hpiwowar's library 1578 articles

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Abstract  Increasingly, funding of academic research is carried out through the support of collaboration, rather than through single awards to a sole grant holder. The practice is well supported by evidence that larger, network-based research achieves high quality while leading to a number of capacity building benefits for the research system, although with significant transaction costs. However, the question of what kind of funding schemes should be made available to researchers is not a simple dichotomy between single grant-holder projects and networks. ...

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ABSTRACT This paper presents a study of incorporating domain-specific knowledge (ie, information about concepts and relationships between concepts in a certain domain) in an information retrieval (IR) system to improve its ...

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OBJECTIVES: Assess query expansion using thesaurus relationships and definitions in the UMLS Metathesaurus for improving searching performance. METHODS: The queries from a MEDLINE test collection (OHSUMED) were expanded using synonym, hierarchical, and related term information as well as term definitions from the UMLS Metathesaurus. Documents were retrieved from a word-statistical retrieval system and assessed for recall and precision based on relevance judgments from the test collection. RESULTS: All types of query expansion degraded aggregate retrieval performance as measured by recall and ...

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1531-605x Evaluation Studies Journal Article

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BACKGROUND: Few meta-analyses of randomised trials assess the quality of the studies included. Yet there is increasing evidence that trial quality can affect estimates of intervention efficacy. We investigated whether different methods of quality assessment provide different estimates of intervention efficacy evaluated in randomised controlled trials (RCTs). METHODS: We randomly selected 11 meta-analyses that involved 127 RCTs on the efficacy of interventions used for circulatory and digestive diseases, mental health, and pregnancy and childbirth. We replicated all the meta-analyses using published ...

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0140-6736 (Print) Journal Article

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There is considerable evidence that the translation rate of major basic science promises to clinical applications has been inefficient and disappointing. The deficiencies of translational science have often been proposed as an explanation for this failure. An alternative explanation is that until recently basic science advances have made oversimplified assumptions that have not matched the true etiological complexity of most common diseases; while clinical science has suffered from poor research practices, overt biases and conflicts of interest. The advent of molecular ...

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1479-5876 (Electronic) Editorial

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Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. We investigated global gene expression in surgical samples of brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower-grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix remodeling. We found that the gene expression ...

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0027-8424 Journal Article

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Global analysis of gene expression by using DNA microarrays is employed increasingly to search for differences in biological properties between normal and diseased tissue. In such studies, expression that deviates from defined thresholds commonly is used for creating genetic signatures that characterize disease vs. normality. Although it is axiomatic that the threshold parameters applied to microarray analysis will alter the contents of such genetic signatures, the extent to which threshold choice can affect the fundamental conclusions made from microarray-based studies has ...

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0027-8424 Journal Article

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Both proteomic and genomic methods offer promise for the classification of human lung carcinomas. This review summarizes the range of proteomic methods in development for lung cancer classification, and describes a number of recent analyses of messenger RNA expression in lung cancer. Multiple independent studies of mRNA expression profiles in lung adenocarcinoma have proven highly reproducible. Analyses of the relationship between expression profiles and tumor development and differentiation, the presence or absence of specific pathogenic mutations, patient prognosis and survival after ...

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Almost two years after instituting the requirement for submitting microarray studies to GEO, Physiological Genomics decided to take a look at the process. In September 2004, we surveyed 76 scientists who have had microarray studies published in this journal and 237 more who reviewed microarray papers for the journal. Overall, 29% of them responded to our survey (Fig. 1). ...

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1531-2267 (Electronic) News

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The Human Genome Project, in accomplishing its goal of sequencing one human genome, heralded a new era of research, a component of which is the systematic study of human genetic variation. Despite delays, the Human Genome Diversity Project has started to make progress in understanding the patterns of this variation and its causes, and also promises to provide important information for biomedical studies. ...

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1471-0056 Journal Article Review

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0140-6736 (Print) Comment Journal Article

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Context The relative merits of various study designs and their placement in hierarchies of evidence are often discussed. However, there is limited knowledge about the relative citation impact of articles using various study designs. Objective To determine whether the type of study design affects the rate of citation in subsequent articles. Design and Setting We measured the citation impact of articles using various study designs--including meta-analyses, randomized controlled trials, cohort studies, case-control studies, case reports, nonsystematic reviews, and decision analysis or ...

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We present an interactive literature based biomedical discovery support system (BITOLA). The goal of the system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database Medline. To make the system more suitable for disease candidate gene discovery and to decrease the number of candidate relations, we integrate background knowledge about the chromosomal location of the starting disease as well as the chromosomal location of the candidate genes from ...

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0926-9630 Journal Article

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The National Library of Medicine's Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain. The UMLS is used for research and development in a range of different applications, including natural language processing (NLP). In this paper we investigate the nature of the strings found in the UMLS Metathesaurus and evaluate them for their usefulness in NLP. We begin by identifying a number of properties that might allow us to predict the likelihood of a given ...

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1531-605x Journal Article

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1568-9972 (Print) Journal Article Review

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Acute lymphoblastic leukemia (ALL) can be cured with combination chemotherapy in over 75% of children, but the cause of treatment failure in the remaining patients is unknown. We determined the sensitivity of ALL cells to individual antileukemic agents in 441 patients and used a genome-wide approach to identify 45 genes differentially expressed in ALL exhibiting crossresistance to prednisolone, vincristine, asparaginase, and daunorubicin. We also identified a distinct phenotype of discordant resistance to asparaginase and vincristine and 139 genes whose expression was ...

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1535-6108 Journal article

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No abstract. ...

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1476-4598 Journal article

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by content- algorithm [20] (see Fig the impact of content- browsing tool on genomics track [7], which employed ten-year ...

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The rapid advances in high-throughput biotechnologies such as DNA microarrays and mass spectrometry have generated vast amounts of data ranging from gene expression to proteomics data. The large size and complexity involved in analyzing such data demand a significant amount of computing power. High-performance computation (HPC) is an attractive and increasingly affordable approach to help meet this challenge. There is a spectrum of techniques that can be used to achieve computational speedup with varying degrees of impact in terms of how ...

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1067-5027 Journal Article

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You’ve long been enamored with the Python language, and have mastered its many nuances. Yet something seems to be missing—a productivity boost that you know is possible but you’re not sure how to go about it. This was the sentiment of so many developers before discovering Agile programming paradigm, which embraces concepts such as automation, effective code management, and test–driven development. Foundations of Agile Python Development is the first book to apply these sought–after principles to Python developers, introducing both the ...

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BACKGROUND: Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed, provide clues to the molecular organization of diverse cells and to the potential roles of the genes. RESULTS: Here we describe ...

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1465-6914 Journal Article

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MOTIVATION: A large volume of experimental data on protein phosphorylation is buried in the fast-growing PubMed literature. While of great value, such information is limited in databases owing to the laborious process of literature-based curation. Computational literature mining holds promise to facilitate database curation. RESULTS: A rule-based system, RLIMS-P (Rule-based LIterature Mining System for Protein Phosphorylation), was used to extract protein phosphorylation information from MEDLINE abstracts. An annotation-tagged literature corpus developed at PIR was used to evaluate the system for finding ...

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1367-4803 Journal Article

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Evaluation 6. Evaluation results and discussion 7 Unsupervised approaches normally define learning-free function between two authors ...

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All the long-standing archives at economics journals do not facilitate the reproduction of published results. The data-only archives at Journal of Business and Economic Statistics and Economic Journal fail in part because most authors do not contribute data. Results published in the FRB St. Louis Review can rarely be reproduced using the data+code in the journal archive. Recently created archives at top journals should avoid the mistakes of their predecessors. We categorize reasons for archives' failures and identify successful policies. ...

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This paper presents the effect of reflecting all query aspects on query expansion using local context analysis and similarity measure in improving MEDLINE document retrieval. For the OHSUMED test collection, a comparison of our experimental results shows that they are more effective than using the standard Rocchio inverted exclamation mark s weight, and all query aspects are better reflected by the local context analysis. ...

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OBJECTIVE: To characterize the relationships among UMLS concepts that co-occur as MeSH descriptors in MEDLINE citations (1990-1999). DESIGN: 18,485 UMLS concepts involved in 7,928,608 directed pairs of co-occurring concepts were studied. For each directed pair of concepts C1-C2: (i) the "family" of C1 was built, using the UMLS Metathesaurus, and we tested whether or not C2 belonged to C1's family; (ii) we used the semantic categorization of Metathesaurus concepts through the UMLS Semantic Network and Semantic Groups to represent the semantics ...

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1569-6332 Journal Article

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An Editors' Comment on " the " by BD McCullough, Kerry Anne McGeary, and Teresa D. Harrison. Author info ...

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The growing numbers of topically relevant biomedical publications readily available due to advances in document retrieval methods pose a challenge to clinicians practicing evidence-based medicine. It is increasingly time consuming to acquire and critically appraise the available evidence. This problem could be addressed in part if methods were available to automatically recognize rigorous studies immediately applicable in a specific clinical situation. We approach the problem of recognizing studies containing useable clinical advice from retrieved topically relevant articles as a binary classification ...

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Political science is a community enterprise; the community of empirical political scientists needs access to the body of data necessary to replicate existing studies to understand, evaluate, and especially build on this work. Unfortunately, the norms we have in place now do not encourage, or in some cases even permit, this aim. Following are suggestions that would facilitate replication and are easy to implement- by teachers, students, dissertation writers, graduate pro- grams, authors, reviewers, funding agencies, and journal and book editors. ...

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Motivation. The UMLS has been used in natural language processing applications such as information retrieval and information extraction systems. The mapping of free-text to UMLS concepts is important for these applications. To improve the mapping, we need a method to disambiguate terms that possess multiple UMLS concepts. In the general English domain, machine-learning techniques have been applied to sense-tagged corpora, in which senses (or concepts) of ambiguous terms have been annotated (mostly manually). Sense disambiguation classifiers are then derived to determine ...

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1067-5027 Evaluation Studies Journal Article

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0212-6567 (Print) Editorial

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Sixteen years ago, the National Academy of Sciences published a report on data archiving for the behavioral sciences entitled Sharing Research Data. Much of the report was devoted to a discussion of objections by behavioral scientists to having databases. In the years since the report was published, the effort to create data archives for psychology has limped along without generating widespread enthusiasm, and the objections to databases have remained unchanged. That lack of change is remarkable because experiences with the databases ...

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Accurate and complete safety data are indispensable for the proper evaluation of the benefit-to-harm ratio of medical interventions. We evaluated whether a systematic review and meta-analysis of standardized safety data is feasible by requesting information on side effects directly from the investigators of all 38 antibiotic trials on acute sinusitis published in the last decade. We requested standardized information on gastrointestinal toxicity outcomes, including hospitalizations, discontinuations, and days with nausea/vomiting, diarrhea, or both. Responses were received only for 16 trials (42%), ...

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0895-4356 (Print) Journal Article