategies, and in the array of tools they deploy to assist users. A small but growing body of evaluation literature, much of it not systematic in nature, indicates that performance effectiveness is difficult to assess in this setting. Significant improvements in general-content search engine retrieval and ranking performance may not be possible, and are probably not worth the effort, although search engine providers have introduced some rudimentary attempts at personalization, summarization, and query expansion. The shift to distributed search across multitype database systems could extend general networked discovery and retrieval to include smaller resource collections with rich metadata and navigation tools.
    BibTeX:
    @article{Schwartz1998,
      author = {Schwartz, C},
      title = {Web search engines},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE},
      year = {1998},
      volume = {49},
      number = {11},
      pages = {973-982}
    }
    
    Schweiger, R., Hoelzer, S., Rudolf, D., Rieger, J. & Dudeck, J. Linking clinical data using XML topic maps {2003} ARTIFICIAL INTELLIGENCE IN MEDICINE
    Vol. {28}({1}), pp. {105-115} 
    article DOI  
    Abstract: Most clinical data is narrative text and often not accessible and searchable at the clinical workstation. We have therefore developed a search engine that allows indexing, searching and linking different kinds of data using web technologies. Text matching methods fail to represent implicit relationships between data, e.g. the relationship between HIV and AIDS. The international organization for standardization (ISO) topic maps standard provides a data model that allows representing arbitrary relationships between resources. Such relationships form the basis for a context sensitive search and accurate search results. The extensible markup language (XML) standards are used for the interchange of data relationships. The approach has been applied to medical classification systems and clinical practice guidelines. The search engine is compared to other XML retrieval methods and the prospect of a ``semantic web'' is discussed. (C) 2003 Elsevier Science B.V. All rights reserved.
    BibTeX:
    @article{Schweiger2003,
      author = {Schweiger, R and Hoelzer, S and Rudolf, D and Rieger, J and Dudeck, J},
      title = {Linking clinical data using XML topic maps},
      journal = {ARTIFICIAL INTELLIGENCE IN MEDICINE},
      year = {2003},
      volume = {28},
      number = {1},
      pages = {105-115},
      doi = {{10.1016/S0933-3657(03)00038-1}}
    }
    
    Seagrave, J., McDonald, J.D., Bedrick, E., Edgerton, E.S., Gigliotti, A.P., Jansen, J.J., Ke, L., Naeher, L.P., Seilkop, S.K., Zheng, M. & Mauderly, J.L. Lung toxicity of ambient particulate matter from southeastern US sites with different contributing sources: Relationships between composition and effects {2006} ENVIRONMENTAL HEALTH PERSPECTIVES
    Vol. {114}({9}), pp. {1387-1393} 
    article DOI  
    Abstract: BACKGROUND: Exposure to air pollution and, more specifically, particulate matter (PM) is associated with adverse health effects. However, the specific PM characteristics responsible for biological effects have not been defined. OBJECTIVES: In this project we examined the composition, sources, and relative toxicity of samples of PM with aerodynamic diameter <= 2.5 mu m (PM2.5) collected from sites within the Southeastern Aerosol Research and Characterization (SEARCH) air monitoring network during two seasons. These sites represent four areas with differing sources of PM2.5, including local urban versus regional sources, urban areas with different contributions of transportation and industrial sources, and a site influenced by Gulf of Mexico weather patterns. METHODS: We collected samples from each site during the winter and summer of 2004 for toxicity testing and for chemical analysis and chemical mass balance-based source apportionment. We also collected PM2.5 downwind of a series of prescribed forest bums. We assessed the toxicity of the samples by instillation into rat lungs and assessed general toxicity, acute cytotoxicity, and inflammation. Statistical dose-response modeling techniques were used to rank the relative toxicity and compare the seasonal differences at each site. Projection-to-latent-surfaces (PLS) techniques examined the relationships among sources, chemical composition, and toxicologic end points. RESULTS AND CONCLUSIONS: Urban sites with high contributions from vehicles and industry were most toxic.
    BibTeX:
    @article{Seagrave2006,
      author = {Seagrave, JeanClare and McDonald, Jacob D. and Bedrick, Edward and Edgerton, Eric S. and Gigliotti, Andrew P. and Jansen, John J. and Ke, Lin and Naeher, Luke P. and Seilkop, Steven K. and Zheng, Mei and Mauderly, Joe L.},
      title = {Lung toxicity of ambient particulate matter from southeastern US sites with different contributing sources: Relationships between composition and effects},
      journal = {ENVIRONMENTAL HEALTH PERSPECTIVES},
      year = {2006},
      volume = {114},
      number = {9},
      pages = {1387-1393},
      doi = {{10.1289/ehp.9234}}
    }
    
    Searle, B.C., Turner, M. & Nesvizhskii, A.I. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies {2008} JOURNAL OF PROTEOME RESEARCH
    Vol. {7}({1}), pp. {245-253} 
    article DOI  
    Abstract: Database-searching programs generally identify only a fraction of the spectra acquired in a standard LC/MS/MS study of digested proteins. Subtle variations in database-searching algorithms for assigning peptides to MS/MS spectra have been known to provide different identification results. To leverage this variation, a probabilistic framework is developed for combining the results of multiple search engines. The scores for each search engine are first independently converted into peptide probabilities. These probabilities can then be readily combined across search engines using Bayesian rules and the expectation maximization learning algorithm. A significant gain in the number of peptides identified with high confidence with each additional search engine is demonstrated using several data sets of increasing complexity, from a control protein mixture to a human plasma sample, searched using SEQUEST, Mascot, and X! Tandem database-searching programs. The increased rate of peptide assignments also translates into a substantially larger number of protein identifications in LC/MS/MS studies compared to a typical analysis using a single database-search tool.
    BibTeX:
    @article{Searle2008,
      author = {Searle, Brian C. and Turner, Mark and Nesvizhskii, Alexey I.},
      title = {Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies},
      journal = {JOURNAL OF PROTEOME RESEARCH},
      year = {2008},
      volume = {7},
      number = {1},
      pages = {245-253},
      doi = {{10.1021/pr070540w}}
    }
    
    Sen, R. Optimal search engine marketing strategy {2005} INTERNATIONAL JOURNAL OF ELECTRONIC COMMERCE
    Vol. {10}({1}), pp. {9-25} 
    article  
    Abstract: Buyers using search engines to look for information tend to trust and follow links displayed in the editorial section of the search-results page. Most on-line sellers, however, do not invest in search engine optimization (SEO) to get higher search-results rankings for their listings, but instead prefer paid placements. They explain that SEO is more expensive than paid placements, produces results that do not justify its cost, and does not consistently lead to high search-results rankings. This implies that sellers would invest in SEO if it were less expensive and its rankings were more consistent. However, even if SEO and paid placement cost the same, and SEO always produced high rankings, paid placement would still be the search engine marketing (SEM) strategy of choice for most on-line sellers. Interestingly, no optimal SEM strategy includes SEO. These findings are especially significant for advertising professionals who have to justify investing in paid placements despite overwhelming evidence that buyers ignore them and follow links in the editorial section of the search-results page.
    BibTeX:
    @article{Sen2005,
      author = {Sen, R},
      title = {Optimal search engine marketing strategy},
      journal = {INTERNATIONAL JOURNAL OF ELECTRONIC COMMERCE},
      year = {2005},
      volume = {10},
      number = {1},
      pages = {9-25}
    }
    
    Seow, D. & Gauthier, S. Pharmacotherapy of Alzheimer disease {2007} CANADIAN JOURNAL OF PSYCHIATRY-REVUE CANADIENNE DE PSYCHIATRIE
    Vol. {52}({10}), pp. {620-629} 
    article  
    Abstract: Objective: To systematically review published clinical trials of the pharmacotherapy of Alzheimer disease (AD). Method: We searched MEDLINE for published English-language medical literature, using Alzheimer disease and treatment as key words. No other search engine was used. Our review focused on randomized clinical trials (RCTs) and corresponding metaanalyses. Results: Although there are many RCTs for the treatment of mild cognitive impairment (MCI), none have been successful in their primary analysis. The cholinesterase inhibitors donepezil, rivastigmine, and galantamine have demonstrated efficacy in 3- to 12-month placebo-controlled RCTs assessing cognitive, functional, behavioural, and global outcomes in patients with mildly to moderately severe AD. Recent data from patients with severe stages of AD demonstrate the efficacy of donepezil on cognitive and functional measures but not on behaviour. The N-methyl-D-aspartate receptor antagonist memantine has been demonstrated to be effective in 6-month, placebo-controlled RCTs of 6 months duration assessing cognitive, functional, and global outcomes of inpatients with moderate-to-severe AD (defined as a Mini Mental State Examination score below 20). Post hoc analyses have demonstrated a benefit in regard to agitation and (or) aggression, but this needs to be confirmed in a prospective RCT across Canada. Disease-modifying treatments are being tested in mild stages of AD in 18-month RCTs with cognitive and global outcomes as primary efficacy outcomes, primarily with drugs reducing amyloid synthesis or aggregation. Successful treatment in mild stages of AD could lead to RCTs in MCI and, possibly, in genetically high-risk asymptomatic individuals. Conclusion: The significant advances in the symptomatic pharmacotherapy of AD may be followed by disease-modification treatments.
    BibTeX:
    @article{Seow2007,
      author = {Seow, Dennis and Gauthier, Serge},
      title = {Pharmacotherapy of Alzheimer disease},
      journal = {CANADIAN JOURNAL OF PSYCHIATRY-REVUE CANADIENNE DE PSYCHIATRIE},
      year = {2007},
      volume = {52},
      number = {10},
      pages = {620-629}
    }
    
    Sevaux, M. & Dauzere-Peres, S. Genetic algorithms to minimize the weighted number of late jobs on a single machine {2003} EUROPEAN JOURNAL OF OPERATIONAL RESEARCH
    Vol. {151}({2}), pp. {296-306} 
    article DOI  
    Abstract: The general one-machine scheduling problem is strongly NP-Hard when the objective is to minimize the weighted number of late jobs. Few methods exist to solve this problem. In an other paper, we developed a Lagrangean relaxation algorithm which gives good results on many instances. However, there is still room for improvement, and a meta-heuristic might lead to better results. In this paper, we decided to use a genetic algorithm (GA). Although a GA is somewhat easy to implement, many variations exist, and we tested some of them to design the best GA for our problem. Three different engines to evaluate the fitness of a chromosome are considered, together with four types of crossover operators and three types of mutation operators. An improved GA is also proposed by applying local search on solutions determined from the chromosome by the engine. Numerical experiments on different tests of instances are reported. They show that starting from an initial population already containing a good solution is very effective. (C) 2003 Elsevier B.V. All rights reserved.
    BibTeX:
    @article{Sevaux2003,
      author = {Sevaux, M and Dauzere-Peres, S},
      title = {Genetic algorithms to minimize the weighted number of late jobs on a single machine},
      journal = {EUROPEAN JOURNAL OF OPERATIONAL RESEARCH},
      year = {2003},
      volume = {151},
      number = {2},
      pages = {296-306},
      note = {18th EURO Summer-Winter-Institute on Meta-Heuristics in Combinatorial Optimization (ESWI XVIII), SWITZERLAND, 2000},
      doi = {{10.1016/S0377-2217(02)00827-5}}
    }
    
    Shafer, R., Jung, D. & Betts, B. Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries {2000} NATURE MEDICINE
    Vol. {6}({11}), pp. {1290-1292} 
    article  
    BibTeX:
    @article{Shafer2000,
      author = {Shafer, RW and Jung, DR and Betts, BJ},
      title = {Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries},
      journal = {NATURE MEDICINE},
      year = {2000},
      volume = {6},
      number = {11},
      pages = {1290-1292}
    }
    
    Shen, C., Yu, J., Lo, Y., Kuo, C., Yue, C., Jou, Y., Huang, C., Lung, J. & Wu, C. Genome-wide search for loss of heterozygosity using laser capture microdissected tissue of breast carcinoma: An implication for mutator phenotype and breast cancer pathogenesis {2000} CANCER RESEARCH
    Vol. {60}({14}), pp. {3884-3892} 
    article  
    Abstract: Breast cancer is considered to display a high degree of intratumor heterogeneity, without any obvious morphological and pathological steps to define sequential evolution, and its progression may vary among individual tumors. In an attempt to elucidate these etiological and phenotypic complexities, the present study, based on the fundamental concept that genomic instability is the engine of both tumor progression and tumor heterogeneity, was conducted to test the hypothesis that breast cancer pathogenesis is driven by double-strand break (DSB)-initiated chromosome instability (CIN). The rationale underlying this hypothesis is derived from the clues provided by family breast cancer syndromes, in which susceptibility genes, including p53, ATM, BRCA1 and BRCA2, are involved within the common functional pathway of DSB-related checkpoint/repair. Because genomic deletion caused by DSB is reflected in the genetic mechanism of loss of heterozygosity (LOH), this genome-wide LOH study was conducted, using 100 tumors and 400 microsatellite markers. To minimize the effect of heterogeneity within tumors, the experimental technique of laser capture microdissection was used to ensure that genetic and phenotypic examinations were based on the same tumor cells. Support for our hypothesis comes from the observations that: (a) the extent of DSB-initiated CIN in tumors significantly increased as tumors progressed to poorer grades or later stages; (b) in the sequential steps toward CIN, the loci of p53 and ATM, the key checkpoint genes against DSB, were lost at the earliest stage; and (c) many loci identified to be important in breast tumorigenesis were the genomic sites possibly harboring the genes involved in DSB-related checkpoint/repair (including RAD51, RAD52, and BRCA1) or CIN (including FA-A, FA-D, and WRN), and a higher number of these loci showing LOH was significantly associated with increased level of DSB-initiated CIN (P < 0.0001). Breast cancers are thus considered to be sequentially progressive with CIN. However, CIN might also cause genetic heterogeneity, which was revealed by the findings that LOH at some markers was observed only in the component of ductal carcinoma ill situ but not in the invasive component of the same tumors. In addition, some markers were found to preferentially lose at specific tumor grades, implying their contribution to genetic heterogeneity during tumor development, Therefore, this study suggests that breast cancer progression is clonal with regard to CIN, but different breast cancers would present distinct molecular profiles resulting from genetic heterogeneity caused by CIN.
    BibTeX:
    @article{Shen2000,
      author = {Shen, CY and Yu, JC and Lo, YL and Kuo, CH and Yue, CT and Jou, YS and Huang, CS and Lung, JC and Wu, CW},
      title = {Genome-wide search for loss of heterozygosity using laser capture microdissected tissue of breast carcinoma: An implication for mutator phenotype and breast cancer pathogenesis},
      journal = {CANCER RESEARCH},
      year = {2000},
      volume = {60},
      number = {14},
      pages = {3884-3892}
    }
    
    Shenton, A. & Dixon, P. A comparison of youngsters' use of CD-ROM and the Internet as information resources {2003} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {54}({11}), pp. {1029-1049} 
    article DOI  
    Abstract: Little research has compared youngsters' use of CDROM and the Internet for information-seeking purposes. Nevertheless, the area has recently been addressed within a largely qualitative project more generally devoted to young people's information universes. Home access to the Internet was seen to be more limited than that to CD-ROM, although the former was consulted to tackle needs of a greater number of types. The strategies employed to exploit each form of information resource were essentially similar. No attempts were reported to check the credibility of any information retrieved from electronic sources. The Internet was, however, used more frequently beyond the informants' own homes than was CD-ROM. There was also greater employment of the Internet by adults acting on the youngsters' behalf. As Internet use for school purposes rose in accordance with age, that of CD-ROM declined. When youngsters themselves compared the two resources as information-seeking tools, CD-ROM software was criticized for its lack of detailed material and the Internet for the problems in locating what was desired. Project findings have implications in a range of areas, including the marketing of CD-ROM packages, research and development and practices within schools.
    BibTeX:
    @article{Shenton2003,
      author = {Shenton, AK and Dixon, P},
      title = {A comparison of youngsters' use of CD-ROM and the Internet as information resources},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2003},
      volume = {54},
      number = {11},
      pages = {1029-1049},
      doi = {{10.1002/asi.10299}}
    }
    
    Sheridan, S., Pignone, M. & Mulrow, C. Framingham-based tools to calculate the global risk of coronary heart disease - A systematic review of tools for clinicians {2003} JOURNAL OF GENERAL INTERNAL MEDICINE
    Vol. {18}({12}), pp. {1039-1052} 
    article  
    Abstract: PURPOSE: To examine the features of available Framingham-based risk calculation tools and review their accuracy and feasibility in clinical practice. DATA SOURCES: MEDLINE, 1966-April 2003, and the GOOGLE search engine on the Internet. TOOL AND STUDY SELECTION: We included risk calculation tools that used the Framingham risk equations to generate a global coronary heart disease (CHD) risk. To determine tool accuracy, we reviewed all articles that compared the performance of various Framingham-based risk tools to that of the continuous Framingham risk equations. To determine the feasibility of tool use in clinical practice, we reviewed articles on the availability of the risk factor information required for risk calculation, subjective preference for 1 risk calculator over another, or subjective ease of use. DATA EXTRACTION: Two reviewers independently reviewed the results of the literature search, all websites, and abstracted all articles for relevant information. DATA SYNTHESIS: Multiple CHD risk calculation tools are available, including risk charts and computerized calculators for personal digital assistants, personal computers, and web-based use. Most are easy to use and available without cost. They require information on age, smoking status, blood pressure, total and HDL cholesterol, and the presence or absence of diabetes. Compared to the full Framingham equations, accuracy for identifying patients at increased risk was generally quite high. Data on the feasibility of tool use was limited. CONCLUSIONS: Several easy-to-use tools are available for estimating patients' CHD risk. Use of such tools could facilitate better decision making about interventions for primary prevention of CHD, but further research about their actual effect on clinical practice and patient outcomes is required. DISCLOSURE: Drs. Sheridan and Pignone have participated in the development of Heart-to-Heart, one of the risk tools evaluated within. They have also received speaking and consulting fees from Bayer, Inc. Bayer, Inc. has licensed the Heart-to-Heart tool.
    BibTeX:
    @article{Sheridan2003,
      author = {Sheridan, S and Pignone, M and Mulrow, C},
      title = {Framingham-based tools to calculate the global risk of coronary heart disease - A systematic review of tools for clinicians},
      journal = {JOURNAL OF GENERAL INTERNAL MEDICINE},
      year = {2003},
      volume = {18},
      number = {12},
      pages = {1039-1052}
    }
    
    Shibuya, T. & Rigoutsos, I. Dictionary-driven prokaryotic gene finding {2002} NUCLEIC ACIDS RESEARCH
    Vol. {30}({12}), pp. {2710-2725} 
    article  
    Abstract: Gene Identification, also known as gene finding or gene recognition, Is among the important problems of molecular biology that have been receiving Increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene Identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified In a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes Is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm's implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method's generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed In detail.
    BibTeX:
    @article{Shibuya2002,
      author = {Shibuya, T and Rigoutsos, I},
      title = {Dictionary-driven prokaryotic gene finding},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2002},
      volume = {30},
      number = {12},
      pages = {2710-2725}
    }
    
    Shilov, I.V., Seymour, S.L., Patel, A.A., Loboda, A., Tang, W.H., Keating, S.P., Hunter, C.L., Nuwaysir, L.M. & Schaeffer, D.A. The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra {2007} MOLECULAR & CELLULAR PROTEOMICS
    Vol. {6}({9}), pp. {1638-1655} 
    article DOI  
    Abstract: The Paragon (TM) Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/ MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user- controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2 - 5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.
    BibTeX:
    @article{Shilov2007,
      author = {Shilov, Ignat V. and Seymour, Sean L. and Patel, Alpesh A. and Loboda, Alex and Tang, Wilfred H. and Keating, Sean P. and Hunter, Christie L. and Nuwaysir, Lydia M. and Schaeffer, Daniel A.},
      title = {The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra},
      journal = {MOLECULAR & CELLULAR PROTEOMICS},
      year = {2007},
      volume = {6},
      number = {9},
      pages = {1638-1655},
      doi = {{10.1074/mcp.T600050-MCP200}}
    }
    
    Shimada, Y., Suzuki, K. & Sayama, H. Computer-aided operability study {1996} COMPUTERS & CHEMICAL ENGINEERING
    Vol. {20}({6-7}), pp. {905-913} 
    article  
    Abstract: Operability study is a systematic technique for identifying hazards or operability problems throughout an entire facility. In this paper, we have proposed an approach using knowledge engineering techniques to the automated operability study. The computer-aided operability study system consists of the plant-specific knowledge-base, the generic knowledge-base and the inference engine. Causal relationships between input and output variable deviations for components are modeled using decision tables. Decision tables for components are developed by the user and stored in a generic knowledge-base in computers. The plant structure (piping and instrumentation diagram) and reaction types are inputted to the plant-specific knowledge-base in computers. Each process variable of equipment is examined in sequence by searching the generic knowledge-base, and operability study is generated resulting from the search. We demonstrate via the Solvey process how the computer-aided operability study can identify hazards, and substantiate the usefulness of the method.
    BibTeX:
    @article{Shimada1996,
      author = {Shimada, Y and Suzuki, K and Sayama, H},
      title = {Computer-aided operability study},
      journal = {COMPUTERS & CHEMICAL ENGINEERING},
      year = {1996},
      volume = {20},
      number = {6-7},
      pages = {905-913},
      note = {5th International Symposium on Process Systems Engineering (PSE 94), KYONGJU, SOUTH KOREA, MAY 30-JUN 03, 1994}
    }
    
    Shu, B. & Kak, S. A neural network-based intelligent metasearch engine {1999} INFORMATION SCIENCES
    Vol. {120}({1-4}), pp. {1-11} 
    article  
    Abstract: Determining the relevancy of web pages to a query term is basic to the working of any search engine. In this paper we present a neural network based algorithm to classify the relevancy of search results on a metasearch engine. The fast learning neural network technology used by us enables the metasearch engine to handle a query term in a reasonably short time and return the search results with high accuracy. (C) 1999 Elsevier Science Inc. All rights reserved.
    BibTeX:
    @article{Shu1999,
      author = {Shu, B and Kak, S},
      title = {A neural network-based intelligent metasearch engine},
      journal = {INFORMATION SCIENCES},
      year = {1999},
      volume = {120},
      number = {1-4},
      pages = {1-11}
    }
    
    Si, L. & Callan, J. A semisupervised learning method to merge search engine results {2003} ACM TRANSACTIONS ON INFORMATION SYSTEMS
    Vol. {21}({4}), pp. {457-491} 
    article  
    Abstract: The proliferation of searchable text databases on local area networks and the Internet causes the problem of finding information that may be distributed among many disjoint text databases ( distributed information retrieval). How to merge the results returned by selected databases is an important subproblem of the distributed information retrieval task. Previous research assumed that either resource providers cooperate to provide normalizing statistics or search clients download all retrieved documents and compute normalized scores without cooperation from resource providers. This article presents a semisupervised learning solution to the result merging problem. The key contribution is the observation that information used to create resource descriptions for resource selection can also be used to create a centralized sample database to guide the normalization of document scores returned by different databases. At retrieval time, the query is sent to the selected databases, which return database-specific document scores, and to a centralized sample database, which returns database-independent document scores. Documents that have both a database-specific score and a database-independent score serve as training data for learning to normalize the scores of other documents. An extensive set of experiments demonstrates that this method is more effective than the well-known CORI result-merging algorithm under a variety of conditions.
    BibTeX:
    @article{Si2003,
      author = {Si, L and Callan, J},
      title = {A semisupervised learning method to merge search engine results},
      journal = {ACM TRANSACTIONS ON INFORMATION SYSTEMS},
      year = {2003},
      volume = {21},
      number = {4},
      pages = {457-491}
    }
    
    Silverman, B., Bachann, M. & Al-Akharas, K. Implications of buyer decision theory for design of e-commerce websites {2001} INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES
    Vol. {55}({5}), pp. {815-844} 
    article  
    Abstract: In the rush to open their website, e-commerce sites too often fail to support buyer decision-making and search, resulting in a loss of sale and the customer's repeat business. This paper reviews why this occurs and the failure of many B2C and B2B website executives to understand that appropriate decision support and search technology cannot be fully bought off-the-shelf. Our contention is that significant investment and effort is required at any given website in order to create the decision support and search agents needed to properly support buyer decision-making. We provide a framework to guide such effort (derived from buyer behavior choice theory); review the open problems that e-catalog sites pose to the framework and to existing search engine technology; discuss underlying design principles and guidelines; validate the framework and guidelines with a case study; and discuss lessons learned and steps needed to better support buyer decision behavior in the future. Future needs are also pinpointed. (C) 2001 Academic Press.
    BibTeX:
    @article{Silverman2001,
      author = {Silverman, BG and Bachann, M and Al-Akharas, K},
      title = {Implications of buyer decision theory for design of e-commerce websites},
      journal = {INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES},
      year = {2001},
      volume = {55},
      number = {5},
      pages = {815-844}
    }
    
    Singh, P., Shaffer, S.A., Scherl, A., Holman, C., Pfuetzner, R.A., Freeman, T.J.L., Miller, S.I., Hernandez, P., Appel, R.D. & Goodlett, D.R. Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy {2008} ANALYTICAL CHEMISTRY
    Vol. {80}({22}), pp. {8799-8806} 
    article DOI  
    Abstract: Protein-protein interactions are key to function and regulation of many biological pathways. To facilitate characterization of protein-protein interactions using mass spectrometry, a new data acquisition/analysis pipeline was designed. The goal for this pipeline was to provide a generic strategy for identifying cross-linked peptides from single LC/MS/MS data sets, without using specialized cross-linkers or custom-written software. To achieve this, each peptide in the pair of cross-linked peptides was considered to be ``post-translationally'' modified with an unknown mass at an unknown amino acid. This allowed use of an open-modification search engine, Popitam, to interpret the tandem mass spectra of cross-linked peptides. False positives were reduced and database selectivity increased by acquiring precursors and fragments at high mass accuracy. Additionally, a high-charge-state-driven data acquisition scheme was utilized to enrich data sets for cross-linked peptides. This open-modification search based pipeline was shown to be useful for characterizing both chemical as well as native cross-links in proteins. The pipeline was validated by characterizing the known interactions in the chemically cross-linked CYP2E1-b5 complex. Utility of this method in identifying native cross-links was demonstrated by mapping disulfide bridges in RcsF, an outer membrane lipoprotein involved in Rcs phosphorelay.
    BibTeX:
    @article{Singh2008,
      author = {Singh, Pragya and Shaffer, Scott A. and Scherl, Alexander and Holman, Carol and Pfuetzner, Richard A. and Freeman, Theodore J. Larson and Miller, Samuel I. and Hernandez, Patricia and Appel, Ron D. and Goodlett, David R.},
      title = {Characterization of Protein Cross-Links via Mass Spectrometry and an Open-Modification Search Strategy},
      journal = {ANALYTICAL CHEMISTRY},
      year = {2008},
      volume = {80},
      number = {22},
      pages = {8799-8806},
      doi = {{10.1021/ac801646f}}
    }
    
    Singh, P., Wu, H., Clark, C. & Owlia, A. Annexin II binds progastrin and gastrin-like peptides, and mediates growth factor effects of autocrine and exogenous gastrins on colon cancer and intestinal epithelial cells {2007} ONCOGENE
    Vol. {26}({3}), pp. {425-440} 
    article  
    Abstract: We and others have reported the presence of novel progastrin (PG)/gastrin receptors on normal and cancerous intestinal cells. We had earlier reported the presence of 33 - 36 kDa gastrin-binding proteins on cellular membranes of colon cancer cells. The goal of the current study was to identify the protein(s) in the 33 - 36 kDa band, and analyse its functional significance. A carbodiimide crosslinker was used for crosslinking radio-labeled gastrins to membrane proteins from gastrin/PG responsive cell lines. Native membrane proteins, crosslinked to the ligand, were solubulized and enriched by > 1000-fold, and analysed by surface-enhanced laser desorption/ionization-time of light-mass spectrometry. The peptide masses were researched against the NCBInr database using the ProFound search engine. Annexin II (ANX II) was identified, and confirmed by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. As HCT-116 cells express autocrine PG, the in situ association of PG with ANX II was demonstrated in pulldown assays. Direct binding of PG with ANX II was confirmed in an in vitro binding assay. In order to confirm a functional importance of these observations, sense and anti-sense (AS) ANX II RNA-expressing clones of intestinal epithelial (IEC-18) and human colon cancer (HCT-116) cell lines were generated. AS clones demonstrated a significant loss in the growth response to exogenous (IEC-18) and autocrine (HCT-116) PG. We have thus discovered that membrane-associated ANX II binds PG/gastrins, and partially mediates growth factor effects of the peptides.
    BibTeX:
    @article{Singh2007,
      author = {Singh, P. and Wu, H. and Clark, C. and Owlia, A.},
      title = {Annexin II binds progastrin and gastrin-like peptides, and mediates growth factor effects of autocrine and exogenous gastrins on colon cancer and intestinal epithelial cells},
      journal = {ONCOGENE},
      year = {2007},
      volume = {26},
      number = {3},
      pages = {425-440}
    }
    
    Smith, J. & Chang, S. An image and video search engine for the World-Wide Web {1997}
    Vol. {3022}STORAGE AND RETRIEVAL FOR IMAGE AND VIDEO DATABASES V, pp. {84-95} 
    inproceedings  
    Abstract: We describe a visual information system prototype for searching for images and videos on the World-Wide Web. New visual information in the form of images, graphics, animations and videos is being published on the Web at an incredible rate. However, cataloging this visual data is beyond the capabilities of current text-based Web search engines. In this paper, we describe a complete system by which visual information on the Web is (1) collected by automated agents, (2) processed in both text and visual feature domains, (3) catalogued and (4) indexed for fast search and retrieval. We introduce an image and video search engine which utilizes both text-based navigation and content-based technology for searching visually through the catalogued images and videos. Finally, we provide an initial evaluation based upon the cataloging of over one half million images and videos collected from the Web.
    BibTeX:
    @inproceedings{Smith1997,
      author = {Smith, JR and Chang, SF},
      title = {An image and video search engine for the World-Wide Web},
      booktitle = {STORAGE AND RETRIEVAL FOR IMAGE AND VIDEO DATABASES V},
      year = {1997},
      volume = {3022},
      pages = {84-95},
      note = {Conference on Storage and Retrieval for Image and Video Databases V, SAN JOSE, CA, FEB 13-14, 1997}
    }
    
    Smyth, B., Balfe, E., Freyne, J., Briggs, P., Coyle, M. & Boydell, O. Exploiting query repetition and regularity in an adaptive community-based Web search engine {2004} USER MODELING AND USER-ADAPTED INTERACTION
    Vol. {14}({5}), pp. {383-423} 
    article DOI  
    Abstract: Search engines continue to struggle with the challenges presented by Web search: vague queries, impatient users and an enormous and rapidly expanding collection of unmoderated, heterogeneous documents all make for an extremely hostile search environment. In this paper we argue that conventional approaches to Web search - those that adopt a traditional, document-centric, information retrieval perspective - are limited by their refusal to consider the past search behaviour of users during future search sessions. In particular, we argue that in many circumstances the search behaviour of users is repetitive and regular; the same sort of queries tend to recur and the same type of results are often selected. We describe how this observation can lead to a novel approach to a more adaptive form of search, one that leverages past search behaviours as a means to re-rank future search results in a way that recognises the implicit preferences of communities of searchers. We describe and evaluate the I-SPY search engine, which implements this approach to collaborative, community-based search. We show that it offers potential improvements in search performance, especially in certain situations where communities of searchers share similar information needs and use similar queries to express these needs. We also show that I-SPY benefits from important advantages when it comes to user privacy. In short, we argue that I-SPY strikes a useful balance between search personalization and user privacy, by offering a unique form of anonymous personalization, and in doing so may very well provide privacy-conscious Web users with an acceptable approach to personalized search.
    BibTeX:
    @article{Smyth2004,
      author = {Smyth, B and Balfe, E and Freyne, J and Briggs, P and Coyle, M and Boydell, O},
      title = {Exploiting query repetition and regularity in an adaptive community-based Web search engine},
      journal = {USER MODELING AND USER-ADAPTED INTERACTION},
      year = {2004},
      volume = {14},
      number = {5},
      pages = {383-423},
      doi = {{10.1007/s11257-004-5270-4}}
    }
    
    Snoek, C.G.M., Worring, M., Koelma, D.C. & Smeulders, A.W.M. A learned lexicon-driven paradigm for interactive video retrieval {2007} IEEE TRANSACTIONS ON MULTIMEDIA
    Vol. {9}({2}), pp. {280-292} 
    article DOI  
    Abstract: Effective video retrieval is the result of an interplay between interactive query selection, advanced visualization of results, and a goal-oriented human user. Traditional interactive video retrieval approaches emphasize paradigms, such as query-by-keyword and query-by-example, to aid the user in the search for relevant footage. However, recent results in automatic indexing indicate that query-by-concept is becoming a viable resource for interactive retrieval also. We propose in this paper a new video retrieval paradigm. The core of the paradigm is formed by first detecting a large lexicon of semantic concepts. From there, we combine query-by-concept, query-by-example, query-by-keyword, and user interaction into the MediaMill semantic video search engine. To measure the impact of increasing lexicon size on interactive video retrieval performance, we performed two experiments against the 2004 and 2005 NIST TRECVID benchmarks, using lexicons containing 32 and 101 concepts, respectively. The results suggest that from all factors that play a role in interactive retrieval, a large lexicon of semantic concepts matters most. Indeed, by exploiting large lexicons, many video search questions are solvable without using query-by-keyword and query-by-example. In addition, we show that the lexicon-driven search engine outperforms all state-of-the-art video retrieval systems in both TRECVID 2004 and 2005.
    BibTeX:
    @article{Snoek2007,
      author = {Snoek, Cees G. M. and Worring, Marcel and Koelma, Dennis C. and Smeulders, Arnold W. M.},
      title = {A learned lexicon-driven paradigm for interactive video retrieval},
      journal = {IEEE TRANSACTIONS ON MULTIMEDIA},
      year = {2007},
      volume = {9},
      number = {2},
      pages = {280-292},
      doi = {{10.1109/TMM.2006.886275}}
    }
    
    Snove, O. & Holen, T. Many commonly used siRNAs risk off-target activity {2004} BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
    Vol. {319}({1}), pp. {256-263} 
    article DOI  
    Abstract: Using small interfering RNA (siRNA) to induce sequence specific gene silencing is fast becoming a standard toot in functional genomics. As siRNAs in some cases tolerate mismatches with the mRNA target, knockdown of genes other than the intended target could make results difficult to interpret. In an investigation of 359 published siRNA sequences, we have found that about 75% of them have a risk of eliciting non-specific effects. A possible cause for this is the popular BLAST search engine, which is inappropriate for such short oligos as siRNAs. Furthermore, we used new special purpose hardware to do a transcriptome-wide screening of all possible siRNAs, and show that many unique siRNAs exist per target even if several mismatches are allowed. Hence, we argue that the risk of off-target effects is unnecessary and should be avoided in future siRNA design. (C) 2004 Elsevier Inc. All rights reserved.
    BibTeX:
    @article{Snove2004,
      author = {Snove, O and Holen, T},
      title = {Many commonly used siRNAs risk off-target activity},
      journal = {BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS},
      year = {2004},
      volume = {319},
      number = {1},
      pages = {256-263},
      doi = {{10.1016/j.bbrc.2004.04.175}}
    }
    
    Snyder, H. & Rosenbaum, H. Can search engines be used as tools for web-link analysis? A critical view {1999} JOURNAL OF DOCUMENTATION
    Vol. {55}({4}), pp. {375-384} 
    article  
    Abstract: The paper investigates the problems of using commercial search engines for web-link research and attempts to clarify the nature of the problems involved in the use of these engines. The research finds that search engines are highly variable in the results they produce, are limited in the search functions they offer, have poorly and/or incorrectly documented functions, use search logics that are opaque, and change the search functions they offer over time. The limitations which are inherent in commercial search engines should cause researchers to have reservations about any conclusions that rely on these tools as primary data-gathering instruments. The shortcomings are market-driven rather than inherent properties of the web or of web-searching technologies. Improved functionalities are within the technical capabilities of search engine programmers and could be made available to the research community. The findings also offer mild support for the validity of the connection between web links and citations as analogues of intellectual linkage.
    BibTeX:
    @article{Snyder1999,
      author = {Snyder, H and Rosenbaum, H},
      title = {Can search engines be used as tools for web-link analysis? A critical view},
      journal = {JOURNAL OF DOCUMENTATION},
      year = {1999},
      volume = {55},
      number = {4},
      pages = {375-384}
    }
    
    Spink, A. A user-centered approach to evaluating human interaction with Web search engines: an exploratory study {2002} INFORMATION PROCESSING & MANAGEMENT
    Vol. {38}({3}), pp. {401-426} 
    article  
    Abstract: A growing body of studies is developing approaches to evaluating human interaction with Web search engines, including the usability and effectiveness of Web search tools. This study explores a user-centered approach to the evaluation of the Web search engine Inquirus - a Web meta-search tool developed by researchers from the NEC Research Institute. The goal of the study reported in this paper was to develop a user-centered approach to the evaluation including: (1) effectiveness: based on the impact of users' interactions on their information problem and information seeking stage, and (2) usability: including screen layout and system capabilities for users. Twenty-two volunteers searched Inquirus on their own personal information topics. Data analyzed included: (1) user pre- and post-search questionnaires and (2) Inquirus search transaction logs. Key findings include: (1) Inquirus was rated highly by users on various usability measures, (2) all users experienced some level of shift/change in their information problem, information seeking, and personal knowledge due to their Inquirus interaction, (3) different users experienced different levels of change/shift, and (4) the search measure precision did not correlate with other user-based measures. Some users experienced major changes/shifts in various user-based variables, such as information problem or information seeking stage with a search of low precision and vice versa. Implications for the development of user-centered approaches to the evaluation of Web and information retrieval (IR) systems and further research are discussed. (C) 2002 Elsevier Science Ltd. All rights reserved.
    BibTeX:
    @article{Spink2002a,
      author = {Spink, A},
      title = {A user-centered approach to evaluating human interaction with Web search engines: an exploratory study},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2002},
      volume = {38},
      number = {3},
      pages = {401-426}
    }
    
    Spink, A., Bateman, J. & Jansen, B. Searching the Web: a survey of EXCITE users {1999} INTERNET RESEARCH-ELECTRONIC NETWORKING APPLICATIONS AND POLICY
    Vol. {9}({2}), pp. {117-128} 
    article  
    Abstract: Web search services are now a major source of information for a growing number of people. We need to know more about how users search Web search engines to improve the effectiveness of their information retrieval. This paper reports results from a major study exploring users' information searching behavior on the EXCITE Web search engine. The study is the fi rst to investigate Web users' success ive searching behavior as they conduct related searches over time on the same or evolving topic. A total of 316 EXCITE users responded to an interactive survey accessed through EXCITE's homepage. Users provided information on their search topics, intended query terms, search frequency for information on their topic, and demographic data. Results show that when searching the Web: users tend to employ simple search strategies; and often conduct more than one search (successive searches) over time to find information related to a particular topic. Implications for the design of Web search services are discussed.
    BibTeX:
    @article{Spink1999,
      author = {Spink, A and Bateman, J and Jansen, BJ},
      title = {Searching the Web: a survey of EXCITE users},
      journal = {INTERNET RESEARCH-ELECTRONIC NETWORKING APPLICATIONS AND POLICY},
      year = {1999},
      volume = {9},
      number = {2},
      pages = {117-128}
    }
    
    Spink, A., Jansen, B., Blakely, C. & Koshman, S. A study of results overlap and uniqueness among major Web search engines {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({5}), pp. {1379-1391} 
    article DOI  
    Abstract: The performance and capabilities of Web search engines is an important and significant area of research. Millions of people world wide use Web search engines very day. This paper reports the results of a major study examining the overlap among results retrieved by multiple Web search engines for a large set of more than 10,000 queries. Previous smaller studies have discussed a lack of overlap in results returned by Web search engines for the same queries. The goal of the current study was to conduct a large-scale study to measure the overlap of search results on the first result page (both non-sponsored and sponsored) across the four most popular Web search engines, at specific points in time using a large number of queries. The Web search engines included in the study were MSN Search, Google, Yahoo! and Ask Jeeves. Our study then compares these results with the first page results retrieved for the same queries by the metasearch engine Dogpile.com. Two sets of randomly selected user-entered queries, one set was 10,316 queries and the other 12,570 queries, from Infospace's Dogpile.com search engine (the first set was from Dogpile, the second was from across the Infospace Network of search properties were submitted to the four single Web search engines). Findings show that the percent of total results unique to only one of the four Web search engines was 84.9 shared by two of the three Web search engines was 11.4 shared by three of the Web search engines was 2.6 and shared by all four Web search engines was 1.1 This small degree of overlap shows the significant difference in the way major Web search engines retrieve and rank results in response to given queries. Results point to the value of metasearch engines in Web retrieval to overcome the biases of individual search engines. (c) 2005 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Spink2006,
      author = {Spink, A and Jansen, BJ and Blakely, C and Koshman, S},
      title = {A study of results overlap and uniqueness among major Web search engines},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {5},
      pages = {1379-1391},
      doi = {{10.1016/j.ipm.2005.11.001}}
    }
    
    Spink, A., Jansen, B. & Ozmultu, H. Use of query reformulation and relevance feedback by Excite users {2000} INTERNET RESEARCH-ELECTRONIC NETWORKING APPLICATIONS AND POLICY
    Vol. {10}({4}), pp. {317-328} 
    article  
    Abstract: Examines the use of query reformulation, and particularly the use of relevance feedback by users of the Excite Web search engine. A total of 985 user search sessions from a data set of 18,113 user search sessions containing 51,473 queries were examined. Includes a qualitative and quantitative analysis of 191 user sessions including more than one query, to examine patterns of user query reformulation; and second, all 804 user sessions including relevance feedback were examined. Results show limited use of query reformulation and relevance feedback by Excite users - only one in five users reformulated queries. Most relevance feedback sessions were successful. Identifies the most common pattern of searching and discusses implications for Web search system design.
    BibTeX:
    @article{Spink2000,
      author = {Spink, A and Jansen, BJ and Ozmultu, HC},
      title = {Use of query reformulation and relevance feedback by Excite users},
      journal = {INTERNET RESEARCH-ELECTRONIC NETWORKING APPLICATIONS AND POLICY},
      year = {2000},
      volume = {10},
      number = {4},
      pages = {317-328}
    }
    
    Spink, A. & Ozmultu, H. Characteristics of question format web queries: an exploratory study {2002} INFORMATION PROCESSING & MANAGEMENT
    Vol. {38}({4}), pp. {453-471} 
    article  
    Abstract: Web queries in question format are becoming a common element of a user's interaction with Web search engines. Web search services such as Ask Jeeves - a publicly accessible question and answer (Q&A) search engine - request users to enter question format queries. This paper provides results from a study examining queries in question format submitted to two different Web search engines - Ask Jeeves that explicitly encourages queries in question format and the Excite search service that does not explicitly encourage queries in question format. We identify the characteristics of queries in question format in two different data sets: (1) 30,000 Ask Jeeves queries and 15.575 Excite queries, including the nature, length, and structure of queries in question format. Findings include: (1) 50% of Ask Jeeves queries and less than 1% of Excite were in question format, (2) most users entered only one query in question format with little query reformulation, (3) limited range of formats for queries in question format - mainly ``where'', ``what'', or ``how'' questions, (4) most common question query format was ``Where can I find..........'' for general information on a topic. and (5) non-question queries may be in request format. Overall, four types of user Web queries were identified: keyword, Boolean, question, and request. These findings provide an initial mapping of the structure and content of queries in question and request format. Implications for Web search services are discussed. (C) 2002 Published by Elsevier Science Ltd.
    BibTeX:
    @article{Spink2002b,
      author = {Spink, A and Ozmultu, HC},
      title = {Characteristics of question format web queries: an exploratory study},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2002},
      volume = {38},
      number = {4},
      pages = {453-471}
    }
    
    Spink, A., Ozmutlu, H. & Ozmutlu, S. Multitasking information seeking and searching processes {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({8}), pp. {639-652} 
    article DOI  
    Abstract: Recent studies show that humans engage in multitasking behaviors as they seek and search information retrieval (IR) systems for information on more than one topic at the same time. For example, a Web search session by a single user may consist of searching on single topics or multitasking. Findings are presented from four separate studies of the prevalence of multitasking information seeking and searching by Web, IR system, and library users. Incidence of multitasking identified in the four different studies included: (1) users of the Excite Web search engine who completed a survey form, (2) Excite Web search engine users filtered from an Excite transaction log from 20 December 1999, (3) mediated on-line databases searches, and (4) academic library users. Findings include: (1) multitasking information seeking and searching is a common human behavior, (2) users may conduct information seeking and searching on related or unrelated topics, (3) Web or IR multitasking search sessions are longer than single topic sessions, (4) mean number of topics per Web search ranged of 1 to more than 10 topics with a mean of 2.11 topic changes per search session, and (4) many Web search topic changes were from hobbies to shopping and vice versa. A more complex model of human seeking and searching levels that incorporates multitasking information behaviors is presented, and a theoretical framework for human information coordinating behavior (HICB) is proposed. Multitasking information seeking and searching is developing as major research area that draws together IR and information seeking studies toward a focus on IR within the context of human information behavior. Implications for models of information seeking and searching, IR/Web systems design, and further research are discussed.
    BibTeX:
    @article{Spink2002,
      author = {Spink, A and Ozmutlu, HC and Ozmutlu, S},
      title = {Multitasking information seeking and searching processes},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {8},
      pages = {639-652},
      doi = {{10.1002/asi.10124}}
    }
    
    Spink, A., Park, M., Jansen, B. & Pedersen, J. Multitasking during Web search sessions {2006} INFORMATION PROCESSING & MANAGEMENT
    Vol. {42}({1}), pp. {264-275} 
    article DOI  
    Abstract: A user's single session with a Web search engine or information retrieval (IR) system may consist of seeking information on single or multiple topics, and switch between tasks or multitasking information behavior. Most Web search sessions consist of two queries of approximately two words. However, some Web search sessions consist of three or more queries. We present findings from two studies. First, a study of two-query search sessions on the AltaVista Web search engine, and second, a study of three or more query search sessions on the AltaVista Web search engine. We examine the degree of multitasking search and information task switching during these two sets of AltaVista Web search sessions. A sample of two-query and three or more query sessions were filtered from AltaVista transaction logs from 2002 and qualitatively analyzed. Sessions ranged in duration from less than a minute to a few hours. Findings include: (1) 81% of two-query sessions included multiple topics, (2) 91.3% of three or more query sessions included multiple topics, (3) there are a broad variety of topics in multitasking search sessions, and (4) three or more query sessions sometimes contained frequent topic changes. Multitasking is found to be a growing element in Web searching. This paper proposes an approach to interactive information retrieval (IR) contextually within a multitasking framework. The implications of our findings for Web design and further research are discussed. (c) 2004 Elsevier Ltd. All rights reserved.
    BibTeX:
    @article{Spink2006a,
      author = {Spink, A and Park, M and Jansen, BJ and Pedersen, J},
      title = {Multitasking during Web search sessions},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {2006},
      volume = {42},
      number = {1},
      pages = {264-275},
      doi = {{10.1016/j.ipm.2004.10.004}}
    }
    
    Spink, A., Wolfram, D., Jansen, M. & Saracevic, T. Searching the Web: The public and their queries {2001} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {52}({3}), pp. {226-234} 
    article  
    Abstract: In studying actual Web searching by the public at large, we analyzed over one million Web queries by users of the Excite search engine. We found that most people use few search terms, few modified queries, view few Web pages, and rarely use advanced search features. A small number of search terms are used with high frequency, and a great many terms are unique; the language of Web queries is distinctive. Queries about recreation and entertainment rank highest. Findings are compared to data from two other large studies of Web queries. This study provides an insight into the public practices and choices in Web searching.
    BibTeX:
    @article{Spink2001,
      author = {Spink, A and Wolfram, D and Jansen, MBJ and Saracevic, T},
      title = {Searching the Web: The public and their queries},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2001},
      volume = {52},
      number = {3},
      pages = {226-234}
    }
    
    St Peter, S., Abbas, M. & Kelly, K. The spectrum of pneumatosis intestinalis {2003} ARCHIVES OF SURGERY
    Vol. {138}({1}), pp. {68-75} 
    article  
    Abstract: Hypothesis: A review of the spectrum of illness associated with pneumatosis intestinalis enables us to identify the probable causes of, the best diagnostic approaches to, and the most appropriate treatments for this condition. Data Sources: A review of all published material in the English language regarding pneumatosis intestinalis was conducted using the PubMed and MEDLINE databases. Any relevant work referenced in those articles and not previously found or published before the limit of the search engine was also retrieved and reviewed. Study Selection: There were no exclusion criteria for published information relevant to the topic. All of the studies cited in the present review make a point that contributes to the portrayal of this condition. In circumstances in which the same point was made in several different studies, not all were cited herein. Data Extraction: All published material on pneumatosis intestinalis was considered. Information, was extracted for preferentially selected ideas and theories supported in multiple studies. Data Synthesis: The collected information was organized by theory. Conclusions: Mucosal integrity, intraluminal pressure, bacterial flora, and intraluminal gas all interact in the formation of pneumatosis intestinalis. Radiography and computed tomography are the best diagnostic tests. Nonoperative management should be pursued in most patients, and underlying illnesses should be treated. When acute complications appear, such as perforation, peritonitis, and necrotic bowel, surgery is indicated.
    BibTeX:
    @article{StPeter2003,
      author = {St Peter, SD and Abbas, MA and Kelly, KA},
      title = {The spectrum of pneumatosis intestinalis},
      journal = {ARCHIVES OF SURGERY},
      year = {2003},
      volume = {138},
      number = {1},
      pages = {68-75}
    }
    
    Stamatakis, A., Blagojevic, F., Nikolopoulos, D.S. & Antonopoulos, C.D. Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell {2007} JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY
    Vol. {48}({3}), pp. {271-286} 
    article DOI  
    Abstract: Phylogenetic inference is considered to be one of the grand challenges in Bioinformatics due to the immense computational requirements. RAxML is currently among the fastest and most accurate programs for phylogenetic tree inference under the Maximum Likelihood (ML) criterion. First, we introduce new tree search heuristics that accelerate RAxML by a factor of 2.43 while returning equally good trees. The performance of the new search algorithm has been assessed on 18 real-world datasets comprising 148 up to 4,843 DNA sequences. We then present the implementation, optimization, and evaluation of RAxML on the IBM Cell Broadband Engine. We address the problems and provide solutions pertaining to the optimization of floating point code, control flow, communication, and scheduling of multi-level parallelism on the Cell.
    BibTeX:
    @article{Stamatakis2007,
      author = {Stamatakis, A. and Blagojevic, F. and Nikolopoulos, D. S. and Antonopoulos, C. D.},
      title = {Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell},
      journal = {JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY},
      year = {2007},
      volume = {48},
      number = {3},
      pages = {271-286},
      doi = {{10.1007/s11265-007-0067-4}}
    }
    
    Stebbings, L. & Mizuguchi, K. HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database {2004} NUCLEIC ACIDS RESEARCH
    Vol. {32}({Sp. Iss. SI}), pp. {D203-D207} 
    article DOI  
    Abstract: HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/ homstrad/) is a collection of protein families, clustered on the basis of sequence and structural similarity. The database is unique in that the protein family sequence alignments have been specially annotated using the program, JOY, to highlight a wide range of structural features. Such data are useful for identifying key structurally conserved residues within the families. Superpositions of the structures within each family are also available and a sensitive structure-aided search engine, FUGUE, can be used to search the database for matches to a query protein sequence. Historically, HOMSTRAD families were generated using several key pieces of software, including COMPARER and MNYFIT, and held in a number of flat files and indexes. A new relational database version of HOMSTRAD, HOMSTRAD BETA (http://www-cryst.bioc.cam. ac.uk/homstradbeta/) is being developed using MySQL. This relational data structure provides more flexibility for future developments, reduces update times and makes data more easily accessible. Consequently it has been possible to add a number of new web features including a custom alignment facility. Altogether, this makes HOMSTRAD and its new BETA version, an excellent resource both for comparative modelling and for identifying distant sequence/structure similarities between proteins.
    BibTeX:
    @article{Stebbings2004,
      author = {Stebbings, LA and Mizuguchi, K},
      title = {HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2004},
      volume = {32},
      number = {Sp. Iss. SI},
      pages = {D203-D207},
      doi = {{10.1093/nar/gkh027}}
    }
    
    Stokes, T.H., Torrance, J.T., Li, H. & Wang, M.D. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses {2008} BMC BIOINFORMATICS
    Vol. {9}({Suppl. 6}) 
    article DOI  
    Abstract: Background: A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the ``curse-of-dimension'' problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create ``intelligent'' microarray repositories that (1) enable update of metadata with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results: To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (Semantic Agents) such as Google to further enhance data discovery. Conclusions: Microarray data and meta information in ArrayWiki are distributed and visualized using a novel and compact data storage format, BioPNG. Also, they are open to the research community for curation, modification, and contribution. By making a small investment of time to learn the syntax and structure common to all sites running MediaWiki software, domain scientists and practioners can all contribute to make better use of microarray technologies in research and medical practices.
    BibTeX:
    @article{Stokes2008,
      author = {Stokes, Todd H. and Torrance, J. T. and Li, Henry and Wang, May D.},
      title = {ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses},
      journal = {BMC BIOINFORMATICS},
      year = {2008},
      volume = {9},
      number = {Suppl. 6},
      note = {Symposium of Computations in Bioinformatics and Bioscience (SCBB07), Iowa City, IA, AUG 13-15, 2007},
      doi = {{10.1186/1471-2105-9-S6-S18}}
    }
    
    Struder-Kypke, M. & Montagnes, D. Development of web-based guides to planktonic protists {2002} AQUATIC MICROBIAL ECOLOGY
    Vol. {27}({2}), pp. {203-207} 
    article  
    Abstract: Computer-based media constitute an ideal tool for disseminating data concerning protist biodiversity. Interactive guides can combine micrographs, illustrations, text and links to molecular data. A standardized web-based guide could collate information collected by researchers and create a mechanism for ecologists to identify taxa. Web-based guides have advantages: they are easily modified and expanded; they are easy to distribute; they can include a search engine to replace a dichotomous key; they can be downloaded to run on stand-alone computers; and they can be structured to provide printed information. We have developed a model for a guide that incorporates these methods of disseminating information. Using this model, we indicate how the web can provide information and act as a tool to identify taxa. We then use a guide to the planktonic ciliates, based on this model, as an example (www.liv.ac.uk/ciliate). Finally we present data from a survey that reviewed our model website; it indicated that the site was well received. Ultimately, we offer this guide as a template to be applied to other taxa.
    BibTeX:
    @article{Struder-Kypke2002,
      author = {Struder-Kypke, MC and Montagnes, DJS},
      title = {Development of web-based guides to planktonic protists},
      journal = {AQUATIC MICROBIAL ECOLOGY},
      year = {2002},
      volume = {27},
      number = {2},
      pages = {203-207}
    }
    
    STRZALKOWSKI, T. NATURAL-LANGUAGE INFORMATION-RETRIEVAL {1995} INFORMATION PROCESSING & MANAGEMENT
    Vol. {31}({3}), pp. {397-417} 
    article  
    Abstract: In this paper we describe an information retrieval system in which advanced natural language processing techniques are used to enhance the effectiveness of term-based document retrieval. The backbone of our system is a traditional statistical engine that builds inverted index files from pre-processed documents, and then searches and ranks the documents in response to user queries. Natural language processing is used to (a) preprocess the documents in order to extract content carrying terms, (b) discover inter-term dependencies and build a conceptual hierarchy specific to the database domain, and (c) process the user's natural language requests into effective search queries. During the course of the Text REtrieval Conferences, TREC-1 and TREC-2, our system has evolved from a scaled-up prototype, originally tested on such collections as CACM-3204 and Cranfield, to its present form which can be effectively used to process hundreds of millions of words of unrestricted text.
    BibTeX:
    @article{STRZALKOWSKI1995,
      author = {STRZALKOWSKI, T},
      title = {NATURAL-LANGUAGE INFORMATION-RETRIEVAL},
      journal = {INFORMATION PROCESSING & MANAGEMENT},
      year = {1995},
      volume = {31},
      number = {3},
      pages = {397-417}
    }
    
    Su, L. A comprehensive and systematic model of user evaluation of Web search engines: II. An evaluation by undergraduates {2003} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {54}({13}), pp. {1193-1223} 
    article DOI  
    Abstract: This paper presents an application of the model described in Part I to the evaluation of Web search engines by undergraduates. The study observed how 36 undergraduate used four major search engines to find information for their own individual problems and how they evaluated these engines based on actual interaction with the search engines. User evaluation was based on 16 performance measures representing five evaluation criteria: relevance, efficiency, utility, user satisfaction, and connectivity. Non-performance (user-related) measures were also applied. Each participant searched his/her own topic on all four engines and provided satisfaction ratings for system features and interaction and reasons for satisfaction. Each also made relevance judgements of retrieved items in relation to his/her own information need and participated in post-search interviews to provide reactions to the search results and overall performance. The study found significant differences in precision P,,, relative recall, user satisfaction with output display, time saving, value of search results, and overall performance among the four engines and also significant engine by discipline interactions on all these measures. In addition, the study found significant differences in user satisfaction with response time among four engines, and significant engine by discipline interaction in user satisfaction with search interface. None of the four search engines dominated in every aspect of the multidimensional evaluation. Content analysis of verbal data identified a number of user criteria and users evaluative comments based on these criteria. Results from both quantitative analysis and content analysis provide insight for system design and development, and useful feedback on strengths and weaknesses of search engines for system improvement.
    BibTeX:
    @article{Su2003,
      author = {Su, LT},
      title = {A comprehensive and systematic model of user evaluation of Web search engines: II. An evaluation by undergraduates},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2003},
      volume = {54},
      number = {13},
      pages = {1193-1223},
      note = {Annual ASIS Meeting, WASHINGTON, D.C., OCT 31-NOV 04, 1999},
      doi = {{10.1002/asi.10334}}
    }
    
    Su, L. A comprehensive and systematic model of user evaluation of Web search engines: I. Theory and background {2003} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {54}({13}), pp. {1175-1192} 
    article DOI  
    Abstract: The project proposes and tests a comprehensive and systematic model of user evaluation of Web search engines. The project contains two parts. Part I describes the background and the model including a set of criteria and measures, and a method for implementation. It includes a literature review for two periods. The early period (1995-1996) portrays the settings for developing the model and the later period (1997-2000) places two applications of the model among contemporary evaluation work. Part 11 presents one of the applications that investigated the evaluation of four major search engines by 36 undergraduates from three academic disciplines. It reports results from statistical analyses of quantitative data for the entire sample and among disciplines, and content analysis of verbal data containing users' reasons for satisfaction. The proposed model aims to provide systematic feedback to engine developers or service providers for system improvement and to generate useful insight for system design and tool choice. The model can be applied to evaluating other compatible information retrieval systems or information retrieval (IR) techniques. It intends to contribute to developing a theory of relevance that goes beyond topicality to include value and usefulness for designing user-oriented information retrieval systems.
    BibTeX:
    @article{Su2003a,
      author = {Su, LT},
      title = {A comprehensive and systematic model of user evaluation of Web search engines: I. Theory and background},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2003},
      volume = {54},
      number = {13},
      pages = {1175-1192},
      note = {61st ASIS Annual Meeting, PITTSBURGH, PENNSYLVANIA, OCT 24-29, 1998},
      doi = {{10.1002/asi.10303}}
    }
    
    Suarez-Almazor, M., Kendall, C. & Dorgan, M. Surfing the Net - Information on the World Wide Web for persons with arthritis: Patient empowerment or patient deceit? {2001} JOURNAL OF RHEUMATOLOGY
    Vol. {28}({1}), pp. {185-191} 
    article  
    Abstract: Objective. In the past few years access to the Internet has become readily available. Patients are increasingly seeking and obtaining health information through the Internet, most often the World Wide Web (WWW). We assessed the content, authorship, and scope of the information available on WWW in relation to rheumatoid arthritis. Methods. In an attempt to replicate use by the average person, a broad search of the Internet was conducted for the phrase ``rheumatoid arthritis'' using WebCrawler, a commonly used search engine. All the ``hits'' were critically assessed after visiting and collecting information from the respective Web sites in relation to relevance, scope, authorship, type of publication, and financial objectives. Results. The search returned 537 hits. We evaluated 531-2 did not exist, 2 could not be contacted, one was not in English, and one required a membership to access. The 531 hits originated from 388 Web sites. Only 198 (51 were considered to be relevant and 7 (2 were of doubtful relevance. Thirty-four (17 were posted by an individual, 57 (28 by a nonprofit organization, 104 (51 by a profit industry, and 10 (5 by universities. Ninety-one (44 promoted alternative therapies, the most common including cetyl-myristoleate, colloidal minerals, Pycnogenol, shark cartilage, and Tahitian Noni. Of the 107 sites with financial interests, 76 (71 promoted alternative medicine. The first 100 hits only identified about a third of the nonprofit organizations or university owned Web pages. Conclusion. Many sites easily accessed by consumers appear to be profit based companies advertising an alternative product claimed to be effective for many conditions. These findings emphasize the need for critical evaluation of Web site contents.
    BibTeX:
    @article{Suarez-Almazor2001,
      author = {Suarez-Almazor, ME and Kendall, CJ and Dorgan, M},
      title = {Surfing the Net - Information on the World Wide Web for persons with arthritis: Patient empowerment or patient deceit?},
      journal = {JOURNAL OF RHEUMATOLOGY},
      year = {2001},
      volume = {28},
      number = {1},
      pages = {185-191}
    }
    
    Suomela, B. & Andrade, M. Ranking the whole MEDLINE database according to a large training set using text indexing {2005} BMC BIOINFORMATICS
    Vol. {6} 
    article DOI  
    Abstract: Background: The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. Results: We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79 than adjectives (73 or verbs (70. The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65 Conclusion: This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.
    BibTeX:
    @article{Suomela2005,
      author = {Suomela, BP and Andrade, MA},
      title = {Ranking the whole MEDLINE database according to a large training set using text indexing},
      journal = {BMC BIOINFORMATICS},
      year = {2005},
      volume = {6},
      doi = {{10.1186/1471-2105-6-75}}
    }
    
    Sutcliffe, A., Ennis, M. & Hu, J. Evaluating the effectiveness of visual user interfaces for information retrieval {2000} INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES
    Vol. {53}({5}), pp. {741-763} 
    article  
    Abstract: An integrated visual thesaurus and results browser to support information retrieval was designed using a task model of information searching. The system provided a hierarchical thesaurus with a results cluster display representing similarity between retrieved documents and relevance ranking using a bullseye metaphor. Latent semantic indexing (LSI) was used as the retrieval engine and to calculate the similarity between documents. The design was tested with two information retrieval tasks. User behaviour, performance and attitude were recorded as well as usability problems. The system had few usability problems and users liked the visualizations, but recall performance was poor. The reasons for poor/good performance were investigated by examining user behaviour and search strategies. Better searchers used the visualizations more effectively and spent longer on the task, whereas poorer performances were attributable to poor motivation, difficulty in assessing article relevance and poor use of system visualizations. The bullseye browser display appeared to encourage limited evaluation of article relevance on titles, leading to poor performance. The bullseye display metaphor for article relevance was understood by users; however, they were confused by the concept of similarity searching expressed as visual clusters. The conclusions from the study are that while visual user interfaces for information searching might seem to be usable, they may not actually improve performance. Training and advisor facilities for effective search strategies need to be incorporated to enhance the effectiveness of visual user interfaces for information retrieval. (C) 2000 Academic Press.
    BibTeX:
    @article{Sutcliffe2000,
      author = {Sutcliffe, AG and Ennis, M and Hu, J},
      title = {Evaluating the effectiveness of visual user interfaces for information retrieval},
      journal = {INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES},
      year = {2000},
      volume = {53},
      number = {5},
      pages = {741-763}
    }
    
    Tabb, D.L., Fernando, C.G. & Chambers, M.C. MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis {2007} JOURNAL OF PROTEOME RESEARCH
    Vol. {6}({2}), pp. {654-661} 
    article DOI  
    Abstract: Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score potential identifications by evaluating the number of fragment ions matched between each peptide sequence and an observed spectrum. These systems, however, generally do not distinguish between matching an intense peak and matching a minor peak. We have developed a statistical model to score peptide matches that is based upon the multivariate hypergeometric distribution. This scorer, part of the ``MyriMatch'' database search engine, places greater emphasis on matching intense peaks. The probability that the best match for each spectrum has occurred by random chance can be employed to separate correct matches from random ones. We evaluated this software on data sets from three different laboratories employing three different ion trap instruments. Employing a novel system for testing discrimination, we demonstrate that stratifying peaks into multiple intensity classes improves the discrimination of scoring. We compare MyriMatch results to those of Sequest and X!Tandem, revealing that it is capable of higher discrimination than either of these algorithms. When minimal peak filtering is employed, performance plummets for a scoring model that does not stratify matched peaks by intensity. On the other hand, we find that MyriMatch discrimination improves as more peaks are retained in each spectrum. MyriMatch also scales well to tandem mass spectra from high-resolution mass analyzers. These findings may indicate limitations for existing database search scorers that count matched peaks without differentiating them by intensity. This software and source code is available under Mozilla Public License at this URL: http://www.mc.vanderbilt.edu/msrc/bioinformatics/.
    BibTeX:
    @article{Tabb2007,
      author = {Tabb, David L. and Fernando, Christopher G. and Chambers, Matthew C.},
      title = {MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis},
      journal = {JOURNAL OF PROTEOME RESEARCH},
      year = {2007},
      volume = {6},
      number = {2},
      pages = {654-661},
      doi = {{10.1021/pr0604054}}
    }
    
    Taguchi, R., Nishijima, M. & Shimizu, T. Basic analytical systems for lipidomics by mass spectrometry in Japan {2007}
    Vol. {432}LIPIDOMICS AND BIOACTIVE LIPIDS: MASS-SPECTROMETRY-BASED LIPID ANALYSIS, pp. {185-211} 
    incollection DOI  
    Abstract: In recent analyses of phospholipids, the application of mass spectrometry (MS) has become increasingly popular. To elucidate the function of phospholipids, it is necessary to analyze not only their classes and subclasses, but also their molecular species. In choosing analytical methods for lipidomics, we selected several different approaches in the identification of phospholipid molecular species. The first approach, global and shotgun liquid chromatographic tandem MS (LC-MS/MS) analysis, uses data-dependent MS/MS scanning, whereas the second approach is structure related, focusing on methods using precursor ion scanning or neutral loss scanning. The third approach uses theoretically expanded multiple reaction monitoring for the analysis of targeted molecules in extremely small amounts. Data from the first and second types of analyses can be obtained with the use of our search engine, Lipid Search (http://lipidsearch.jp), and most probabte molecular species can be obtained with their compensated ion intensities. Identified individual molecular species can be automatically profiled according to their compensated ion intensities. Profiled data can be visualized in the state of relative increase or decrease. These data are available via the Lipid Bank (http://lipidbank.jp) and the MassBank (http://www.massbank.jp).
    BibTeX:
    @incollection{Taguchi2007,
      author = {Taguchi, Ryo and Nishijima, Mashahiro and Shimizu, Takao},
      title = {Basic analytical systems for lipidomics by mass spectrometry in Japan},
      booktitle = {LIPIDOMICS AND BIOACTIVE LIPIDS: MASS-SPECTROMETRY-BASED LIPID ANALYSIS},
      year = {2007},
      volume = {432},
      pages = {185-211},
      doi = {{10.1016/S0076-6879(07)32008-9}}
    }
    
    Tamura, M., Hendrix, D., Klosterman, P., Schimmelman, N., Brenner, S. & Holbrook, S. SCOR: Structural Classification of RNA, version 2.0 {2004} NUCLEIC ACIDS RESEARCH
    Vol. {32}({Sp. Iss. SI}), pp. {D182-D184} 
    article DOI  
    Abstract: SCOR, the Structural Classification of RNA (http:// scor.lbl.gov), is a database designed to provide a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. SCOR 2.0 represents a major expansion and introduces a new classification organization. The new version represents the classification as a Directed Acyclic Graph (DAG), which allows a classification node to have multiple parents, in contrast to the strictly hierarchical classification used in SCOR 1.2. SCOR 2.0 supports three types of query terms in the updated search engine: PDB or NDB identifier, nucleotide sequence and keyword. We also provide parseable XML files for all information. This new release contains 511 RNA entries from the PDB as of 15 May 2003. A total of 5880 secondary structural elements are classified: 2104 hairpin loops and 3776 internal loops. RNA motifs reported in the literature, such as `Kink turn' and `GNRA loops', are now incorporated into the structural classification along with definitions and descriptions.
    BibTeX:
    @article{Tamura2004,
      author = {Tamura, M and Hendrix, DK and Klosterman, PS and Schimmelman, NRB and Brenner, SE and Holbrook, SR},
      title = {SCOR: Structural Classification of RNA, version 2.0},
      journal = {NUCLEIC ACIDS RESEARCH},
      year = {2004},
      volume = {32},
      number = {Sp. Iss. SI},
      pages = {D182-D184},
      doi = {{10.1093/nar/gkh080}}
    }
    
    Tanev, I., Ray, T. & Buller, A. Automated evolutionary design, robustness, and adaptation of sidewinding locomotion of a simulated snake-like robot {2005} IEEE TRANSACTIONS ON ROBOTICS
    Vol. {21}({4}), pp. {632-645} 
    article DOI  
    Abstract: Inspired by the efficient method of locomotion of the rattlesnake Crotalus cerastes, the objective of this work is automatic design through genetic programming (GP) of the fastest possible (sidewinding) locomotion of simulated limbless, wheelless snake-like robot (Snakebot). The realism of simulation is ensured by employing the Open Dynamics Engine (ODE), which facilitates implementation of all physical forces, resulting from the actuators, joints constrains, frictions, gravity, and cohisions. Reduction of the search space of the GP is achieved by representation of Snakebot as a system comprising identical morphological segments and by automatic definition of code fragments, shared among (and expressing the correlation between) the evolved dynamics of the vertical and horizontal turning angles of the actuators of Snakebot. Empirically obtained results demonstrate the emergence of sidewinding locomotion from relatively simple motion patterns of morphological segments. Robustness of the sidewinding Snakebot, which is considered to be the ability to retain its velocity when situated in an unanticipated environment, is illustrated by the ease with which Snakebot overcomes various types of obstacles such as a pile of or burial under boxes, rugged terrain, and small walls. The ability of Snakebot to adapt to partial damage by gradually improving its velocity characteristics is discussed. Discovering compensatory locomotion traits, Snakebot recovers completely from single damage and recovers a major extent of its original velocity when more significant damage is inflicted. Exploring the opportunity for automatic design and adaptation of a simulated artifact, this work could be considered as a step toward building real Snakebots, which are able to perform robustly in difficult environments.
    BibTeX:
    @article{Tanev2005,
      author = {Tanev, I and Ray, T and Buller, A},
      title = {Automated evolutionary design, robustness, and adaptation of sidewinding locomotion of a simulated snake-like robot},
      journal = {IEEE TRANSACTIONS ON ROBOTICS},
      year = {2005},
      volume = {21},
      number = {4},
      pages = {632-645},
      doi = {{10.1109/TRO.2005.851028}}
    }
    
    Tang, H. & Ng, J.H.K. Googling for a diagnosis - use of Googgle as a diagnostic aid: internet based study {2006} BRITISH MEDICAL JOURNAL
    Vol. {333}({7579}), pp. {1143-1145} 
    article DOI  
    Abstract: Objective To determine how often searching with Google (the most popular search engine on the world wide web) leads doctors to the correct diagnosis. Design Internet based study using Google to search for diagnoses; researchers were blind to the correct diagnoses. Setting One year's (2005) diagnostic cases published in the case records of the New England journal of Medicine. Cases 26 cases from the New England journal of Medicine; management cases were excluded. Main outcome measure Percentage of correct diagnoses from Google searches (compared with the diagnoses as published in the New England journal of Medicine). Results Google searches revealed the correct diagnosis in 15 (5895% confidence interval 38% to 77 cases. Conclusion As internet access becomes more readily available in outpatient clinics and hospital wards, the web is rapidly becoming an important clinical tool for doctors. The use of web based searching may help doctors to diagnose difficult cases.
    BibTeX:
    @article{Tang2006,
      author = {Tang, Hangwri and Ng, Jennifer Hwee Kwoon},
      title = {Googling for a diagnosis - use of Googgle as a diagnostic aid: internet based study},
      journal = {BRITISH MEDICAL JOURNAL},
      year = {2006},
      volume = {333},
      number = {7579},
      pages = {1143-1145},
      doi = {{10.1136/bmj.39003.640567.AE}}
    }
    
    Tang, W., Halpern, B., Shilov, I., Seymour, S., Keating, S., Loboda, A., Patel, A., Schaeffer, D. & Nuwaysir, L. Discovering known and unanticipated protein modifications using MS/MS database searching {2005} ANALYTICAL CHEMISTRY
    Vol. {77}({13}), pp. {3931-3946} 
    article DOI  
    Abstract: We present an MS/MS database search algorithm with the following novel features: (1) a novel protein database structure containing extensive preindexing and (2) zone modification searching, which enables the rapid discovery of protein modifications of known (i.e., user-specified) and unanticipated delta masses. All of these features are implemented in Interrogator, the search engine that runs behind the Pro ID, Pro ICAT, and Pro QUANT software products. Speed benchmarks demonstrate that our modification-tolerant database search algorithm is 100-fold faster than traditional database search algorithms when used for comprehensive searches for a broad variety of modification species. The ability to rapidly search for a large variety of known as well as unanticipated modifications allows a significantly greater percentage of MS/MS scans to be identified. We demonstrate this with an example in which, out of a total of 473 identified MS/MS scans, 315 of these scans correspond to unmodified peptides, while 158 scans correspond to a wide variety of modified peptides. In addition, we provide specific examples where the ability to search for unanticipated modifications allows the scientist to discover: unexpected modifications that have biological significance; amino acid mutations; salt-adducted peptides in a sample that has nominally been desalted; peptides arising from nontryptic cleavage in a sample that has nominally been digested using trypsin; other unintended consequences of sample handling procedures.
    BibTeX:
    @article{Tang2005,
      author = {Tang, WH and Halpern, BR and Shilov, IV and Seymour, SL and Keating, SP and Loboda, A and Patel, AA and Schaeffer, DA and Nuwaysir, LM},
      title = {Discovering known and unanticipated protein modifications using MS/MS database searching},
      journal = {ANALYTICAL CHEMISTRY},
      year = {2005},
      volume = {77},
      number = {13},
      pages = {3931-3946},
      doi = {{10.1021/ac0481046}}
    }
    
    Taskiran, C., Chen, J., Albiol, A., Torres, L., Bouman, C. & Delp, E. ViBE: A compressed video database structured for active browsing and search {2004} IEEE TRANSACTIONS ON MULTIMEDIA
    Vol. {6}({1}), pp. {103-118} 
    article DOI  
    Abstract: In this paper, we describe a unique new paradigm for video database management known as ViBE (video indexing and browsing environment). ViBE is a browseable/searchable paradigm for organizing video data containing a large number of sequences. The system first segments video sequences into shots by using a new feature vector known as the Generalized Trace obtained from the DC-sequence of the compressed data. Each video shot is then represented by a hierarchical structure known as the shot tree. The shots are then classified into pseudo-semantic classes that describe the shot content. Finally, the results are presented to the user in an active browsing environment using a similarity pyramid data structure. The similarity pyramid allows the user to view the video database at various levels of detail. The user can also define semantic classes and reorganize the browsing environment based on relevance feedback. We describe how ViBE performs on a database of MPEG sequences.
    BibTeX:
    @article{Taskiran2004,
      author = {Taskiran, C and Chen, JY and Albiol, A and Torres, L and Bouman, CA and Delp, EJ},
      title = {ViBE: A compressed video database structured for active browsing and search},
      journal = {IEEE TRANSACTIONS ON MULTIMEDIA},
      year = {2004},
      volume = {6},
      number = {1},
      pages = {103-118},
      doi = {{10.1109/TMM.2003.819783}}
    }
    
    Taylor, G., Kim, Y., Forbes, A., Meng, F., McCarthy, R. & Kelleher, N. Web and database software for identification of intact proteins using ``top down'' mass spectrometry {2003} ANALYTICAL CHEMISTRY
    Vol. {75}({16}), pp. {4081-4086} 
    article DOI  
    Abstract: For the identification and characterization of proteins harboring posttranslational modifications (PTMs), a ``top down'' strategy using mass spectrometry has been forwarded recently but languishes without tailored software widely available. We describe a Web-based software and database suite called ProSight PTM constructed for large-scale proteome projects involving direct fragmentation of intact protein ions. Four main components of ProSight PTM are a database retrieval algorithm (Retriever), MySQL protein databases, a file/data manager, and a project tracker. Retriever performs probability-based identifications from absolute fragment ion masses, automatically compiled sequence tags, or a combination of the two, with graphical rendering and browsing of the results. The database structure allows known and putative protein forms to be searched, with prior or predicted PTM knowledge used during each search. Initial functionality is illustrated with a 36-kDa yeast protein identified from a processed cell extract after automated data acquisition using a quadrupole-FT hybrid mass spectrometer. A +142-Da Deltam on glyceraldehyde-3-phosphate dehydrogenase was automatically localized between Asp(90) and Asp(192), consistent with its two cystine residues (149 and 153) alkylated by acrylamide (+71 Da each) during the gel-based sample preparation. ProSight PTM is the first search engine and Web environment for identification of intact proteins (https://prosightptm.scs.uiuc.edu/).
    BibTeX:
    @article{Taylor2003,
      author = {Taylor, GK and Kim, YB and Forbes, AJ and Meng, FY and McCarthy, R and Kelleher, NL},
      title = {Web and database software for identification of intact proteins using ``top down'' mass spectrometry},
      journal = {ANALYTICAL CHEMISTRY},
      year = {2003},
      volume = {75},
      number = {16},
      pages = {4081-4086},
      doi = {{10.1021/ac0341721}}
    }
    
    Thelwall, M. Conceptualizing documentation on the Web: An evaluation of different heuristic-based models for counting links between university Web sites {2002} JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY
    Vol. {53}({12}), pp. {995-1005} 
    article DOI  
    Abstract: All known previous Web link studies have used the Web page as the primary indivisible source document for counting purposes. Arguments are presented to explain why this is not necessarily optimal and why other alternatives have the potential to produce better results. This is despite the fact that individual Web files are often the only choice if search engines are used for raw data and are the easiest basic Web unit to identify. The central issue is of defining the Web ``document'': that which should comprise the single indissoluble unit of coherent material. Three alternative heuristics are defined for the educational arena based upon the directory, the domain and the whole university site. These are then compared by implementing them on a set of 108 UK university institutional Web sites under the assumption that a more effective heuristic will tend to produce results that correlate more highly with institutional research productivity. It was discovered that the domain and directory models were able to successfully reduce the impact of anomalous linking behavior between pairs of Web sites, with the latter being the method of choice. Reasons are then given as to why a document model on its own cannot eliminate all anomalies in Web linking behavior. Finally, the results from all models give a clear confirmation of the very strong association between the research productivity of a UK university and the number of incoming links from its peers' Web sites.
    BibTeX:
    @article{Thelwall2002,
      author = {Thelwall, M},
      title = {Conceptualizing documentation on the Web: An evaluation of different heuristic-based models for counting links between university Web sites},
      journal = {JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY},
      year = {2002},
      volume = {53},
      number = {12},
      pages = {995-1005},
      doi = {{10.1002/asi.10135}}
    }
    
    Thelwall, M. Research dissemination and invocation on the Web {2002} ONLINE INFORMATION REVIEW
    Vol. {26}({6}), pp. {413-420} 
    article