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  1. Improving accuracy for identifying related PubMed queries by an integrated approach.

    PubMed

    Lu, Zhiyong; Wilbur, W John

    2009-10-01

    PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments.

  2. Improving accuracy for identifying related PubMed queries by an integrated approach

    PubMed Central

    Lu, Zhiyong; Wilbur, W. John

    2009-01-01

    PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users’ search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1,539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1,396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments. PMID:19162232

  3. Validation of a search strategy to identify nutrition trials in PubMed using the relative recall method.

    PubMed

    Durão, Solange; Kredo, Tamara; Volmink, Jimmy

    2015-06-01

    To develop, assess, and maximize the sensitivity of a search strategy to identify diet and nutrition trials in PubMed using relative recall. We developed a search strategy to identify diet and nutrition trials in PubMed. We then constructed a gold standard reference set to validate the identified trials using the relative recall method. Relative recall was calculated by dividing the number of references from the gold standard our search strategy identified by the total number of references in the gold standard. Our gold standard comprised 298 trials, derived from 16 included systematic reviews. The initial search strategy identified 242 of 298 references, with a relative recall of 81.2% [95% confidence interval (CI): 76.3%, 85.5%]. We analyzed titles and abstracts of the 56 missed references for possible additional terms. We then modified the search strategy accordingly. The relative recall of the final search strategy was 88.6% (95% CI: 84.4%, 91.9%). We developed a search strategy to identify diet and nutrition trials in PubMed with a high relative recall (sensitivity). This could be useful for establishing a nutrition trials register to support the conduct of future research, including systematic reviews. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Enriching PubMed Related Article Search with Sentence Level Co-citations

    PubMed Central

    Tran, Nam; Alves, Pedro; Ma, Shuangge

    2009-01-01

    PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. In this paper, we propose to enrich PubMed with a new type of related article link based on citations within a single sentence (i.e. sentence level co-citations or SLCs). Using different similarity metrics, we demonstrated that articles linked by SLCs are highly related. We also showed that only half of SLCs are found among PubMed related article links. Additionally, we discuss how the citing sentence of an SLC explains the connection between two articles. PMID:20351935

  5. Validation of search filters for identifying pediatric studies in PubMed.

    PubMed

    Leclercq, Edith; Leeflang, Mariska M G; van Dalen, Elvira C; Kremer, Leontien C M

    2013-03-01

    To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity, precision, specificity, accuracy, and number needed to read (NNR). An optimal search filter will have a high sensitivity and high precision with a low NNR. In addition to the PubMed Limits: All Child: 0-18 years filter (in May 2012 renamed to PubMed Filter Child: 0-18 years), 6 search filters for identifying studies including children were identified: 3 developed by Kastner et al, 1 developed by BestBets, one by the Child Health Field, and 1 by the Cochrane Childhood Cancer Group. Three search filters (Cochrane Childhood Cancer Group, Child Health Field, and BestBets) had the highest sensitivity (99.3%, 99.5%, and 99.3%, respectively) but a lower precision (64.5%, 68.4%, and 66.6% respectively) compared with the other search filters. Two Kastner search filters had a high precision (93.0% and 93.7%, respectively) but a low sensitivity (58.5% and 44.8%, respectively). They failed to identify many pediatric studies in our datasets. The search terms responsible for false-positive results in the reference dataset were determined. With these data, we developed a new search filter for identifying studies with children in PubMed with an optimal sensitivity (99.5%) and precision (69.0%). Search filters to identify studies including children either have a low sensitivity or a low precision with a high NNR. A new pediatric search filter with a high sensitivity and a low NNR has been developed. Copyright © 2013 Mosby, Inc. All rights reserved.

  6. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    PubMed

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  7. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

    PubMed Central

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as ‘CHEMICAL-1 compared to CHEMICAL-2.’ With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical–disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked

  8. Evaluation of PubMed filters used for evidence-based searching: validation using relative recall.

    PubMed

    Hoogendam, Arjen; de Vries Robbé, Pieter F; Stalenhoef, Anton F H; Overbeke, A John P M

    2009-07-01

    The research sought to determine the value of PubMed filters and combinations of filters in literature selected for systematic reviews on therapy-related clinical questions. References to 35,281 included and 48,514 excluded articles were extracted from 2,629 reviews published prior to January 2008 in the Cochrane Database of Systematic Reviews and sent to PubMed with and without filters. Sensitivity, specificity, and precision were calculated from the percentages of unfiltered and filtered references retrieved for each review and averaged over all reviews. Sensitivity of the Sensitive Clinical Queries filter was reasonable (92.7%, 92.1-93.3); specificity (16.1%, 15.1-17.1) and precision were low (49.5%, 48.5-50.5). The Specific Clinical Queries and the Single Term Medline Specific filters performed comparably (sensitivity, 78.2%, 77.2-79.2 vs. 78.0%; 77.0-79.0; specificity, 52.0%, 50.8-53.2 vs. 52.3%, 51.1-53.5; precision, 60.4%, 59.4-61.4 vs. 60.6%, 59.6-61.6). Combining the Abridged Index Medicus (AIM) and Single Term Medline Specific (65.2%, 63.8-66.6), Two Terms Medline Optimized (64.2%, 62.8-65.6), or Specific Clinical Queries filters (65.0%, 63.6-66.4) yielded the highest precision. Sensitive and Specific Clinical Queries filters used to answer questions about therapy will result in a list of clinical trials but cannot be expected to identify only methodologically sound trials. The Specific Clinical Queries filters are not suitable for questions regarding therapy that cannot be answered with randomized controlled trials. Combining AIM with specific PubMed filters yields the highest precision in the Cochrane dataset.

  9. Evaluation of PubMed filters used for evidence-based searching: validation using relative recall

    PubMed Central

    Hoogendam, Arjen; de Vries Robbé, Pieter F.; Stalenhoef, Anton F.H.; Overbeke, A. John P.M.

    2009-01-01

    Objectives: The research sought to determine the value of PubMed filters and combinations of filters in literature selected for systematic reviews on therapy-related clinical questions. Methods: References to 35,281 included and 48,514 excluded articles were extracted from 2,629 reviews published prior to January 2008 in the Cochrane Database of Systematic Reviews and sent to PubMed with and without filters. Sensitivity, specificity, and precision were calculated from the percentages of unfiltered and filtered references retrieved for each review and averaged over all reviews. Results: Sensitivity of the Sensitive Clinical Queries filter was reasonable (92.7%, 92.1–93.3); specificity (16.1%, 15.1–17.1) and precision were low (49.5%, 48.5–50.5). The Specific Clinical Queries and the Single Term Medline Specific filters performed comparably (sensitivity, 78.2%, 77.2–79.2 vs. 78.0%; 77.0–79.0; specificity, 52.0%, 50.8–53.2 vs. 52.3%, 51.1–53.5; precision, 60.4%, 59.4–61.4 vs. 60.6%, 59.6–61.6). Combining the Abridged Index Medicus (AIM) and Single Term Medline Specific (65.2%, 63.8–66.6), Two Terms Medline Optimized (64.2%, 62.8–65.6), or Specific Clinical Queries filters (65.0%, 63.6–66.4) yielded the highest precision. Conclusions: Sensitive and Specific Clinical Queries filters used to answer questions about therapy will result in a list of clinical trials but cannot be expected to identify only methodologically sound trials. The Specific Clinical Queries filters are not suitable for questions regarding therapy that cannot be answered with randomized controlled trials. Combining AIM with specific PubMed filters yields the highest precision in the Cochrane dataset. PMID:19626144

  10. Google Scholar versus PubMed in locating primary literature to answer drug-related questions.

    PubMed

    Freeman, Maisha Kelly; Lauderdale, Stacy A; Kendrach, Michael G; Woolley, Thomas W

    2009-03-01

    were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

  11. The Relation between Iranian Medical Science Research in PubMed and Burden of Disease.

    PubMed

    Foroughi, Zahra; Siamian, Hasan; Alizadeh-Navaei, Reza; Davodi, Ali

    2016-07-16

    Scientific productions have been accelerated in Iran in past decades but its association with health problems and disease burden is doubtful. The aim of this study is assessment of the relationship between scientific productions with disease burden in Iran in PubMed dataset during 2010 to 2014. The study was performed with the library method. Data Gathered using Scientometrics indicators and direct observation. The current research includes all articles written by Iranian researchers during 2010 to 2014 which were published in PubMed-indexed journals. The search was performed using keywords included road accident, ischaemic heart diseases, major depression disorders and cerebral vascular diseases. In total 910 articles had been published PubMed -indexed journals. Among them Substance-Related Disorders and Accidents, Traffic had the highest (263 records) and lowest (94 records) records respectively. There was not a direct correlation between Years of Life Lost, Years Lost due to Disability and mortality rate with scientific productions. our results showed Iranian scientific productions in PubMed data set are not related to disease burden however they are not related to high mortality diseases.

  12. The Relation between Iranian Medical Science Research in PubMed and Burden of Disease

    PubMed Central

    Foroughi, Zahra; Siamian, Hasan; Alizadeh-Navaei, Reza; Davodi, Ali

    2016-01-01

    Introduction: Scientific productions have been accelerated in Iran in past decades but its association with health problems and disease burden is doubtful. The aim of this study is assessment of the relationship between scientific productions with disease burden in Iran in PubMed dataset during 2010 to 2014. Method: The study was performed with the library method. Data Gathered using Scientometrics indicators and direct observation. The current research includes all articles written by Iranian researchers during 2010 to 2014 which were published in PubMed–indexed journals. The search was performed using keywords included road accident, ischaemic heart diseases, major depression disorders and cerebral vascular diseases. Results: In total 910 articles had been published PubMed -indexed journals. Among them Substance-Related Disorders and Accidents, Traffic had the highest (263 records) and lowest (94 records) records respectively. There was not a direct correlation between Years of Life Lost, Years Lost due to Disability and mortality rate with scientific productions. Conclusions: our results showed Iranian scientific productions in PubMed data set are not related to disease burden however they are not related to high mortality diseases. PMID:27708491

  13. Updating a bibliography using the related articles function within PubMed.

    PubMed Central

    Liu, X.; Altman, R. B.

    1998-01-01

    Comprehensive bibliographies are useful for conducting reviews of the literature, and for assessing the progress within a field. These bibliographies may be broad and inclusive, or focused and precise in their inclusion criteria. In either case, the task of maintaining a complete bibliography within a particular area of research is made difficult by the diversity, complexity and huge volume of newly published literature. In an effort to effectively and automatically retrieve relevant literature, different search strategies and indexing tools have been developed, including the RELATED ARTICLES function provided with the PubMed system. In this paper, we report a program for incremental updates of a bibliography using the PubMed RELATED ARTICLES function. Given a highly specialized starting bibliography of experimental measurements of the structure of the 30S bacterial ribosomal subunit, the system was applied to find additional relevant references. For this particular task, the system has a recall of 75%, a strict precision of 32% and a partial precision of 42%. Our results are notable because although the RELATED ARTICLES function is purely statistical, it is nonetheless able to select a very narrowly defined set of articles from the literature. We discuss the tradeoffs between having a user to evaluate many articles of possible interest in a single session, versus asking a user to evaluate a small set of articles on a periodic basis. PMID:9929319

  14. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

    PubMed

    Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

    2010-08-23

    The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the

  15. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface

    PubMed Central

    2010-01-01

    Background The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. Methods A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). Results The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). Conclusions As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized

  16. Identifying outcome reporting bias in randomised trials on PubMed: review of publications and survey of authors

    PubMed Central

    Chan, An-Wen; Altman, Douglas G

    2005-01-01

    Objective To examine the extent and nature of outcome reporting bias in a broad cohort of published randomised trials. Design Retrospective review of publications and follow up survey of authors. Cohort All journal articles of randomised trials indexed in PubMed whose primary publication appeared in December 2000. Main outcome measures Prevalence of incompletely reported outcomes per trial; reasons for not reporting outcomes; association between completeness of reporting and statistical significance. Results 519 trials with 553 publications and 10 557 outcomes were identified. Survey responders (response rate 69%) provided information on unreported outcomes but were often unreliable—for 32% of those who denied the existence of such outcomes there was evidence to the contrary in their publications. On average, over 20% of the outcomes measured in a parallel group trial were incompletely reported. Within a trial, such outcomes had a higher odds of being statistically non-significant compared with fully reported outcomes (odds ratio 2.0 (95% confidence interval 1.6 to 2.7) for efficacy outcomes; 1.9 (1.1 to 3.5) for harm outcomes). The most commonly reported reasons for omitting efficacy outcomes included space constraints, lack of clinical importance, and lack of statistical significance. Conclusions Incomplete reporting of outcomes within published articles of randomised trials is common and is associated with statistical non-significance. The medical literature therefore represents a selective and biased subset of study outcomes, and trial protocols should be made publicly available. PMID:15681569

  17. TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations

    PubMed Central

    Miyao, Yusuke; Collier, Nigel

    2017-01-01

    Background Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. Objective This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. Methods We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. Results The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. Conclusions We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. PMID:28468748

  18. [A statistical analysis and perspective of headache-related papers covered in 2011 PubMed].

    PubMed

    Zhang, Ming-jie; Yu, Sheng-yuan; Chu, Bing-qian; Dai, Wei

    2013-01-01

    To investigate the distribution and hot spots of literatures on headache by bibliometric analysis in order to provide reference for further study. Literatures that contained headache or migraine in text words published in 2011 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were searched. Journals, countries and subjects were bibliometrically analysed. There were 3683 papers involved to headache published in PubMed in 2011, of which 1527 papers were on headache research. The number of papers on headache research published by USA was the most followed by Italy and Germany (USA 23.25%, Italy 10.74%, Germany 5.83%). The mainly studied subjects were therapy (29.60%), pathophysiology (18.66%) and etiology (16.31%). 14.86% papers published in Cephalalgia, which is one of the most important journals, reported negative results. The emphasis of headache research was on migraine. Therapy, pathophysiology and etiology were the hot spot. Literatures with negative result attracted authors to give the more attention.

  19. Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature

    PubMed Central

    Song, Michael M.; Simonsen, Cheryl K.; Wilson, Joanna D.

    2016-01-01

    Abstract Background: An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. Methods: PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Results: Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. Conclusions: The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH. PMID:26555409

  20. Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature.

    PubMed

    Song, Michael M; Simonsen, Cheryl K; Wilson, Joanna D; Jenkins, Marjorie R

    2016-02-01

    An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH.

  1. Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level.

    PubMed

    Spiroski, Mirko

    2016-06-15

    The aim of this study was to analyze relative citation ratio (RCR) of top twenty Macedonian biomedical scientists with a new metric that uses citation rates to measure influence at the article level. Top twenty Macedonian biomedical scientists were identified by GoPubMed on the base of the number of deposited abstracts in PubMed, corrected with the data from previously published paper, and completed with the Macedonian biomedical scientists working in countries outside the Republic of Macedonia, but born or previously worked in the country. iCite was used as a tool to access a dashboard of bibliometrics for papers associated with a portfolio. The biggest number of top twenty Macedonian biomedical scientists has RCR lower than one. Only four Macedonian biomedical scientists have bigger RCR in comparison with those in PubMed. The most prominent RCR of 2.29 has Rosoklija G. RCR of the most influenced individual papers deposited in PubMed has shown the biggest value for the paper of Efremov D (35.19). This paper has the biggest number of authors (860). It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists.

  2. Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level

    PubMed Central

    Spiroski, Mirko

    2016-01-01

    AIM: The aim of this study was to analyze relative citation ratio (RCR) of top twenty Macedonian biomedical scientists with a new metric that uses citation rates to measure influence at the article level. MATERIAL AND METHODS: Top twenty Macedonian biomedical scientists were identified by GoPubMed on the base of the number of deposited abstracts in PubMed, corrected with the data from previously published paper, and completed with the Macedonian biomedical scientists working in countries outside the Republic of Macedonia, but born or previously worked in the country. iCite was used as a tool to access a dashboard of bibliometrics for papers associated with a portfolio. RESULTS: The biggest number of top twenty Macedonian biomedical scientists has RCR lower than one. Only four Macedonian biomedical scientists have bigger RCR in comparison with those in PubMed. The most prominent RCR of 2.29 has Rosoklija G. RCR of the most influenced individual papers deposited in PubMed has shown the biggest value for the paper of Efremov D (35.19). This paper has the biggest number of authors (860). CONCLUSION: It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists. PMID:27335586

  3. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  4. The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly "The Emperor of All Maladies"?

    PubMed

    Reyes-Aldasoro, Constantino Carlos

    2017-01-01

    In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain "DNA", "Computational" or "Mathematical" have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK's Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material.

  5. The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly “The Emperor of All Maladies”?

    PubMed Central

    2017-01-01

    In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain “DNA”, “Computational” or “Mathematical” have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK’s Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material. PMID:28282418

  6. Concern noted: A descriptive study of editorial expressions of concern in PubMed and PubMed Central

    PubMed Central

    Vaught, Melissa; Jordan, Diana C.; Bastian, Hilda

    2017-01-01

    Background An editorial expression of concern (EEoC) is issued by editors or publishers to draw attention to potential problems in a publication, without itself constituting a retraction or correction. Methods We searched PubMed, PubMed Central (PMC), and Google Scholar to identify EEoCs issued for publications in PubMed and PMC up to 22 August 2016. We also searched the archives of the Retraction Watch blog, some journal and publisher websites, and studies of EEoCs. In addition, we searched for retractions of EEoCs and affected articles in PubMed up to 8 December 2016. We analyzed overall historical trends, as well as reported reasons and subsequent editorial actions related to EEoCs issued between August 2014 and August 2016. Results After screening 5,076 records, we identified 230 EEoCs that affect 300 publications indexed in PubMed, the earliest issued in 1985. Half of the primary EEoCs were issued between 2014 and 2016 (52%). We found evidence of some EEoCs that had been removed by the publisher without leaving a record and some were not submitted for PubMed or PMC indexing. A minority of publications affected by EEoCs had been retracted by early December 2016 (25%). For the subset of 92 EEoCs issued between August 2014 and August 2016, affecting 99 publications, the rate of retraction was similar (29%). The majority of EEoCs were issued because of concerns with validity of data, methods, or interpretation of the publication (68%), and 31% of cases remained open. Issues with images were raised in 40% of affected publications. Ongoing monitoring after the study identified another 17 EEoCs to year’s end in 2016, increasing the number of EEoCs to 247 and publications in PubMed known to be affected by EEoCs to 320 at the end of 2016. Conclusions EEoCs have been rare publishing events in the biomedical literature, but their use has been increasing. Most have not led to retractions, and many remain unresolved. Lack of prominence and inconsistencies in management

  7. Scientific publications and research groups on alcohol consumption and related problems worldwide: authorship analysis of papers indexed in PubMed and Scopus databases (2005 to 2009).

    PubMed

    González-Alcaide, Gregorio; Castelló-Cogollos, Lourdes; Castellano-Gómez, Miguel; Agullo-Calatayud, Víctor; Aleixandre-Benavent, Rafael; Alvarez, Francisco Javier; Valderrama-Zurián, Juan Carlos

    2013-01-01

    The research of alcohol consumption-related problems is a multidisciplinary field. The aim of this study is to analyze the worldwide scientific production in the area of alcohol-drinking and alcohol-related problems from 2005 to 2009. A MEDLINE and Scopus search on alcohol (alcohol-drinking and alcohol-related problems) published from 2005 to 2009 was carried out. Using bibliometric indicators, the distribution of the publications was determined within the journals that publish said articles, specialty of the journal (broad subject terms), article type, language of the publication, and country where the journal is published. Also, authorship characteristics were assessed (collaboration index and number of authors who have published more than 9 documents). The existing research groups were also determined. About 24,100 documents on alcohol, published in 3,862 journals, and authored by 69,640 authors were retrieved from MEDLINE and Scopus between the years 2005 and 2009. The collaboration index of the articles was 4.83 ± 3.7. The number of consolidated research groups in the field was identified as 383, with 1,933 authors. Documents on alcohol were published mainly in journals covering the field of "Substance-Related Disorders," 23.18%, followed by "Medicine," 8.7%, "Psychiatry," 6.17%, and "Gastroenterology," 5.25%. Research on alcohol is a consolidated field, with an average of 4,820 documents published each year between 2005 and 2009 in MEDLINE and Scopus. Alcohol-related publications have a marked multidisciplinary nature. Collaboration was common among alcohol researchers. There is an underrepresentation of alcohol-related publications in languages other than English and from developing countries, in MEDLINE and Scopus databases. Copyright © 2012 by the Research Society on Alcoholism.

  8. Predicting clicks of PubMed articles.

    PubMed

    Mao, Yuqing; Lu, Zhiyong

    2013-01-01

    Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed.

  9. Predicting clicks of PubMed articles

    PubMed Central

    Mao, Yuqing; Lu, Zhiyong

    2013-01-01

    Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed. PMID:24551386

  10. Identifying Health-Related Topics on Twitter

    NASA Astrophysics Data System (ADS)

    Prier, Kyle W.; Smith, Matthew S.; Giraud-Carrier, Christophe; Hanson, Carl L.

    Public health-related topics are difficult to identify in large conversational datasets like Twitter. This study examines how to model and discover public health topics and themes in tweets. Tobacco use is chosen as a test case to demonstrate the effectiveness of topic modeling via LDA across a large, representational dataset from the United States, as well as across a smaller subset that was seeded by tobacco-related queries. Topic modeling across the large dataset uncovers several public health-related topics, although tobacco is not detected by this method. However, topic modeling across the tobacco subset provides valuable insight about tobacco use in the United States. The methods used in this paper provide a possible toolset for public health researchers and practitioners to better understand public health problems through large datasets of conversational data.

  11. GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

    PubMed

    Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

    2010-02-01

    Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

  12. Gaps in affiliation indexing in Scopus and PubMed

    PubMed Central

    Schmidt, Cynthia M.; Cox, Roxanne; Fial, Alissa V.; Hartman, Teresa L.; Magee, Martha L.

    2016-01-01

    Objective The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. Methods First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. Results We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Conclusions Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators. PMID:27076801

  13. Gaps in affiliation indexing in Scopus and PubMed.

    PubMed

    Schmidt, Cynthia M; Cox, Roxanne; Fial, Alissa V; Hartman, Teresa L; Magee, Martha L

    2016-04-01

    The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators.

  14. [Bibliometric analysis of current glaucoma research based on Pubmed database].

    PubMed

    Huang, Wen-bin; Wang, Wei; Zhou, Min-wen; Chen, Shi-da; Zhang, Xiu-lan

    2013-11-01

    To survey the distribution pattern and subject domain knowledge of worldwide glaucoma research based on literatures in Pubmed database. Literatures on glaucoma published in 2007 to 2011 were identified in Pubmed database. The analytic items of an article include published year, country, language author, and journal. After core mesh terms had been characterized by BICOMS, the co-occurrence matrix was built. Cluster analysis was finished by SPSS 20.0. Then visualized network was drawn using ucinet 6.0. Totally 6427 literatures were included, the number of annual articles changed slightly between 2007 and 2011. The United States, England, Germany, Australia, and France together accounted for 77.63% of articles. There were 52 high-frequency subjects and hot topics were clustered into the following 10 categories: (1) Pathology of optic disc and nerve fibers and OCT application, (2) METHODS: of visual field (VF) and visual function examination, (3) Glaucoma drug medications, (4) Pathology and physiology of primary open angle glaucoma (POAG) including VF and intraocular pressure (IOP), (5) Glaucoma surgery, (6) Gene research related to POAG, (7) Glaucoma disease pathology and animal models, (8) Ocular hypertension (OHT) induced complications and corneal changes, (9) Etiology of congenital glaucoma and complications, (10) Etiology and epidemiology of glaucoma. The visualized domain knowledge mapping was successfully built. The pathology of optic disc and nerve fibers, medications, and surgery were well developed. Study on IOP and visual field was in the core domain, which have an important link to etiology, diagnosis, and therapy. The researches on glaucomatous gene, disease pathology model, congenital glaucoma, etiology and epidemiology were not developed well, which are of great promotion space. The distribution pattern and subject domain knowledge of worldwide glaucoma research in the recent five years were shown by using bibliometric analysis.Western developed

  15. Comparison of PubMed and Google Scholar literature searches.

    PubMed

    Anders, Michael E; Evans, Dennis P

    2010-05-01

    Literature searches are essential to evidence-based respiratory care. To conduct literature searches, respiratory therapists rely on search engines to retrieve information, but there is a dearth of literature on the comparative efficiencies of search engines for researching clinical questions in respiratory care. To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark. We performed literature searches with PubMed and Google Scholar, on 3 clinical topics. In PubMed we used the Clinical Queries search filter. In Google Scholar we used the search filters in the Advanced Scholar Search option. We used the reference list of a related Cochrane Collaboration evidence-based systematic review as the benchmark for each of the search results. We calculated recall (sensitivity) and precision (positive predictive value) with 2 x 2 contingency tables. We compared the results with the chi-square test of independence and Fisher's exact test. PubMed and Google Scholar had similar recall for both overall search results (71% vs 69%) and full-text results (43% vs 51%). PubMed had better precision than Google Scholar for both overall search results (13% vs 0.07%, P < .001) and full-text results (8% vs 0.05%, P < .001). Our results suggest that PubMed searches with the Clinical Queries filter are more precise than with the Advanced Scholar Search in Google Scholar for respiratory care topics. PubMed appears to be more practical to conduct efficient, valid searches for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes.

  16. Risk factors for bladder cancer: challenges of conducting a literature search using PubMed.

    PubMed

    Joshi, Ashish; Preslan, Elicia

    2011-04-01

    The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term "urinary bladder cancer" and a risk factor term (e.g., "cigarette smoking") and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F-measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms.

  17. Author Name Disambiguation for PubMed.

    PubMed

    Liu, Wanli; Islamaj Doğan, Rezarta; Kim, Sun; Comeau, Donald C; Kim, Won; Yeganova, Lana; Lu, Zhiyong; Wilbur, W John

    2014-04-01

    Log analysis shows that PubMed users frequently use author names in queries for retrieving scientific literature. However, author name ambiguity may lead to irrelevant retrieval results. To improve the PubMed user experience with author name queries, we designed an author name disambiguation system consisting of similarity estimation and agglomerative clustering. A machine-learning method was employed to score the features for disambiguating a pair of papers with ambiguous names. These features enable the computation of pairwise similarity scores to estimate the probability of a pair of papers belonging to the same author, which drives an agglomerative clustering algorithm regulated by 2 factors: name compatibility and probability level. With transitivity violation correction, high precision author clustering is achieved by focusing on minimizing false-positive pairing. Disambiguation performance is evaluated with manual verification of random samples of pairs from clustering results. When compared with a state-of-the-art system, our evaluation shows that among all the pairs the lumping error rate drops from 10.1% to 2.2% for our system, while the splitting error rises from 1.8% to 7.7%. This results in an overall error rate of 9.9%, compared with 11.9% for the state-of-the-art method. Other evaluations based on gold standard data also show the increase in accuracy of our clustering. We attribute the performance improvement to the machine-learning method driven by a large-scale training set and the clustering algorithm regulated by a name compatibility scheme preferring precision. With integration of the author name disambiguation system into the PubMed search engine, the overall click-through-rate of PubMed users on author name query results improved from 34.9% to 36.9%.

  18. Searching the literature using medical subject headings versus text word with PubMed.

    PubMed

    Chang, Angela A; Heskett, Karen M; Davidson, Terence M

    2006-02-01

    This study was conducted to investigate the performance of two search strategies in the retrieval of information from the National Library of Medicine (NLM) on otolaryngology-head and neck surgery related conditions and diagnoses using PubMed. Two search strategies-one based on the use of Medical Subject Headings (MeSH) and the second based on text word searching-were compared. The MeSH search provided a more efficient search than the text word search. Head and neck surgeons can most efficiently search the NLM using PubMed as a search engine by initiating the search with MeSH terms. Once a key article is identified, the searcher should use the "Related Articles" feature.

  19. Acta informatica medica is indexed in pubmed and archived in pubmed central.

    PubMed

    Masic, Izet

    2013-03-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries.

  20. Acta Informatica Medica Is Indexed In Pubmed And Archived In Pubmed Central

    PubMed Central

    Masic, Izet

    2013-01-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries. PMID:23572852

  1. How Complementary and Alternative Medicine Practitioners Use PubMed

    PubMed Central

    Quint-Rapoport, Mia

    2007-01-01

    Background PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research. Objective This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners. Methods In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent. Results The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were

  2. SPELLING CORRECTION IN THE PUBMED SEARCH ENGINE.

    PubMed

    Wilbur, W John; Kim, Won; Xie, Natalie

    2006-11-01

    It is known that users of internet search engines often enter queries with misspellings in one or more search terms. Several web search engines make suggestions for correcting misspelled words, but the methods used are proprietary and unpublished to our knowledge. Here we describe the methodology we have developed to perform spelling correction for the PubMed search engine. Our approach is based on the noisy channel model for spelling correction and makes use of statistics harvested from user logs to estimate the probabilities of different types of edits that lead to misspellings. The unique problems encountered in correcting search engine queries are discussed and our solutions are outlined.

  3. SPELLING CORRECTION IN THE PUBMED SEARCH ENGINE

    PubMed Central

    Wilbur, W. John; Kim, Won; Xie, Natalie

    2007-01-01

    It is known that users of internet search engines often enter queries with misspellings in one or more search terms. Several web search engines make suggestions for correcting misspelled words, but the methods used are proprietary and unpublished to our knowledge. Here we describe the methodology we have developed to perform spelling correction for the PubMed search engine. Our approach is based on the noisy channel model for spelling correction and makes use of statistics harvested from user logs to estimate the probabilities of different types of edits that lead to misspellings. The unique problems encountered in correcting search engine queries are discussed and our solutions are outlined. PMID:18080004

  4. How Do Users Find Things with PubMed? Towards Automatic Utility Evaluation with User Simulations

    DTIC Science & Technology

    2008-02-01

    experimental variable was the algorithm for suggesting related articles. We considered two: • Using language modeling retrieval, implemented with Lemur [16...similarity algorithm in PubMed, accessed through the PubMed eUtils API.5 Quite explicitly, our goal was not to compare Lemur with PubMed, but rather to...for the simulation (utility). The top graph shows the greedy browsing strategy and the bottom graph the breadth-like browsing strategy, both with Lemur

  5. LGscore: A method to identify disease-related genes using biological literature and Google data.

    PubMed

    Kim, Jeongwoo; Kim, Hyunjin; Yoon, Youngmi; Park, Sanghyun

    2015-04-01

    Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which identifies disease-related genes using Google data and literature data. To implement this method, first, we construct a disease-related gene network using text-mining results. We then extract gene-gene interactions based on co-occurrences in abstract data obtained from PubMed, and calculate the weights of edges in the gene network by means of Z-scoring. The weights contain two values: the frequency and the Google search results. The frequency value is extracted from literature data, and the Google search result is obtained using Google. We assign a score to each gene through a network analysis. We assume that genes with a large number of links and numerous Google search results and frequency values are more likely to be involved in disease. For validation, we investigated the top 20 inferred genes for five different diseases using answer sets. The answer sets comprised six databases that contain information on disease-gene relationships. We identified a significant number of disease-related genes as well as candidate genes for Alzheimer's disease, diabetes, colon cancer, lung cancer, and prostate cancer. Our method was up to 40% more accurate than existing methods.

  6. Complex event extraction at PubMed scale

    PubMed Central

    Björne, Jari; Ginter, Filip; Pyysalo, Sampo; Tsujii, Jun'ichi; Salakoski, Tapio

    2010-01-01

    Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction. Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information. Availability: The event detection system and extracted data are open source licensed and available at http://bionlp.utu.fi/. Contact: jari.bjorne@utu.fi PMID:20529932

  7. Identifying redundant and missing relations in the gene ontology.

    PubMed

    Mougin, Fleur

    2015-01-01

    Significant efforts have been undertaken for providing the Gene Ontology (GO) in a computable format as well as for enriching it with logical definitions. Automated approaches can thus be applied to GO for assisting its maintenance and for checking its internal coherence. However, inconsistencies may still remain within GO. In this frame, the objective of this work was to audit GO relationships. First, reasoning over relationships was exploited for detecting redundant relations existing between GO concepts. Missing necessary and sufficient conditions were then identified based on the compositional structure of the preferred names of GO concepts. More than one thousand redundant relations and 500 missing necessary and sufficient conditions were found. The proposed approach was thus successful for detecting inconsistencies within GO relations. The application of lexical approaches as well as the exploitation of synonyms and textual definitions could be useful for identifying additional necessary and sufficient conditions. Multiple necessary and sufficient conditions for a given GO concept may be indicative of inconsistencies.

  8. Connecting the Dots between PubMed Abstracts

    PubMed Central

    Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren

    2012-01-01

    Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. Methodology We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for “connecting the dots” across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. Conclusions We demonstrate the application of our storytelling algorithm to three case studies: i) a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii) a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii) a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only around a hundred

  9. Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews.

    PubMed

    Agoritsas, Thomas; Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

    2012-06-12

    Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed's Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%-25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%-30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help clinicians apply effective strategies to answer their

  10. Identifying molecular subtypes related to clinicopathologic factors in pancreatic cancer

    PubMed Central

    2014-01-01

    Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal tumors and usually presented with locally advanced and distant metastasis disease, which prevent curative resection or treatments. In this regard, we considered identifying molecular subtypes associated with clinicopathological factor as prognosis factors to stratify PDAC for appropriate treatment of patients. Results In this study, we identified three molecular subtypes which were significant on survival time and metastasis. We also identified significant genes and enriched pathways represented for each molecular subtype. Considering R0 resection patients included in each subtype, metastasis and survival times are significantly associated with subtype 1 and subtype 2. Conclusions We observed three PDAC molecular subtypes and demonstrated that those subtypes were significantly related with metastasis and survival time. The study may have utility in stratifying patients for cancer treatment. PMID:25560450

  11. Automatically identifying health- and clinical-related content in wikipedia.

    PubMed

    Liu, Feifan; Moosavinasab, Soheil; Agarwal, Shashank; Bennett, Andrew S; Yu, Hong

    2013-01-01

    Physicians are increasingly using the Internet for finding medical information related to patient care. Wikipedia is a valuable online medical resource to be integrated into existing clinical question answering (QA) systems. On the other hand, Wikipedia contains a full spectrum of world's knowledge and therefore comprises a large partition of non-health-related content, which makes disambiguation more challenging and consequently leads to large overhead for existing systems to effectively filter irrelevant information. To overcome this, we have developed both unsupervised and supervised approaches to identify health-related articles as well as clinically relevant articles. Furthermore, we explored novel features by extracting health related hierarchy from the Wikipedia category network, from which a variety of features were derived and evaluated. Our experiments show promising results and also demonstrate that employing the category hierarchy can effectively improve the system performance.

  12. Materia Socio Medica is Indexed in Pubmed and Archived in PubMed Central.

    PubMed

    Masic, Izet

    2013-01-01

    Materia Socio Medica Journal has been accepted for archiving in PubMed Central from 2011. The journal started in 1993 as offi cial journal of Social Medicine Association of B&H. During last 3 years Mat Soc Med has included in almost all femous on-line databases (except WoS). All issues of Mat Soc Med published in 2012 are now visible on PubMed/PubMed Central.

  13. Identifying concealment-related responses in the concealed information test.

    PubMed

    Matsuda, Izumi; Nittono, Hiroshi; Ogawa, Tokihiro

    2013-07-01

    The concealed information test (CIT) assesses an examinee's recognition of a crime-relevant item using physiological measures. However, a guilty examinee not only recognizes the crime-relevant item but also conceals the recognition intentionally. In this study, we attempted to identify the effect of concealing the recognition on event-related potentials and autonomic responses. After committing a mock theft of two items, 30 participants received two CITs: one for an item that they had to conceal, and the other for an item that they had disclosed. N2, P3, heart rate, skin conductance, and cutaneous blood flow differed between crime-relevant and irrelevant items in both CITs. In contrast, late positive potential and respiration differed between crime-relevant and irrelevant items only when the examinee needed to conceal. The former measures appear to be related to orienting process, whereas the latter to controlled process related to concealment.

  14. A vector space model approach to identify genetically related diseases

    PubMed Central

    2012-01-01

    Objective The relationship between diseases and their causative genes can be complex, especially in the case of polygenic diseases. Further exacerbating the challenges in their study is that many genes may be causally related to multiple diseases. This study explored the relationship between diseases through the adaptation of an approach pioneered in the context of information retrieval: vector space models. Materials and Methods A vector space model approach was developed that bridges gene disease knowledge inferred across three knowledge bases: Online Mendelian Inheritance in Man, GenBank, and Medline. The approach was then used to identify potentially related diseases for two target diseases: Alzheimer disease and Prader-Willi Syndrome. Results In the case of both Alzheimer Disease and Prader-Willi Syndrome, a set of plausible diseases were identified that may warrant further exploration. Discussion This study furthers seminal work by Swanson, et al. that demonstrated the potential for mining literature for putative correlations. Using a vector space modeling approach, information from both biomedical literature and genomic resources (like GenBank) can be combined towards identification of putative correlations of interest. To this end, the relevance of the predicted diseases of interest in this study using the vector space modeling approach were validated based on supporting literature. Conclusion The results of this study suggest that a vector space model approach may be a useful means to identify potential relationships between complex diseases, and thereby enable the coordination of gene-based findings across multiple complex diseases. PMID:22227640

  15. Analysis of queries sent to PubMed at the point of care: observation of search behaviour in a medical teaching hospital.

    PubMed

    Hoogendam, Arjen; Stalenhoef, Anton F H; Robbé, Pieter F de Vries; Overbeke, A John P M

    2008-09-24

    The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2-161 articles. Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research.

  16. Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

    PubMed Central

    Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

    2008-01-01

    Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

  17. Analysis of PubMed User Sessions Using a Full-Day PubMed Query Log: A Comparison of Experienced and Nonexperienced PubMed Users

    PubMed Central

    2015-01-01

    Background PubMed is the largest biomedical bibliographic information source on the Internet. PubMed has been considered one of the most important and reliable sources of up-to-date health care evidence. Previous studies examined the effects of domain expertise/knowledge on search performance using PubMed. However, very little is known about PubMed users’ knowledge of information retrieval (IR) functions and their usage in query formulation. Objective The purpose of this study was to shed light on how experienced/nonexperienced PubMed users perform their search queries by analyzing a full-day query log. Our hypotheses were that (1) experienced PubMed users who use system functions quickly retrieve relevant documents and (2) nonexperienced PubMed users who do not use them have longer search sessions than experienced users. Methods To test these hypotheses, we analyzed PubMed query log data containing nearly 3 million queries. User sessions were divided into two categories: experienced and nonexperienced. We compared experienced and nonexperienced users per number of sessions, and experienced and nonexperienced user sessions per session length, with a focus on how fast they completed their sessions. Results To test our hypotheses, we measured how successful information retrieval was (at retrieving relevant documents), represented as the decrease rates of experienced and nonexperienced users from a session length of 1 to 2, 3, 4, and 5. The decrease rate (from a session length of 1 to 2) of the experienced users was significantly larger than that of the nonexperienced groups. Conclusions Experienced PubMed users retrieve relevant documents more quickly than nonexperienced PubMed users in terms of session length. PMID:26139516

  18. Identifying and relating biological concepts in the Catalogue of Life

    PubMed Central

    2011-01-01

    Background In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world's known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals' opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life. Results We describe how we are using Life Science Identifiers (LSIDs) as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible entities, events, documents

  19. Identifying and relating nurses' attitudes toward computer use.

    PubMed

    Burkes, M

    1991-01-01

    The purpose of this study was to measure nurses' attitudes toward computer use based on an adaptation of Vroom's expectancy theory, and identify variables that may correlate with these attitudes. Content validity and reliability for internal consistency were determined for the developed attitude questionnaire. Nurses' individual characteristics and computer-use satisfaction, beliefs, and motivation were correlated. Data analysis revealed that nurses' attitudes were significantly related (satisfaction to beliefs, r = 0.783, p less than 0.001; satisfaction to motivation, r = 0.598, p less than 0.001; and beliefs to motivation r = 0.651, p less than 0.001), supporting the model based on Vroom's expectancy theory. Computer knowledge significantly related to computer-use beliefs (r = 0.229, p less than 0.05). Length of computer experience (r = -0.265, p less than 0.05) and nursing experience (r = -0.239, p less than 0.05) related negatively to nurses' computer-use satisfaction.

  20. Sensitivity and Predictive Value of 15 PubMed Search Strategies to Answer Clinical Questions Rated Against Full Systematic Reviews

    PubMed Central

    Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

    2012-01-01

    Background Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. Objective To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. Methods We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed’s Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. Results The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%–25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%–30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. Conclusions The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help

  1. Bosnian and Herzegovinian medical scientists in PubMed database.

    PubMed

    Masic, Izet

    2013-01-01

    In this paper it is shortly presented PubMed as one of the most important on-line databases of the scientific biomedical literature. Also, the author has analyzed the most cited authors, professors of the medical faculties in Bosnia and Herzegovina, from the published papers in the biomedical journals abstracted and indexed in PubMed.

  2. Classification methods for finding articles describing protein-protein interactions in PubMed.

    PubMed

    Matos, Sérgio; Oliveira, José Luís

    2011-09-16

    With the rapid expansion in the number of published papers in the biomedical field, finding relevant articles has become a demanding task for researchers. This has led to increasing interest in the use of text mining tools that help search the literature and identify the most relevant documents or information. One specific topic of interest is related to the identification of articles that might be used for extracting protein-protein interactions. Using the BioCreative III Article Classification Task dataset, composed of PubMed abstracts classified as relevant or non-relevant for describing protein-protein interactions, we compare different classification methods with different sets of features. The best results--area under the interpolated precision-recall curve of 0.654--indicate that the proposed classification strategy could be incorporated in the database curation workflows in order to prioritize articles for extraction of protein-protein interactions. Furthermore, we also analysed the use of this method for ranking documents resulting from general PubMed queries, and propose that this approach could be useful for general researchers looking for publications describing protein-protein interactions within a particular topic of interest.

  3. History and Trends of "Personal Health Record" Research in PubMed

    PubMed Central

    Kim, Jeongeun; Bates, David W.

    2011-01-01

    Objectives The purpose of this study was to review history and trends of personal health record research in PubMed and to provide accurate understanding and categorical analysis of expert opinions. Methods For the search strategy, PubMed was queried for 'personal health record, personal record, and PHR' in the title and abstract fields. Those containing different definitions of the word were removed by one-by-one analysis from the results, 695 articles. In the end, total of 229 articles were analyzed in this research. Results The results show that the changes in terms over the years and the shift to patient centeredness and mixed usage. And we identified history and trend of PHR research in some category that the number of publications by year, topic, methodologies and target diseases. Also from analysis of MeSH terms, we can show the focal interest in regards the PHR boundaries and related subjects. Conclusions For PHRs to be efficiently used by general public, initial understanding of the history and trends of PHR research may be helpful. Simultaneously, accurate understanding and categorical analysis of expert opinions that can lead to the development and growth of PHRs will be valuable to their adoption and expansion. PMID:21818452

  4. Relational Aggression: Understanding, Identifying, and Responding in Schools

    ERIC Educational Resources Information Center

    Young, Ellie L.; Boye, America E.; Nelson, David A.

    2006-01-01

    Relational aggression, harm through injury or manipulation of a relationship, has become fashionable, particularly in the popular press. Mental health professionals in schools can better serve students when they understand what is known about relational aggression, how it influences social behavior, and how it is related to children's well-being.…

  5. Relational Aggression: Understanding, Identifying, and Responding in Schools

    ERIC Educational Resources Information Center

    Young, Ellie L.; Boye, America E.; Nelson, David A.

    2006-01-01

    Relational aggression, harm through injury or manipulation of a relationship, has become fashionable, particularly in the popular press. Mental health professionals in schools can better serve students when they understand what is known about relational aggression, how it influences social behavior, and how it is related to children's well-being.…

  6. Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

    PubMed

    Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

    2012-06-01

    We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

  7. PubMed search filters for the study of putative outdoor air pollution determinants of disease.

    PubMed

    Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

    2016-12-21

    Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one 'more specific', one 'more sensitive'). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. The 'more specific' filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The 'more sensitive' filter was based on the combination of all search terms under study. When compared with the gold standard, the 'more specific' filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the 'more sensitive' one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the 'more specific' filter and 3.3 for the 'more sensitive' one. The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  8. PubMed search filters for the study of putative outdoor air pollution determinants of disease

    PubMed Central

    Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

    2016-01-01

    Objectives Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. Methods We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one ‘more specific’, one ‘more sensitive’). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. Results The ‘more specific’ filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The ‘more sensitive’ filter was based on the combination of all search terms under study. When compared with the gold standard, the ‘more specific’ filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the ‘more sensitive’ one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the ‘more specific’ filter and 3.3 for the ‘more sensitive’ one. Conclusions The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. PMID:28003291

  9. Identifying Indicators Related to Constructs for Engineering Design Outcome

    ERIC Educational Resources Information Center

    Wilhelmsen, Cheryl A.; Dixon, Raymond A.

    2016-01-01

    This study ranked constructs articulated by Childress and Rhodes (2008) and identified the key indicators for each construct as a starting point to explore what should be included on an instrument to measure the engineering design process and outcomes of students in high schools that use the PLTW and EbDTM curricula in Idaho. A case-study design…

  10. Simple search techniques in PubMed are potentially suitable for evaluating the completeness of systematic reviews.

    PubMed

    Waffenschmidt, Siw; Janzen, Tatjana; Hausner, Elke; Kaiser, Thomas

    2013-06-01

    The Institute for Quality and Efficiency in Health Care (IQWiG) assesses the added benefit of new drugs by means of company dossiers. The pharmaceutical company performs the information retrieval, which is then assessed by IQWiG. Our aim was to determine whether PubMed's Related Citations (RelCits) and/or a simple-structured Boolean search (SSBS) are efficient and reliable search techniques to assess the completeness of an evidence base consisting of published randomized controlled trials (RCTs). Retrospective analysis of citations included as relevant in systematic reviews (SRs) of drugs. The proportion of relevant citations identified by the above-mentioned search techniques was determined. Relative sensitivity, precision, and the number needed to read (NNR) were then calculated. A total of 19 SRs included 330 relevant PubMed citations. The single techniques yielded either insufficient completeness, reliability, or efficiency. The first 20 RelCits plus SSBS achieved high completeness and reliability (sensitivity: 98.1%, range: 80-100%) and sufficient efficiency (precision: 5.0%, NNR: 25). The first 50 RelCit plus SSBS achieved slightly better completeness and reliability, but slightly worse efficiency. Combining the first 20 RelCits and an SSBS in PubMed is a suitable method to assess the completeness of an evidence base of published RCTs. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Identifying synonymy between relational phrases using word embeddings.

    PubMed

    Nguyen, Nhung T H; Miwa, Makoto; Tsuruoka, Yoshimasa; Tojo, Satoshi

    2015-08-01

    Many text mining applications in the biomedical domain benefit from automatic clustering of relational phrases into synonymous groups, since it alleviates the problem of spurious mismatches caused by the diversity of natural language expressions. Most of the previous work that has addressed this task of synonymy resolution uses similarity metrics between relational phrases based on textual strings or dependency paths, which, for the most part, ignore the context around the relations. To overcome this shortcoming, we employ a word embedding technique to encode relational phrases. We then apply the k-means algorithm on top of the distributional representations to cluster the phrases. Our experimental results show that this approach outperforms state-of-the-art statistical models including latent Dirichlet allocation and Markov logic networks.

  12. Mermaid health - identifying health issues related to mermaiding.

    PubMed

    Guitton, Matthieu J

    2017-01-01

    Mermaiding - swimming with a leg-covering monofin mimicking the tail of a mermaid - is an emerging aquatic activity, which has gained a marked popularity over the last few years. However, no study so far has documented the potential health issues or risks of injuries related to this practice. This study surveyed professional mermaids cumulating an estimated total of 19,147 h of in-water mermaiding, regarding their health issues and injuries. While mermaiding bears some risks, the occurrence of problematic conditions appears limited. Interestingly, the profile of health issues experienced by professional mermaids is unique and specific, and clearly different from both professional swimmers and surfers. Self-reported health issues related to mermaiding could be divided into issues specifically related to mermaiding activities (ear issues, reported by 87.5% of the respondents; sea life encounters, 50%; cold-related issues, 37.5%; compromised access to air, 25%), issues related to the tail and fins (back pain, 50%; lower limbs issues, 37.5%), and issues related to water quality (eye issues, 25%; waterborne diseases, 12.5%). Clear differences appear between professional and recreational mermaiding activities. The results presented here will help to build safer conditions for mermaiding activities and to develop adapted responses from health specialists to help this unique yet growing population of aquatic performers and athletes.

  13. MET network in PubMed: a text-mined network visualization and curation system.

    PubMed

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway.

  14. MET network in PubMed: a text-mined network visualization and curation system

    PubMed Central

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET. Database URL: http://btm.tmu.edu.tw/metastasisway PMID:27242035

  15. Identifying Fracture Types and Relative Ages Using Fluid Inclusion Stratigraphy

    SciTech Connect

    Dilley, Lorie M.; Norman, David; Owens, Lara

    2008-06-30

    Enhanced Geothermal Systems (EGS) are designed to recover heat from the subsurface by mechanically creating fractures in subsurface rocks. Understanding the life cycle of a fracture in a geothermal system is fundamental to the development of techniques for creating fractures. Recognizing the stage of a fracture, whether it is currently open and transmitting fluids; if it recently has closed; or if it is an ancient fracture would assist in targeting areas for further fracture stimulation. Identifying dense fracture areas as well as large open fractures from small fracture systems will also assist in fracture stimulation selection. Geothermal systems are constantly generating fractures, and fluids and gases passing through rocks in these systems leave small fluid and gas samples trapped in healed microfractures. Fluid inclusions trapped in minerals as the fractures heal are characteristic of the fluids that formed them, and this signature can be seen in fluid inclusion gas analysis. Our hypothesis is that fractures over their life cycle have different chemical signatures that we can see in fluid inclusion gas analysis and by using the new method of fluid inclusion stratigraphy (FIS) the different stages of fractures, along with an estimate of fracture size can be identified during the well drilling process. We have shown with this study that it is possible to identify fracture locations using FIS and that different fractures have different chemical signatures however that signature is somewhat dependent upon rock type. Open, active fractures correlate with increase concentrations of CO2, N2, Ar, and to a lesser extent H2O. These fractures would be targets for further enhancement. The usefulness of this method is that it is low cost alternative to current well logging techniques and can be done as a well is being drilled.

  16. Using PubMed effectively to access the orthopaedic literature.

    PubMed

    Clough, J F Myles; Hitchcock, Kristin; Nelson, David L

    2011-01-01

    PubMed is the free public Internet interface to the US National Library of Medicine's MEDLINE database of citations to medical scientific articles. Many orthopaedic surgeons use PubMed on a regular basis, but most orthopaedic surgeons have received little or no training in how to use PubMed effectively and express frustration with the experience. Typical problems encountered are data overload with very large numbers of returns to look through, failure to find a specific article, and a concern that a search has missed important papers. It is helpful to understand the system used to enter journal articles into the database and the classification of the common types of searches and to review suggestions for the best ways to use the PubMed interface and find sources for search teaching and assistance.

  17. Identifying patterns of immune-related disease: use in disease prevention and management.

    PubMed

    Dietert, Rodney R; Zelikoff, Judith T

    2010-05-01

    Childhood susceptibility to diseases linked with immune dysfunction affects over a quarter of the pediatric population in some countries. While this alone is a significant health issue, the actual impact of immune-related diseases extends over a lifetime and involves additional secondary conditions. Some comorbidities are well known (e.g., allergic rhinitis and asthma). However, no systematic approach has been used to identify life-long patterns of immune-based disease where the primary condition arises in childhood. Such information is useful for both disease prevention and treatment approaches. Recent primary research papers as well as review articles were obtained from PubMed, Chem Abstracts, Biosis and from the personal files of the authors. Search words used were: the diseases and conditions shown Figs. 1 and 2 in conjunction with comorbid, comorbidities, pediatric, childhood, adult, immune, immune dysfunction, allergy, autoimmune, inflammatory, infectious, health risks, environment, risk factors. Childhood diseases such as asthma, type-1 diabetes, inflammatory bowel disease, respiratory infections /rhinitis, recurrent otitis media, pediatric celiac, juvenile arthritis and Kawasaki disease are examples of significant childhood health problems where immune dysfunction plays a significant role. Each of these pediatric diseases is associated with increased risk of several secondary conditions, many of which appear only later in life. To illustrate, four prototypes of immune-related disease patterns (i.e., allergy, autoimmunity, inflammation and infectious disease) are shown as tools for: 1) enhanced disease prevention; 2) improved management of immune-based pediatric diseases; and 3) better recognition of underlying pediatric immune dysfunction. Identification of immune-related disease patterns beginning in childhood provides the framework for examining the underlying immune dysfunctions that can contribute to additional diseases in later life. Many pediatric

  18. Identifying Girls Who Use Relational Aggression: A Proposed Model

    ERIC Educational Resources Information Center

    Page, Angela; Smith, Lisa F.

    2012-01-01

    This study used mixed methods to compare perceptions of relational aggression (RA) of adolescent girls (n = 282) and their teachers (n = 15) in New Zealand, and to explore strategies for teachers to effectively manage RA in the classroom. Results indicated that younger adolescent girls view physical aggression as more acceptable than older girls,…

  19. Identifying genes related with rheumatoid arthritis via system biology analysis.

    PubMed

    Liu, Tao; Lin, Xinmei; Yu, Hongjian

    2015-10-15

    Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease that mainly attacks synovial joints. However, the underlying systematic relationship among different genes and biological processes involved in the pathogenesis are still unclear. By analyzing and comparing the transcriptional profiles from RA, OA (osteoarthritis) patients as well as ND (normal donors) with bioinformatics methods, we tend to uncover the potential molecular networks and critical genes which play important roles in RA and OA development. Initially, hierarchical clustering was performed to classify the overall transcriptional profiles. Differentially expressed genes (DEGs) between ND and RA and OA patients were identified. Furthermore, PPI networks were constructed, functional modules were extracted, and functional annotation was also applied. Our functional analysis identifies 22 biological processes and 2 KEGG pathways enriched in the commonly-regulated gene set. However, we found that number of set of genes differentially expressed genes only between RA and ND reaches up to 244, indicating this gene set may specifically accounts for processing to disease of RA. Additionally, 142 biological processes and 19 KEGG pathways are over-represented by these 244 genes. Meanwhile, although another 21 genes were differentially expressed only in OA and ND, no biological process nor pathway is over-represented by them.

  20. PubMed searches: overview and strategies for clinicians.

    PubMed

    Lindsey, Wesley T; Olin, Bernie R

    2013-04-01

    PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

  1. PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

    PubMed

    Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

    2011-07-01

    To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

  2. Identifying Dyscalculia Symptoms Related to Magnocellular Reasoning Using Smartphones.

    PubMed

    Knudsen, Greger Siem; Babic, Ankica

    2016-01-01

    This paper presents a study that has developed a mobile software application for assisting diagnosis of learning disabilities in mathematics, called dyscalculia, and measuring correlations between dyscalculia symptoms and magnocellular reasoning. Usually, software aids for dyscalculic individuals are focused on both assisting diagnosis and teaching the material. The software developed in this study however maintains a specific focus on the former, and in the process attempts to capture alleged correlations between dyscalculia symptoms and possible underlying causes of the condition. Classification of symptoms is performed by k-Nearest Neighbor algorithm classifying five parameters evaluating user's skills, returning calculated performance in each category as well as correlation strength between detected symptoms and magnocellular reasoning abilities. Expert evaluations has found the application to be appropriate and productive for its intended purpose, proving that mobile software is a suitable and valuable tool for assisting dyscalculia diagnosis and identifying root causes of developing the condition.

  3. Transformation-Related Antigens Identified by Monoclonal Antibodies

    NASA Astrophysics Data System (ADS)

    Strand, Mette

    1980-06-01

    Tumor-cell proteins that were antigenic in a syngeneic animal were identified by immunoprecipitation with monoclonal antibodies. Spleen cells of BALB/c mice immunized with plasma membranes of Kirsten RNA sarcoma virus-transformed BALB/3T3 cells were fused with NS-l myeloma cells. Antibodies secreted into the culture fluid from these hybridomas were distinguished by their reactivity against proteins of different target cells. A total of 191 cultures were established; 143 produced antibodies that bound to BALB/3T3 cells transformed by the RNA sarcoma virus, of which antibodies from 82 bound to BALB/3T3 transformed with simian virus 40, and antibodies from 56 bound to BALB/3T3 cells. Thus, more than 50% of the cultures produced antibodies that possibly were specific to antigens of the transformed cell. Twenty different hybridomas have been cloned, and antibodies from eight of these were found to immunoprecipitate five different proteins. A protein of approximately 32,000 daltons was precipitated from BALB/3T3 cells transformed by the RNA sarcoma virus, simian virus 40, or methylcholanthrene but not from untransformed BALB/3T3 cells. A protein of about 300,000 daltons was precipitated from all four cell lines; precipitation was enhanced in the viral transformed cells. Proteins of approximately 57,000, 54,000, and 8500 daltons were immunoprecipitated from all four cell lines.

  4. Using Facility Condition Assessments to Identify Actions Related to Infrastructure

    NASA Technical Reports Server (NTRS)

    Rubert, Kennedy F.

    2010-01-01

    To support cost effective, quality research it is essential that laboratory and testing facilities are maintained in a continuous and reliable state of availability at all times. NASA Langley Research Center (LaRC) and its maintenance contractor, Jacobs Technology, Inc. Research Operations, Maintenance, and Engineering (ROME) group, are in the process of implementing a combined Facility Condition Assessment (FCA) and Reliability Centered Maintenance (RCM) program to improve asset management and overall reliability of testing equipment in facilities such as wind tunnels. Specific areas are being identified for improvement, the deferred maintenance cost is being estimated, and priority is being assigned against facilities where conditions have been allowed to deteriorate. This assessment serves to assist in determining where to commit available funds on the Center. RCM methodologies are being reviewed and enhanced to assure that appropriate preventive, predictive, and facilities/equipment acceptance techniques are incorporated to prolong lifecycle availability and assure reliability at minimum cost. The results from the program have been favorable, better enabling LaRC to manage assets prudently.

  5. Identifying Key Concepts and Student Misconceptions Related to the Cryosphere

    NASA Astrophysics Data System (ADS)

    Ferguson, J. E.

    2016-12-01

    The cryosphere is a vital part of the earth system which is undergoing very rapid change as a result of anthropogenic climate change. Melting ice and thawing permafrost have severe consequences for our society from dwindling freshwater supplies to accelerating sea level rise and climate change. It is therefore important that both geoscience majors and also the broader undergraduate population develop a better understanding of the cryosphere. However, in various locations around the world, students rarely encounter ice and snow in their everyday life and many undergraduate students have misconceptions about how the cryosphere functions. In several scientific fields the creation of concept inventories, including the geoscience concept inventory, has been extremely helpful in allowing instructors to assess student learning and the success of new instructional strategies. This project aims to take the first steps towards creating a cryosphere concept inventory by 1) reporting expert opinions about the key concepts related to the cryosphere, and 2) by examining undergraduate student understanding of the cryosphere using open-ended and multiple choice questions in large ( 350-450 student) general education classes at the University of California, Irvine.

  6. Revisiting amino acid substitution matrices for identifying distantly related proteins.

    PubMed

    Yamada, Kazunori; Tomii, Kentaro

    2014-02-01

    Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence-profile and profile-profile comparison methods can be improved further. Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/.

  7. Net improvement of correct answers to therapy questions after pubmed searches: pre/post comparison.

    PubMed

    McKibbon, Kathleen Ann; Lokker, Cynthia; Keepanasseril, Arun; Wilczynski, Nancy L; Haynes, R Brian

    2013-11-08

    Clinicians search PubMed for answers to clinical questions although it is time consuming and not always successful. To determine if PubMed used with its Clinical Queries feature to filter results based on study quality would improve search success (more correct answers to clinical questions related to therapy). We invited 528 primary care physicians to participate, 143 (27.1%) consented, and 111 (21.0% of the total and 77.6% of those who consented) completed the study. Participants answered 14 yes/no therapy questions and were given 4 of these (2 originally answered correctly and 2 originally answered incorrectly) to search using either the PubMed main screen or PubMed Clinical Queries narrow therapy filter via a purpose-built system with identical search screens. Participants also picked 3 of the first 20 retrieved citations that best addressed each question. They were then asked to re-answer the original 14 questions. We found no statistically significant differences in the rates of correct or incorrect answers using the PubMed main screen or PubMed Clinical Queries. The rate of correct answers increased from 50.0% to 61.4% (95% CI 55.0%-67.8%) for the PubMed main screen searches and from 50.0% to 59.1% (95% CI 52.6%-65.6%) for Clinical Queries searches. These net absolute increases of 11.4% and 9.1%, respectively, included previously correct answers changing to incorrect at a rate of 9.5% (95% CI 5.6%-13.4%) for PubMed main screen searches and 9.1% (95% CI 5.3%-12.9%) for Clinical Queries searches, combined with increases in the rate of being correct of 20.5% (95% CI 15.2%-25.8%) for PubMed main screen searches and 17.7% (95% CI 12.7%-22.7%) for Clinical Queries searches. PubMed can assist clinicians answering clinical questions with an approximately 10% absolute rate of improvement in correct answers. This small increase includes more correct answers partially offset by a decrease in previously correct answers.

  8. Contribution of Indian Psychiatrists to PubMed Listed Mental Health Literature During 1995–2013: an Exploratory Study

    PubMed Central

    Mohandoss, Anusa Arunachalam; Thavarajah, Rooban

    2016-01-01

    Introduction: Contribution of Indian Psychiatrists as publications in peer-reviewed journals listed with PubMed and their impact has not been studied. The aim of this manuscript is to assess such contribution using a new article level metric measure. The relative citation ratio (RCR) has been used to assess the quality, quantity, and impact of research output of Indian Psychiatrists. Materials and Methods: Publications by Indian psychiatrists in PubMed during 1995–2013 were collected, their RCR and associated factors estimated. The nationality of the journals, type of manuscripts, PubMed Central (PMC) visibility and the type of the journals were factored in. The data collected was analyzed. Descriptive statistics, Chi-square tests, correlations, and linear regression were performed. P ≤ 0.05 was taken as significant. Results: Using the criteria set, 1914 manuscripts were identified. Of the 1914 manuscripts, 1007 were cited at least once and among this, 40.7% were listed with PubMed while of the 907 non-PMC listed manuscripts, only 180 were never cited (P = 0.000). Of the 1032 manuscripts published in Indian journals, 474 were never cited while 214 of the manuscripts published with non-India based journals were never cited even once (P = 0.000). Discussion: The difference in terms of manuscripts visibility in PMC, nationality of journals and article type in analysis indicate that there exists an innate difference between the cited and noncited manuscripts. The probable explanation behind this and its associated phenomenon are discussed. PMID:27570340

  9. Demystifying the Search Button: A Comprehensive PubMed Search Strategy for Performing an Exhaustive Literature Review.

    PubMed

    McKeever, Liam; Nguyen, Van; Peterson, Sarah J; Gomez-Perez, Sandra; Braunschweig, Carol

    2015-08-01

    A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the "related citations feature," the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through "MyNCBI" to receive search query updates by email as new citations become available.

  10. Revisiting amino acid substitution matrices for identifying distantly related proteins

    PubMed Central

    Yamada, Kazunori; Tomii, Kentaro

    2014-01-01

    Motivation: Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. Results: Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence–profile and profile–profile comparison methods can be improved further. Availability and implementation: Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/. Contact: k-tomii@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online PMID:24281694

  11. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed.

    PubMed

    Williams, Shirley Ann; Terras, Melissa; Warwick, Claire

    2013-01-01

    Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper's title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that researchers are starting to use knowledge

  12. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed

    PubMed Central

    2013-01-01

    Background Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. Objective This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Methods Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper’s title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. Results As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that

  13. An automatic method to generate domain-specific investigator networks using PubMed abstracts.

    PubMed

    Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

    2007-06-20

    Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70-90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. We successfully created a web-based prototype capable of creating domain

  14. An automatic method to generate domain-specific investigator networks using PubMed abstracts

    PubMed Central

    Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

    2007-01-01

    Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype

  15. Information management and complementary alternative medicine: the anatomy of information about CAMs through PubMed.

    PubMed

    Corrao, Salvatore; Argano, Christiano; Colomba, Daniela; Ippolito, Calogero; Gargano, Vincenzo; Arcoraci, Vincenzo; Licata, Giuseppe

    2013-10-01

    In recent years, there has been a growing interest about complementary and alternative medicine (CAM), and the use of CAM interventions has become more common among people. For these reasons, health professionals must be able to effectively manage information in this field of knowledge according to an evidence-based point of view. This study assessed the anatomy of the available information about CAMs using PubMed, to give practical instructions to manage information in this field. We also analyzed the anatomy of information according to each alternative medicine branch, narrow and broad search methods, subset filters for indexed-for-Medline and non-indexed citations, and different publication types including randomized controlled trials (RCTs) and meta-analyses. Our results demonstrated that the use of CAMs subset (supplied by PubMed search engine) leads to a great number of citations determining an information overload. Our data reveal that it would be more useful to search for the CAM separately, identifying specific items and study design. Moreover, we found the largest number of randomized clinical trials and meta-analyses related to herbal medicine and acupuncture, neither RCTs nor meta-analyses were available for bach and flower remedies, auriculoacupuncture, iridology, and pranotherapy. For the first time, our study gives a comprehensive view of the anatomy of information regarding CAMs and each branch of them. We suggest a methodological approach to face with searching information about this emerging issue from an evidence-based point of view. Finally, our data pointed out some "grey zones" since neither RCTs nor meta-analyses were available for some CAMs.

  16. pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts.

    PubMed

    Rani, Jyoti; Shah, A B Rauf; Ramachandran, Srinivasan

    2015-10-01

    The PubMed literature database is a valuable source of information for scientific research. It is rich in biomedical literature with more than 24 million citations. Data-mining of voluminous literature is a challenging task. Although several text-mining algorithms have been developed in recent years with focus on data visualization, they have limitations such as speed, are rigid and are not available in the open source. We have developed an R package, pubmed.mineR, wherein we have combined the advantages of existing algorithms, overcome their limitations, and offer user flexibility and link with other packages in Bioconductor and the Comprehensive R Network (CRAN) in order to expand the user capabilities for executing multifaceted approaches. Three case studies are presented, namely, 'Evolving role of diabetes educators', 'Cancer risk assessment' and 'Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus sizes and with compute intensive functions. The pubmed.mineR is available at http://cran.rproject. org/web/packages/pubmed.mineR.

  17. PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords.

    PubMed

    Chen, Chou-Cheng; Ho, Chung-Liang

    2014-01-01

    While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research. http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx.

  18. Use of scientific social networking to improve the research strategies of PubMed readers.

    PubMed

    Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

    2016-02-18

    Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users. A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users. We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users. A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

  19. PubMed Central Canada: Beyond an Open Access Repository?

    ERIC Educational Resources Information Center

    Nariani, Rajiv

    2013-01-01

    PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

  20. PubMed Central Canada: Beyond an Open Access Repository?

    ERIC Educational Resources Information Center

    Nariani, Rajiv

    2013-01-01

    PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

  1. Impact of PubMed search filters on the retrieval of evidence by physicians

    PubMed Central

    Shariff, Salimah Z.; Sontrop, Jessica M.; Haynes, R. Brian; Iansavichus, Arthur V.; McKibbon, K. Ann; Wilczynski, Nancy L.; Weir, Matthew A.; Speechley, Mark R.; Thind, Amardeep; Garg, Amit X.

    2012-01-01

    Background: Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians. Methods: We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries “therapy”) and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles. Results: The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were nonrelevant (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55). Interpretation: The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care. PMID:22249990

  2. Impact of PubMed search filters on the retrieval of evidence by physicians.

    PubMed

    Shariff, Salimah Z; Sontrop, Jessica M; Haynes, R Brian; Iansavichus, Arthur V; McKibbon, K Ann; Wilczynski, Nancy L; Weir, Matthew A; Speechley, Mark R; Thind, Amardeep; Garg, Amit X

    2012-02-21

    Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians. We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries "therapy") and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles. The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were relevant (corrected) (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55). The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.

  3. AliBaba: PubMed as a graph.

    PubMed

    Plake, Conrad; Schiemann, Torsten; Pankalla, Marcus; Hakenberg, Jörg; Leser, Ulf

    2006-10-01

    The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. http://alibaba.informatik.hu-berlin.de/

  4. Research methodology search filters: are they effective for locating research for evidence-based veterinary medicine in PubMed?

    PubMed Central

    Murphy, Sarah Anne

    2003-01-01

    Objective: The study examined the effectiveness of research methodology search filters developed by Haynes and colleagues and utilized by the Clinical Query feature of PubMed for locating literature for evidence-based veterinary medicine (EBVM). Methods: A manual review of articles published in 6 commonly read veterinary journals was conducted. Articles were classified by format (original study, review, general article, conference report, decision analysis, and case report) and purpose category (etiology, prognosis, diagnosis, and treatment). Search strategies listed in PubMed's Clinical Query feature were then tested and compared to the manually reviewed data to calculate sensitivity, specificity, and precision. Results: The author manually reviewed 914 articles to identify 702 original studies. Search #1 included terms determined to have the highest sensitivity and returned acceptable sensitivities over 75% for diagnosis and treatment. Search #2 included terms identified as providing the highest specificity and returned results with specificities over 75% for etiology, prognosis, and treatment. Discussion: The low precision for each search prompts the question: Are research methodology search filters practical for locating literature for the practice of EBVM? A study examining terms related to appropriate research methodologies for advanced clinical veterinary research is necessary to develop filters designed to locate literature for EBVM. PMID:14566380

  5. Research methodology search filters: are they effective for locating research for evidence-based veterinary medicine in PubMed?

    PubMed

    Murphy, Sarah Anne

    2003-10-01

    The study examined the effectiveness of research methodology search filters developed by Haynes and colleagues and utilized by the Clinical Query feature of PubMed for locating literature for evidence-based veterinary medicine (EBVM). A manual review of articles published in 6 commonly read veterinary journals was conducted. Articles were classified by format (original study, review, general article, conference report, decision analysis, and case report) and purpose category (etiology, prognosis, diagnosis, and treatment). Search strategies listed in PubMed's Clinical Query feature were then tested and compared to the manually reviewed data to calculate sensitivity, specificity, and precision. The author manually reviewed 914 articles to identify 702 original studies. Search #1 included terms determined to have the highest sensitivity and returned acceptable sensitivities over 75% for diagnosis and treatment. Search #2 included terms identified as providing the highest specificity and returned results with specificities over 75% for etiology, prognosis, and treatment. The low precision for each search prompts the question: Are research methodology search filters practical for locating literature for the practice of EBVM? A study examining terms related to appropriate research methodologies for advanced clinical veterinary research is necessary to develop filters designed to locate literature for EBVM.

  6. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters

    PubMed Central

    Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

    2011-01-01

    Objective Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Materials and methods Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. Results For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Discussion Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Conclusion Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval. PMID:21680559

  7. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters.

    PubMed

    Lokker, Cynthia; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

    2011-01-01

    Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval.

  8. Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

    PubMed

    Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

    2015-01-01

    In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

  9. pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

    PubMed Central

    Baran, Joachim; Gerner, Martin; Haeussler, Maximilian; Nenadic, Goran; Bergman, Casey M.

    2011-01-01

    Background The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions. Methodology/Principal Findings To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data. Conclusion/Significance By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much

  10. A systematic review of validated methods for identifying infection related to blood products, tissue grafts, or organ transplants using administrative data.

    PubMed

    Carnahan, Ryan M; Moores, Kevin G; Perencevich, Eli N

    2012-01-01

    To systematically review algorithms to identify infections related to blood products, tissue grafts, or organ transplants in administrative and claims data, focusing on studies that have examined the validity of the algorithms. A literature search was conducted using PubMed and the database of the Iowa Drug Information Service. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada because these data sources were most likely to reflect the coding practices of Mini-Sentinel data sources. Searches identified one study that examined the validity of an algorithm to identify aspergillosis in transplant recipients and 16 studies that used nonvalidated algorithms to identify infections in recipients of blood products, tissue grafts, or organ transplants. Transfusion was studied as a risk factor for infection, but no studies attempted to identify infection transmitted by any of the exposures under review. Two studies reported sensitivity ranging from 21% to 83% and specificity of 100% of codes to identify allogeneic blood transfusion. No validation studies of algorithms to identify tissue grafts or organ transplant were identified. There is little evidence to support the validity of algorithms to identify infections related to blood products, tissue grafts, or organ transplants in administrative data or algorithms to identify the exposures. Although it may be possible to validate algorithms to identify the exposures and infectious outcomes, the use of administrative data to identify infections transmitted by these exposures may be challenging. Codes indicating infections acquired through medical care may be useful. Copyright © 2012 John Wiley & Sons, Ltd.

  11. Medical literature searches: a comparison of PubMed and Google Scholar.

    PubMed

    Nourbakhsh, Eva; Nugent, Rebecca; Wang, Helen; Cevik, Cihan; Nugent, Kenneth

    2012-09-01

    Medical literature searches provide critical information for clinicians. However, the best strategy for identifying relevant high-quality literature is unknown. We compared search results using PubMed and Google Scholar on four clinical questions and analysed these results with respect to article relevance and quality. Abstracts from the first 20 citations for each search were classified into three relevance categories. We used the weighted kappa statistic to analyse reviewer agreement and nonparametric rank tests to compare the number of citations for each article and the corresponding journals' impact factors. Reviewers ranked 67.6% of PubMed articles and 80% of Google Scholar articles as at least possibly relevant (P = 0.116) with high agreement (all kappa P-values < 0.01). Google Scholar articles had a higher median number of citations (34 vs. 1.5, P < 0.0001) and came from higher impact factor journals (5.17 vs. 3.55, P = 0.036). PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals. The identification of frequently cited articles using Google Scholar for searches probably has value for initial literature searches. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

  12. RESPIRATORY INFECTIONS RESEARCH IN AFGHANISTAN: BIBLIOMETRIC ANALYSIS WITH THE DATABASE PUBMED.

    PubMed

    Pilsczek, Florian H

    2015-01-01

    Infectious diseases research in a low-income country like Afghanistan is important. In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11 (4.9%); multi-drug resistant bacteria (MDR) 18 (8.0%); polio 31 (13.7%); leishmania 31 (13.7%); malaria 46 (20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions.

  13. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.

    PubMed

    Barbosa-Silva, Adriano; Fontaine, Jean-Fred; Donnard, Elisa R; Stussi, Fernanda; Ortega, J Miguel; Andrade-Navarro, Miguel A

    2011-11-09

    Biological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation. To help the concept-oriented exploration of such data we developed PESCADOR, a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts. We illustrate its use in exploring protein aggregation in neurodegenerative disease and in the expansion of pathways associated to colon cancer. PESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador/

  14. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

    PubMed Central

    2011-01-01

    Background Biological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation. Results To help the concept-oriented exploration of such data we developed PESCADOR, a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts. We illustrate its use in exploring protein aggregation in neurodegenerative disease and in the expansion of pathways associated to colon cancer. Conclusions PESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador/ PMID:22070195

  15. PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

    PubMed Central

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2006-01-01

    Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

  16. Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid

    PubMed Central

    Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

    2016-01-01

    Objective The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Methods Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Results Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Conclusion Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews. PMID:27822154

  17. Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

    PubMed

    Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

    2016-10-01

    The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

  18. PubMed search strings for the study of agricultural workers' diseases.

    PubMed

    Mattioli, Stefano; Gori, Davide; Di Gregori, Valentina; Ricotta, Lara; Baldasseroni, Alberto; Farioli, Andrea; Zanardi, Francesca; Galletti, Stefania; Colosio, Claudio; Curti, Stefania; Violante, Francesco S

    2013-12-01

    Several optimized search strategies have been developed in Medicine, and more recently in Occupational Medicine. The aim of this study was to identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of agricultural workers' diseases. We selected the Medical Subjects Heading (MeSH) term agricultural workers' diseases and six MeSH terms describing farm work (agriculture, agrochemicals NOT pesticides, animal husbandry, pesticides, rural health, rural population) alongside 61 other promising terms. We estimated proportions of articles containing potentially pertinent information regarding occupational etiology to formulate two search strategies (one "more specific," one "more sensitive"). We applied these strategies to retrieve information on the possible occupational etiology among agricultural workers of kidney cancer, knee osteoarthritis, and multiple sclerosis. We evaluated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these pathologies. The "more specific" search string was based on the combination of terms that yielded the highest proportion (40%) of potentially pertinent abstracts. The "more sensitive" string was based on use of broader search fields and additional coverage provided by other search terms under study. Using the "more specific" string, the NNR to find one potentially pertinent article were: 1.1 for kidney cancer; 1.4 for knee osteoarthritis; 1.2 for multiple sclerosis. Using the sensitive strategy, the NNR were 1.4, 3.6, and 6.3, respectively. The proposed strings could help health care professionals explore putative occupational etiology for agricultural workers' diseases (even if not generally thought to be work related). © 2013 Wiley Periodicals, Inc.

  19. Acta stomatologica Croatica and PubMed Central

    PubMed Central

    Brkić, Hrvoje

    2016-01-01

    April 15 2016 marked the 50th anniversary of continuous publishing of the journal Acta stomatologica Croatica (ASCRO). The celebration was held in the great hall of the Croatian Medical Association, with numerous guests from the biomedical field. The history of the journal was presented by Goran Knežević (editor-in-chief 1996-2006) and Hrvoje Brkić (current editor-in-chief), who presented all the current information on the electronical editing and its current indexation. Only a few days later, the Editorial Office received the information that ASCRO has been included in PubMed Central since volume 48, an impulse for the members of the Editorial Board and the Editor-in-Chief to make ASCRO better and more cited PMID:27789906

  20. A Study on Pubmed Search Tag Usage Pattern: Association Rule Mining of a Full-day Pubmed Query Log

    PubMed Central

    2013-01-01

    Background The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. Methods A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. Results The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. Conclusions The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed’s Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE. PMID:23302604

  1. GO2PUB: Querying PubMed with semantic expansion of gene ontology terms

    PubMed Central

    2012-01-01

    Background With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are necessary. We developed GO2PUB to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a GO term of interest or one of its descendants. Results GO2PUB enriches PubMed queries based on selected GO terms and keywords. It processes the result and displays the PMID, title, authors, abstract and bibliographic references of the articles. Gene names, symbols and synonyms that have been generated as extra keywords from the GO terms are also highlighted. GO2PUB is based on a semantic expansion of PubMed queries using the semantic inheritance between terms through the GO graph. Two experts manually assessed the relevance of GO2PUB, GoPubMed and PubMed on three queries about lipid metabolism. Experts’ agreement was high (kappa = 0.88). GO2PUB returned 69% of the relevant articles, GoPubMed: 40% and PubMed: 29%. GO2PUB and GoPubMed have 17% of their results in common, corresponding to 24% of the total number of relevant results. 70% of the articles returned by more than one tool were relevant. 36% of the relevant articles were returned only by GO2PUB, 17% only by GoPubMed and 14% only by PubMed. For determining whether these results can be generalized, we generated twenty queries based on random GO terms with a granularity similar to those of the first three queries and compared the proportions of GO2PUB and GoPubMed results. These were respectively of 77% and 40% for the first queries, and of 70% and 38% for the random queries. The two experts also assessed the relevance of seven of the twenty queries (the three related to lipid metabolism and four related to other domains). Expert agreement was high (0.93 and 0.8). GO2PUB and GoPubMed performances

  2. National efforts to identify research issues related to prevention of work-related musculoskeletal disorders.

    PubMed

    Waters, Thomas R

    2004-02-01

    Musculoskeletal disorders (MSDs), including low back and upper extremity disorders, represent one of the greatest work-related health concerns facing industrialized nations. Recently, two national groups were charged with developing research agendas aimed at increasing our knowledge of the prevention of these disorders. The first agenda, developed by the National Institute for Occupational Safety and Health's (NIOSH) National Occupational Research Agenda (NORA) MSD team, was based on input from several hundred practitioners and safety and health experts representing industry, labor, and academia. The second agenda, developed by the National Research Council (NRC) and the Institute of Medicine's (IOM) National Panel on Musculoskeletal Disorders and the Workplace, was based on input from leading researchers in the fields of medicine, information science, and ergonomics. This paper summarizes the findings of the two groups and compares the two research agendas.

  3. Dialysis Search Filters for PubMed, Ovid MEDLINE, and Embase Databases

    PubMed Central

    Iansavichus, Arthur V.; Haynes, R. Brian; Lee, Christopher W.C.; Wilczynski, Nancy L.; McKibbon, Ann; Shariff, Salimah Z.; Blake, Peter G.; Lindsay, Robert M.

    2012-01-01

    Summary Background and objectives Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. Design, setting, participants, & measurements A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. Results The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words “dialy” (truncated), “uremic,” “catheters,” and “renal transplant wait list.” These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters’ performance remained robust in an independent validation subset of articles. Conclusions These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase. PMID:22917701

  4. Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

    PubMed

    Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

    2012-10-01

    Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

  5. PubMed and beyond: a survey of web tools for searching biomedical literature

    PubMed Central

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

  6. PubMed search strategies for the identification of etiologic associations between hypothalamic-pituitary disorders and other medical conditions.

    PubMed

    Guaraldi, Federica; Grottoli, Silvia; Arvat, Emanuela; Mattioli, Stefano; Ghigo, Ezio; Gori, Davide

    2013-12-01

    Biomedical literature has enormously grown in the last decades and become broadly available through online databases. Ad-hoc search methods, created on the basis of research field and goals, are required to enhance the quality of searching. Aim of this study was to formulate efficient, evidence-based PubMed search strategies to retrieve articles assessing etiologic associations between a condition of interest and hypothalamic-pituitary disorders (HPD). Based on expert knowledge, 17 MeSH (Medical Subjects Headings) and 79 free terms related to HPD were identified to search PubMed. Using random samples of abstracts retrieved by each term, we estimated the proportion of articles containing pertinent information and formulated two strings (one more specific, one more sensitive) for the detection of articles focusing on the etiology of HPD, that were then applied to retrieve articles identifying possible etiologic associations between HPD and three diseases (malaria, LHON and celiac disease) considered not associated to HPD, and define the number of abstracts needed to read (NNR) to find one potentially pertinent article. We propose two strings: one sensitive string derived from the combination of articles providing the largest literature coverage in the field and one specific including combined terms retrieving ≥40% of potentially pertinent articles. NNR were 2.1 and 1.6 for malaria, 3.36 and 2.29 for celiac disease, 2.8 and 2.2 for LHON, respectively. For the first time, two reliable, readily applicable strings are proposed for the retrieval of medical literature assessing putative etiologic associations between HPD and other medical conditions of interest.

  7. Publication Trends in Acupuncture Research: A 20-Year Bibliometric Analysis Based on PubMed

    PubMed Central

    Dong, Ming; Zhou, Kehua; Mita, Carol; Liu, Jianping; Wayne, Peter M.

    2016-01-01

    Objective Acupuncture has become popular and widely practiced in many countries around the world. Despite the large amount of acupuncture-related literature that has been published, broader trends in the prevalence and scope of acupuncture research remain underexplored. The current study quantitatively analyzes trends in acupuncture research publications in the past 20 years. Methods A bibliometric approach was used to search PubMed for all acupuncture-related research articles including clinical and animal studies. Inclusion criteria were articles published between 1995 and 2014 with sufficient information for bibliometric analyses. Rates and patterns of acupuncture publication within the 20 year observational period were estimated, and compared with broader publication rates in biomedicine. Identified eligible publications were further analyzed with respect to study type/design, clinical condition addressed, country of origin, and journal impact factor. Results A total of 13,320 acupuncture-related publications were identified using our search strategy and eligibility criteria. Regression analyses indicated an exponential growth in publications over the past two decades, with a mean annual growth rate of 10.7%. This compares to a mean annual growth rate of 4.5% in biomedicine. A striking trend was an observed increase in the proportion of randomized clinical trials (RCTs), from 7.4% in 1995 to 20.3% in 2014, exceeding the 4.5% proportional growth of RCTs in biomedicine. Over the 20 year period, pain was consistently the most common focus of acupuncture research (37.9% of publications). Other top rankings with respect to medical focus were arthritis, neoplasms/cancer, pregnancy or labor, mood disorders, stroke, nausea/vomiting, sleep, and paralysis/palsy. Acupuncture research was conducted in 60 countries, with the top 3 contributors being China (47.4%), United States (17.5%), and United Kingdom (8.2%). Retrieved articles were published mostly in complementary and

  8. Publication Trends in Acupuncture Research: A 20-Year Bibliometric Analysis Based on PubMed.

    PubMed

    Ma, Yan; Dong, Ming; Zhou, Kehua; Mita, Carol; Liu, Jianping; Wayne, Peter M

    2016-01-01

    Acupuncture has become popular and widely practiced in many countries around the world. Despite the large amount of acupuncture-related literature that has been published, broader trends in the prevalence and scope of acupuncture research remain underexplored. The current study quantitatively analyzes trends in acupuncture research publications in the past 20 years. A bibliometric approach was used to search PubMed for all acupuncture-related research articles including clinical and animal studies. Inclusion criteria were articles published between 1995 and 2014 with sufficient information for bibliometric analyses. Rates and patterns of acupuncture publication within the 20 year observational period were estimated, and compared with broader publication rates in biomedicine. Identified eligible publications were further analyzed with respect to study type/design, clinical condition addressed, country of origin, and journal impact factor. A total of 13,320 acupuncture-related publications were identified using our search strategy and eligibility criteria. Regression analyses indicated an exponential growth in publications over the past two decades, with a mean annual growth rate of 10.7%. This compares to a mean annual growth rate of 4.5% in biomedicine. A striking trend was an observed increase in the proportion of randomized clinical trials (RCTs), from 7.4% in 1995 to 20.3% in 2014, exceeding the 4.5% proportional growth of RCTs in biomedicine. Over the 20 year period, pain was consistently the most common focus of acupuncture research (37.9% of publications). Other top rankings with respect to medical focus were arthritis, neoplasms/cancer, pregnancy or labor, mood disorders, stroke, nausea/vomiting, sleep, and paralysis/palsy. Acupuncture research was conducted in 60 countries, with the top 3 contributors being China (47.4%), United States (17.5%), and United Kingdom (8.2%). Retrieved articles were published mostly in complementary and alternative medicine (CAM

  9. Sensitivity and specificity of administrative mortality data for identifying prescription opioid–related deaths

    PubMed Central

    Gladstone, Emilie; Smolina, Kate; Morgan, Steven G.; Fernandes, Kimberly A.; Martins, Diana; Gomes, Tara

    2016-01-01

    Background: Comprehensive systems for surveilling prescription opioid–related harms provide clear evidence that deaths from prescription opioids have increased dramatically in the United States. However, these harms are not systematically monitored in Canada. In light of a growing public health crisis, accessible, nationwide data sources to examine prescription opioid–related harms in Canada are needed. We sought to examine the performance of 5 algorithms to identify prescription opioid–related deaths from vital statistics data against data abstracted from the Office of the Chief Coroner of Ontario as a gold standard. Methods: We identified all prescription opioid–related deaths from Ontario coroners’ data that occurred between Jan. 31, 2003, and Dec. 31, 2010. We then used 5 different algorithms to identify prescription opioid–related deaths from vital statistics death data in 2010. We selected the algorithm with the highest sensitivity and a positive predictive value of more than 80% as the optimal algorithm for identifying prescription opioid–related deaths. Results: Four of the 5 algorithms had positive predictive values of more than 80%. The algorithm with the highest sensitivity (75%) in 2010 improved slightly in its predictive performance from 2003 to 2010. Interpretation: In the absence of specific systems for monitoring prescription opioid–related deaths in Canada, readily available national vital statistics data can be used to study prescription opioid–related mortality with considerable accuracy. Despite some limitations, these data may facilitate the implementation of national surveillance and monitoring strategies. PMID:26622006

  10. Net Improvement of Correct Answers to Therapy Questions After PubMed Searches: Pre/Post Comparison

    PubMed Central

    Keepanasseril, Arun

    2013-01-01

    Background Clinicians search PubMed for answers to clinical questions although it is time consuming and not always successful. Objective To determine if PubMed used with its Clinical Queries feature to filter results based on study quality would improve search success (more correct answers to clinical questions related to therapy). Methods We invited 528 primary care physicians to participate, 143 (27.1%) consented, and 111 (21.0% of the total and 77.6% of those who consented) completed the study. Participants answered 14 yes/no therapy questions and were given 4 of these (2 originally answered correctly and 2 originally answered incorrectly) to search using either the PubMed main screen or PubMed Clinical Queries narrow therapy filter via a purpose-built system with identical search screens. Participants also picked 3 of the first 20 retrieved citations that best addressed each question. They were then asked to re-answer the original 14 questions. Results We found no statistically significant differences in the rates of correct or incorrect answers using the PubMed main screen or PubMed Clinical Queries. The rate of correct answers increased from 50.0% to 61.4% (95% CI 55.0%-67.8%) for the PubMed main screen searches and from 50.0% to 59.1% (95% CI 52.6%-65.6%) for Clinical Queries searches. These net absolute increases of 11.4% and 9.1%, respectively, included previously correct answers changing to incorrect at a rate of 9.5% (95% CI 5.6%-13.4%) for PubMed main screen searches and 9.1% (95% CI 5.3%-12.9%) for Clinical Queries searches, combined with increases in the rate of being correct of 20.5% (95% CI 15.2%-25.8%) for PubMed main screen searches and 17.7% (95% CI 12.7%-22.7%) for Clinical Queries searches. Conclusions PubMed can assist clinicians answering clinical questions with an approximately 10% absolute rate of improvement in correct answers. This small increase includes more correct answers partially offset by a decrease in previously correct answers

  11. Using PubMed search strings for efficient retrieval of manual therapy research literature.

    PubMed

    Pillastrini, Paolo; Vanti, Carla; Curti, Stefania; Mattioli, Stefano; Ferrari, Silvano; Violante, Francesco Saverio; Guccione, Andrew

    2015-02-01

    The aim of this study was to construct PubMed search strings that could efficiently retrieve studies on manual therapy (MT), especially for time-constrained clinicians. Our experts chose 11 Medical Subject Heading terms describing MT along with 84 additional potential terms. For each term that was able to retrieve more than 100 abstracts, we systematically extracted a sample of abstracts from which we estimated the proportion of studies potentially relevant to MT. We then constructed 2 search strings: 1 narrow (threshold of pertinent articles ≥40%) and 1 expanded (including all terms for which a proportion had been calculated). We tested these search strings against articles on 2 conditions relevant to MT (thoracic and temporomandibular pain). We calculated the number of abstracts needed to read (NNR) to identify 1 potentially pertinent article in the context of these conditions. Finally, we evaluated the efficiency of the proposed PubMed search strings to identify relevant articles included in a systematic review on spinal manipulative therapy for chronic low back pain. Fifty-five search terms were able to extract more than 100 citations. The NNR to find 1 potentially pertinent article using the narrow string was 1.2 for thoracic pain and 1.3 for temporomandibular pain, and the NNR for the expanded string was 1.9 and 1.6, respectively. The narrow search strategy retrieved all the randomized controlled trials included in the systematic review selected for comparison. The proposed PubMed search strings may help health care professionals locate potentially pertinent articles and review a large number of MT studies efficiently to better implement evidence-based practice. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

  12. Using Active Learning to Identify Health Information Technology Related Patient Safety Events.

    PubMed

    Fong, Allan; Howe, Jessica L; Adams, Katharine T; Ratwani, Raj M

    2017-01-18

    The widespread adoption of health information technology (HIT) has led to new patient safety hazards that are often difficult to identify. Patient safety event reports, which are self-reported descriptions of safety hazards, provide one view of potential HIT-related safety events. However, identifying HIT-related reports can be challenging as they are often categorized under other more predominate clinical categories. This challenge of identifying HIT-related reports is exacerbated by the increasing number and complexity of reports which pose challenges to human annotators that must manually review reports. In this paper, we apply active learning techniques to support classification of patient safety event reports as HIT-related. We evaluated different strategies and demonstrated a 30% increase in average precision of a confirmatory sampling strategy over a baseline no active learning approach after 10 learning iterations.

  13. Combat-Related Heterotopic Ossification: Development of Animal Models for Identifying Mechanisms and Testing Therapeutics

    DTIC Science & Technology

    2016-03-01

    1 Award Number: W81XWH-14-2-0010 TITLE: Combat-Related Heterotopic Ossification: Development of Animal Models for Identifying Mechanisms and...June 2014 - 14 December 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Combat-Related Heterotopic Ossification: Development of Animal Models for...etiology, treatment, and prevention is the absence of a reliable and reproducible small animal model that can be used to characterize combat‐related HO

  14. OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content.

    PubMed

    Damarell, Raechel A; Tieman, Jennifer J; Sladek, Ruth M

    2013-07-02

    PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed's unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms ('textwords'), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed's unique heart failure literature. We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter's MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as 'textwords'). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this 'lost set'. This string, restricted to searching on PubMed's unique content, was then combined with the validated PubMed translation to extend the filter's performance in this database. The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed

  15. GeneView: a comprehensive semantic search engine for PubMed.

    PubMed

    Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

    2012-07-01

    Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.

  16. GeneView: a comprehensive semantic search engine for PubMed

    PubMed Central

    Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

    2012-01-01

    Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein–protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271 000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/. PMID:22693219

  17. Non-lexical approaches to identifying associative relations in the gene ontology.

    PubMed

    Bodenreider, Olivier; Aubry, Marc; Burgun, Anita

    2005-01-01

    The Gene Ontology (GO) is a controlled vocabulary widely used for the annotation of gene products. GO is organized in three hierarchies for molecular functions, cellular components, and biological processes but no relations are provided among terms across hierarchies. The objective of this study is to investigate three non-lexical approaches to identifying such associative relations in GO and compare them among themselves and to lexical approaches. The three approaches are: computing similarity in a vector space model, statistical analysis of co-occurrence of GO terms in annotation databases, and association rule mining. Five annotation databases (FlyBase, the Human subset of GOA, MGI, SGD, and WormBase) are used in this study. A total of 7,665 associations were identified by at least one of the three non-lexical approaches. Of these, 12% were identified by more than one approach. While there are almost 6,000 lexical relations among GO terms, only 203 associations were identified by both non-lexical and lexical approaches. The associations identified in this study could serve as the starting point for adding associative relations across hierarchies to GO, but would require manual curation. The application to quality assurance of annotation databases is also discussed.

  18. A mutation-centric approach to identifying pharmacogenomic relations in text.

    PubMed

    Rance, Bastien; Doughty, Emily; Demner-Fushman, Dina; Kann, Maricel G; Bodenreider, Olivier

    2012-10-01

    To explore the notion of mutation-centric pharmacogenomic relation extraction and to evaluate our approach against reference pharmacogenomic relations. From a corpus of MEDLINE abstracts relevant to genetic variation, we identify co-occurrences between drug mentions extracted using MetaMap and RxNorm, and genetic variants extracted by EMU. The recall of our approach is evaluated against reference relations curated manually in PharmGKB. We also reviewed a random sample of 180 relations in order to evaluate its precision. One crucial aspect of our strategy is the use of biological knowledge for identifying specific genetic variants in text, not simply gene mentions. On the 104 reference abstracts from PharmGKB, the recall of our mutation-centric approach is 33-46%. Applied to 282,000 abstracts from MEDLINE, our approach identifies pharmacogenomic relations in 4534 abstracts, with a precision of 65%. Compared to a relation-centric approach, our mutation-centric approach shows similar recall, but slightly lower precision. We show that both approaches have limited overlap in their results, but are complementary and can be used in combination. Rather than a solution for the automatic curation of pharmacogenomic knowledge, we see these high-throughput approaches as tools to assist biocurators in the identification of pharmacogenomic relations of interest from the published literature. This investigation also identified three challenging aspects of the extraction of pharmacogenomic relations, namely processing full-text articles, sequence validation of DNA variants and resolution of genetic variants to reference databases, such as dbSNP. Published by Elsevier Inc.

  19. Retrieval comparison of EndNote to search MEDLINE (Ovid and PubMed) versus searching them directly.

    PubMed

    Gall, Carole; Brahmi, Frances A

    2004-01-01

    Using EndNote version 7.0, the authors tested the search capabilities of the EndNote search engine for retrieving citations from MEDLINE for importation into EndNote, a citation management software package. Ovid MEDLINE and PubMed were selected for the comparison. Several searches were performed on Ovid MEDLINE and PubMed using EndNote as the search engine, and the same searches were run on both Ovid and PubMed directly. Findings indicate that it is preferable to search MEDLINE directly rather than using EndNote. The publishers of EndNote do warn its users about the limitations of their product as a search engine when searching external databases. In this article, the limitations of EndNote as a search engine for searching MEDLINE were explored as related to MeSH, non-MeSH, citation verification, and author searching.

  20. Human-Relations Training with Seventh-Grade Boys Identified as Behavior Problems

    ERIC Educational Resources Information Center

    McCurdy, Betty; And Others

    1977-01-01

    Boys (N=12), identified as constituting behavior problems in a class of underachievers, were given group human-relations training. Self-esteem was improved by training procedures including videotape as well as facilitative communication. Group experiences seemed to affect classroom behavior positively, as evidenced by a decrease in behavior…

  1. Prospective Mathematics Teachers' Ability to Identify Mistakes Related to Angle Concept of Sixth Grade Students

    ERIC Educational Resources Information Center

    Arslan, Cigdem; Erbay, Hatice Nur; Guner, Pinar

    2017-01-01

    In the present study we try to highlight prospective mathematics teachers' ability to identify mistakes of sixth grade students related to angle concept. And also we examined prospective mathematics teachers' knowledge of angle concept. Study was carried out with 30 sixth-grade students and 38 prospective mathematics teachers. Sixth grade students…

  2. Identifying wild relatives of subtropical and temperate fruit and nut crops

    USDA-ARS?s Scientific Manuscript database

    In 2008 the Plant Exchange Office (PEO) of the Agricultural Research Service began a concentrated effort to identify, classify, and provide a full treatment in the taxonomy area of the Germplasm Resources Information Network (GRIN) for all primary, secondary, and tertiary genetic wild relatives (CWR...

  3. Contingency Space Analysis: An Alternative Method for Identifying Contingent Relations from Observational Data

    ERIC Educational Resources Information Center

    Martens, Brian K.; DiGennaro, Florence D.; Reed, Derek D.; Szczech, Frances M.; Rosenthal, Blair D.

    2008-01-01

    Descriptive assessment methods have been used in applied settings to identify consequences for problem behavior, thereby aiding in the design of effective treatment programs. Consensus has not been reached, however, regarding the types of data or analytic strategies that are most useful for describing behavior-consequence relations. One promising…

  4. EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts.

    PubMed

    Yeniterzi, Süveyda; Sezerman, Ugur

    2009-08-27

    A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes' databases are currently available, scientific literature still remains at large for up-to-date source of learning the effects of a mutation on an enzyme. However, going through vast amounts of scientific documents to extract the information on desired mutation has always been a time consuming process. In this paper, therefore, we describe an unique method, termed as EnzyMiner, which automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability and/or the activity of a given enzyme. We present an automated system which identifies the abstracts that contain an amino-acid-level mutation and then classifies them according to the mutation's effect on the enzyme. In the case of mutation identification, MuGeX, an automated mutation-gene extraction system has an accuracy of 93.1% with a 91.5 F-measure. For impact analysis, document classification is performed to identify the abstracts that contain a change in enzyme's stability or activity resulting from the mutation. The system was trained on lipases and tested on amylases with an accuracy of 85%. EnzyMiner identifies the abstracts that contain a protein mutation for a given enzyme and checks whether the abstract is related to a disease with the help of information extraction and machine learning techniques. For disease related abstracts, the mutation list and direct links to the abstracts are retrieved from the system and displayed on the Web. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme's stability or functionality followed by displaying these on the web.

  5. Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

    PubMed

    Uchiyama, Ikuo

    2008-10-31

    Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

  6. Multiple genome alignment for identifying the core structure among moderately related microbial genomes

    PubMed Central

    Uchiyama, Ikuo

    2008-01-01

    Background Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. Results The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. Conclusion The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes. PMID:18976470

  7. Identification of risk conditions for the development of adrenal disorders: how optimized PubMed search strategies makes the difference.

    PubMed

    Guaraldi, Federica; Parasiliti-Caprino, Mirko; Goggi, Riccardo; Beccuti, Guglielmo; Grottoli, Silvia; Arvat, Emanuela; Ghizzoni, Lucia; Ghigo, Ezio; Giordano, Roberta; Gori, Davide

    2014-12-01

    The exponential growth of scientific literature available through electronic databases (namely PubMed) has increased the chance of finding interesting articles. At the same time, search has become more complicated, time consuming, and at risk of missing important information. Therefore, optimized strategies have to be adopted to maximize searching impact. The aim of this study was to formulate efficient strings to search PubMed for etiologic associations between adrenal disorders (ADs) and other conditions. A comprehensive list of terms identifying endogenous conditions primarily affecting adrenals was compiled. An ad hoc analysis was performed to find the best way to express each term in order to find the highest number of potentially pertinent articles in PubMed. A predefined number of retrieved abstracts were read to assess their association with ADs' etiology. A more sensitive (providing the largest literature coverage) and a more specific (including only those terms retrieving >40 % of potentially pertinent articles) string were formulated. Various researches were performed to assess strings' ability to identify articles of interest in comparison with non-optimized literature searches. We formulated optimized, ready applicable tools for the identification of the literature assessing etiologic associations in the field of ADs using PubMed, and demonstrated the advantages deriving from their application. Detailed description of the methodological process is also provided, so that this work can easily be translated to other fields of practice.

  8. Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

    PubMed

    Lu, Yin; Figler, Bryan; Huang, Hong; Tu, Yi-Cheng; Wang, Ju; Cheng, Feng

    2017-01-01

    Identifying drug-drug interaction (DDI) is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings) terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

  9. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    PubMed Central

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

  10. Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm

    PubMed Central

    Guo, Wei; Shang, Dong-Mei; Cao, Jing-Hui; Feng, Kaiyan; Wang, ShaoPeng

    2017-01-01

    As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients' personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR) algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases. PMID:28255556

  11. Qatar biomedical and cancer publications in PubMed between 2000 and 2012.

    PubMed

    Zeeneldin, Ahmed A; Taha, Fatma Mohamed

    2014-01-01

    obvious increase in Qatar biomedical and cancer publications in PubMed, the absolute numbers were relatively small. While strategies are in place, leaders of Qatar biomedical research need to consider increasing cancer research and clinical trials to meet the country's needs. Linking research output to researchers, research facilities and research funding is needed.

  12. Identifying work related injuries: comparison of methods for interrogating text fields

    PubMed Central

    2010-01-01

    Background Work-related injuries in Australia are estimated to cost around $57.5 billion annually, however there are currently insufficient surveillance data available to support an evidence-based public health response. Emergency departments (ED) in Australia are a potential source of information on work-related injuries though most ED's do not have an 'Activity Code' to identify work-related cases with information about the presenting problem recorded in a short free text field. This study compared methods for interrogating text fields for identifying work-related injuries presenting at emergency departments to inform approaches to surveillance of work-related injury. Methods Three approaches were used to interrogate an injury description text field to classify cases as work-related: keyword search, index search, and content analytic text mining. Sensitivity and specificity were examined by comparing cases flagged by each approach to cases coded with an Activity code during triage. Methods to improve the sensitivity and/or specificity of each approach were explored by adjusting the classification techniques within each broad approach. Results The basic keyword search detected 58% of cases (Specificity 0.99), an index search detected 62% of cases (Specificity 0.87), and the content analytic text mining (using adjusted probabilities) approach detected 77% of cases (Specificity 0.95). Conclusions The findings of this study provide strong support for continued development of text searching methods to obtain information from routine emergency department data, to improve the capacity for comprehensive injury surveillance. PMID:20374657

  13. Using noun phrases for navigating biomedical literature on Pubmed: how many updates are we losing track of?

    PubMed

    Srikrishna, Devabhaktuni; Coram, Marc A

    2011-01-01

    Author-supplied citations are a fraction of the related literature for a paper. The "related citations" on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed "related citations." We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper--many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper.

  14. Identifying content-based and relational techniques to change behaviour in motivational interviewing.

    PubMed

    Hardcastle, Sarah J; Fortier, Michelle; Blake, Nicola; Hagger, Martin S

    2017-03-01

    Motivational interviewing (MI) is a complex intervention comprising multiple techniques aimed at changing health-related motivation and behaviour. However, MI techniques have not been systematically isolated and classified. This study aimed to identify the techniques unique to MI, classify them as content-related or relational, and evaluate the extent to which they overlap with techniques from the behaviour change technique taxonomy version 1 [BCTTv1; Michie, S., Richardson, M., Johnston, M., Abraham, C., Francis, J., Hardeman, W., … Wood, C. E. (2013). The behavior change technique taxonomy (v1) of 93 hierarchically clustered techniques: Building an international consensus for the reporting of behavior change interventions. Annals of Behavioral Medicine, 46, 81-95]. Behaviour change experts (n = 3) content-analysed MI techniques based on Miller and Rollnick's [(2013). Motivational interviewing: Preparing people for change (3rd ed.). New York: Guildford Press] conceptualisation. Each technique was then coded for independence and uniqueness by independent experts (n = 10). The experts also compared each MI technique to those from the BCTTv1. Experts identified 38 distinct MI techniques with high agreement on clarity, uniqueness, preciseness, and distinctiveness ratings. Of the identified techniques, 16 were classified as relational techniques. The remaining 22 techniques were classified as content based. Sixteen of the MI techniques were identified as having substantial overlap with techniques from the BCTTv1. The isolation and classification of MI techniques will provide researchers with the necessary tools to clearly specify MI interventions and test the main and interactive effects of the techniques on health behaviour. The distinction between relational and content-based techniques within MI is also an important advance, recognising that changes in motivation and behaviour in MI is a function of both intervention content and the interpersonal style

  15. Time-dependent migration of citations through PubMed and OvidSP subsets: a study on a series of simultaneous PubMed and OvidSP searches.

    PubMed

    Boeker, Martin; Vach, Werner; Motschall, Edith

    2013-01-01

    To quantitatively describe (1) differences between search results derived at consecutive time points with the PubMed and OvidSP literature search interfaces over a five day interval, and (2) the migration of citations through different subsets to estimate the timeliness of OvidSP. PubMed-Identifiers (PMIDs) of the following subsets were retrieved from PubMed and OvidSP simultaneously (within 8 h) at 11 days in March and April 2010 including 5 consecutive days: as supplied by publisher, in process, PubMed not MEDLINE, and OLDMEDLINE. Search results were compared for difference and intersection sets. The migration of citations on individual level was determined by comparison of corresponding sets over several days. The "in process" set was stable with about 446,000 - 452,000 citations; a small fraction of up to 3 % of the total subsets were in PubMed only and OvidSP only subsets. About 96 % of the ca. 10,500 citations in the OvidSP only subset migrated within 2 days out of the "in process" subset. The database of OvidSP is updated within a period of two days.

  16. Conducting literature searches on Ayurveda in PubMed, Indian, and other databases.

    PubMed

    Narahari, Saravu R; Aggithaya, Madhur Guruprasad; Suraj, Kumbla R

    2010-11-01

    Literature searches for articles on Ayurveda provide special challenges, since many of the Indian journals in which such articles appear are not indexed by current medical databases such as PubMed and Cochrane Central Register of Controlled Trials. The aim of this study was to develop a comprehensive search strategy on Ayurveda topics and to map the existing databases containing Ayurveda journal publications. We have developed a literature search procedure that can recover the great majority of articles on any given topic associated with Ayurveda. Our system is formulated in an easily reproducible fashion that all researchers can use. Using the keywords related to Ayurveda and vitiligo, we searched 41 databases that may contain complementary and alternative medicine publications. Only 11 databases yielded results; PubMed contained 9 articles. Each of 14 other databases named in our search procedure averaged 23 articles. International Bibliographic Information of Dietary Supplements, for example, gave 22, of which 1 satisfied our eligibility criteria. "Annotated Bibliography of Indian Medicine" gave 47, of which 7 satisfied eligibility criteria. This article proposes guidelines enabling comprehensive searches to locate all types of Ayurvedic articles, not necessarily only randomized controlled trials.

  17. Bioinformatic profiling identifies an immune-related risk signature for glioblastoma.

    PubMed

    Cheng, Wen; Ren, Xiufang; Zhang, Chuanbao; Cai, Jinquan; Liu, Yang; Han, Sheng; Wu, Anhua

    2016-06-14

    To investigate the local immune status and its prognostic value in glioma. A cohort of 297 glioma samples with whole genome microarray expression data from the Chinese Glioma Genome Atlas database were included for discovery. The Cancer Genome Atlas (TCGA) database was used for validation. Principal components analysis and gene set enrichment analysis were used to explore the bioinformatic implication. Distinct local immune status was identified according to histologic grade. Glioblastoma (GBM) exhibited an enhanced immune phenotype compared to lower grade glioma. We profiled the immune-related gene set and identified 8 genes (FOXO3, IL6, IL10, ZBTB16, CCL18, AIMP1, FCGR2B, and MMP9) with the greatest prognostic value in GBM. A local immune-related risk signature was developed from the genes to distinguish cases as high or low risk of unfavorable prognosis, which could be validated in TCGA database. High-risk patients conferred an enhanced intensity of local immune response compared to low-risk ones. Additionally, the signature exhibited different distribution based on molecular features. The signature had prognostic significance in the stratified cohorts and was identified as an independent prognostic factor for GBM. We profiled the immune status in glioma and established a local immune signature for GBM, which could independently identify patients with a high risk of reduced survival, indicating the relationship between prognosis and local immune response. © 2016 American Academy of Neurology.

  18. Refined phenotyping identifies links between preeclampsia and related diseases in a Norwegian preeclampsia family cohort

    PubMed Central

    Thomsen, Liv Cecilie V.; Melton, Phillip E.; Tollaksen, Kjersti; Lyslo, Ingvill; Roten, Linda T.; Odland, Maria L.; Strand, Kristin M.; Nygård, Ottar; Sun, Chen; Iversen, Ann-Charlotte; Austgulen, Rigmor; Moses, Eric K.; Bjørge, Line

    2015-01-01

    Objective: Preeclampsia is a complex genetic disease of pregnancy with a heterogenous presentation, unknown cause and potential severe outcomes for both mother and child. Preeclamptic women have increased risk for atherothrombotic cardiovascular disease. We aimed to identify heritabilities and phenotypic correlations of preeclampsia and related conditions in the Norwegian Preeclampsia Family Biobank. Methods: By applying a variance components model, a total of 493 individuals (from 138 families with increased occurrence of preeclampsia) were classified according to 30 disease-related phenotypes. Results: Of parous women, 75.7% (263/338) had experienced preeclampsia and 35.7% of women with and 22.4% without preeclampsia delivered children small for gestational age (SGA). We identified 11 phenotypes as heritable. The increased occurrence of preeclampsia was reflected by the presence [heritability (H2r) = 0.60)] and severity (H2r = 0.15) of preeclampsia and being born in a preeclamptic pregnancy (H2r = 0.25). Other heritable phenotypes identified included SGA (H2r = 0.40), chronic hypertension (H2r = 0.57), severity of atherothrombotic cardiovascular disease (H2r = 0.31), BMI (H2r = 0.60) and pulmonary disease (H2r = 0.91). The heritable phenotype preeclampsia overlapped with SGA (P = 0.03), whereas pulmonary disease was phenotypically correlated with atherothrombotic cardiovascular disease (P < 0.01), SGA (P = 0.02) and BMI (P = 0.02). Conclusion: This is the first study identifying the H2r of a range of health-related conditions in preeclamptic families. Our study demonstrates how refinement of phenotypes leads to better H2r estimation and the identification of a biological relationship between preeclampsia and related traits. PMID:26259119

  19. Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches.

    PubMed

    Shariff, Salimah Z; Bejaimal, Shayna Ad; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

    2013-08-15

    Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. To compare the performance of searches in PubMed and Google Scholar. We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; P<.001). Precision was similar in both databases (PubMed: 6%; Google Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; P<.001). For quick clinical searches, Google Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles.

  20. Identifying the Structure and Effect of Drinking-Related Self-Schemas.

    PubMed

    Domenico, Lisa H; Strobbe, S; Stein, Karen Farchaus; Giordani, Bruno J; Hagerty, Bonnie M; Pressler, Susan J

    2016-07-13

    Self-schemas have received increased attention as favorable targets for therapeutic intervention because of their central role in self-perception and behavior. The purpose of this integrative review was to identify, evaluate, and synthesize existing research pertaining to drinking-related self-schemas. Russell's integrative review strategy guided the search. Sixteen published works were identified, meeting criteria for evaluation (n = 12 data-based publications and n = 4 models). The retrieved data-based publications rated fair-good using Polit and Beck's criteria; the overall body of literature rated "B" using Grimes and Schulz criteria. Retrieved models rated 4 to 7 using Fitzpatrick and Whall's criteria. The existing literature strongly supports the availability of a drinking-related self-schema among moderate-to-heavy drinking samples, and suggests a positive relationship between elaboration and drinking behavior. The relationship between valenced content of the schema and drinking behavior remains unexplored. Identifying variation in the structural properties of drinking-related self-schemas could lay the foundation for future interventions.

  1. Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

    PubMed

    Vellay, S G P; Latimer, N E Miller; Paillard, G

    2009-06-01

    Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

  2. Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

    PubMed Central

    Niu, Yun; Otasek, David; Jurisica, Igor

    2010-01-01

    Motivation: Identification and characterization of protein–protein interactions (PPIs) is one of the key aims in biological research. While previous research in text mining has made substantial progress in automatic PPI detection from literature, the need to improve the precision and recall of the process remains. More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction. Results: We developed an interaction detection method and explored the usefulness of various features in automatically identifying PPIs in text. The results show that our approach outperforms other systems using the AImed dataset. In the tests where our system achieves better precision with reduced recall, we discuss possible approaches for improvement. In addition to test datasets, we evaluated the performance on interactions from five human-curated databases—BIND, DIP, HPRD, IntAct and MINT—where our system consistently identified evidence for ∼60% of interactions when both proteins appear in at least one sentence in the PubMed abstract. We then applied the system to extract articles from PubMed to annotate known, high-throughput and interologous interactions in I2D. Availability: The data and software are available at: http://www.cs.utoronto.ca/∼juris/data/BI09/. Contact: yniu@uhnres.utoronto.ca; juris@ai.utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19850753

  3. Age-related remodeling of neuromuscular junctions on type-identified diaphragm fibers.

    PubMed

    Prakash, Y S; Sieck, G C

    1998-07-01

    Previous studies have reported fiber-type differences in the morphological adaptations of neuromuscular junctions (NMJs) to aging by comparing limb muscles consisting of predominantly type I or II fibers. A confounding factor in these studies is age-related change in activity, which may differ between muscles. In the present study, we assessed age-related changes of the NMJ in type-identified fibers of the rat diaphragm muscle, which maintains consistent inspiratory-related activation throughout life. In 6- and 24-month-old rats, a fluorescent triple-labeling technique was used to visualize phrenic axons, presynaptic nerve terminals, and postsynaptic acetylcholine receptors (end-plates) on type-identified fibers. The NMJs were then imaged using three-dimensional (3D) confocal microscopy. On type IIx and IIb fibers, nerve terminal and end-plate 2D planar and 3D surface areas expanded, and the number of nerve terminal and end-plate branches increased, indicating fragmentation of the NMJ with aging. On the other hand, NMJs on type I and IIa fibers displayed little adaptation. These morphological adaptations may be geared toward maintaining the efficacy of inspiratory-related activity of the diaphragm muscle, but may affect the functional reserve of the aging diaphragm.

  4. Answers to Questions Posed During Daily Patient Care Are More Likely to Be Answered by UpToDate Than PubMed

    PubMed Central

    Stalenhoef, Anton FH; de Vries Robbé, Pieter F; Overbeke, A John PM

    2008-01-01

    Background UpToDate and PubMed are popular sources for medical information. Data regarding the efficiency of PubMed and UpToDate in daily medical care are lacking. Objective The purpose of this observational study was to describe the percentage of answers retrieved by these information sources, comparing search results with regard to different medical topics and the time spent searching for an answer. Methods A total of 40 residents and 30 internists in internal medicine working in an academic medical center searched PubMed and UpToDate using an observation portal during daily medical care. The information source used for searching and the time needed to find an answer to the question were recorded by the portal. Information was provided by searchers regarding the topic of the question, the situation that triggered the question, and whether an answer was found. Results We analyzed 1305 patient-related questions sent to PubMed and/or UpToDate between October 1, 2005 and March 31, 2007 using our portal. A complete answer was found in 594/1125 (53%) questions sent to PubMed or UpToDate. A partial or full answer was obtained in 729/883 (83%) UpToDate searches and 152/242 (63%) PubMed searches (P < .001). UpToDate answered more questions than PubMed on all major medical topics, but a significant difference was detected only when the question was related to etiology (P < .001) or therapy (P = .002). Time to answer was 241 seconds (SD 24) for UpToDate and 291 seconds (SD 7) for PubMed. Conclusions Specialists and residents in internal medicine generally use less than 5 minutes to answer patient-related questions in daily care. More questions are answered using UpToDate than PubMed on all major medical topics. PMID:18926978

  5. Answers to questions posed during daily patient care are more likely to be answered by UpToDate than PubMed.

    PubMed

    Hoogendam, Arjen; Stalenhoef, Anton F H; Robbé, Pieter F de Vries; Overbeke, A John P M

    2008-10-03

    UpToDate and PubMed are popular sources for medical information. Data regarding the efficiency of PubMed and UpToDate in daily medical care are lacking. The purpose of this observational study was to describe the percentage of answers retrieved by these information sources, comparing search results with regard to different medical topics and the time spent searching for an answer. A total of 40 residents and 30 internists in internal medicine working in an academic medical center searched PubMed and UpToDate using an observation portal during daily medical care. The information source used for searching and the time needed to find an answer to the question were recorded by the portal. Information was provided by searchers regarding the topic of the question, the situation that triggered the question, and whether an answer was found. We analyzed 1305 patient-related questions sent to PubMed and/or UpToDate between October 1, 2005 and March 31, 2007 using our portal. A complete answer was found in 594/1125 (53%) questions sent to PubMed or UpToDate. A partial or full answer was obtained in 729/883 (83%) UpToDate searches and 152/242 (63%) PubMed searches (P < .001). UpToDate answered more questions than PubMed on all major medical topics, but a significant difference was detected only when the question was related to etiology (P < .001) or therapy (P = .002). Time to answer was 241 seconds (SD 24) for UpToDate and 291 seconds (SD 7) for PubMed. Specialists and residents in internal medicine generally use less than 5 minutes to answer patient-related questions in daily care. More questions are answered using UpToDate than PubMed on all major medical topics.

  6. Identifying Novel Candidate Genes Related to Apoptosis from a Protein-Protein Interaction Network

    PubMed Central

    Wang, Baoman; Yuan, Fei; Kong, Xiangyin; Hu, Lan-Dian; Cai, Yu-Dong

    2015-01-01

    Apoptosis is the process of programmed cell death (PCD) that occurs in multicellular organisms. This process of normal cell death is required to maintain the balance of homeostasis. In addition, some diseases, such as obesity, cancer, and neurodegenerative diseases, can be cured through apoptosis, which produces few side effects. An effective comprehension of the mechanisms underlying apoptosis will be helpful to prevent and treat some diseases. The identification of genes related to apoptosis is essential to uncover its underlying mechanisms. In this study, a computational method was proposed to identify novel candidate genes related to apoptosis. First, protein-protein interaction information was used to construct a weighted graph. Second, a shortest path algorithm was applied to the graph to search for new candidate genes. Finally, the obtained genes were filtered by a permutation test. As a result, 26 genes were obtained, and we discuss their likelihood of being novel apoptosis-related genes by collecting evidence from published literature. PMID:26543496

  7. Identifying biological concepts from a protein-related corpus with a probabilistic topic model.

    PubMed

    Zheng, Bin; McLean, David C; Lu, Xinghua

    2006-02-08

    Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE titles and abstracts by applying a probabilistic topic model. The latent Dirichlet allocation (LDA) model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO) terms based on mutual information. The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text.

  8. Identifying biological concepts from a protein-related corpus with a probabilistic topic model

    PubMed Central

    Zheng, Bin; McLean, David C; Lu, Xinghua

    2006-01-01

    Background Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE© titles and abstracts by applying a probabilistic topic model. Results The latent Dirichlet allocation (LDA) model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO) terms based on mutual information. Conclusion The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text. PMID:16466569

  9. Examination of relative reinforcement effects of stimuli identified through pretreatment and daily brief preference assessments.

    PubMed

    DeLeon, I G; Fisher, W W; Rodriguez-Catter, V; Maglieri, K; Herman, K; Marhefka, J M

    2001-01-01

    Several brief preference assessments have recently been developed to identify reinforcers for individuals with developmental disabilities. One purported advantage of brief assessments is that they can be administered frequently, thus accommodating shifts in preference and presumably enhancing reinforcement effects. In this study, we initially conducted lengthy paired-choice preference assessments and identified a hierarchy of preferred items for 5 individuals with developmental disabilities. Subsequently, brief multiple-stimulus-without-replacement assessments using the same items were completed each day prior to work sessions. On days when results of the daily brief assessment differed from the one-time lengthy assessment, the relative reinforcing effects of the top items from each assessment were compared in a concurrent-schedule arrangement. The results revealed that when the two assessments differed, participants generally allocated more responses to the task associated with the daily top-ranked item.

  10. Real-time analysis application for identifying bursty local areas related to emergency topics.

    PubMed

    Sakai, Tatsuhiro; Tamura, Keiichi

    2015-01-01

    Since social media started getting more attention from users on the Internet, social media has been one of the most important information source in the world. Especially, with the increasing popularity of social media, data posted on social media sites are rapidly becoming collective intelligence, which is a term used to refer to new media that is displacing traditional media. In this paper, we focus on geotagged tweets on the Twitter site. These geotagged tweets are referred to as georeferenced documents because they include not only a short text message, but also the documents' posting time and location. Many researchers have been tackling the development of new data mining techniques for georeferenced documents to identify and analyze emergency topics, such as natural disasters, weather, diseases, and other incidents. In particular, the utilization of geotagged tweets to identify and analyze natural disasters has received much attention from administrative agencies recently because some case studies have achieved compelling results. In this paper, we propose a novel real-time analysis application for identifying bursty local areas related to emergency topics. The aim of our new application is to provide new platforms that can identify and analyze the localities of emergency topics. The proposed application is composed of three core computational intelligence techniques: the Naive Bayes classifier technique, the spatiotemporal clustering technique, and the burst detection technique. Moreover, we have implemented two types of application interface: a Web application interface and an android application interface. To evaluate the proposed application, we have implemented a real-time weather observation system embedded the proposed application. we used actual crawling geotagged tweets posted on the Twitter site. The weather observation system successfully detected bursty local areas related to observed emergency weather topics.

  11. Enriching plausible new hypothesis generation in PubMed

    PubMed Central

    Baek, Seung Han; Lee, Dahee; Kim, Minjoo; Lee, Jong Ho

    2017-01-01

    Background Most of earlier studies in the field of literature-based discovery have adopted Swanson's ABC model that links pieces of knowledge entailed in disjoint literatures. However, the issue concerning their practicability remains to be solved since most of them did not deal with the context surrounding the discovered associations and usually not accompanied with clinical confirmation. In this study, we aim to propose a method that expands and elaborates the existing hypothesis by advanced text mining techniques for capturing contexts. We extend ABC model to allow for multiple B terms with various biological types. Results We were able to concretize a specific, metabolite-related hypothesis with abundant contextual information by using the proposed method. Starting from explaining the relationship between lactosylceramide and arterial stiffness, the hypothesis was extended to suggest a potential pathway consisting of lactosylceramide, nitric oxide, malondialdehyde, and arterial stiffness. The experiment by domain experts showed that it is clinically valid. Conclusions The proposed method is designed to provide plausible candidates of the concretized hypothesis, which are based on extracted heterogeneous entities and detailed relation information, along with a reliable ranking criterion. Statistical tests collaboratively conducted with biomedical experts provide the validity and practical usefulness of the method unlike previous studies. Applying the proposed method to other cases, it would be helpful for biologists to support the existing hypothesis and easily expect the logical process within it. PMID:28678852

  12. A Case Study on Sepsis Using PubMed and Deep Learning for Ontology Learning.

    PubMed

    Arguello Casteleiro, Mercedes; Maseda Fernandez, Diego; Demetriou, George; Read, Warren; Fernandez Prieto, Maria Jesus; Des Diz, Julio; Nenadic, Goran; Keane, John; Stevens, Robert

    2017-01-01

    We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora. Term extraction is used as the first step of an ontology learning process that aims to (semi-)automatic annotation of biomedical concepts and relations from more than 300K PubMed titles and abstracts. We experimented with both traditional distributional semantics methods such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) as well as the neural language models CBOW and Skip-gram from Deep Learning. The evaluation conducted concentrates on sepsis, a major life-threatening condition, and shows that Deep Learning models outperform LSA and LDA with much higher precision.

  13. Identifying Liver Cancer and Its Relations with Diseases, Drugs, and Genes: A Literature-Based Approach

    PubMed Central

    Song, Min

    2016-01-01

    In biomedicine, scientific literature is a valuable source for knowledge discovery. Mining knowledge from textual data has become an ever important task as the volume of scientific literature is growing unprecedentedly. In this paper, we propose a framework for examining a certain disease based on existing information provided by scientific literature. Disease-related entities that include diseases, drugs, and genes are systematically extracted and analyzed using a three-level network-based approach. A paper-entity network and an entity co-occurrence network (macro-level) are explored and used to construct six entity specific networks (meso-level). Important diseases, drugs, and genes as well as salient entity relations (micro-level) are identified from these networks. Results obtained from the literature-based literature mining can serve to assist clinical applications. PMID:27195695

  14. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome.

    PubMed

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-06-13

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, "conronavirus", "case", "transmission" and "detection" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened.

  15. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome

    PubMed Central

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-01-01

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, “conronavirus”, “case”, “transmission” and “detection” were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened. PMID:27304963

  16. Developing topic-specific search filters for PubMed with click-through data.

    PubMed

    Li, J; Lu, Z

    2013-01-01

    Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters. We present an automated method to develop topic-specific filters on the basis of users' search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance. We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters. Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/

  17. Developing Topic-Specific Search Filters for PubMed with Click-Through Data

    PubMed Central

    Li, Jiao; Lu, Zhiyong

    2013-01-01

    Summary Objectives Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters. Methods We present an automated method to develop topic-specific filters on the basis of users’ search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance. Results We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters. Conclusion Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/ PMID:23666447

  18. The development of PubMed search strategies for patient preferences for treatment outcomes.

    PubMed

    van Hoorn, Ralph; Kievit, Wietske; Booth, Andrew; Mozygemba, Kati; Lysdahl, Kristin Bakke; Refolo, Pietro; Sacchini, Dario; Gerhardus, Ansgar; van der Wilt, Gert Jan; Tummers, Marcia

    2016-07-29

    The importance of respecting patients' preferences when making treatment decisions is increasingly recognized. Efficiently retrieving papers from the scientific literature reporting on the presence and nature of such preferences can help to achieve this goal. The objective of this study was to create a search filter for PubMed to help retrieve evidence on patient preferences for treatment outcomes. A total of 27 journals were hand-searched for articles on patient preferences for treatment outcomes published in 2011. Selected articles served as a reference set. To develop optimal search strategies to retrieve this set, all articles in the reference set were randomly split into a development and a validation set. MeSH-terms and keywords retrieved using PubReMiner were tested individually and as combinations in PubMed and evaluated for retrieval performance (e.g. sensitivity (Se) and specificity (Sp)). Of 8238 articles, 22 were considered to report empirical evidence on patient preferences for specific treatment outcomes. The best search filters reached Se of 100 % [95 % CI 100-100] with Sp of 95 % [94-95 %] and Sp of 97 % [97-98 %] with 75 % Se [74-76 %]. In the validation set these queries reached values of Se of 90 % [89-91 %] with Sp 94 % [93-95 %] and Se of 80 % [79-81 %] with Sp of 97 % [96-96 %], respectively. Narrow and broad search queries were developed which can help in retrieving literature on patient preferences for treatment outcomes. Identifying such evidence may in turn enhance the incorporation of patient preferences in clinical decision making and health technology assessment.

  19. Testing search strategies for systematic reviews in the Medline literature database through PubMed.

    PubMed

    Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

    2014-04-01

    A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

  20. Improved Methods to Identify Stable, Highly Heritable Subtypes of Opioid Use and Related Behaviors

    PubMed Central

    Sun, Jiangwen; Bi, Jinbo; Chan, Grace; Oslin, David; Farrer, Lindsay; Gelernter, Joel; Kranzler, Henry R.

    2012-01-01

    Although there is evidence that opioid dependence (OD) is heritable, efforts to identify genes contributing to risk for the disorder have been hampered by its complex etiology and variable clinical manifestations. Decomposition of a complex set of opioid users into homogeneous subgroups could enhance genetic analysis. We applied a series of data mining techniques, including multiple correspondence analysis, variable selection and cluster analysis, to 69 opioid-related measures from 5,390 subjects aggregated from family-based and case-control genetic studies to identify homogeneous subtypes and estimate their heritability. Novel aspects of this work include our use of 1) heritability estimates of specific clinical features of OD to enhance the heritability of the subtypes and 2) a k-medoids clustering method in combination with hierarchical clustering to yield replicable clusters that are less sensitive to noise than previous methods. We identified five homogeneous groups, including two large groups comprised of 762 and 1,353 heavy opioid users, with estimated heritability of 0.69 and 0.76, respectively. These methods represent a promising approach to the identification of highly heritable subtypes in complex, heterogeneous disorders. PMID:22694982

  1. Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network.

    PubMed

    Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

    2016-05-05

    Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.

  2. Metabolism-related enzyme alterations identified by proteomic analysis in human renal cell carcinoma

    PubMed Central

    Lu, Zejun; Yao, Yuqin; Song, Qi; Yang, Jinliang; Zhao, Xiangfei; Yang, Ping; Kang, Jingbo

    2016-01-01

    The renal cell carcinoma (RCC) is one of the most common types of kidney neoplasia in Western countries; it is relatively resistant to conventional chemotherapy and radiotherapy. Metabolic disorders have a profound effect on the degree of malignancy and treatment resistance of the tumor. However, the molecular characteristics related to impaired metabolism leading to the initiation of RCC are still not very clear. In this study, two-dimensional electrophoresis (2-DE) and mass spectra (MS) technologies were utilized to identify the proteins involved in energy metabolism of RCC. A total of 73 proteins that were differentially expressed in conventional RCC, in comparison with the corresponding normal kidney tissues, were identified. Bioinformatics analysis has shown that these proteins are involved in glycolysis, urea cycle, and the metabolic pathways of pyruvate, propanoate, and arginine/proline. In addition, some were also involved in the signaling network of p53 and FAS. These results provide some clues for new therapeutic targets and treatment strategies of RCC. PMID:27022288

  3. Soil geomorphology: Identifying relations between the scale of spatial variation and soil processes using the variogram

    NASA Astrophysics Data System (ADS)

    Kerry, Ruth; Oliver, Margaret A.

    2011-07-01

    Practitioners of geostatistics often fail to make associations between the patterns of variation on their maps of kriged predictions and the physical processes that might generate them. Geostatistical approaches that use knowledge of the underlying process have been proposed to reduce the number of soil samples required. Also, if the scale of variation identified by the variogram can be linked to process, it could be incorporated as a scale factor into existing deterministic models. To attempt to relate the scale and pattern of variation in topsoil properties to processes, the topsoil of four field sites in southern England on different parent materials and with a variety of topography was sampled. Relations between variogram range, topography and parent material were examined. The variogram ranges for parent materials that result in heavier soil textures tended to be longer as were those for plateau and valley areas compared with slopes. Possible links between these patterns and soil processes were investigated by examining: 1) changes in soil characteristics with depth, 2) moving correlations, 3) variation in soil properties with topography within fields, 4) directional variograms and 5) derived topographic attributes. The predominance of vertical rather than lateral movements of water through the soil in plateau and valley positions was identified as responsible for the longer range of variograms in these locations. Hydraulic conductivity was suggested as a possible underlying cause of differences in the scale of variation in the topsoil between parent materials.

  4. Rare Copy Number Variants Identified Suggest the Regulating Pathways in Hypertension-Related Left Ventricular Hypertrophy

    PubMed Central

    Marshall, Christian R.; Majid, Fadhlina; Danuri, Norlaila; Basir, Fashieha; Thiruvahindrapuram, Bhooma; Scherer, Stephen W.; Yusoff, Khalid

    2016-01-01

    Left ventricular hypertrophy (LVH) is an independent risk factor for cardiovascular morbidity and mortality, and a powerful predictor of adverse cardiovascular outcomes in the hypertensive patients. It has complex multifactorial and polygenic basis for its pathogenesis. We hypothesized that rare copy number variants (CNVs) contribute to the LVH pathogenesis in hypertensive patients. Copy number variants (CNV) were identified in 258 hypertensive patients, 95 of whom had LVH, after genotyping with a high resolution SNP array. Following stringent filtering criteria, we identified 208 rare, or private CNVs that were only present in our patients with hypertension related LVH. Preliminary findings from Gene Ontology and pathway analysis of this study confirmed the involvement of the genes known to be functionally involved in cardiac development and phenotypes, in line with previously reported transcriptomic studies. Network enrichment analyses suggested that the gene-set was, directly or indirectly, involved in the transcription factors regulating the “foetal cardiac gene programme” which triggered the hypertrophic cascade, confirming previous reports. These findings suggest that multiple, individually rare copy number variants altering genes may contribute to the pathogenesis of hypertension-related LVH. In summary, we have provided further supporting evidence that rare CNV could potentially impact this common and complex disease susceptibility with lower heritability. PMID:26930585

  5. Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network

    PubMed Central

    Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

    2016-01-01

    Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer. PMID:27149165

  6. Sleep-related eye symptoms and their potential for identifying driver sleepiness.

    PubMed

    Filtness, Ashleigh J; Anund, Anna; Fors, Carina; Ahlström, Christer; Akerstedt, Torbjørn; Kecklund, Göran

    2014-10-01

    The majority of individuals appear to have insight into their own sleepiness, but there is some evidence that this does not hold true for all, for example treated patients with obstructive sleep apnoea. Identification of sleep-related symptoms may help drivers determine their sleepiness, eye symptoms in particular show promise. Sixteen participants completed four motorway drives on two separate occasions. Drives were completed during daytime and night-time in both a driving simulator and on the real road. Ten eye symptoms were rated at the end of each drive, and compared with driving performance and subjective and objective sleep metrics recorded during driving. 'Eye strain', 'difficulty focusing', 'heavy eyelids' and 'difficulty keeping the eyes open' were identified as the four key sleep-related eye symptoms. Drives resulting in these eye symptoms were more likely to have high subjective sleepiness and more line crossings than drives where similar eye discomfort was not reported. Furthermore, drivers having unintentional line crossings were likely to have 'heavy eyelids' and 'difficulty keeping the eyes open'. Results suggest that drivers struggling to identify sleepiness could be assisted with the advice 'stop driving if you feel sleepy and/or have heavy eyelids or difficulty keeping your eyes open'.

  7. Using relative handgrip strength to identify children at risk of sarcopenic obesity.

    PubMed

    Steffl, Michal; Chrudimsky, Jan; Tufano, James J

    2017-01-01

    Identifying children at risk of developing childhood sarcopenic obesity often requires specialized equipment and costly testing procedures, so cheaper and quicker methods would be advantageous, especially in field-based settings. The purpose of this study was to determine the relationships between the muscle-to-fat ratio (MFR) and relative handgrip strength, and to determine the ability of handgrip strength relative to body mass index (grip-to-BMI) to identify children who are at risk of developing sarcopenic obesity. Grip-to-BMI was measured in 730 Czech children (4 to 14 yrs). Bioelectrical impedance was used to estimate body fat mass and skeletal muscle mass, from which the MFR was calculated. The area under the curve (AUC) was 0.791 (95% CI 0.692-0.890, p ˂ 0.001) in girls 4-9; 0.789 (95% CI 0.688-0.890, p ˂ 0.001) in girls 10-14 years old; 0.719 (95% CI 0.607-0.831, p = 0.001) in boys 4-9; and 0.896 (95% CI 0.823-0.969, p ˂ 0.001) in boys 10-14 years old. Calculated using the grip-to-BMI ratio, the OR (95% CI) for girls to be at risk of sarcopenic obesity identified by MFR was 9.918 (4.243-23.186, p ˂ 0.001) and was 11.515 (4.280-30.982, p ˂ 0.001) for boys. The grip-to-BMI ratio can be used to predict the presence of sarcopenic obesity in children, which can play a role in pediatric health interventions.

  8. Soil Incubations Synthesis Study to Identify and Constrain Relations of Soil Properties and Carbon Mineralization

    NASA Astrophysics Data System (ADS)

    Moyano, F. E.; Chenu, C.

    2010-12-01

    , which can be better applied to a wide range of (non-waterlogged) soils. Such relations will ultimately serve to improve the performance of soil models. An overview of the data shows a large variability among datasets in the relations between moisture and respiration fluxes. Data from a wide variety of soils has been submitted to the database, ranging from Mediterranean to Boreal climates. More data is still being provided by researchers worldwide. A projected analysis of the database will serve to test the applicability of currently used soil respiration functions on different data, to derive new functions describing relations and potential interacting effects, and to find where further studies are necessary by identifying poorly characterized soils or processes. The database is open to further contributions of data, and to the option of establishing a dynamic database accessible to data owners or for open access.

  9. Sports medicine clinical trial research publications in academic medical journals between 1996 and 2005: an audit of the PubMed MEDLINE database.

    PubMed

    Nichols, A W

    2008-11-01

    To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and the internationality of authorships. Sports medicine research is international in scope with improving study methodology and an evolution of topics. Structured review of articles identified in a search of a large electronic medical database. PubMed MEDLINE database. Sports medicine-related clinical research trials published between 1996 and 2005. Review and analysis of articles that meet inclusion criteria. Articles were examined for study topics, research methods, experimental subject characteristics, journal of publication, lead authors and journal countries of origin and language of publication. The search retrieved 414 articles, of which 379 (345 English language and 34 non-English language) met the inclusion criteria. The number of publications increased steadily during the study period. Randomised clinical trials were the most common study type and the "diagnosis, management and treatment of sports-related injuries and conditions" was the most popular study topic. The knee, ankle/foot and shoulder were the most frequent anatomical sites of study. Soccer players and runners were the favourite study subjects. The American Journal of Sports Medicine had the highest number of publications and shared the greatest international diversity of authorships with the British Journal of Sports Medicine. The USA, Australia, Germany and the UK produced a good number of the lead authorships. In all, 91% of articles and 88% of journals were published in English. Sports medicine-related research is internationally diverse, clinical trial publications are increasing and the sophistication of research design may be improving.

  10. Three PubMed skills to support evidence-based dentistry.

    PubMed

    Deahl, S Thomas

    2011-02-01

    The National Library of Medicine's PubMed database can powerfully assist dentists in evidence-based practice. Three useful PubMed skills can improve the efficiency of the clinician's search: (1) Use of MeSH terms; (2) Use of Limits; (3) Use of Clinical Queries.

  11. Use of a twin dataset to identify AMD-related visual patterns controlled by genetic factors

    NASA Astrophysics Data System (ADS)

    Quellec, Gwénolé; Abràmoff, Michael D.; Russell, Stephen R.

    2010-03-01

    The mapping of genotype to the phenotype of age-related macular degeneration (AMD) is expected to improve the diagnosis and treatment of the disease in a near future. In this study, we focused on the first step to discover this mapping: we identified visual patterns related to AMD which seem to be controlled by genetic factors, without explicitly relating them to the genes. For this purpose, we used a dataset of eye fundus photographs from 74 twin pairs, either monozygotic twins, who have the same genotype, or dizygotic twins, whose genes responsible for AMD are less likely to be identical. If we are able to differentiate monozygotic twins from dizygotic twins, based on a given visual pattern, then this pattern is likely to be controlled by genetic factors. The main visible consequence of AMD is the apparition of drusen between the retinal pigment epithelium and Bruch's membrane. We developed two automated drusen detectors based on the wavelet transform: a shape-based detector for hard drusen, and a texture- and color- based detector for soft drusen. Forty visual features were evaluated at the location of the automatically detected drusen. These features characterize the texture, the shape, the color, the spatial distribution, or the amount of drusen. A distance measure between twin pairs was defined for each visual feature; a smaller distance should be measured between monozygotic twins for visual features controlled by genetic factors. The predictions of several visual features (75.7% accuracy) are comparable or better than the predictions of human experts.

  12. Using PubMed in radiology: Ten useful tips for radiologists

    PubMed Central

    Sriganesh, Vasumathi

    2011-01-01

    PubMed contains a bibliography of articles published in around 4800 journals. It combines MEDLINE and OLDMEDLINE (articles from 1960, going back till the 1940s). PubMed is updated on a daily basis; to include both published and ahead of print references. As a radiologist, one can use PubMed to track several journals, track topics, search for specific topics, verify incomplete or incorrect references, store one's own publications, and save selected references; one can also create filters depending on one's own search needs for some regular topics. This article provides some key background knowledge on searching PubMed and also describes some features that are often left unexplored. The PubMed site has undergone many changes in the last few years and this article will update users on the current features. PMID:22013289

  13. Using PubMed in radiology: Ten useful tips for radiologists.

    PubMed

    Sriganesh, Vasumathi

    2011-07-01

    PubMed contains a bibliography of articles published in around 4800 journals. It combines MEDLINE and OLDMEDLINE (articles from 1960, going back till the 1940s). PubMed is updated on a daily basis; to include both published and ahead of print references. As a radiologist, one can use PubMed to track several journals, track topics, search for specific topics, verify incomplete or incorrect references, store one's own publications, and save selected references; one can also create filters depending on one's own search needs for some regular topics. This article provides some key background knowledge on searching PubMed and also describes some features that are often left unexplored. The PubMed site has undergone many changes in the last few years and this article will update users on the current features.

  14. De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

    PubMed Central

    2011-01-01

    Background Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV) by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the E. fischeriana transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds. Results In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of E. fischeriana. We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (> = 75%) to Ricinus communis, a close relative to E. fischeriana. We also evaluated the conservation of E. fischeriana genes against EST datasets from the Euphorbeacea family, which included R. communis, Hevea brasiliensis and Euphorbia esula. We identified a core set of 1,145 gene clusters conserved in all four species and 1,487 E. fischeriana paralogous genes. Furthermore, we screened E. fischeriana transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (HDS) and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS), which are required for multiple

  15. Drug related problems identified by community pharmacists on hospital discharge prescriptions in New Zealand.

    PubMed

    Braund, Rhiannon; Coulter, Carolyn V; Bodington, Amy Jane; Giles, Lauren Margaret; Greig, Anna-Marie; Heaslip, Larissa Jane; Marshall, Brooke Jane

    2014-06-01

    There can be a lack of transfer of information between hospitals and community pharmacies following patient discharge, which puts patients at a high risk of suffering drug related problems (DRPs). Community pharmacy plays a vital role in identifying and solving these discharge DRPs and taking action before these DRPs can lead to patient harm. To identify the types and quantities of DRPs that community pharmacies detect within a single district health board (DHB) in New Zealand. One DHB in New Zealand that contains 50 community pharmacies, which receive discharge prescriptions from two local hospitals. All community pharmacies in the DHB area (n = 50) were invited to participate in the 2 week study which involved documenting the number of hospital discharge prescriptions received, and then the number and type of DRPs identified and what interventions were required. The number and type of DRPs identified as a proportion of all discharge prescriptions received during the 2 week study period. Initially a total of 38 pharmacies agreed to participate in this study, however only 32 pharmacies provided data for the entire 2 week period. Over a 2 week period a total of 1,374 hospital discharge prescriptions were presented to these pharmacies. From these prescriptions 344 (25 %) required further action to be taken by the pharmacist. These 344 prescriptions consisted of a total of 396 individual DRPs. Actions classified as "Supply and/or Funding" accounted for 43 % (171), which represented the largest class of all actions required from hospital discharge prescriptions. This class consisted of "Special Authority" problems, medications not being available, non-subsidised items on the prescription and other supply/funding problems. "Errors" accounted for 38 % (151) which included errors of omission (20 %) and errors of commission (18 %). This study found a significant number of DRPs identified by community pharmacists on hospital discharge prescriptions. These included missing

  16. QTLs for Seed Vigor-Related Traits Identified in Maize Seeds Germinated under Artificial Aging Conditions

    PubMed Central

    Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, ShuLei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

    2014-01-01

    High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R2>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R2>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes. PMID:24651614

  17. QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

    PubMed

    Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, Shulei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

    2014-01-01

    High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R(2)>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2)>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

  18. Retrieving Clinical Evidence: A Comparison of PubMed and Google Scholar for Quick Clinical Searches

    PubMed Central

    Bejaimal, Shayna AD; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

    2013-01-01

    Background Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. Objective To compare the performance of searches in PubMed and Google Scholar. Methods We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Results Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; P<.001). Precision was similar in both databases (PubMed: 6%; Google Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; P<.001). Conclusions For quick clinical searches, Google Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles. PMID:23948488

  19. Identifying Tinnitus-Related Genes Based on a Side-Effect Network Analysis

    PubMed Central

    Elgoyhen, A B; Langguth, B; Nowak, W; Schecklmann, M; De Ridder, D; Vanneste, S

    2014-01-01

    Tinnitus, phantom sound perception, is a worldwide highly prevalent disorder for which no clear underlying pathology has been established and for which no approved drug is on the market. Thus, there is an urgent need for new approaches to understand this condition. We used a network pharmacology side-effect analysis to search for genes that are involved in tinnitus generation. We analyzed a network of 1,313 drug–target pairs, based on 275 compounds that elicit tinnitus as side effect and their targets reported in databases, and used a quantitative score to identify emergent significant targets that were more common than expected at random. Cyclooxigenase 1 and 2 were significant, which validates our approach, since salicylate is a known tinnitus generator. More importantly, we predict previously unknown tinnitus-related targets. The present results have important implications toward understanding tinnitus pathophysiology and might pave the way toward the design of novel pharmacotherapies. PMID:24477090

  20. [Italian Program for Surveillance of Acute Pesticide-Related Illnesses: cases identified in 2005].

    PubMed

    Settimi, L; Davanzo, F; Travaglia, A; Locatelli, C; Cilento, I; Volpe, C; Russo, A; Miceli, G; Fracassi, A; Maiozzi, P; Marcello, I; Sesan, F; Urbani, E

    2007-01-01

    In 2005, the Italian System for Surveillance of Acute Pesticide-Related Illnesses (SIAF) identified 625 cases, among which 520 unintentionally exposed. The majority of these subjects were men (75%) and aged 26-65 years (65%). About 63% of all exposures occurred at work. Severity for these illnesses was low for 94% and moderate for 5%. Four cases were classified as illnesses of high severity. Some 70% of all the reported exposures occurred between May and September. The active ingredients responsible for the largest number of cases were: glyphosate (n. 56), copper sulphate (n. 55), methomyl (n. = 52), metam-sodium (n. 24). Three episodes of collective environmental exposure to soil fumigants involving 23 subjects were also detected.

  1. An event-related potential paradigm for identifying (rare negative) attitude stimuli that people intentionally misreport.

    PubMed

    Crites, Stephen L; Mojica, Andrew J; Corral, Guadalupe; Taylor, Jennifer H

    2010-09-01

    This experiment explored whether a late positive potential (LPP) of the event-related brain potential is useful for examining attitudes that people attempt to conceal. Participants identified a set of liked, neutral, and disliked people and viewed sequences consisting of either names or pictures of these people. Disliked people appeared rarely among liked people, and participants either: (1) always accurately reported their negative attitudes toward the people; (2) misreported negative attitudes as positive when they saw a picture of a disliked person; or (3) misreported negative attitudes as positive when they saw a name of a disliked person. Rare negative stimuli evoked a larger-amplitude LPP than frequent positive stimuli. Misreporting attitudes significantly reduced the amplitude difference between rare negative and frequent positive stimuli, though it remained significant.

  2. Aberrant drug-related behaviors: Unsystematic documentation does not identify prescription drug use disorder

    PubMed Central

    Meltzer, Ellen C.; Rybin, Dennis; Meshesha, Lidia Z.; Saitz, Richard; Samet, Jeffrey H.; Rubens, Sonia L.; Liebschutz, Jane M.

    2012-01-01

    Objective No evidence-based methods exist to identify prescription drug use disorder (PDUD) in primary care (PC) patients prescribed controlled substances. Aberrant drug-related behaviors (ADRBs) are suggested as a proxy. Our objective was to determine whether ADRBs documented in electronic medical records (EMRs) of patients prescribed opioids and benzodiazepines could serve as a proxy for identifying PDUD. Design A cross-sectional study of PC patients at an urban, academic medical center. Subjects 264 English-speaking patients (ages 18–60) with chronic pain (≥3 months), receiving ≥1 opioid analgesic or benzodiazepine prescription in the past year, were recruited during outpatient PC visits. Outcome Measures Composite International Diagnostic Interview defined DSM-IV diagnoses of past-year PDUD and no disorder. EMRs were reviewed for 15 pre-specified ADRBs (e.g. early refill, stolen medications) in the year before and after study entry. Fisher’s exact test compared frequencies of each ADRB between participants with and without PDUD. Results 61 participants (23%) met DSM-IV PDUD criteria and 203 (77%) had no disorder; 85% had one or more ADRB documented. Few differences in frequencies of individual behaviors were noted between groups, with only “appearing intoxicated or high” documented more frequently among participants with PDUD (n=10, 16%) vs. no disorder (n=8, 4%), p=0.002. The only common ADRB, “emergency visit for pain,” did not discriminate between those with and without the disorder (82% PDUD vs. 78% no disorder, p=0.6). Conclusions EMR documentation of ADRBs is common among PC patients prescribed opioids or benzodiazepines, but unsystematic clinician documentation does not identify PDUDs. Evidence-based approaches are needed. PMID:23057631

  3. Potential Susceptibility Loci Identified for Renal Cell Carcinoma by Targeting Obesity-Related Genes.

    PubMed

    Shu, Xiang; Purdue, Mark P; Ye, Yuanqing; Tu, Huakang; Wood, Christopher G; Tannir, Nizar M; Wang, Zhaoming; Albanes, Demetrius; Gapstur, Susan M; Stevens, Victoria L; Rothman, Nathaniel; Chanock, Stephen J; Wu, Xifeng

    2017-09-01

    Background: Obesity is an established risk factor for renal cell carcinoma (RCC). Although genome-wide association studies (GWAS) of RCC have identified several susceptibility loci, additional variants might be missed due to the highly conservative selection.Methods: We conducted a multiphase study utilizing three independent genome-wide scans at MD Anderson Cancer Center (MDA RCC GWAS and MDA RCC OncoArray) and National Cancer Institute (NCI RCC GWAS), which consisted of a total of 3,530 cases and 5,714 controls, to investigate genetic variations in obesity-related genes and RCC risk.Results: In the discovery phase, 32,946 SNPs located at ±10 kb of 2,001 obesity-related genes were extracted from MDA RCC GWAS and analyzed using multivariable logistic regression. Proxies (R(2) > 0.8) were searched or imputation was performed if SNPs were not directly genotyped in the validation sets. Twenty-one SNPs with P < 0.05 in both MDA RCC GWAS and NCI RCC GWAS were subsequently evaluated in MDA RCC OncoArray. In the overall meta-analysis, significant (P < 0.05) associations with RCC risk were observed for SNP mapping to IL1RAPL2 [rs10521506-G: ORmeta = 0.87 (0.81-0.93), Pmeta = 2.33 × 10(-5)], PLIN2 [rs2229536-A: ORmeta = 0.87 (0.81-0.93), Pmeta = 2.33 × 10(-5)], SMAD3 [rs4601989-A: ORmeta = 0.86 (0.80-0.93), Pmeta = 2.71 × 10(-4)], MED13L [rs10850596-A: ORmeta = 1.14 (1.07-1.23), Pmeta = 1.50 × 10(-4)], and TSC1 [rs3761840-G: ORmeta = 0.90 (0.85-0.97), Pmeta = 2.47 × 10(-3)]. We did not observe any significant cis-expression quantitative trait loci effect for these SNPs in the TCGA KIRC data.Conclusions: Taken together, we found that genetic variation of obesity-related genes could influence RCC susceptibility.Impact: The five identified loci may provide new insights into disease etiology that reveal importance of obesity-related genes in RCC development. Cancer Epidemiol Biomarkers Prev; 26(9); 1436-42. ©2017 AACR. ©2017 American Association for Cancer Research.

  4. Acute Aortic Dissection Biomarkers Identified Using Isobaric Tags for Relative and Absolute Quantitation

    PubMed Central

    Xiao, Ziya; Xue, Yuan; Gu, Guorong; Zhang, Yaping; Zhang, Jin; Fan, Fan; Luan, Xiao; Deng, Zhi; Tao, Zhengang; Song, Zhen-ju; Tong, Chaoyang; Wang, Haojun

    2016-01-01

    The purpose of this study was to evaluate the utility of potential serum biomarkers for acute aortic dissection (AAD) that were identified by isobaric Tags for Relative and Absolute Quantitation (iTRAQ) approaches. Serum samples from 20 AAD patients and 20 healthy volunteers were analyzed using iTRAQ technology. Protein validation was performed using samples from 120 patients with chest pain. A total of 355 proteins were identified with the iTRAQ approach; 164 proteins reached the strict quantitative standard, and 125 proteins were increased or decreased more than 1.2-fold (64 and 61 proteins were up- and downregulated, resp.). Lumican, C-reactive protein (CRP), thrombospondin-1 (TSP-1), and D-dimer were selected as candidate biomarkers for the validation tests. Receiver operating characteristic (ROC) curves show that Lumican and D-dimer have diagnostic value (area under the curves [AUCs] 0.895 and 0.891, P < 0.05). For Lumican, the diagnostic sensitivity and specificity were 73.33% and 98.33%, while the corresponding values for D-dimer were 93.33% and 68.33%. For Lumican and D-dimer AAD combined diagnosis, the sensitivity and specificity were 88.33% and 95%, respectively. In conclusion, Lumican has good specificity and D-dimer has good sensitivity for the diagnosis of AAD, while the combined detection of D-dimer and Lumican has better diagnostic value. PMID:27403433

  5. Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity.

    PubMed

    Fortney, Kristen; Dobriban, Edgar; Garagnani, Paolo; Pirazzini, Chiara; Monti, Daniela; Mari, Daniela; Atzmon, Gil; Barzilai, Nir; Franceschi, Claudio; Owen, Art B; Kim, Stuart K

    2015-12-01

    We developed a new statistical framework to find genetic variants associated with extreme longevity. The method, informed GWAS (iGWAS), takes advantage of knowledge from large studies of age-related disease in order to narrow the search for SNPs associated with longevity. To gain support for our approach, we first show there is an overlap between loci involved in disease and loci associated with extreme longevity. These results indicate that several disease variants may be depleted in centenarians versus the general population. Next, we used iGWAS to harness information from 14 meta-analyses of disease and trait GWAS to identify longevity loci in two studies of long-lived humans. In a standard GWAS analysis, only one locus in these studies is significant (APOE/TOMM40) when controlling the false discovery rate (FDR) at 10%. With iGWAS, we identify eight genetic loci to associate significantly with exceptional human longevity at FDR < 10%. We followed up the eight lead SNPs in independent cohorts, and found replication evidence of four loci and suggestive evidence for one more with exceptional longevity. The loci that replicated (FDR < 5%) included APOE/TOMM40 (associated with Alzheimer's disease), CDKN2B/ANRIL (implicated in the regulation of cellular senescence), ABO (tags the O blood group), and SH2B3/ATXN2 (a signaling gene that extends lifespan in Drosophila and a gene involved in neurological disease). Our results implicate new loci in longevity and reveal a genetic overlap between longevity and age-related diseases and traits, including coronary artery disease and Alzheimer's disease. iGWAS provides a new analytical strategy for uncovering SNPs that influence extreme longevity, and can be applied more broadly to boost power in other studies of complex phenotypes.

  6. Identifying metabolites related to nitrogen mineralisation using 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    . T McDonald, Noeleen; Graham, Stewart; Watson, Catherine; Gordon, Alan; Lalor, Stan; Laughlin, Ronnie; Elliott, Chris; . P Wall, David

    2015-04-01

    Exploring new analysis techniques to enhance our knowledge of the various metabolites within our soil systems is imperative. Principally, this knowledge would allow us to link key metabolites with functional influences on critical nutrient processes, such as the nitrogen (N) mineralisation in soils. Currently there are few studies that utilize proton nuclear magnetic resonance spectroscopy (1H NMR) to characterize multiple metabolites within a soil sample. The aim of this research study was to examine the effectiveness of 1H NMR for isolating multiple metabolites that are related to the mineralizable N (MN) capacity across a range of 35 Irish grassland soils. Soils were measured for MN using the standard seven day anaerobic incubation (AI-7). Additionally, soils were also analysed for a range of physio-chemical properties [e.g. total N, total C, mineral N, texture and soil organic matter (SOM)]. Proton NMR analysis was carried on these soils by extracting with 40% methanol:water, lyophilizing and reconstituting in deuterium oxide and recording the NMR spectra on a 400MHz Bruker AVANCE III spectrometer. Once the NMR data were spectrally processed and analysed using multivariate statistical analysis, seven metabolites were identified as having significant relationships with MN (glucose, trimethylamine, glutamic acid, serine, aspartic acid, 4-aminohippuirc acid and citric acid). Following quantification, glucose was shown to explain the largest percentage variability in MN (72%). These outcomes suggest that sources of labile carbon are essential in regulating N mineralisation and the capacity of plant available N derived from SOM-N pools in these soils. Although, smaller in concentration, the amino acids; 4-aminohippuirc acid, glutamic acid and serine also significantly (P<0.05) explained 43%, 27% and 19% of the variability in MN, respectively. This novel study highlights the effectiveness of using 1H NMR as a practical approach to profile multiple metabolites in

  7. Identifying and Characterizing Climate-related Changes Influencing Accessiblity to Ecosystem Services in Rural Boreal Alaska

    NASA Astrophysics Data System (ADS)

    Hollingsworth, T. N.; Cold, H.; Brinkman, T. J.; Brown, C.; Verbyla, D.

    2016-12-01

    Increasingly, subsistence harvesters within the Alaska boreal region are experiencing changes in the environment that are influencing their ability to access traditional hunting, fishing, and gathering areas. However, few data have been collected on the mechanisms of environmental disturbances and their biophysical characteristics that affect human movement across landscapes. In addition, the prevalence and spatial-temporal characteristics of subsistence-altering disturbances have not been quantified within this region. The overarching objectives of this project are to: 1) Collaborate with subsistence harvesters to map travel networks and locate sites of ecosystem disturbances influencing access to subsistence resources, 2) Identify biophysical characteristics and underlying mechanisms of access corridors and disturbances, 3) Using remote sensing, expand the sample size of disturbance observations and determine spatial and temporal extent (frequency, duration, area, severity) of influential disturbances. Here, we present initial data from subsistence harvesters about climate change effects on their ability to access resources. Furthermore, we describe our conceptual framework for accomplishing these goals, including modifications of our data collection based on participatory response. Across nine rural villages in interior Alaska, we have identified eight general categories of climatic change: ice and snow conditions (40%), hydrological changes including erosion (35%), changes in shoulder season length (14%), weather anomalies (4%), phenological changes (3%), thermokarst (2%), fire (1%), and undetermined (3%). We discuss how to combine the data and knowledge we have collected through participatory research with natural science approaches to expand our understanding of landscape-level climate-related changes. We will use results and locations collected from participants to assess ecosystem and landscape-level biophysical factors related to areas where travel is

  8. Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity

    PubMed Central

    Fortney, Kristen; Dobriban, Edgar; Garagnani, Paolo; Pirazzini, Chiara; Monti, Daniela; Mari, Daniela; Atzmon, Gil; Barzilai, Nir; Franceschi, Claudio; Owen, Art B.; Kim, Stuart K.

    2015-01-01

    We developed a new statistical framework to find genetic variants associated with extreme longevity. The method, informed GWAS (iGWAS), takes advantage of knowledge from large studies of age-related disease in order to narrow the search for SNPs associated with longevity. To gain support for our approach, we first show there is an overlap between loci involved in disease and loci associated with extreme longevity. These results indicate that several disease variants may be depleted in centenarians versus the general population. Next, we used iGWAS to harness information from 14 meta-analyses of disease and trait GWAS to identify longevity loci in two studies of long-lived humans. In a standard GWAS analysis, only one locus in these studies is significant (APOE/TOMM40) when controlling the false discovery rate (FDR) at 10%. With iGWAS, we identify eight genetic loci to associate significantly with exceptional human longevity at FDR < 10%. We followed up the eight lead SNPs in independent cohorts, and found replication evidence of four loci and suggestive evidence for one more with exceptional longevity. The loci that replicated (FDR < 5%) included APOE/TOMM40 (associated with Alzheimer’s disease), CDKN2B/ANRIL (implicated in the regulation of cellular senescence), ABO (tags the O blood group), and SH2B3/ATXN2 (a signaling gene that extends lifespan in Drosophila and a gene involved in neurological disease). Our results implicate new loci in longevity and reveal a genetic overlap between longevity and age-related diseases and traits, including coronary artery disease and Alzheimer’s disease. iGWAS provides a new analytical strategy for uncovering SNPs that influence extreme longevity, and can be applied more broadly to boost power in other studies of complex phenotypes. PMID:26677855

  9. A methodological survey identified eight proposed frameworks for the adaptation of health related guidelines.

    PubMed

    Darzi, Andrea; Abou-Jaoude, Elias A; Agarwal, Arnav; Lakis, Chantal; Wiercioch, Wojtek; Santesso, Nancy; Brax, Hneine; El-Jardali, Fadi; Schünemann, Holger J; Akl, Elie A

    2017-06-01

    five key steps strategy for adaptation of guidelines to the local context. The SGR method consists of nine steps and takes into consideration both methodological gaps and context-specific normative issues in source guidelines. We identified through searching personal files two abandoned methods. We identified and described eight proposed frameworks for the adaptation of health-related guidelines. There is a need to evaluate these different frameworks to assess rigor, efficiency, and transparency of their proposed processes. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Characterization of drug-related problems identified by clinical pharmacy staff at Danish hospitals.

    PubMed

    Kjeldsen, Lene Juel; Birkholm, Trine; Fischer, Hanne; Graabæk, Trine; Kibsdal, Karina Porsborg; Ravn-Nielsen, Lene Vestergaard; Truelshøj, Tania Holtum

    2014-08-01

    In 2010, a database of drug related problems (DRPs) was implemented to assist clinical pharmacy staff in documenting clinical pharmacy activities locally. A study of quality, reliability and generalisability showed that national analyses of the data could be conducted. Analyses at the national level may help identify and prevent DRPs by performing national interventions. The aim of the study was to explore the DRP characteristics as documented by clinical pharmacy staff at hospital pharmacies in the Danish DRP-database during a 3-year period. Danish hospital pharmacies. Data documented in the DRP-database during the initial 3 years after implementation were analyzed retrospectively. The DRP-database contains DRPs reported at hospitals by clinical pharmacy staff. The analyses focused on DRP categories, implementation rates and drugs associated with the DRPs. Characteristics of DRPs. In total, 72,044 DRPs were documented in the DRP-database during the first 3 years of implementation, and the number of documented DRPs increased every year. An overall stable implementation rate of approximately 58 % was identified. The DRPs identified were multi-facetted, however evenly distributed for each of the 3 years. The most frequently identified DRP categories were: "Dose", followed by "Nonadherence to guidelines" and "Supplement to treatment". The highest implementation rates were found for the following DRP categories: "Non-adherence to guidelines" (79 %) followed by "Therapeutic duplication" (73 %) and "Dosing time and interval" (70 %). Even though the top 25 drugs were involved in 58 % of all DRPs, multiple drugs were associated with DRPs. The drugs most frequently involved in DRPs were paracetamol (4.6 % of all DRPs), simvastatin (3.0 %), lansoprazole (2.7 %), morphine (2.6 %) and alendronic acid (2.4 %). The study found that a national database on DRPs contained multi-facetted DRPs, however evenly distributed for each of the 3 years. Even though the top 25 drugs were

  11. VEGF-related polymorphisms identified by GWAS and risk for major depression

    PubMed Central

    Xie, T; Stathopoulou, M G; de Andrés, F; Siest, G; Murray, H; Martin, M; Cobaleda, J; Delgado, A; Lamont, J; Peñas-LIedó, E; LLerena, A; Visvikis-Siest, S

    2017-01-01

    Depression is a common, severe, disabling mental disease that affects millions of people of all ages worldwide. Various studies have shown that neurotrophic/growth factors have a key role in depression and, more specifically, vascular endothelial growth factor (VEGF) is implicated in the pathogenesis of depression. The purpose of this study was to investigate the potential links between four VEGF-related single-nucleotide polymorphisms (SNPs), previously identified through a genome-wide association study (GWAS) and depression. The direct effects and epistatic interactions of the four VEGF-related SNPs (rs10738760, rs6921438, rs6993770 and rs4416670) on depression were investigated through a case–control study including 437 individuals diagnosed with depression and 477 healthy volunteers as controls. Gender, age and body mass index influence was additionally analyzed. The SNP rs4416670 was associated with increased risk for depression (OR: 1.60, P: 0.010). This result demonstrates the existence of relationships between VEGF genetic determinants and depression. This novel association reveals new molecular mechanisms suggesting the potential role of VEGF in depression development that could help to promote a personalized prediction for this severe common disease. PMID:28267147

  12. VEGF-related polymorphisms identified by GWAS and risk for major depression.

    PubMed

    Xie, T; Stathopoulou, M G; de Andrés, F; Siest, G; Murray, H; Martin, M; Cobaleda, J; Delgado, A; Lamont, J; Peñas-LIedó, E; LLerena, A; Visvikis-Siest, S

    2017-03-07

    Depression is a common, severe, disabling mental disease that affects millions of people of all ages worldwide. Various studies have shown that neurotrophic/growth factors have a key role in depression and, more specifically, vascular endothelial growth factor (VEGF) is implicated in the pathogenesis of depression. The purpose of this study was to investigate the potential links between four VEGF-related single-nucleotide polymorphisms (SNPs), previously identified through a genome-wide association study (GWAS) and depression. The direct effects and epistatic interactions of the four VEGF-related SNPs (rs10738760, rs6921438, rs6993770 and rs4416670) on depression were investigated through a case-control study including 437 individuals diagnosed with depression and 477 healthy volunteers as controls. Gender, age and body mass index influence was additionally analyzed. The SNP rs4416670 was associated with increased risk for depression (OR: 1.60, P: 0.010). This result demonstrates the existence of relationships between VEGF genetic determinants and depression. This novel association reveals new molecular mechanisms suggesting the potential role of VEGF in depression development that could help to promote a personalized prediction for this severe common disease.

  13. Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition.

    PubMed

    Tao, Xuan; Liang, Yan; Yang, Xuemei; Pang, Jianhui; Zhong, Zhijun; Chen, Xiaohui; Yang, Yuekui; Zeng, Kai; Kang, Runming; Lei, Yunfeng; Ying, Sancheng; Gong, Jianjun; Gu, Yiren; Lv, Xuebin

    2017-01-01

    Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.

  14. EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts

    PubMed Central

    Yeniterzi, Süveyda; Sezerman, Uğur

    2009-01-01

    Background A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes' databases are currently available, scientific literature still remains at large for up-to-date source of learning the effects of a mutation on an enzyme. However, going through vast amounts of scientific documents to extract the information on desired mutation has always been a time consuming process. In this paper, therefore, we describe an unique method, termed as EnzyMiner, which automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability and/or the activity of a given enzyme. Results We present an automated system which identifies the abstracts that contain an amino-acid-level mutation and then classifies them according to the mutation's effect on the enzyme. In the case of mutation identification, MuGeX, an automated mutation-gene extraction system has an accuracy of 93.1% with a 91.5 F-measure. For impact analysis, document classification is performed to identify the abstracts that contain a change in enzyme's stability or activity resulting from the mutation. The system was trained on lipases and tested on amylases with an accuracy of 85%. Conclusion EnzyMiner identifies the abstracts that contain a protein mutation for a given enzyme and checks whether the abstract is related to a disease with the help of information extraction and machine learning techniques. For disease related abstracts, the mutation list and direct links to the abstracts are retrieved from the system and displayed on the Web. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme's stability or functionality followed by displaying

  15. Quantity and quality assessment of randomized controlled trials on orthodontic practice in PubMed.

    PubMed

    Shimada, Tatsuo; Takayama, Hisako; Nakamura, Yoshiki

    2010-07-01

    To find current high-quality evidence for orthodontic practice within a reasonable time, we tested the performance of a PubMed search. PubMed was searched using publication type randomized controlled trial and medical subject heading term "orthodontics" for articles published between 2003 and 2007. The PubMed search results were compared with those from a hand search of four orthodontic journals to determine the sensitivity of PubMed search. We evaluated the precision of the PubMed search result and assessed the quality of individual randomized controlled trials using the Jadad scale. Sensitivity and precision were 97.46% and 58.12%, respectively. In PubMed, of the 277 articles retrieved, 161 (58.12%) were randomized controlled trials on orthodontic practice, and 115 of the 161 articles (71.42%) were published in four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics. Assessment by the Jadad scale revealed 60 high-quality randomized controlled trials on orthodontic practice, of which 45 (75%) were published in these four journals. PubMed is a highly desirable search engine for evidence-based orthodontic practice. To stay current and get high-quality evidence, it is reasonable to look through four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics.

  16. LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts.

    PubMed

    Maier, Holger; Döhr, Stefanie; Grote, Korbinian; O'Keeffe, Sean; Werner, Thomas; Hrabé de Angelis, Martin; Schneider, Ralf

    2005-07-01

    The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene-gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser.

  17. LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts

    PubMed Central

    Maier, Holger; Döhr, Stefanie; Grote, Korbinian; O'Keeffe, Sean; Werner, Thomas; de Angelis, Martin Hrabé; Schneider, Ralf

    2005-01-01

    The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene–gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner () and WikiGene () can be used unrestricted with any Internet browser. PMID:15980584

  18. Design of a score to identify hospitalized patients at risk of drug-related problems.

    PubMed

    Urbina, Olatz; Ferrández, Olivia; Grau, Santiago; Luque, Sonia; Mojal, Sergi; Marin-Casino, Monica; Mateu-de-Antonio, Javier; Carmona, Alexia; Conde-Estévez, David; Espona, Merce; González, Elena; Riu, Marta; Salas, Esther

    2014-09-01

    The potential impact of drug-related problems (DRP) on morbidity and mortality is a serious concern in hospitalized patients. This study aimed to design a risk score to identify patients most at risk of a DRP. Data from patients admitted to a tertiary university hospital between January and August 2009 were used to design the risk score (training set). DRP were detected through a pharmacy warning system integrated in the computerized medical history. The variables associated with developing a DRP were identified through a binary multivariate logistic regression analysis and were used to compute the DRP risk score, which was subsequently validated in patients admitted between September and December 2009 (validation set). Of the 8713 patients included in the training set, at least one DRP was detected in 2425 (27.8%). Prescription of a higher number of drugs, higher comorbidity, advanced age, certain groups of the Anatomical Therapeutic Chemical classification system, and some major diagnostic categories were associated with risk of DRP. These variables were used to compute the DRP risk score. The area under the receiver operator characteristic curve was 0.778 (95%CI [0.768, 0.789]). Of the 4058 admissions included in the validation set, at least one DRP was detected in 876 (21.6%). The area under the receiver operator characteristic curve was 0.776 (95%CI [0.759, 0.792]). Knowledge of the variables associated with DRP could aid their early detection in at-risk patients. The use of an application that can be continually updated in daily clinical practice helps to optimize resources. Copyright © 2014 John Wiley & Sons, Ltd.

  19. Allatotropin-related peptide in cockroaches: identification via mass spectrometric analysis of single identified neurons.

    PubMed

    Neupert, Susanne; Schattschneider, Sebastian; Predel, Reinhard

    2009-03-01

    The first insect allatotropin-related peptide (ATRP) was isolated from head extracts of the adult sphinx moth Manduca sexta [Kataoka H, Toschi A, Li JP, Carney RL, Schooley DA, Kramer SJ. Identification of an allatotropin from adult Manduca sexta. Science 1989;243:1481-3.]. Meanwhile ATRPs are known from different holometabolous insects but only a single ATRP could be identified from hemimetabolous insects [Paemen L, Tips A, Schoofs L, Proost P, Van Damme J, De Loof A. Lom-AG-myotropin: a novel myotropic peptide from the male accessory glands of Locusta migratoria. Peptides 1991;12:7-10.]. This means that the extensive analysis of neuropeptides from Leucophaea maderae and Periplaneta americana, which led to the discovery of many novel insect neuropeptides, did not result in the detection of any ATRP. In this study, we used another approach to find a cockroach ATRP by first identifying Manse-AT immunoreactive neurons in the terminal ganglion that can be stained by retrograde labeling and are suitable for dissection and subsequent mass spectrometric analysis. The peptidomic analysis of these putative ATRP neurons paved the way for the identification of the first cockroach ATRP. MALDI-TOF/TOF tandem mass spectrometry revealed a sequence identity with Locmi-AG-MT-1 which classifies this ATRP as a highly conserved neuropeptide. A mass spectrometric screening of the nervous system allowed the detection of ATRP-ion signals in different parts of the CNS of P. americana as well as L. maderae. The data obtained in this study will be incorporated in a map of peptidergic neurons from the CNS of the American cockroach, P. americana.

  20. Scientific publication productivity of Libyan medical schools: a bibliometric study of papers listed in PubMed, 1988-2007.

    PubMed

    Benamer, H T S; Bredan, A; Bakoush, O

    2009-08-01

    Scientific publication is a vital mission of medical schools and it is important to periodically document how well schools fulfil this mission. This study aimed to analyse the publication record of Libyan medical schools in international journals indexed in PubMed between 1988 and 2007. Medline was searched using PubMed for publications affiliated to Libya during 1988-2007. Out of 417 papers related to Libya, 348 (84%) are affiliated to the medical schools and related hospitals. More than 60% of the 348 papers are affiliated to Al-Arab Medical University, Benghazi, while Al-Fateh Medical University, Tripoli, contributed 103 papers (30%). The rest of the papers (n=25, 7%) were published by medical schools in other parts of the country. The publication rate declined by 3% annually between 1988 and 2007. The decline was mainly due to a decrease in the publication rate by Al-Arab Medical University, Benghazi. Overall, nine departments produced 10 or more papers each. Out of about 1675 staff members, there are only 148 first authors and 207 last authors. The estimated annual publication rate is 0.7 papers per 100 academic staff members. This study reveals that published scholarship of the Libyan medical schools is extremely low, that the publication rate has declined, and that most academic staff have no publications listed in PubMed. This issue needs urgent attention.

  1. Quertle and KNALIJ: searching PubMed has never been so easy and effective.

    PubMed

    Giglia, E

    2011-12-01

    Quertle and KNALIJ are two innovative tools created to search PubMed in a easier and more effective way. They dramatically reduce time to discover meaningful results. Quertle allows a semantic search in multiple biomedical databases (PubMed included) and runs a query via relationships between concepts, so that you retrieve at ease more pertinent results and can navigate them by "key concepts". KNALIJ is a visualization tool which searches PubMed and presents the results in the form of visual, interactive maps you can zoom, scale, and explore according to new paths.

  2. Automatic Export of PubMed Citations to EndNote.

    PubMed

    London, Sue; Gurdal, Osman; Gall, Carole

    2010-04-01

    The export of MEDLINE references to EndNote can be accomplished in various ways. Unlike Ovid MEDLINE, PubMed does not have a direct export feature to EndNote. Until recently, PubMed references had to be saved as a text file to import into EndNote. Now, the automatic export of PubMed references can be done using Internet Explorer (IE) or Mozilla Firefox Web browsers. The development and teaching of seamless citation management is a value-added service to health professionals.

  3. Expression-based network biology identifies immune-related functional modules involved in plant defense.

    PubMed

    Tully, Joel P; Hill, Aubrey E; Ahmed, Hadia M R; Whitley, Ryan; Skjellum, Anthony; Mukhtar, M Shahid

    2014-06-03

    Plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. These intricate transcriptional regulatory interactions depend on the recognition of specific promoter sequences by regulatory transcription factors. The combinatorial and cooperative action of multiple transcription factors defines a regulatory network that enables plant cells to respond to distinct biological signals. The identification of immune-related modules in large-scale transcriptional regulatory networks can reveal the mechanisms by which exposure to a pathogen elicits a precise phenotypic immune response. We have generated a large-scale immune co-expression network using a comprehensive set of Arabidopsis thaliana (hereafter Arabidopsis) transcriptomic data, which consists of a wide spectrum of immune responses to pathogens or pathogen-mimicking stimuli treatments. We employed both linear and non-linear models to generate Arabidopsis immune co-expression regulatory (AICR) network. We computed network topological properties and ascertained that this newly constructed immune network is densely connected, possesses hubs, exhibits high modularity, and displays hallmarks of a "real" biological network. We partitioned the network and identified 156 novel modules related to immune functions. Gene Ontology (GO) enrichment analyses provided insight into the key biological processes involved in determining finely tuned immune responses. We also developed novel software called OCCEAN (One Click Cis-regulatory Elements ANalysis) to discover statistically enriched promoter elements in the upstream regulatory regions of Arabidopsis at a whole genome level. We demonstrated that OCCEAN exhibits higher precision than the existing promoter element discovery tools. In light of known and newly discovered cis-regulatory elements, we evaluated biological significance of two key immune-related functional modules and proposed mechanism(s) to explain

  4. Identifying genes related to choriogenesis in insect panoistic ovaries by Suppression Subtractive Hybridization

    PubMed Central

    Irles, Paula; Bellés, Xavier; Piulachs, M Dolors

    2009-01-01

    Background Insect ovarioles are classified into two categories: panoistic and meroistic, the later having apparently evolved from an ancestral panoistic type. Molecular data on oogenesis is practically restricted to meroistic ovaries. If we aim at studying the evolutionary transition from panoistic to meroistic, data on panoistic ovaries should be gathered. To this end, we planned the construction of a Suppression Subtractive Hybridization (SSH) library to identify genes involved in panoistic choriogenesis, using the cockroach Blattella germanica as model. Results We constructed a post-vitellogenic ovary library by SSH to isolate genes involved in choriogenesis in B. germanica. The tester library was prepared with an ovary pool from 6- to 7-day-old females, whereas the driver library was prepared with an ovary pool from 3- to 4-day-old females. From the SSH library, we obtained 258 high quality sequences which clustered into 34 unique sequences grouped in 19 contigs and 15 singlets. The sequences were compared against non-redundant NCBI databases using BLAST. We found that 44% of the unique sequences had homologous sequences in known genes of other organisms, whereas 56% had no significant similarity to any of the databases entries. A Gene Ontology analysis was carried out, classifying the 34 sequences into different functional categories. Seven of these gene sequences, representative of different categories and processes, were chosen to perform expression studies during the first gonadotrophic cycle by real-time PCR. Results showed that they were mainly expressed during post-vitellogenesis, which validates the SSH technique. In two of them corresponding to novel genes, we demonstrated that they are specifically expressed in the cytoplasm of follicular cells in basal oocytes at the time of choriogenesis. Conclusion The SSH approach has proven to be useful in identifying ovarian genes expressed after vitellogenesis in B. germanica. For most of the genes, functions

  5. Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

    PubMed Central

    Srikrishna, Devabhaktuni; Coram, Marc A.

    2011-01-01

    Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMedrelated citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper. PMID:21935487

  6. GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

    PubMed

    Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

    2008-04-22

    Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

  7. GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

    PubMed Central

    Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

    2008-01-01

    Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge. PMID:18430222

  8. Kelvin Absolute Temperature Scale Identified as Length Scale and Related to de Broglie Thermal Wavelength

    NASA Astrophysics Data System (ADS)

    Sohrab, Siavash

    Thermodynamic equilibrium between matter and radiation leads to de Broglie wavelength λdβ = h /mβvrβ and frequency νdβ = k /mβvrβ of matter waves and stochastic definitions of Planck h =hk =mk <λrk > c and Boltzmann k =kk =mk <νrk > c constants, λrkνrk = c , that respectively relate to spatial (λ) and temporal (ν) aspects of vacuum fluctuations. Photon massmk =√{ hk /c3 } , amu =√{ hkc } = 1 /No , and universal gas constant Ro =No k =√{ k / hc } result in internal Uk = Nhνrk = Nmkc2 = 3 Nmkvmpk2 = 3 NkT and potential pV = uN\\vcirc / 3 = N\\ucirc / 3 = NkT energy of photon gas in Casimir vacuum such that H = TS = 4 NkT . Therefore, Kelvin absolute thermodynamic temperature scale [degree K] is identified as length scale [meter] and related to most probable wavelength and de Broglie thermal wavelength as Tβ =λmpβ =λdβ / 3 . Parallel to Wien displacement law obtained from Planck distribution, the displacement law λwS T =c2 /√{ 3} is obtained from Maxwell -Boltzmann distribution of speed of ``photon clusters''. The propagation speeds of sound waves in ideal gas versus light waves in photon gas are described in terms of vrβ in harmony with perceptions of Huygens. Newton formula for speed of long waves in canals √{ p / ρ } is modified to √{ gh } =√{ γp / ρ } in accordance with adiabatic theory of Laplace.

  9. Anticoagulant-related hospital admissions: serious adverse reactions identified through hospital databases.

    PubMed

    Heng, Charles; Rybarczyk-Vigouret, Marie Christine; Michel, Bruno

    2015-02-01

    A growing number of patients today receive anticoagulants. These drugs can cause serious adverse reactions leading to patients' hospitalization. The present study aimed to assess the number of hospital admissions as a result of anticoagulant adverse reactions in Alsace, a French region of 1.8 million inhabitants, and to estimate the economic burden associated with their management. A retrospective analysis was performed using data extracted from the regional and anonymous hospital Programme de Médicalisation des Systèmes d'Information (PMSI) database to assess the number of hospital admissions and the associated costs. Stays from public and private hospitals were extracted from the database using two International Classification of Diseases, 10th revision, codes referring to anticoagulant drugs: 'T45.5-Poisoning by anticoagulants' and 'Y44.2-Anticoagulants' adverse effect in therapeutic use'. Costs were calculated from official French tariffs. Within a 2-year period from 1 Januray 2010 to 31 December 2011, 462 anticoagulant-related hospital admissions, predominantly in elderly patients, were identified in Alsace. These stays, as a result of anticoagulant adverse reactions, represented a cost of 2 050 127.86 euros (including hospitalization and expensive drugs). Regional PMSI database constitutes an effective tool to explore anticoagulant-related hospital admissions. Based on our study, one can state that the cost of anticoagulation therapies lies not only in the price of the drugs but also in the cost of adverse reaction management. Policy makers should be aware of this reality and should focus on better medication supervision in order to improve patient safety and reduce expenses. Copyright © 2014 John Wiley & Sons, Ltd.

  10. Identifying flavor preference subgroups. Genetic basis and related eating behavior traits.

    PubMed

    Törnwall, Outi; Silventoinen, Karri; Hiekkalinna, Tero; Perola, Markus; Tuorila, Hely; Kaprio, Jaakko

    2014-04-01

    Subgroups based on flavor preferences were identified and their genetic and behavior related characteristics investigated using extensive data from 331 Finnish twins (21-25years, 146 men) including 47 monozygotic (MZ) and 93 dizygotic (DZ) pairs, and 51 twin individuals. The subgroup identification (hierarchical and K-means clustering) was based on liking responses to food names representing sour, umami, and spicy flavor qualities. Furthermore, sensory tests were conducted, a questionnaire on food likes completed, and various eating behavior related traits measured with validated scales. Sensory data included intensity ratings of PROP (6-n-propylthiouracil-impregnated filter paper), hedonic and intensity responses to sourness (orange juice with and without added citric acid, 0.42%), pungency (strawberry jelly with and without added capsaicin 0.00013%) and umami ('mouthfeel flavor' taste solution). Ratings of liking of 41 general food names were categorized into salty-and-fatty, sweet-and-fatty, fruits and vegetables and fish foods. Subgroup differences (complex samples procedure) and the genetics underlying the subgroups (structural equation modeling) were investigated. Of the resulting two groups (basic, n=140, adventurous n=152; non-grouped n=39), the adventurous expressed higher liking for sour and spicy foods, and had more tolerance for capsaicin burn in the sensory-hedonic test. The adventurous were also less food neophobic (25.9±9.1 vs. 32.5±10.6, respectively) and expressed higher liking for fruits and vegetables compared to the basic group. Genetic effects were shown to underlie the subgroups (heritability 72%, CI: 36-92%). Linkage analysis for 27 candidate gene regions revealed suggestively that being adventurous is linked to TAS1R1 and PKD1L3 genes. These results indicate that food neophobia and genetic differences may form a barrier through which individual flavor preferences are generated.

  11. Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia

    PubMed Central

    Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

    2016-01-01

    Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors. PMID:27511178

  12. Utilization of digital differential display to identify differentially expressed genes related to rumen development.

    PubMed

    Kato, Daichi; Suzuki, Yutaka; Haga, Satoshi; So, KyoungHa; Yamauchi, Eri; Nakano, Miwa; Ishizaki, Hiroshi; Choi, Kichoon; Katoh, Kazuo; Roh, Sang-Gun

    2016-04-01

    This study aimed to identify the genes associated with the development of the rumen epithelium by screening for candidate genes by digital differential display (DDD) in silico. Using DDD in NCBI's UniGene database, expressed sequence tag (EST)-based gene expression profiles were analyzed in rumen, reticulum, omasum, abomasum and other tissues in cattle. One hundred and ten candidate genes with high expression in the rumen were derived from a library of all tissues. The expression levels of 11 genes in all candidate genes were analyzed in the rumen, reticulum, omasum and abomasum of nine Japanese Black male calves (5-week-old pre-weaning: n = 3; 15-week-old weaned calves: n = 6). Among the 11 genes, only 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), aldo-keto reductase family 1, member C1-like (AKR1C1), and fatty acid binding protein 3 (FABP3) showed significant changes in the levels of gene expression in the rumen between the pre- and post-weaning of calves. These results indicate that DDD analysis in silico can be useful for screening candidate genes related to rumen development, and that the changes in expression levels of three genes in the rumen may have been caused by weaning, aging or both.

  13. Feasibility of Identifying the Tobacco-related Global Metabolome in Blood by UPLC–QTOF-MS

    PubMed Central

    2012-01-01

    Metabolomics is likely an ideal tool to assess tobacco smoke exposure and the impact of cigarette smoke on human exposure and health. To assess reproducibility and feasibility of this by UPLC–QTOF-MS, three experiments were designed for the assessment of smokers’ blood. Experiment I was an analysis of 8 smokers with 8 replicates. Experiment II was an analysis of 62 pooled quality control (QC) samples from 7 nonsmokers’ plasma placed as every tenth sample among a study of 613 samples from 160 smokers. Finally, to examine the feasibility of metabolomic study in assessing smoke exposure, Experiment III consisted of 9 smokers and 10 nonsmokers’ serum to evaluate differences in their global metabolome. There was minimal measurement and sample preparation variation in all experiments, although some caution is needed when analyzing specific parts of the chromatogram. When assessing QC samples in the large scale study, QC clustering indicated high stability, reproducibility, and consistency. Finally, in addition to the identification of nicotine metabolites as expected, there was a characteristic profile distinguishing smokers from nonsmokers. Metabolites selected from putative identifications were verified by MS/MS, showing the potential to identify metabolic phenotypes and new metabolites relating to cigarette smoke exposure and toxicity. PMID:23240883

  14. Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

    PubMed

    Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

    2016-08-11

    Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

  15. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

    PubMed

    Zapiola, Maria L; Cronn, Richard C; Mallory-Smith, Carol A

    2010-07-01

    We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape level study of gene flow from transgenic glyphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of transgenic pollen both within the Agrostis complex and the related genera Polypogon.

  16. [Use of PubMed to improve evidence-based medicine in routine urological practice].

    PubMed

    Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

    2013-03-01

    Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment.

  17. Acupuncture for Neoplasms: An Update from the PubMed Database

    PubMed Central

    Wang, Guangjun

    2015-01-01

    Abstract Background: The therapeutic mainstays of cancer remain surgery, radiotherapy, and chemotherapy. However, radiotherapy and chemotherapy are often associated with serious side-effects, such as nausea and vomiting. Acupuncture has been used widely to treat disorders in clinical practice for at least 3000 years. According to the National Institutes of Health (NIH) Consensus Statement, chemotherapy-induced nausea and vomiting are suitable for acupuncture intervention. Objectives: The goal of this review is to analyze the applications of acupuncture for treating cancer and to look ahead at the potential advantages of acupuncture for patients with cancer. Materials and Methods: The PubMed database was searched for articles on acupuncture therapy and neoplasms. The different distributions of scientific papers were analyzed preliminarily. Results: The articles found showed that acupuncture was used to address various symptoms related to different types of cancer. Conclusions: The results of clinical trials in acupuncture have provided important clues in oncologic practice. The evidence suggests that acupuncture is a safe and effective therapy for managing cancer and treatment-related symptoms, such as nausea and vomiting and fatigue caused by chemotherapy. As more evidence emerges, the potential advantages of acupuncture in tumor treatment will eventually be clear. PMID:26155320

  18. Kidney transplantation search filters for PubMed, Ovid Medline, and Embase.

    PubMed

    Lee, Christopher W C; Iansavichus, Arthur V; Haynes, R Brian; Shariff, Salimah Z; Wilczynski, Nancy; McKibbon, Ann; Rehman, Faisal; Garg, Amit X

    2012-03-15

    Clinicians commonly search bibliographic databases such as Medline to find sound evidence to guide patient care. Unfortunately, this can be a frustrating experience because database searches often miss relevant articles. We addressed this problem for transplant professionals by developing kidney transplantation search filters for use in Medline through PubMed and Ovid Technologies, and Embase. We began by reading the full-text versions of 22,992 articles from 39 journals published across 5 years. These articles were labeled relevant to kidney transplantation or not forming our "gold standard." We then developed close to five million kidney transplantation filters using different terms and their combinations. Afterward, these filters were applied to development and validation subsets of the articles to determine their accuracy and reliability in identifying articles with kidney transplantation content. The final kidney transplantation filters used multiple terms in combination. The best performing filters achieved 97.5% sensitivity (95% confidence interval, 96.4%-98.5%), and 98.0% specificity (95% confidence interval, 97.8%-98.3%). Similar high performance was achieved for filters developed for Ovid Medline and Embase. Proof-of-concept searches confirmed more relevant articles are retrieved using these filters. These kidney transplantation filters can now be used in Medline and Embase databases to improve clinician searching.

  19. Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation

    PubMed Central

    Ye, Wei; Wu, Hongqing; He, Xin; Wang, Lei; Zhang, Weimin; Li, Haohua; Fan, Yunfei; Tan, Guohui; Liu, Taomei; Gao, Xiaoxia

    2016-01-01

    Background Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation. Methodology/Principal Findings A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant–pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation. Conclusions/Significance The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of

  20. A Multi-sensor Approach to Identify Crop Sensitivity Related to Climate Variability in Central India

    NASA Astrophysics Data System (ADS)

    Mondal, P.; DeFries, R. S.; Jain, M.; Robertson, A. W.; Galford, G. L.; Small, C.

    2012-12-01

    Agriculture is a primary source of livelihood for over 70% of India's population, with staple crops (e.g. winter wheat) playing a pivotal role in satisfying an ever-increasing food-demand of a growing population. Agricultural yield in India has been reported to be highly correlated with the timing and total amount of monsoon rainfall and/or temperature depending on crop type. With expected change in future climate (temperature and precipitation), significant fluctuations in crop yields are projected for near future. To date, little work has identified the sensitivity of cropping intensity, or the number of crops planted in a given year, to climate variability. The objective of this study is to shed light on relative importance of different climate parameters through a statistical analysis of inter-annual variations in cropping intensity at a regional scale, which may help identify adaptive strategies in response to future climate anomalies. Our study focuses on a highly human-modified landscape in central India, and uses a multi-sensor approach to determine the sensitivity of agriculture to climate variability. First, we assembled the 16-day time-series of 250m Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI), and applied a spline function-based smoothing algorithm to develop maps of monsoon and winter crops in Central India for a decadal time-span. A hierarchical model involving moderate resolution Landsat (30m) data was used to estimate the heterogeneity of the spectral signature within the MODIS dataset (250m). We then compared the season-specific cropping patterns with spatio-temporal variability in climate parameters derived from the Tropical Rainfall Measuring Mission (TRMM) data. Initial data indicates that the existence of a monsoon crop has moderate to strong correlation with wet season end date (ρ = .522), wet season length (ρ = .522), and the number of rainy days during wet season (ρ = .829). Existence of a winter

  1. Tracking Australian health and medical research expenditure with a PubMed bibliometric method.

    PubMed

    Mendis, Kumara; Bailey, Jannine; McLean, Rick

    2015-06-01

    To assess Australian health and medical research (HMR) investment returns by measuring the trends in HMR expenditure and PubMed publications by Australian authors. Bibliometric analysis collating Australian HMR expenditure reported by the Australian Institute of Health and Welfare and Australian HMR publications indexed in PubMed. Similar methods were applied to data from the United Kingdom and New Zealand. From financial year 2000/01 through 2011/12, HMR investment increased by 232% from $1.49 to $4.94 billion (current prices adjusted for inflation), while PubMed publications increased by 123% from 10,696 to 23,818. The average HMR investment required for a single PubMed publication rose by 49% from $139,304 in 2000/01 to $207,364 in 2011/12. Quality analyses showed an increase in systematic reviews, cohort studies and clinical trials, and a decrease in publications in PubMed's core clinical journal collection. Comparisons with New Zealand and the United Kingdom showed that Australia has had the greatest overall percentage increase in gross publication numbers and publications per capita. Our analyses confirm that increased HMR expenditure is associated with an increase in HMR publications in PubMed. Tracking HMR investment outcomes using this method could be useful for future policy and funding decisions at a federal and specific institution level. © 2015 Public Health Association of Australia.

  2. Genome-Wide Association Study to Identify Genes Related to Renal Mercury Concentrations in Mice

    PubMed Central

    Alkaissi, Hammoudi; Ekstrand, Jimmy; Jawad, Aksa; Nielsen, Jesper Bo; Havarinasab, Said; Soderkvist, Peter; Hultman, Per

    2016-01-01

    , Hultman P. 2016. Genome-wide association study to identify genes related to renal mercury concentrations in mice. Environ Health Perspect 124:920–926; http://dx.doi.org/10.1289/ehp.1409284 PMID:26942574

  3. Joint spatial modeling to identify shared patterns among chronic related potentially preventable hospitalizations

    PubMed Central

    2014-01-01

    Background Rates of Potentially Preventable Hospitalizations (PPH) are used to evaluate access of territorially delimited populations to high quality ambulatory care. A common geographic pattern of several PPH would reflect the performance of healthcare providers. This study is aimed at modeling jointly the geographical variation in six chronic PPH conditions in one Spanish Autonomous Community for describing common and discrepant patterns, and to assess the relative weight of the common pattern on each condition. Methods Data on the 39,970 PPH hospital admissions for diabetes short term complications, chronic obstructive pulmonary disease (COPD), congestive heart failure, dehydration, angina admission and adult asthma, between 2007 and 2009 were extracted from the Hospital Discharge Administrative Databases and assigned to one of the 240 Basic Health Zones. Rates and Standardized Hospitalization Ratios per geographic unit were estimated. The spatial analysis was carried out jointly for PPH conditions using Shared Component Models (SCM). Results The component shared by the six PPH conditions explained about the 36% of the variability of each PPH condition, ranging from the 25.9 for dehydration to 58.7 for COPD. The geographical pattern found in the latent common component identifies territorial clusters with particularly high risk. The specific risk pattern that each isolated PPH does not share with the common pattern for all six conditions show many non-significant areas for most PPH, but with some exceptions. Conclusions The geographical distribution of the risk of the PPH conditions is captured in a 36% by a unique latent pattern. The SCM modeling may be useful to evaluate healthcare system performance. PMID:24899214

  4. Identifying seasonal and temporal trends in the pressures experienced by hospitals related to unscheduled care.

    PubMed

    Walker, N J; Van Woerden, H C; Kiparoglou, V; Yang, Y

    2016-07-26

    As part of an electronic dashboard operated by Public Health Wales, senior managers at hospitals in Wales report daily "escalation" scores which reflect management opinion on the pressure a hospital is experiencing and ability to meet ongoing demand with respect to unscheduled care. An analysis was undertaken of escalation scores returned for 18 hospitals in Wales between the years 2006 and 2014 inclusive, with a view to identifying systematic temporal patterns in pressure experienced by hospitals in relation to unscheduled care. Exploratory data analysis indicated the presence of within-year cyclicity in average daily scores over all hospitals. In order to quantify this cyclicity, a Generalised Linear Mixed Model was fitted which incorporated a trigonometric function (sine and cosine) to capture within-year change in escalation. In addition, a 7-level categorical day of the week effect was fitted as well as a 3-level categorical Christmas holiday variable based on patterns observed in exploration of the raw data. All of the main effects investigated were found to be statistically significant. Firstly, significant differences emerged in terms of overall pressure reported by individual hospitals. Furthermore, escalation scores were found to vary systematically within-year in a wave-like fashion for all hospitals (but not between hospitals) with the period of highest pressure consistently observed to occur in winter and lowest pressure in summer. In addition to this annual variation, pressure reported by hospitals was also found to be influenced by day of the week (low at weekends, high early in the working week) and especially low over the Christmas period but high immediately afterwards. Whilst unpredictable to a degree, quantifiable pressure experienced by hospitals can be anticipated according to models incorporating systematic temporal patterns. In the context of finite resources for healthcare services, these findings could optimise staffing schedules and

  5. Association of eGFR-Related Loci Identified by GWAS with Incident CKD and ESRD

    PubMed Central

    Böger, Carsten A.; Gorski, Mathias; Li, Man; Hoffmann, Michael M.; Huang, Chunmei; Yang, Qiong; Teumer, Alexander; Krane, Vera; O'Seaghdha, Conall M.; Kutalik, Zoltán; Wichmann, H.-Erich; Haak, Thomas; Boes, Eva; Coassin, Stefan; Coresh, Josef; Kollerits, Barbara; Haun, Margot; Paulweber, Bernhard; Köttgen, Anna; Li, Guo; Shlipak, Michael G.; Powe, Neil; Hwang, Shih-Jen; Dehghan, Abbas; Rivadeneira, Fernando; Uitterlinden, André; Hofman, Albert; Beckmann, Jacques S.; Krämer, Bernhard K.; Witteman, Jacqueline; Bochud, Murielle; Siscovick, David; Rettig, Rainer; Kronenberg, Florian; Wanner, Christoph; Thadhani, Ravi I.; Heid, Iris M.

    2011-01-01

    Family studies suggest a genetic component to the etiology of chronic kidney disease (CKD) and end stage renal disease (ESRD). Previously, we identified 16 loci for eGFR in genome-wide association studies, but the associations of these single nucleotide polymorphisms (SNPs) for incident CKD or ESRD are unknown. We thus investigated the association of these loci with incident CKD in 26,308 individuals of European ancestry free of CKD at baseline drawn from eight population-based cohorts followed for a median of 7.2 years (including 2,122 incident CKD cases defined as eGFR <60ml/min/1.73m2 at follow-up) and with ESRD in four case-control studies in subjects of European ancestry (3,775 cases, 4,577 controls). SNPs at 11 of the 16 loci (UMOD, PRKAG2, ANXA9, DAB2, SHROOM3, DACH1, STC1, SLC34A1, ALMS1/NAT8, UBE2Q2, and GCKR) were associated with incident CKD; p-values ranged from p = 4.1e-9 in UMOD to p = 0.03 in GCKR. After adjusting for baseline eGFR, six of these loci remained significantly associated with incident CKD (UMOD, PRKAG2, ANXA9, DAB2, DACH1, and STC1). SNPs in UMOD (OR = 0.92, p = 0.04) and GCKR (OR = 0.93, p = 0.03) were nominally associated with ESRD. In summary, the majority of eGFR-related loci are either associated or show a strong trend towards association with incident CKD, but have modest associations with ESRD in individuals of European descent. Additional work is required to characterize the association of genetic determinants of CKD and ESRD at different stages of disease progression. PMID:21980298

  6. Threshold crossing of device-based intrathoracic impedance trends identifies relatively increased mortality risk

    PubMed Central

    Tang, Wai Hong Wilson; Warman, Eduardo N.; Johnson, James W.; Small, Roy S.; Heywood, James Thomas

    2012-01-01

    Aims Threshold crossings of impedance trends detected by implanted devices have been associated with clinically relevant heart failure events, but long-term prognosis of such events has not been demonstrated. The aim of this study is to examine the relationship between alterations in intrathoracic impedance and mortality risk in patients with implantable devices. Methods and results We reviewed remote monitoring data in the de-identified Medtronic CareLink® Discovery Link that captured intrathoracic impedance trends for >6 months. The initial 6 months of the cardiac and impedance trends were used as the observation period to create the patient groups and cross-referenced with the Social Security Death Index for mortality data. In our study cohort of 21 217 patients, 36% experienced impedance threshold crossing within the initial 6 months of monitoring (defined as the ‘early threshold crossing’ group). Patients with early threshold crossings demonstrated an increased risk of age- and gender-adjusted all-cause mortality [hazard ratio (HR) 2.15, 95% confidence interval (CI) 1.95–2.38, P< 0.0001]. Increased mortality risk remained significant when analysed in subgroups of patients without defibrillator shock (HR 2.10, 95% CI 1.90–2.34, P< 0.0001, n= 1621) or within those patients without device-detectable atrial fibrillation (AF) during the initial 6 months of monitoring (HR 2.09, 95% CI 1.86–2.34, P< 0.0001, n= 17 235). Both the number and the duration of early threshold crossings of impedance trends detectable by implanted devices were associated with increased mortality risk. Furthermore, the improvement of altered impedance trends portends more favourable prognosis. Conclusions Threshold crossing of impedance trends detectable by implanted devices is associated with relatively increased mortality risk even after adjusted for demographic, device-detected AF, or defibrillator shocks. PMID:22677137

  7. Threshold crossing of device-based intrathoracic impedance trends identifies relatively increased mortality risk.

    PubMed

    Tang, Wai Hong Wilson; Warman, Eduardo N; Johnson, James W; Small, Roy S; Heywood, James Thomas

    2012-09-01

    Threshold crossings of impedance trends detected by implanted devices have been associated with clinically relevant heart failure events, but long-term prognosis of such events has not been demonstrated. The aim of this study is to examine the relationship between alterations in intrathoracic impedance and mortality risk in patients with implantable devices. We reviewed remote monitoring data in the de-identified Medtronic CareLink(®) Discovery Link that captured intrathoracic impedance trends for >6 months. The initial 6 months of the cardiac and impedance trends were used as the observation period to create the patient groups and cross-referenced with the Social Security Death Index for mortality data. In our study cohort of 21 217 patients, 36% experienced impedance threshold crossing within the initial 6 months of monitoring (defined as the 'early threshold crossing' group). Patients with early threshold crossings demonstrated an increased risk of age- and gender-adjusted all-cause mortality [hazard ratio (HR) 2.15, 95% confidence interval (CI) 1.95-2.38, P< 0.0001]. Increased mortality risk remained significant when analysed in subgroups of patients without defibrillator shock (HR 2.10, 95% CI 1.90-2.34, P< 0.0001, n= 1621) or within those patients without device-detectable atrial fibrillation (AF) during the initial 6 months of monitoring (HR 2.09, 95% CI 1.86-2.34, P< 0.0001, n= 17 235). Both the number and the duration of early threshold crossings of impedance trends detectable by implanted devices were associated with increased mortality risk. Furthermore, the improvement of altered impedance trends portends more favourable prognosis. Threshold crossing of impedance trends detectable by implanted devices is associated with relatively increased mortality risk even after adjusted for demographic, device-detected AF, or defibrillator shocks.

  8. A fibrinogen-related protein identified from hepatopancreas of crayfish is a potential pattern recognition receptor.

    PubMed

    Chen, Qiming; Bai, Suhua; Dong, Chaohua

    2016-09-01

    Fibrinogen-related protein (FREP) family is a large group of proteins containing fibrinogen-like (FBG) domain and plays multiple physiological roles in animals. However, their immune functions in crayfish are not fully explored. In the present study, a novel fibrinogen-like protein (designated as PcFBN1) was identified and characterized from hepatopancreas of red swamp crayfish Procambarus clarkii. The cDNA sequence of PcFBN1 contains an open reading frame (ORF) of 1353 bp encoding a protein of 450 amino acids. Sequence and structural analysis indicated that PcFBN1 contains an FBG domain in C-terminal and a putative signal peptide of 19 amino acids in N-terminal. Semi-quantitative PCR revealed that the main expression of PcFBN1 was observed in hepatopancreas and hemocyte. Temporal expression analysis exhibited that PcFBN1 expression could be significantly induced by heat-killed Aeromonas hydrophila. Tissue distribution and temporal change of PcFBN1 suggested that PcFBN1 may be involved in immune responses of red swamp crayfish. Recombinant PcFBN1 protein binds and agglutinates both gram-negative bacteria Escherichia coli and gram-positive bacteria Micrococcus lysodeikticus. Moreover, binding and agglutination is Ca(2+) dependent. Further analysis indicated that PcFBN1 recognizes some acetyl group-containing substance LPS and PGN. RNAi experiment revealed that PcFBN1 is required for bacterial clearance and survival from A. hydrophila infection. Reduction of PcFBN1 expression significantly decreased the survival and enhanced the number of A. hydrophila in the hemolymph. These results indicated that PcFBN1 plays an important role in the innate immunity of red swamp crayfish as a potential pattern recognition receptor.

  9. OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content

    PubMed Central

    2013-01-01

    Background PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed’s unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms (‘textwords’), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed’s unique heart failure literature. Methods We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter’s MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as ‘textwords’). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this ‘lost set’. This string, restricted to searching on PubMed’s unique content, was then combined with the validated PubMed translation to extend the filter’s performance in this database. Results The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and

  10. High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

    PubMed

    Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

    2014-04-01

    We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

  11. Find Duplicates among the PubMed, EMBASE, and Cochrane Library Databases in Systematic Review

    PubMed Central

    Wang, Juan; Han, Guohong; Fan, Daiming

    2013-01-01

    Background Finding duplicates is an important phase of systematic review. However, no consensus regarding the methods to find duplicates has been provided. This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates. Methods and Findings Literatures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers. They were divided into type-I (duplicates among different databases) and type-II (duplicate publications in different journals/issues) duplicates. For type-I duplicates, reference items were further compared between index and redundant papers. Of 10936 papers regarding PVT, 2399 and 1307 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 11.0% (1201/10936) and 6.1% (665/10936), respectively. They included 3431 type-I and 275 type-II duplicates. Of 11403 papers regarding BCS, 3275 and 2064 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 14.4% (1640/11403) and 9.1% (1039/11403), respectively. They included 5053 type-I and 286 type-II duplicates. Most of type-I duplicates were identified by auto-searching method (69.5%, 2385/3431 in PVT literatures; 64.6%, 3263/5053 in BCS literatures). Nearly all type-II duplicates were identified by hand-searching method (94.9%, 261/275 in PVT literatures; 95.8%, 274/286 in BCS literatures). Compared with those identified by auto-searching method, type-I duplicates identified by hand-searching method had a significantly higher prevalence of wrong items (47/2385 versus 498/1046, p<0.0001 in PVT literatures; 30/3263 versus 778/1790, p<0.0001 in BCS literatures). Most of wrong items originated from

  12. Differences in Alcohol Use and Alcohol-Related Problems between Transgender- and Nontransgender-identified Young Adults

    PubMed Central

    Coulter, Robert W.S.; Blosnich, John R.; Bukowski, Leigh A.; Herrick, A. L.; Siconolfi, Daniel E.; Stall, Ron D.

    2015-01-01

    Background Little is known about differences in alcohol use and alcohol-related problems between transgender- and nontransgender-identified populations. Using data from a large-scale health survey, we compare the drinking patterns and prevalence of alcohol-related problems of transgender-identified individuals to nontransgender-identified males and females. For transgender-identified people, we examine how various forms of victimization relate to heavy episodic drinking (HED). Methods Cross-sectional surveys were completed by 75,192 students aged 18–29 years attending 120 post-secondary educational institutions in the United States from 2011–2013. Self-reported measures included alcohol use, alcohol-related problems, victimization, and sociodemographics, including 3 gender-identity groups: transgender-identified individuals; nontransgender-identified males; and nontransgender-identified females. Results Compared to transgender-identified individuals, nontransgender-identified males were more likely to report HED in the past 2 weeks (relative risk=1.42; p=0.006); however, nontransgender-identified males and females reported HED on fewer days than transgender-identified people (incidence-rate ratios [IRRs] ranged from 0.28–0.43; p-values<0.001). Compared to transgender-identified people, nontransgender-identified males and females had lower odds of past-year alcohol-related sexual assault and suicidal ideation (odds ratios ranged from 0.24–0.45; p-values<0.05). Among transgender-identified people, individuals who were sexually assaulted (IRR=3.21, p=0.011) or verbally threatened (IRR=2.42, p=0.021) in the past year had greater HED days than those who did not experience those forms of victimization. Conclusions Compared to transgender-identified people, nontransgender-identified males and females: have fewer HED occasions (despite nontransgender-identified males having greater prevalence of HED); and are at lower risk for alcohol-related sexual assaults and

  13. Differences in alcohol use and alcohol-related problems between transgender- and nontransgender-identified young adults.

    PubMed

    Coulter, Robert W S; Blosnich, John R; Bukowski, Leigh A; Herrick, A L; Siconolfi, Daniel E; Stall, Ron D

    2015-09-01

    Little is known about differences in alcohol use and alcohol-related problems between transgender- and nontransgender-identified populations. Using data from a large-scale health survey, we compare the drinking patterns and prevalence of alcohol-related problems of transgender-identified individuals to nontransgender-identified males and females. For transgender-identified people, we examine how various forms of victimization relate to heavy episodic drinking (HED). Cross-sectional surveys were completed by 75,192 students aged 18-29 years attending 120 post-secondary educational institutions in the United States from 2011 to 2013. Self-reported measures included alcohol use, alcohol-related problems, victimization, and sociodemographics, including 3 gender-identity groups: transgender-identified individuals; nontransgender-identified males; and nontransgender-identified females. Compared to transgender-identified individuals, nontransgender-identified males were more likely to report HED in the past 2 weeks (relative risk=1.42; p=0.006); however, nontransgender-identified males and females reported HED on fewer days than transgender-identified people (incidence-rate ratios [IRRs] ranged from 0.28 to 0.43; p-values<0.001). Compared to transgender-identified people, nontransgender-identified males and females had lower odds of past-year alcohol-related sexual assault and suicidal ideation (odds ratios ranged from 0.24 to 0.45; p-values<0.05). Among transgender-identified people, individuals who were sexually assaulted (IRR=3.21, p=0.011) or verbally threatened (IRR=2.42, p=0.021) in the past year had greater HED days than those who did not experience those forms of victimization. Compared to transgender-identified people, nontransgender-identified males and females: have fewer HED occasions (despite nontransgender-identified males having greater prevalence of HED); and are at lower risk for alcohol-related sexual assaults and suicidal ideation. Experiences of sexual

  14. GLAD4U: deriving and prioritizing gene lists from PubMed literature

    PubMed Central

    2012-01-01

    Background Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors. Results We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis. Conclusions GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient

  15. CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions.

    PubMed

    Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine

    2011-02-01

    Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not

  16. [An analysis of Chilean biomedical publications in PubMed in the years 2008-2009].

    PubMed

    Valdés S, Gloria; Pérez G, Fernanda; Reyes B, Humberto

    2015-08-01

    During the years 2008 and 2009, 1,191 biomedical articles authored by Chilean investigators working in Chile were indexed in PubMed. To evaluate the potential visibility of those articles, according to scientometric indexes of the journals where they were published. Those journals where the articles had been published were identified and each journal’s Impact Factor (JIF), 5-year JIF, SCImago Journal Rank (SJR), SCImago Quartiles (Q) for 2010 and the Source Normalized Impact per Paper (SNIP) for 2008-2009 were identified. Three hundred and twelve articles (26,2%) were dedicated to experimental studies in animals, tissues or cells and they were classified as “Biomedicine”, while 879 (73,8%) were classified as “Clinical Medicine”; in both areas the main type of articles were original reports (90% and 73.6%, respectively). Revista Médica de Chile and Revista Chilena de Infectología concentrated the greater number of publications. Articles classified in Biomedicine were published more frequently in English and in journals with higher scientometric indexes than those classified in Clinical Medicine. Biomedical articles dealing with clinical topics, particularly case reports, were published mostly in national journals or in foreign journals with low scientometric indexes. It can be partly attributable to the authors’ interest in reaching local readers. The evaluation of research productivity should combine several scientometric indexes, selected according to the field of research, the institution's and investigators’ interests, with a qualitative and multifactorial assessment.

  17. Managing more than the mean: using quantile regression to identify factors related to large elk groups.

    PubMed

    Brennan, Angela; Cross, Paul C; Creel, Scott

    2015-12-01

    Animal group size distributions are often right-skewed, whereby most groups are small, but most individuals occur in larger groups that may also disproportionately affect ecology and policy. In this case, examining covariates associated with upper quantiles of the group size distribution could facilitate better understanding and management of large animal groups.We studied wintering elk groups in Wyoming, where group sizes span several orders of magnitude, and issues of disease, predation and property damage are affected by larger group sizes. We used quantile regression to evaluate relationships between the group size distribution and variables of land use, habitat, elk density and wolf abundance to identify conditions important to larger elk groups.We recorded 1263 groups ranging from 1 to 1952 elk and found that across all quantiles of group size, group sizes were larger in open habitat and on private land, but the largest effect occurred between irrigated and non-irrigated land [e.g. the 90th quantile group size increased by 135 elk (95% CI = 42, 227) on irrigation].Only upper quantile group sizes were positively related to broad-scale measures of elk density and wolf abundance. For wolf abundance, this effect was greater on elk groups found in open habitats and private land than those in closed habitats or public land. If we had limited our analysis to mean or median group sizes, we would not have detected these effects. Synthesis and applications. Our analysis of elk group size distributions using quantile regression suggests that private land, irrigation, open habitat, elk density and wolf abundance can affect large elk group sizes. Thus, to manage larger groups by removal or dispersal of individuals, we recommend incentivizing hunting on private land (particularly if irrigated) during the regular and late hunting seasons, promoting tolerance of wolves on private land (if elk aggregate in these areas to avoid wolves) and creating more winter range and

  18. Measuring Medical Student Preference: A Comparison of Classroom Versus Online Instruction for Teaching Pubmed*EC

    PubMed Central

    Schimming, Laura M.

    2008-01-01

    Objective: The research analyzed evaluation data to assess medical student satisfaction with the learning experience when required PubMed training is offered entirely online. Methods: A retrospective study analyzed skills assessment scores and student feedback forms from 455 first-year medical students who completed PubMed training either through classroom sessions or an online tutorial. The class of 2006 (n = 99) attended traditional librarian-led sessions in a computer classroom. The classes of 2007 (n = 120), 2008 (n = 121), and 2009 (n = 115) completed the training entirely online through a self-paced tutorial. PubMed skills assessment scores and student feedback about the training were compared for all groups. Results: As evidenced by open-ended comments about the training, students who took the online tutorial were equally or more satisfied with the learning experience than students who attended classroom sessions, with the classes of 2008 and 2009 reporting greater satisfaction (P<0.001) than the other 2 groups. The mean score on the PubMed skills assessment (91%) was the same for all groups of students. Conclusions: Student satisfaction improved and PubMed assessment scores did not change when instruction was offered online to first-year medical students. Comments from the students who received online training suggest that the increased control and individual engagement with the web-based content led to their satisfaction with the online tutorial. PMID:18654658

  19. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

    Treesearch

    Maria L. Zapiola; Richard C. Cronn; Carol A. Mallory-Smith

    2010-01-01

    We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape-level study of gene flow from transgenic gylphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of...

  20. Distributed Leadership and Relational Trust: Bridging Two Frameworks to Identify Effective Leadership Behaviors and Practices

    ERIC Educational Resources Information Center

    Abdul-Jabbar, Mustafa

    2013-01-01

    This dissertation investigates how relational trust manifests within schools that have recently enacted the distributed leadership framework, a program implementation by the Penn Center for Educational Leadership. First, the dissertation highlights research that connects the distributed leadership and relational trust frameworks in the task of…

  1. Distributed Leadership and Relational Trust: Bridging Two Frameworks to Identify Effective Leadership Behaviors and Practices

    ERIC Educational Resources Information Center

    Abdul-Jabbar, Mustafa

    2013-01-01

    This dissertation investigates how relational trust manifests within schools that have recently enacted the distributed leadership framework, a program implementation by the Penn Center for Educational Leadership. First, the dissertation highlights research that connects the distributed leadership and relational trust frameworks in the task of…

  2. Social Networking Privacy Control: Exploring University Variables Related to Young Adults' Sharing of Personally Identifiable Information

    ERIC Educational Resources Information Center

    Zimmerman, Melisa S.

    2014-01-01

    The growth of the Internet, and specifically social networking sites (SNSs) like Facebook, create opportunities for individuals to share private and identifiable information with a closed or open community. Internet crime has been on the rise and research has shown that criminals are using individuals' personal information pulled from social…

  3. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.

    PubMed

    Beecham, Ashley H; Patsopoulos, Nikolaos A; Xifara, Dionysia K; Davis, Mary F; Kemppinen, Anu; Cotsapas, Chris; Shah, Tejas S; Spencer, Chris; Booth, David; Goris, An; Oturai, Annette; Saarela, Janna; Fontaine, Bertrand; Hemmer, Bernhard; Martin, Claes; Zipp, Frauke; D'Alfonso, Sandra; Martinelli-Boneschi, Filippo; Taylor, Bruce; Harbo, Hanne F; Kockum, Ingrid; Hillert, Jan; Olsson, Tomas; Ban, Maria; Oksenberg, Jorge R; Hintzen, Rogier; Barcellos, Lisa F; Agliardi, Cristina; Alfredsson, Lars; Alizadeh, Mehdi; Anderson, Carl; Andrews, Robert; Søndergaard, Helle Bach; Baker, Amie; Band, Gavin; Baranzini, Sergio E; Barizzone, Nadia; Barrett, Jeffrey; Bellenguez, Céline; Bergamaschi, Laura; Bernardinelli, Luisa; Berthele, Achim; Biberacher, Viola; Binder, Thomas M C; Blackburn, Hannah; Bomfim, Izaura L; Brambilla, Paola; Broadley, Simon; Brochet, Bruno; Brundin, Lou; Buck, Dorothea; Butzkueven, Helmut; Caillier, Stacy J; Camu, William; Carpentier, Wassila; Cavalla, Paola; Celius, Elisabeth G; Coman, Irène; Comi, Giancarlo; Corrado, Lucia; Cosemans, Leentje; Cournu-Rebeix, Isabelle; Cree, Bruce A C; Cusi, Daniele; Damotte, Vincent; Defer, Gilles; Delgado, Silvia R; Deloukas, Panos; di Sapio, Alessia; Dilthey, Alexander T; Donnelly, Peter; Dubois, Bénédicte; Duddy, Martin; Edkins, Sarah; Elovaara, Irina; Esposito, Federica; Evangelou, Nikos; Fiddes, Barnaby; Field, Judith; Franke, Andre; Freeman, Colin; Frohlich, Irene Y; Galimberti, Daniela; Gieger, Christian; Gourraud, Pierre-Antoine; Graetz, Christiane; Graham, Andrew; Grummel, Verena; Guaschino, Clara; Hadjixenofontos, Athena; Hakonarson, Hakon; Halfpenny, Christopher; Hall, Gillian; Hall, Per; Hamsten, Anders; Harley, James; Harrower, Timothy; Hawkins, Clive; Hellenthal, Garrett; Hillier, Charles; Hobart, Jeremy; Hoshi, Muni; Hunt, Sarah E; Jagodic, Maja; Jelčić, Ilijas; Jochim, Angela; Kendall, Brian; Kermode, Allan; Kilpatrick, Trevor; Koivisto, Keijo; Konidari, Ioanna; Korn, Thomas; Kronsbein, Helena; Langford, Cordelia; Larsson, Malin; Lathrop, Mark; Lebrun-Frenay, Christine; Lechner-Scott, Jeannette; Lee, Michelle H; Leone, Maurizio A; Leppä, Virpi; Liberatore, Giuseppe; Lie, Benedicte A; Lill, Christina M; Lindén, Magdalena; Link, Jenny; Luessi, Felix; Lycke, Jan; Macciardi, Fabio; Männistö, Satu; Manrique, Clara P; Martin, Roland; Martinelli, Vittorio; Mason, Deborah; Mazibrada, Gordon; McCabe, Cristin; Mero, Inger-Lise; Mescheriakova, Julia; Moutsianas, Loukas; Myhr, Kjell-Morten; Nagels, Guy; Nicholas, Richard; Nilsson, Petra; Piehl, Fredrik; Pirinen, Matti; Price, Siân E; Quach, Hong; Reunanen, Mauri; Robberecht, Wim; Robertson, Neil P; Rodegher, Mariaemma; Rog, David; Salvetti, Marco; Schnetz-Boutaud, Nathalie C; Sellebjerg, Finn; Selter, Rebecca C; Schaefer, Catherine; Shaunak, Sandip; Shen, Ling; Shields, Simon; Siffrin, Volker; Slee, Mark; Sorensen, Per Soelberg; Sorosina, Melissa; Sospedra, Mireia; Spurkland, Anne; Strange, Amy; Sundqvist, Emilie; Thijs, Vincent; Thorpe, John; Ticca, Anna; Tienari, Pentti; van Duijn, Cornelia; Visser, Elizabeth M; Vucic, Steve; Westerlind, Helga; Wiley, James S; Wilkins, Alastair; Wilson, James F; Winkelmann, Juliane; Zajicek, John; Zindler, Eva; Haines, Jonathan L; Pericak-Vance, Margaret A; Ivinson, Adrian J; Stewart, Graeme; Hafler, David; Hauser, Stephen L; Compston, Alastair; McVean, Gil; De Jager, Philip; Sawcer, Stephen J; McCauley, Jacob L

    2013-11-01

    Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.

  4. Identifying Students Difficulties in Understanding Concepts Pertaining to Cell Water Relations: An Exploratory Study.

    ERIC Educational Resources Information Center

    Friedler, Y.; And Others

    This study identified students' conceptual difficulties in understanding concepts and processes associated with cell water relationships (osmosis), determined possible reasons for these difficulties, and pilot-tested instruments and research strategies for a large scale comprehensive study. Research strategies used included content analysis of…

  5. Identifying Students Difficulties in Understanding Concepts Pertaining to Cell Water Relations: An Exploratory Study.

    ERIC Educational Resources Information Center

    Friedler, Y.; And Others

    This study identified students' conceptual difficulties in understanding concepts and processes associated with cell water relationships (osmosis), determined possible reasons for these difficulties, and pilot-tested instruments and research strategies for a large scale comprehensive study. Research strategies used included content analysis of…

  6. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

    PubMed Central

    Beecham, Ashley H; Patsopoulos, Nikolaos A; Xifara, Dionysia K; Davis, Mary F; Kemppinen, Anu; Cotsapas, Chris; Shahi, Tejas S; Spencer, Chris; Booth, David; Goris, An; Oturai, Annette; Saarela, Janna; Fontaine, Bertrand; Hemmer, Bernhard; Martin, Claes; Zipp, Frauke; D’alfonso, Sandra; Martinelli-Boneschi, Filippo; Taylor, Bruce; Harbo, Hanne F; Kockum, Ingrid; Hillert, Jan; Olsson, Tomas; Ban, Maria; Oksenberg, Jorge R; Hintzen, Rogier; Barcellos, Lisa F; Agliardi, Cristina; Alfredsson, Lars; Alizadeh, Mehdi; Anderson, Carl; Andrews, Robert; Søndergaard, Helle Bach; Baker, Amie; Band, Gavin; Baranzini, Sergio E; Barizzone, Nadia; Barrett, Jeffrey; Bellenguez, Céline; Bergamaschi, Laura; Bernardinelli, Luisa; Berthele, Achim; Biberacher, Viola; Binder, Thomas M C; Blackburn, Hannah; Bomfim, Izaura L; Brambilla, Paola; Broadley, Simon; Brochet, Bruno; Brundin, Lou; Buck, Dorothea; Butzkueven, Helmut; Caillier, Stacy J; Camu, William; Carpentier, Wassila; Cavalla, Paola; Celius, Elisabeth G; Coman, Irène; Comi, Giancarlo; Corrado, Lucia; Cosemans, Leentje; Cournu-Rebeix, Isabelle; Cree, Bruce A C; Cusi, Daniele; Damotte, Vincent; Defer, Gilles; Delgado, Silvia R; Deloukas, Panos; di Sapio, Alessia; Dilthey, Alexander T; Donnelly, Peter; Dubois, Bénédicte; Duddy, Martin; Edkins, Sarah; Elovaara, Irina; Esposito, Federica; Evangelou, Nikos; Fiddes, Barnaby; Field, Judith; Franke, Andre; Freeman, Colin; Frohlich, Irene Y; Galimberti, Daniela; Gieger, Christian; Gourraud, Pierre-Antoine; Graetz, Christiane; Graham, Andrew; Grummel, Verena; Guaschino, Clara; Hadjixenofontos, Athena; Hakonarson, Hakon; Halfpenny, Christopher; Hall, Gillian; Hall, Per; Hamsten, Anders; Harley, James; Harrower, Timothy; Hawkins, Clive; Hellenthal, Garrett; Hillier, Charles; Hobart, Jeremy; Hoshi, Muni; Hunt, Sarah E; Jagodic, Maja; Jelčić, Ilijas; Jochim, Angela; Kendall, Brian; Kermode, Allan; Kilpatrick, Trevor; Koivisto, Keijo; Konidari, Ioanna; Korn, Thomas; Kronsbein, Helena; Langford, Cordelia; Larsson, Malin; Lathrop, Mark; Lebrun-Frenay, Christine; Lechner-Scott, Jeannette; Lee, Michelle H; Leone, Maurizio A; Leppä, Virpi; Liberatore, Giuseppe; Lie, Benedicte A; Lill, Christina M; Lindén, Magdalena; Link, Jenny; Luessi, Felix; Lycke, Jan; Macciardi, Fabio; Männistö, Satu; Manrique, Clara P; Martin, Roland; Martinelli, Vittorio; Mason, Deborah; Mazibrada, Gordon; McCabe, Cristin; Mero, Inger-Lise; Mescheriakova, Julia; Moutsianas, Loukas; Myhr, Kjell-Morten; Nagels, Guy; Nicholas, Richard; Nilsson, Petra; Piehl, Fredrik; Pirinen, Matti; Price, Siân E; Quach, Hong; Reunanen, Mauri; Robberecht, Wim; Robertson, Neil P; Rodegher, Mariaemma; Rog, David; Salvetti, Marco; Schnetz-Boutaud, Nathalie C; Sellebjerg, Finn; Selter, Rebecca C; Schaefer, Catherine; Shaunak, Sandip; Shen, Ling; Shields, Simon; Siffrin, Volker; Slee, Mark; Sorensen, Per Soelberg; Sorosina, Melissa; Sospedra, Mireia; Spurkland, Anne; Strange, Amy; Sundqvist, Emilie; Thijs, Vincent; Thorpe, John; Ticca, Anna; Tienari, Pentti; van Duijn, Cornelia; Visser, Elizabeth M; Vucic, Steve; Westerlind, Helga; Wiley, James S; Wilkins, Alastair; Wilson, James F; Winkelmann, Juliane; Zajicek, John; Zindler, Eva; Haines, Jonathan L; Pericak-Vance, Margaret A; Ivinson, Adrian J; Stewart, Graeme; Hafler, David; Hauser, Stephen L; Compston, Alastair; McVean, Gil; De Jager, Philip; Sawcer, Stephen; McCauley, Jacob L

    2013-01-01

    Using the ImmunoChip custom genotyping array, we analysed 14,498 multiple sclerosis subjects and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (p-value < 1.0 × 10-4). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 multiple sclerosis subjects and 26,703 healthy controls. In these 80,094 individuals of European ancestry we identified 48 new susceptibility variants (p-value < 5.0 × 10-8); three found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants in 103 discrete loci outside of the Major Histocompatibility Complex. With high resolution Bayesian fine-mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalogue of multiple sclerosis risk variants and illustrates the value of fine-mapping in the resolution of GWAS signals. PMID:24076602

  7. [The iberoamerican scientific production in nutritional sciences: the indexation in PubMed and Google Scholar].

    PubMed

    Franco-Pérez, Alvaro Moisés; Sanz-Valero, Javier; Wanden-Berghe, Carmina; Melian-Fleitas, Liliana

    2014-11-01

    Analyze by bibliometric technique, the Iberoamerican scientific literature related to the nutritional sciences and retrieved on main search engines with free access through Internet (PubMed and Google Scholar). Bibliometric analysis of scientific production recovered in the different selected search tools. The data were obtained by applying to each of them, a composed search equation according to the scheme: Population (neoplasms), Intervention (nutritional status), Outcome (quality of life). 789 references were reviewed, 604 of those were papers published in 277 journals, presenting 20 or more references: Supportive Care in Cancer 27 (4.47%; CI 95% 2.82-6.12) and Clinical Nutrition 20 (3.31%; CI 95% 1.88-4.74). Mean age of documents: 8.08 ± 6.40 (CI 95% 7.63-8.53), median 6 years (Burton Kleber Index), maximum 34 years and Price Index of 43.90%. The predominant geographical distribution among the authors was American, while the articles were written primarily in English. Dispersion of literature (Bradford Law): core (1st tertile), 22 journals (7.94%; CI 95% 4.76-11.13) with 202 articles published (33.44%; CI 95% 29.68-37.21). Statistics related to the impact factor of the core: mean 4.033 ± 4.022 and maximum 18,038 (Journal of Clinical Oncology). The studied thematic continues in force according to the current indicators, with a dominance of English as language of publication and United States filiation. The most referenced journals matching with high Impact publications on nutritional sciences and oncology. Highlighting the presence of an Iberoamerican journal (Nutrición Hospitalaria) with a clear international vocation. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  8. Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

    PubMed

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2015-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.

  9. PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

    PubMed

    Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

    2009-11-15

    PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

  10. High-performance information search filters for CKD content in PubMed, Ovid MEDLINE, and EMBASE.

    PubMed

    Iansavichus, Arthur V; Hildebrand, Ainslie M; Haynes, R Brian; Wilczynski, Nancy L; Levin, Adeera; Hemmelgarn, Brenda R; Tu, Karen; Nesrallah, Gihad E; Nash, Danielle M; Garg, Amit X

    2015-01-01

    Finding relevant articles in large bibliographic databases such as PubMed, Ovid MEDLINE, and EMBASE to inform care and future research is challenging. Articles relevant to chronic kidney disease (CKD) are particularly difficult to find because they are often published under different terminology and are found across a wide range of journal types. We used computer automation within a diagnostic test assessment framework to develop and validate information search filters to identify CKD articles in large bibliographic databases. 22,992 full-text articles in PubMed, Ovid MEDLINE, or EMBASE. 1,374,148 unique search filters. We established the reference standard of article relevance to CKD by manual review of all full-text articles using prespecified criteria to determine whether each article contained CKD content or not. We then assessed filter performance by calculating sensitivity, specificity, and positive predictive value for the retrieval of CKD articles. Filters with high sensitivity and specificity for the identification of CKD articles in the development phase (two-thirds of the sample) were then retested in the validation phase (remaining one-third of the sample). We developed and validated high-performance CKD search filters for each bibliographic database. Filters optimized for sensitivity reached at least 99% sensitivity, and filters optimized for specificity reached at least 97% specificity. The filters were complex; for example, one PubMed filter included more than 89 terms used in combination, including "chronic kidney disease," "renal insufficiency," and "renal fibrosis." In proof-of-concept searches, physicians found more articles relevant to the topic of CKD with the use of these filters. As knowledge of the pathogenesis of CKD grows and definitions change, these filters will need to be updated to incorporate new terminology used to index relevant articles. PubMed, Ovid MEDLINE, and EMBASE can be filtered reliably for articles relevant to CKD. These

  11. A study on PubMed search tag usage pattern: association rule mining of a full-day PubMed query log.

    PubMed

    Mosa, Abu Saleh Mohammad; Yoo, Illhoi

    2013-01-09

    The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed's Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE.

  12. Carbapenem resistance in a human clinical isolate identified to be closely related to Acinetobacter indicus.

    PubMed

    Bonnin, Rémy A; Poirel, Laurent; van der Reijden, Tanny J K; Dijkshoorn, Lenie; Lescat, Mathilde; Nordmann, Patrice

    2014-10-01

    Here we report a case of carbapenem resistance in a human clinical isolate that was found to be closely related to the newly described environmental species Acinetobacter indicus. This strain harboured the blaOXA-23 carbapenemase gene located on a conjugative plasmid. Partial sequencing of 16S rDNA and rpoB genes, together with matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) analysis, showed that this strain was distantly related to the Acinetobacter baumannii-calcoaceticus complex and was closely related to A. indicus.

  13. Generating parity relations for detecting and identifying control system component failures

    NASA Technical Reports Server (NTRS)

    Vander Velder, Wallace E.; Massoumnia, Mohammad-Ali

    1988-01-01

    The monitoring of control system sensors and actuators for failures is presently undertaken by means of an exceptionally simple form of generalized parity relations based on a discrete-time model of the dynamics of linear, time-invariant systems. These generalized parity relations are constructed by recourse to a transfer matrix-description of the system that is additionally useful in the interpretation of their properties. Attention is given to a novel method for constructing the parity relation of minimum length that depends on the output of only a single sensor.

  14. Semantically linking and browsing PubMed abstracts with gene ontology

    PubMed Central

    Vanteru, Bhanu C; Shaik, Jahangheer S; Yeasin, Mohammed

    2008-01-01

    Background The technological advances in the past decade have lead to massive progress in the field of biotechnology. The documentation of the progress made exists in the form of research articles. The PubMed is the current most used repository for bio-literature. PubMed consists of about 17 million abstracts as of 2007 that require methods to efficiently retrieve and browse large volume of relevant information. The State-of-the-art technologies such as GOPubmed use simple keyword-based techniques for retrieving abstracts from the PubMed and linking them to the Gene Ontology (GO). This paper changes the paradigm by introducing semantics enabled technique to link the PubMed to the Gene Ontology, called, SEGOPubmed for ontology-based browsing. Latent Semantic Analysis (LSA) framework is used to semantically interface PubMed abstracts to the Gene Ontology. Results The Empirical analysis is performed to compare the performance of the SEGOPubmed with the GOPubmed. The analysis is initially performed using a few well-referenced query words. Further, statistical analysis is performed using GO curated dataset as ground truth. The analysis suggests that the SEGOPubmed performs better than the classic GOPubmed as it incorporates semantics. Conclusions The LSA technique is applied on the PubMed abstracts obtained based on the user query and the semantic similarity between the query and the abstracts. The analyses using well-referenced keywords show that the proposed semantic-sensitive technique outperformed the string comparison based techniques in associating the relevant abstracts to the GO terms. The SEGOPubmed also extracted the abstracts in which the keywords do not appear in isolation (i.e. they appear in combination with other terms) that could not be retrieved by simple term matching techniques. PMID:18366599

  15. Genome-wide association analysis identifies multiple loci related to resting heart rate

    PubMed Central

    Eijgelsheim, Mark; Newton-Cheh, Christopher; Sotoodehnia, Nona; de Bakker, Paul I.W.; Müller, Martina; Morrison, Alanna C.; Smith, Albert V.; Isaacs, Aaron; Sanna, Serena; Dörr, Marcus; Navarro, Pau; Fuchsberger, Christian; Nolte, Ilja M.; de Geus, Eco J.C.; Estrada, Karol; Hwang, Shih-Jen; Bis, Joshua C.; Rückert, Ina-Maria; Alonso, Alvaro; Launer, Lenore J.; Hottenga, Jouke Jan; Rivadeneira, Fernando; Noseworthy, Peter A.; Rice, Kenneth M.; Perz, Siegfried; Arking, Dan E.; Spector, Tim D.; Kors, Jan A.; Aulchenko, Yurii S.; Tarasov, Kirill V.; Homuth, Georg; Wild, Sarah H.; Marroni, Fabio; Gieger, Christian; Licht, Carmilla M.; Prineas, Ronald J.; Hofman, Albert; Rotter, Jerome I.; Hicks, Andrew A.; Ernst, Florian; Najjar, Samer S.; Wright, Alan F.; Peters, Annette; Fox, Ervin R.; Oostra, Ben A.; Kroemer, Heyo K.; Couper, David; Völzke, Henry; Campbell, Harry; Meitinger, Thomas; Uda, Manuela; Witteman, Jacqueline C.M.; Psaty, Bruce M.; Wichmann, H-Erich; Harris, Tamara B.; Kääb, Stefan; Siscovick, David S.; Jamshidi, Yalda; Uitterlinden, André G.; Folsom, Aaron R.; Larson, Martin G.; Wilson, James F.; Penninx, Brenda W.; Snieder, Harold; Pramstaller, Peter P.; van Duijn, Cornelia M.; Lakatta, Edward G.; Felix, Stephan B.; Gudnason, Vilmundur; Pfeufer, Arne; Heckbert, Susan R.; Stricker, Bruno H.Ch.; Boerwinkle, Eric; O'Donnell, Christopher J.

    2010-01-01

    Higher resting heart rate is associated with increased cardiovascular disease and mortality risk. Though heritable factors play a substantial role in population variation, little is known about specific genetic determinants. This knowledge can impact clinical care by identifying novel factors that influence pathologic heart rate states, modulate heart rate through cardiac structure and function or by improving our understanding of the physiology of heart rate regulation. To identify common genetic variants associated with heart rate, we performed a meta-analysis of 15 genome-wide association studies (GWAS), including 38 991 subjects of European ancestry, estimating the association between age-, sex- and body mass-adjusted RR interval (inverse heart rate) and ∼2.5 million markers. Results with P < 5 × 10−8 were considered genome-wide significant. We constructed regression models with multiple markers to assess whether results at less stringent thresholds were likely to be truly associated with RR interval. We identified six novel associations with resting heart rate at six loci: 6q22 near GJA1; 14q12 near MYH7; 12p12 near SOX5, c12orf67, BCAT1, LRMP and CASC1; 6q22 near SLC35F1, PLN and c6orf204; 7q22 near SLC12A9 and UfSp1; and 11q12 near FADS1. Associations at 6q22 400 kb away from GJA1, at 14q12 MYH6 and at 1q32 near CD34 identified in previously published GWAS were confirmed. In aggregate, these variants explain ∼0.7% of RR interval variance. A multivariant regression model including 20 variants with P < 10−5 increased the explained variance to 1.6%, suggesting that some loci falling short of genome-wide significance are likely truly associated. Future research is warranted to elucidate underlying mechanisms that may impact clinical care. PMID:20639392

  16. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals.

    PubMed

    Eicher, John D; Chami, Nathalie; Kacprowski, Tim; Nomura, Akihiro; Chen, Ming-Huei; Yanek, Lisa R; Tajuddin, Salman M; Schick, Ursula M; Slater, Andrew J; Pankratz, Nathan; Polfus, Linda; Schurmann, Claudia; Giri, Ayush; Brody, Jennifer A; Lange, Leslie A; Manichaikul, Ani; Hill, W David; Pazoki, Raha; Elliot, Paul; Evangelou, Evangelos; Tzoulaki, Ioanna; Gao, He; Vergnaud, Anne-Claire; Mathias, Rasika A; Becker, Diane M; Becker, Lewis C; Burt, Amber; Crosslin, David R; Lyytikäinen, Leo-Pekka; Nikus, Kjell; Hernesniemi, Jussi; Kähönen, Mika; Raitoharju, Emma; Mononen, Nina; Raitakari, Olli T; Lehtimäki, Terho; Cushman, Mary; Zakai, Neil A; Nickerson, Deborah A; Raffield, Laura M; Quarells, Rakale; Willer, Cristen J; Peloso, Gina M; Abecasis, Goncalo R; Liu, Dajiang J; Deloukas, Panos; Samani, Nilesh J; Schunkert, Heribert; Erdmann, Jeanette; Fornage, Myriam; Richard, Melissa; Tardif, Jean-Claude; Rioux, John D; Dube, Marie-Pierre; de Denus, Simon; Lu, Yingchang; Bottinger, Erwin P; Loos, Ruth J F; Smith, Albert Vernon; Harris, Tamara B; Launer, Lenore J; Gudnason, Vilmundur; Velez Edwards, Digna R; Torstenson, Eric S; Liu, Yongmei; Tracy, Russell P; Rotter, Jerome I; Rich, Stephen S; Highland, Heather M; Boerwinkle, Eric; Li, Jin; Lange, Ethan; Wilson, James G; Mihailov, Evelin; Mägi, Reedik; Hirschhorn, Joel; Metspalu, Andres; Esko, Tõnu; Vacchi-Suzzi, Caterina; Nalls, Mike A; Zonderman, Alan B; Evans, Michele K; Engström, Gunnar; Orho-Melander, Marju; Melander, Olle; O'Donoghue, Michelle L; Waterworth, Dawn M; Wallentin, Lars; White, Harvey D; Floyd, James S; Bartz, Traci M; Rice, Kenneth M; Psaty, Bruce M; Starr, J M; Liewald, David C M; Hayward, Caroline; Deary, Ian J; Greinacher, Andreas; Völker, Uwe; Thiele, Thomas; Völzke, Henry; van Rooij, Frank J A; Uitterlinden, André G; Franco, Oscar H; Dehghan, Abbas; Edwards, Todd L; Ganesh, Santhi K; Kathiresan, Sekar; Faraday, Nauder; Auer, Paul L; Reiner, Alex P; Lettre, Guillaume; Johnson, Andrew D

    2016-07-07

    Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets' important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.

  17. Creating a Community Capacity Assessment to Identify Agency Outcomes Related to Occupational Therapy Student Community Partnerships.

    PubMed

    Kramlinger, Anne; Strecker Neufeld, Peggy; Berg, Christine

    2016-07-01

    Service-learning experiences immerse students in authentic situations and build partnerships with community agencies to support the health of those we serve in practice. Most occupational therapy curriculum evaluations do not systematically capture community agency benefits. Through the use of qualitative interviews and Q Methodology, the Community Agency Capacity Questionnaire (CACQ) was developed to capture the agency experience in these partnerships. This paper describes the iterative analytic process that resulted in the CACQ with 29 statements covering 6 domains: programming, evaluation, partnership, staff, funding, and marketing. The CACQ offers a means to identify outcomes from the service-learning partners' perspective.

  18. [Spanish scientific production in obesity research published in PubMed (1988-2007)].

    PubMed

    Vioque, Jesús; Manuel Ramos, José; Navarrete-Muñoz, Eva María; García De La Hera, Manuela

    2010-01-01

    To analyse Spanish scientific research output related to obesity during a 20-year period from 1988 to 2007 into context with the European Union productivity The bibliometric study was based on research of the MEDLINE database in PubMed. Search terms were "obesity" appearing in MeSH. Linear regression was used to estimate trends in number of publications. We retrieved 50,120 documents on obesity in the study period, and 1,407 were by Spanish authors (2.7% of the world production). Spain, accounting for 8.1% of scientific output in this area, was the fifth most productive country in the European Union; 932 (69.1%) of papers were published in English. The average yearly increase in publications was 15%, from 91 documents in the first five-year period to 702 in the last five-period. The most frequent specialty of first author was endocrinology (279 documents, or 22.8%), followed by physiology-nutrition-bromatology (203, or 16.6%), and biochemistry (161, or 13.2%). Journals publishing the largest numbers of papers on obesity were Medicina Clínica (83 or 6.1%), Obesity Surgery (79 or 5.8%), International Journal of Obesity (73) and Nutricion Hospitalaria (59). The most productive regions in Spain were Cataluña (338 or 24.9%), Madrid (286 or 20,6%), and Navarra (159 or 11,7%). The most productive institutions were hospitals, with 708 titles (52.1%), followed by universities, with 521 (38.5%). Obesity research in Spain has increased over the last 20 years and accounted for a substantial proportion of European Union research in this field. Half of the papers by Spanish authors were published in international non-Spanish journals. Most of papers were carried out from hospital settings and universities. Copyright 2009 SESPAS. Published by Elsevier Espana. All rights reserved.

  19. An Event-Related Potentials Study of Mental Rotation in Identifying Chemical Structural Formulas

    ERIC Educational Resources Information Center

    Huang, Chin-Fei; Liu, Chia-Ju

    2012-01-01

    The purpose of this study was to investigate how mental rotation strategies affect the identification of chemical structural formulas. This study conducted event-related potentials (ERPs) experiments. In addition to the data collected in the ERPs, a Chemical Structure Conceptual Questionnaire and interviews were also admin-istered for data…

  20. Identifying the non-linearities in the period-luminosity relations of Cepheids

    NASA Astrophysics Data System (ADS)

    Dassa-Terrier, J.

    2016-12-01

    The period-luminosity relation of Cepheids is essential to characterize the second step of the cosmological distance ladder. However, the possible non-linearity and breaking points around a period of 10 days have important consequences for their use. We review and challenge four different statistical methods on our simulations. We constrain the conditions in which these methods can be applied.

  1. Oximetry Signal Processing Identifies REM Sleep-Related Vulnerability Trait in Asthmatic Children

    PubMed Central

    Perez, Geovanny F.; Gutierrez, Maria J.; Huseni, Shehlanoor; Pancham, Khrisna; Rodriguez-Martinez, Carlos E.; Nino, Cesar L.; Nino, Gustavo

    2013-01-01

    Rationale. The sleep-related factors that modulate the nocturnal worsening of asthma in children are poorly understood. This study addressed the hypothesis that asthmatic children have a REM sleep-related vulnerability trait that is independent of OSA. Methods. We conducted a retrospective cross-sectional analysis of pulse-oximetry signals obtained during REM and NREM sleep in control and asthmatic children (n = 134). Asthma classification was based on preestablished clinical criteria. Multivariate linear regression model was built to control for potential confounders (significance level P ≤ 0.05). Results. Our data demonstrated that (1) baseline nocturnal respiratory parameters were not significantly different in asthmatic versus control children, (2) the maximal % of SaO2 desaturation during REM, but not during NREM, was significantly higher in asthmatic children, and (3) multivariate analysis revealed that the association between asthma and REM-related maximal % SaO2 desaturation was independent of demographic variables. Conclusion. These results demonstrate that children with asthma have a REM-related vulnerability trait that impacts oxygenation independently of OSA. Further research is needed to delineate the REM sleep neurobiological mechanisms that modulate the phenotypical expression of nocturnal asthma in children. PMID:24288619

  2. The engagement of children with disabilities in health-related technology design processes: identifying methodology.

    PubMed

    Allsop, Matthew J; Holt, Raymond J; Levesley, Martin C; Bhakta, Bipinchandra

    2010-01-01

    This review aims to identify research methodology that is suitable for involving children with disabilities in the design of healthcare technology, such as assistive technology and rehabilitation equipment. A review of the literature included the identification of methodology that is available from domains outside of healthcare and suggested a selection of available methods. The need to involve end users within the design of healthcare technology was highlighted, with particular attention to the need for greater levels of participation from children with disabilities within all healthcare research. Issues that may arise when trying to increase such involvement included the need to consider communication via feedback and tailored information, the need to measure levels of participation occurring in current research, and caution regarding the use of proxy information. Additionally, five suitable methods were highlighted that are available for use with children with disabilities in the design of healthcare technology. The methods identified in the review need to be put into practice to establish effective and, if necessary, novel ways of designing healthcare technology when end users are children with disabilities.

  3. Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins.

    PubMed

    Lu, Yuwen; McGavin, Wendy; Cock, Peter J A; Schnettler, Esther; Yan, Fei; Chen, Jianping; MacFarlane, Stuart

    2015-11-01

    Members of the genus Emaravirus, including Raspberry leaf blotch virus (RLBV), are enveloped plant viruses with segmented genomes of negative-strand RNA, although the complete genome complement for any of these viruses is not yet clear. Currently, wheat mosaic virus has the largest emaravirus genome comprising eight RNAs. Previously, we identified five genomic RNAs for RLBV; here, we identify a further three RNAs (RNA6-8). RNA6-8 encode proteins that have clear homologies to one another, but not to any other emaravirus proteins. The proteins self-interacted in yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments, and the P8 protein interacted with the virus nucleocapsid protein (P3) using BiFC. Expression of two of the proteins (P6 and P7) using potato virus X led to an increase in virus titre and symptom severity, suggesting that these proteins may play a role in RLBV pathogenicity; however, using two different tests, RNA silencing suppression activity was not detected for any of the RLBV proteins encoded by RNA2-8.

  4. In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access.

    PubMed

    Garcia Castro, Leyla Jael; Berlanga, Rafael; Garcia, Alexander

    2015-10-01

    Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript. We have benchmarked three similarity metrics - BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles. We have found that the PubMed Related Articles similarity metric is the most suitable for

  5. An integrated approach towards identifying age-related mechanisms of slip initiated falls

    PubMed Central

    Lockhart, Thurmon E.

    2008-01-01

    The causes of slip and fall accidents, both in terms of extrinsic and intrinsic factors and their associations are not yet fully understood. Successful intervention solutions for reducing slip and fall accidents require a more complete understanding of the mechanisms involved. Before effective fall prevention strategies can be put into practice, it is central to examine the chain of events in an accident, comprising the exposure to hazards, initiation of events and the final outcome leading to injury and disability. These events can be effectively identified and analyzed by applying epidemiological, psychophysical, biomechanical and tribological research principles and methodologies. In this manuscript, various methods available to examine fall accidents and their underlying mechanisms are presented to provide a comprehensive array of information to help pinpoint the needs and requirements of new interventions aimed at reducing the risk of falls among the growing elderly population. PMID:17768070

  6. A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes

    PubMed Central

    Xie, Ruiqiang; Chen, Binbin; Huang, Hao; Li, Yiran; He, Yuehan; Lv, Junjie; He, Weiming; Chen, Lina

    2016-01-01

    Identifying the genes involved in venous thromboembolism (VTE) recurrence is important not only for understanding the pathogenesis but also for discovering the therapeutic targets. We proposed a novel prioritization method called Function-Interaction-Pearson (FIP) by creating gene-disease similarity scores to prioritize candidate genes underling VTE. The scores were calculated by integrating and optimizing three types of resources including gene expression, gene ontology and protein-protein interaction. As a result, 124 out of top 200 prioritized candidate genes had been confirmed in literature, among which there were 34 antithrombotic drug targets. Compared with two well-known gene prioritization tools Endeavour and ToppNet, FIP was shown to have better performance. The approach provides a valuable alternative for drug targets discovery and disease therapy. PMID:27050193

  7. What makes astronomical heritage valuable? Identifying potential Outstanding Universal Value in cultural properties relating to astronomy

    NASA Astrophysics Data System (ADS)

    Cotte, Michel

    2015-08-01

    The communication will present the today situation of astronomical and archaeo-astronomical heritage related to the World Heritage Convention along the past years till today. Some parallel events and works promoted strongly as the IAU - UNESCO initiative for the “year of astronomy” (2009). It was followed by a joint program by IAU and ICOMOS who is an official advisory body assessing the World Heritage Committee for the evaluation of nomination dossiers. Result of that works is an important publication by around 40 authors coming from 20 different countries all around the World: Heritage Sites of Astronomy and Archaeoastronomy in context of the UNESCO World Heritage Convention (2010-2011). A second volume is under preparation (2015). It was also accompanied by some initiatives like “Windows to the Universe” organisation and parallel constitution of local “Starlight Reserves”. Some regional meetings studying specific facets or regional heritage in the field giving significant knowledge progresses also accompanied global trend for astronomical heritage.WH assessment is defined by a relatively strict format and methodology. Key word is “demonstration of an Outstanding Universal Value” to justify the WH Listing by the Committee. Communication first examines requirements and evaluation practices about of the OUV demonstration for a given place in context of astronomical or archaeo-astronomical heritage. That means examination of the tangible attributes, inventory of the property in terms of unmoveable and moveable components and inventory of intangible issues related to the history (history of the place in context of the history of astronomy and cultural history). That is also related to apply to the site concept of integrity and authenticity level of the place and comparison with other similar places (WH site already listed, national WH Tentative List, other similar places in the region).Second issue of the communication is to give a glimpse on the

  8. Insights from an international stakeholder consultation to identify informational needs related to seafood safety.

    PubMed

    Tediosi, Alice; Fait, Gabriella; Jacobs, Silke; Verbeke, Wim; Álvarez-Muñoz, Diana; Diogene, Jorge; Reuver, Marieke; Marques, António; Capri, Ettore

    2015-11-01

    Food safety assessment and communication have a strong importance in reducing human health risks related to food consumption. The research carried out within the ECsafeSEAFOOD project aims to assess seafood safety issues, mainly related to non-regulated priority environmental contaminants, and to evaluate their impact on public health. In order to make the research results accessible and exploitable, and to respond to actual stakeholders' demands, a consultation with international stakeholders was performed by means of a survey. The focus was on policy and decision makers, food producers and processors, and agencies (i.e. EU and National or Regional agencies related to Food Safety or Public Health) and consumer organisations. The survey considered questions related to: seafood safety assessment and mitigation strategies, availability of data, such as the level of information on different contaminants, and communication among different stakeholder groups. Furthermore, stakeholders were asked to give their opinion on how they believe consumers perceive risks associated with environmental contaminants. The survey was distributed to 531 key stakeholders and 91 responses were received from stakeholders from 30 EU and non-EU countries. The main results show that communication between different groups of stakeholders needs to be improved and that there is a deficit of information and data in the field of seafood safety. This pertains mainly to the transfer of contaminants between the environment and seafood, and to the diversity of environmental contaminants such as plastic additives, algal toxins and hormones. On-line tools were perceived to be the most useful communication channel. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Lectin microarray technology identifies specific lectins related to lymph node metastasis of advanced gastric cancer.

    PubMed

    Yamashita, Keishi; Kuno, Atsushi; Matsuda, Atsushi; Ikehata, Yuzuru; Katada, Natsuya; Hirabayashi, Jun; Narimatsu, Hisashi; Watanabe, Masahiko

    2016-04-01

    Although various molecular profiling technologies have the potential to predict specific tumor phenotypes, the comprehensive profiling of lectin-bound glycans in human cancer tissues has not yet been achieved. We examined 242 advanced gastric cancer (AGC) patients without or with lymph node metastasis-N0 (n = 62) or N+ (n = 180)-by lectin microarray, and identified the specific lectins highly associated with AGC phenotypes. In seven gastric cancer cell lines, in contrast to expressed-in-cancer lectins, not-expressed-in-cancer (NEC) lectins were tentatively designated by lectin microarray. Binding signals of the specific lectins were robustly reduced in AGC patients with N+ status as compared with those with N0 status. The receiver operating characteristic curve determined the optimal cutoff value to differentiate N0 status from N+ status, and subsequent profiling of NEC lectins identified Vicia villosa agglutinin (VVA) association with the significant other lectins involved in lymph node metastasis. VVA reaction was clearly found on cancer cells, suggesting that it may result from carcinoma-stroma interaction in primary AGC, because VVA is an NEC lectin. Most intriguingly, VVA reaction was remarkably attenuated in the tumor cells of the metastatic lymph nodes, even if it was recognized in primary AGC. In AGC, histological type was strongly associated with soybean agglutinin and Bauhinia purpurea lectin, whereas p53 mutation was the best correlated with Griffonia simplicifolia lectin II. Lectin microarrays can be used to very accurately quantify the reaction of glycans with tumor tissues, and such profiles may represent the specific phenotypes, including N+ status, histological type, or p53 mutation of AGC.

  10. Use of multiple correspondence analysis (MCA) to identify interactive meteorological conditions affecting relative throughfall

    NASA Astrophysics Data System (ADS)

    Van Stan, John T.; Gay, Trent E.; Lewis, Elliott S.

    2016-02-01

    Forest canopies alter rainfall reaching the surface by redistributing it as throughfall. Throughfall supplies water and nutrients to a variety of ecohydrological components (soil microbial communities, stream water discharge/chemistry, and stormflow pathways) and is controlled by canopy structural interactions with meteorological conditions across temporal scales. This work introduces and applies multiple correspondence analyses (MCAs) to a range of meteorological thresholds (median intensity, median absolute deviation (MAD) of intensity, median wind-driven droplet inclination angle, and MAD of wind speed) for an example throughfall problem: identification of interacting storm conditions corresponding to temporal concentration in relative throughfall beyond the median observation (⩾73% of rain). MCA results from the example show that equalling or exceeding rain intensity thresholds (median and MAD) corresponded with temporal concentration of relative throughfall across all storms. Under these intensity conditions, two wind mechanisms produced significant correspondences: (1) high, steady wind-driven droplet inclination angles increased surface wetting; and (2) sporadic winds shook entrained droplets from surfaces. A discussion is provided showing that these example MCA findings agree well with previous work relying on more historically common methods (e.g., multiple regression and analytical models). Meteorological threshold correspondences to temporal concentration of relative throughfall at our site may be a function of heavy Tillandsia usneoides coverage. Applications of MCA within other forests may provide useful insights to how temporal throughfall dynamics are affected for drainage pathways dependent on different structures (leaves, twigs, branches, etc.).

  11. Finding the evidence for protein-protein interactions from PubMed abstracts.

    PubMed

    Jang, Hyunchul; Lim, Jaesoo; Lim, Joon-Ho; Park, Soo-Jun; Lee, Kyu-Chul; Park, Seon-Hee

    2006-07-15

    Protein-protein interactions play critical roles in biological processes, and many biologists try to find or to predict crucial information concerning these interactions. Before verifying interactions in biological laboratory work, validating them from previous research is necessary. Although many efforts have been made to create databases that store verified information in a structured form, much interaction information still remains as unstructured text. As the amount of new publications has increased rapidly, a large amount of research has sought to extract interactions from the text automatically. However, there remain various difficulties associated with the process of applying automatically generated results into manually annotated databases. For interactions that are not found in manually stored databases, researchers attempt to search for abstracts or full papers. As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts. A query is generated from two given proteins automatically and abstracts are then collected from PubMed. Following this, target proteins and their synonyms are recognized and their interaction information is extracted from the collection. It was found that 67.37% of the interactions from DIP-PPI corpus were found from the PubMed abstracts and 87.37% of interactions were found from the given full texts. Contact authors.

  12. Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

    PubMed

    Darmoni, Stéfan J; Soualmia, Lina F; Griffon, Nicolas; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse

    2013-01-01

    PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese.

  13. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

    PubMed

    Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

    2008-02-01

    The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

  14. City-scale analysis of water-related energy identifies more cost-effective solutions.

    PubMed

    Lam, Ka Leung; Kenway, Steven J; Lant, Paul A

    2017-02-01

    Energy and greenhouse gas management in urban water systems typically focus on optimising within the direct system boundary of water utilities that covers the centralised water supply and wastewater treatment systems, despite a greater energy influence by the water end use. This work develops a cost curve of water-related energy management options from a city perspective for a hypothetical Australian city. It is compared with that from the water utility perspective. The curves are based on 18 water-related energy management options that have been implemented or evaluated in Australia. In the studied scenario, the cost-effective energy saving potential from a city perspective (292 GWh/year) is far more significant than that from a utility perspective (65 GWh/year). In some cases, for similar capital cost, if regional water planners invested in end use options instead of utility options, a greater energy saving potential at a greater cost-effectiveness could be achieved in urban water systems. For example, upgrading a wastewater treatment plant for biogas recovery at a capital cost of $27.2 million would save 31 GWh/year with a marginal cost saving of $63/MWh, while solar hot water system rebates at a cost of $28.6 million would save 67 GWh/year with a marginal cost saving of $111/MWh. Options related to hot water use such as water-efficient shower heads, water-efficient clothes washers and solar hot water system rebates are among the most cost-effective city-scale opportunities. This study demonstrates the use of cost curves to compare both utility and end use options in a consistent framework. It also illustrates that focusing solely on managing the energy use within the utility would miss substantial non-utility water-related energy saving opportunities. There is a need to broaden the conventional scope of cost curve analysis to include water-related energy and greenhouse gas at the water end use, and to value their management from a city perspective. This

  15. Parkinson's disease-related perfusion and glucose metabolic brain patterns identified with PCASL-MRI and FDG-PET imaging.

    PubMed

    Teune, Laura K; Renken, Remco J; de Jong, Bauke M; Willemsen, Antoon T; van Osch, Matthias J; Roerdink, Jos B T M; Dierckx, Rudi A; Leenders, Klaus L

    2014-01-01

    Under normal conditions, the spatial distribution of resting cerebral blood flow and cerebral metabolic rate of glucose are closely related. A relatively new magnetic resonance (MR) technique, pseudo-continuous arterial spin labeling (PCASL), can be used to measure regional brain perfusion. We identified a Parkinson's disease (PD)-related perfusion and metabolic covariance pattern in the same patients using PCASL and FDG-PET imaging and assessed (dis)similarities in the disease-related pattern between perfusion and metabolism in PD patients. Nineteen PD patients and seventeen healthy controls underwent [(18)F]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging. Of 14 PD patients and all healthy controls PCASL-MRI could be obtained. Data were analyzed using scaled subprofile model/principal component analysis (SSM/PCA). Unique Parkinson's disease-related perfusion and metabolic covariance patterns were identified using PCASL and FDG-PET in the same patients. The PD-related metabolic covariance brain pattern is in high accordance with previously reports. Also our disease-related perfusion pattern is comparable to the earlier described perfusion pattern. The most marked difference between our perfusion and metabolic patterns is the larger perfusion decrease in cortical regions including the insula. We identified PD-related perfusion and metabolic brain patterns using PCASL and FDG-PET in the same patients which were comparable with results of existing research. In this respect, PCASL appears to be a promising addition in the early diagnosis of individual parkinsonian patients.

  16. Parkinson's disease-related perfusion and glucose metabolic brain patterns identified with PCASL-MRI and FDG-PET imaging

    PubMed Central

    Teune, Laura K.; Renken, Remco J.; de Jong, Bauke M.; Willemsen, Antoon T.; van Osch, Matthias J.; Roerdink, Jos B.T.M.; Dierckx, Rudi A.; Leenders, Klaus L.

    2014-01-01

    Introduction Under normal conditions, the spatial distribution of resting cerebral blood flow and cerebral metabolic rate of glucose are closely related. A relatively new magnetic resonance (MR) technique, pseudo-continuous arterial spin labeling (PCASL), can be used to measure regional brain perfusion. We identified a Parkinson's disease (PD)-related perfusion and metabolic covariance pattern in the same patients using PCASL and FDG-PET imaging and assessed (dis)similarities in the disease-related pattern between perfusion and metabolism in PD patients. Methods Nineteen PD patients and seventeen healthy controls underwent [18F]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging. Of 14 PD patients and all healthy controls PCASL-MRI could be obtained. Data were analyzed using scaled subprofile model/principal component analysis (SSM/PCA). Results Unique Parkinson's disease-related perfusion and metabolic covariance patterns were identified using PCASL and FDG-PET in the same patients. The PD-related metabolic covariance brain pattern is in high accordance with previously reports. Also our disease-related perfusion pattern is comparable to the earlier described perfusion pattern. The most marked difference between our perfusion and metabolic patterns is the larger perfusion decrease in cortical regions including the insula. Conclusion We identified PD-related perfusion and metabolic brain patterns using PCASL and FDG-PET in the same patients which were comparable with results of existing research. In this respect, PCASL appears to be a promising addition in the early diagnosis of individual parkinsonian patients. PMID:25068113

  17. Mobile app versus Web app: a comparison using 2008-2012 "PubMed for Handhelds" server data.

    PubMed

    Fontelo, Paul; Liu, Fang

    2013-01-01

    Recent surveys show that mobile apps are more popular than Web apps. Apple's iTunes Store, now has about 800,000 apps and reported to have about 40 billion downloads. Android apps, although fewer, is available to the most number of smartphones today. About 40,000 apps are medical or health related. We developed a PubMed4Hh mobile app for iPhone/iPad users to search MEDLINE/PubMed with same features as our Web-based search tools, in use since 2002. Five-year (2008-2012) server data for PubMed4Hh and Web app were analyzed. Searches using the mobile app significantly increased compared to the same five-year time period. Month-by-month comparison showed a 3 to 5-fold increase in queries. The six-month total accesses comparison increased 280% from the previous four-year average. A review of 500 randomly selected queries revealed that the majority of queries were clinical questions ((97.8%) and 61% of these queries are searches related to therapy.

  18. What is covered by "cancer rehabilitation" in PubMed? A review of randomized controlled trials 1990-2011.

    PubMed

    Gudbergsson, Sævar Berg; Dahl, Alv A; Loge, Jon Håvard; Thorsen, Lene; Oldervoll, Line M; Grov, Ellen K

    2015-02-01

    This focused review examines randomized controlled studies included by the term "cancer rehabilitation" in PubMed. The research questions concern the type of interventions performed and their methodological quality. Using the Medical Subject Headings (MeSH) terms: neoplasm AND rehabilitation, all articles with randomized controlled studies that included adult cancer patients, written in English, were extracted from PubMed. Papers covering physical exercise, psychiatric/psychological treatment or social support only were excluded as they had been reviewed recently. Abstracts and papers were assessed by 3 pairs of reviewers, and descriptive information was extracted systematically. Methodological quality was rated on a 10-item index scale, and the cut-off for acceptable quality was set at ≥ 8. A total of 132 (19%) of the 683 identified papers met the eligibility criteria and were assessed in detail. The papers were grouped into 5 thematic categories: 44 physical; 15 art and expressive; 47 psycho-educative; 21 emotionally supportive; and 5 others. Good quality of design was observed in 32 studies, 18 of them uni-dimensional and 14 multi-dimensional. Published randomized controlled studies on cancer rehabilitation are heterogeneous in terms of content and samples, and are mostly characterized by suboptimal design quality. Future studies should be more specific and well-designed with sufficient statistical strength.

  19. Identifying cancer patients who alter care or lifestyle due to treatment-related financial distress.

    PubMed

    Nipp, Ryan D; Zullig, Leah L; Samsa, Gregory; Peppercorn, Jeffrey M; Schrag, Deborah; Taylor, Donald H; Abernethy, Amy P; Zafar, S Yousuf

    2016-06-01

    Cancer patients may experience financial distress as a side effect of their care. Little is known about which patients are at greatest risk for altering their care or lifestyle due to treatment-related financial distress. We conducted a cross-sectional survey study to determine which patients are at greatest risk for altering their care or lifestyle due to treatment-related financial distress. Eligible patients were adults receiving cancer treatment enrolled between June 2010 and May 2011. We grouped coping strategies as lifestyle altering or care altering. We assessed coping strategies and relationships between covariates using descriptive statistics and analysis of variance. Among 174 participants, 89% used at least one lifestyle-altering coping strategy, while 39% used a care-altering strategy. Care-altering coping strategies adopted by patients included the following: not filling a prescription (28%) and taking less medication than prescribed (23%). Lifestyle-altering strategies included the following: spending less on leisure activities (77%), spending less on basics like food and clothing (57%), borrowing money (54%), and spending savings (50%). Younger patients were more likely than older patients to use coping strategies (p < 0.001). Lower-income patients adopted care-altering strategies more than higher-income patients (p = 0.03). Participants with more education and shorter duration of chemotherapy used lifestyle-altering strategies more than their counterparts (both p < 0.05). As a means of coping with treatment-related financial distress, patients were more likely to use lifestyle-altering approaches, but more than one-third adopted potentially harmful care-altering strategies. Younger age, lower income, higher education, and shorter duration of chemotherapy were characteristics associated with greater use of coping strategies. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Individual variability in human blood metabolites identifies age-related differences

    PubMed Central

    Murakami, Itsuo; Takada, Junko; Kondoh, Hiroshi; Yanagida, Mitsuhiro

    2016-01-01

    Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and lifestyle factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed nontargeted, quantitative metabolomics analysis in blood of 15 young (29 ± 4 y of age) and 15 elderly (81 ± 7 y of age) individuals. Coefficients of variation (CV = SD/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found 14 blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine, N-acetyl-arginine, N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD+, and NADP+. Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in antioxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson’s coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. Although our CV values are mostly consistent with those CVs previously published, we here report previously unidentified CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4–2.5) are often modified. Compounds having low CV values, such as ATP and glutathione, may be related to various diseases because their concentrations are strictly controlled, and changes in them would compromise health. Thus, human blood is a rich source of information about individual metabolic differences. PMID:27036001

  1. What makes astronomical heritage valuable? Identifying potential Outstanding Universal Value in cultural properties relating to astronomy

    NASA Astrophysics Data System (ADS)

    Cotte, Michel

    2016-10-01

    This communication presents the situation regarding astronomical and archaeoastronomical heritage related to the World Heritage Convention through recent years up until today. Some parallel events and works were promoted strongly within the IAU-UNESCO Initiative during the International Year of Astronomy (2009). This was followed by a joint program by the IAU and ICOMOS-an official advisory body assisting the World Heritage Committee in the evaluation of nomination dossiers. The result of that work is an important publication by around 40 authors from 20 different countries all around the world: Heritage Sites of Astronomy and Archaeoastronomy in the Context of the UNESCO World Heritage Convention (Ruggles & Cotte 2010). A second volume is under preparation (2015). It was also accompanied by some initiatives such as the ``Windows to the Universe" organisation and the parallel constitution of local ``Starlight Reserves''. Some regional meetings studying specific facets or regional heritage in the field giving significant knowledge progresses also accompanied the global trend for astronomical heritage. WH assessment is defined by a relatively strict format and methodology. A key phrase is ``demonstration of Outstanding Universal Value'' to justify the WH Listing by the Committee. This communication first examines the requirements and evaluation practices about of demonstrating OUV for a given place in the context of astronomical or archaeoastronomical heritage. That means the examination of the tangible attributes, an inventory of the property in terms of immoveable and moveable components and an inventory of intangible issues related to the history (history of the place in the context of the history of astronomy and cultural history). This is also related to the application to the site of the concept of integrity and authenticity, as regards the place itself and in comparison with other similar places (WH sites already listed, sites on national WH Tentative Lists

  2. Contribution of WUSCHEL-related homeobox (WOX) genes to identify the phylogenetic relationships among Petunia species.

    PubMed

    Segatto, Ana Lúcia Anversa; Thompson, Claudia Elizabeth; Freitas, Loreta Brandão

    2016-01-01

    Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes.

  3. Contribution of WUSCHEL-related homeobox (WOX) genes to identify the phylogenetic relationships among Petunia species

    PubMed Central

    Segatto, Ana Lúcia Anversa; Thompson, Claudia Elizabeth; Freitas, Loreta Brandão

    2016-01-01

    Abstract Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes. PMID:27768156

  4. Identifying Flood-Related Infectious Diseases in Anhui Province, China: A Spatial and Temporal Analysis

    PubMed Central

    Gao, Lu; Zhang, Ying; Ding, Guoyong; Liu, Qiyong; Jiang, Baofa

    2016-01-01

    The aim of this study was to explore infectious diseases related to the 2007 Huai River flood in Anhui Province, China. The study was based on the notified incidences of infectious diseases between June 29 and July 25 from 2004 to 2011. Daily incidences of notified diseases in 2007 were compared with the corresponding daily incidences during the same period in the other years (from 2004 to 2011, except 2007) by Poisson regression analysis. Spatial autocorrelation analysis was used to test the distribution pattern of the diseases. Spatial regression models were then performed to examine the association between the incidence of each disease and flood, considering lag effects and other confounders. After controlling the other meteorological and socioeconomic factors, malaria (odds ratio [OR] = 3.67, 95% confidence interval [CI] = 1.77–7.61), diarrhea (OR = 2.16, 95% CI = 1.24–3.78), and hepatitis A virus (HAV) infection (OR = 6.11, 95% CI = 1.04–35.84) were significantly related to the 2007 Huai River flood both from the spatial and temporal analyses. Special attention should be given to develop public health preparation and interventions with a focus on malaria, diarrhea, and HAV infection, in the study region. PMID:26903612

  5. Identifying Attentional Bias and Emotional Response After Appearance-Related Stimuli Exposure

    PubMed Central

    Cho, Ara; Kwak, Soo-Min

    2013-01-01

    Abstract The effect of media images has been regarded as a significant variable in the construction or in the activation of body images. Individuals who have a negative body image use avoidance coping strategies to minimize damage to their body image. We identified attentional biases and negative emotional responses following exposure to body stimuli. Female university students were divided into two groups based on their use of avoidance coping strategies (high-level group: high avoidance [HA]; low-group: low avoidance [LA]), and were assigned to two different conditions (exposure to thin body pictures, ET, and exposure to oversized body pictures, EO). Results showed that the HA group paid more attention to slim bodies and reported more negative emotions than the LA group, and that the EO had more negative effects than the ET. We suggest that HAs may attend more to slim bodies as a way of avoiding overweight bodies, influenced by social pressure, and in the search for a compensation of a positive emotional balance. However, attentional bias toward slim bodies can cause an upward comparison process, leading to increased body dissatisfaction, which is the main factor in the development of eating disorders (EDs). Therefore, altering avoidance coping strategies should be considered for people at risk of EDs. PMID:23098249

  6. DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks.

    PubMed

    Castellani, Christina A; Laufer, Benjamin I; Melka, Melkaye G; Diehl, Eric J; O'Reilly, Richard L; Singh, Shiva M

    2015-05-06

    Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental, random, and epigenetic factors. The involvement of DNA methylation in this disease appears logical, but remains to be established. We have used blood DNA from two pairs of monozygotic twins discordant for schizophrenia and their parents in order to assess genome-wide methylation using a NimbleGen Methylation Promoter Microarray. The genome-wide results show that differentially methylated regions (DMRs) exist between members representing discordant monozygotic twins. Some DMRs are shared with parent(s) and others appear to be de novo. We found twenty-seven genes affected by DMR changes that were shared in the affected member of two discordant monozygotic pairs from unrelated families. Interestingly, the genes affected by pair specific DMRs share specific networks. Specifically, this study has identified two networks; "cell death and survival" and a "cellular movement and immune cell trafficking". These two networks and the genes affected have been previously implicated in the aetiology of schizophrenia. The results are compatible with the suggestion that DNA methylation may contribute to the discordance of monozygotic twins for schizophrenia. Also, this may be accomplished by the direct effect of gene specific methylation changes on specific biological networks rather than individual genes. It supports the extensive genetic, epigenetic and phenotypic heterogeneity implicated in schizophrenia.

  7. Identifying attentional bias and emotional response after appearance-related stimuli exposure.

    PubMed

    Cho, Ara; Kwak, Soo-Min; Lee, Jang-Han

    2013-01-01

    The effect of media images has been regarded as a significant variable in the construction or in the activation of body images. Individuals who have a negative body image use avoidance coping strategies to minimize damage to their body image. We identified attentional biases and negative emotional responses following exposure to body stimuli. Female university students were divided into two groups based on their use of avoidance coping strategies (high-level group: high avoidance [HA]; low-group: low avoidance [LA]), and were assigned to two different conditions (exposure to thin body pictures, ET, and exposure to oversized body pictures, EO). Results showed that the HA group paid more attention to slim bodies and reported more negative emotions than the LA group, and that the EO had more negative effects than the ET. We suggest that HAs may attend more to slim bodies as a way of avoiding overweight bodies, influenced by social pressure, and in the search for a compensation of a positive emotional balance. However, attentional bias toward slim bodies can cause an upward comparison process, leading to increased body dissatisfaction, which is the main factor in the development of eating disorders (EDs). Therefore, altering avoidance coping strategies should be considered for people at risk of EDs.

  8. Identifying and tracking attacks on networks: C3I displays and related technologies

    NASA Astrophysics Data System (ADS)

    Manes, Gavin W.; Dawkins, J.; Shenoi, Sujeet; Hale, John C.

    2003-09-01

    Converged network security is extremely challenging for several reasons; expanded system and technology perimeters, unexpected feature interaction, and complex interfaces all conspire to provide hackers with greater opportunities for compromising large networks. Preventive security services and architectures are essential, but in and of themselves do not eliminate all threat of compromise. Attack management systems mitigate this residual risk by facilitating incident detection, analysis and response. There are a wealth of attack detection and response tools for IP networks, but a dearth of such tools for wireless and public telephone networks. Moreover, methodologies and formalisms have yet to be identified that can yield a common model for vulnerabilities and attacks in converged networks. A comprehensive attack management system must coordinate detection tools for converged networks, derive fully-integrated attack and network models, perform vulnerability and multi-stage attack analysis, support large-scale attack visualization, and orchestrate strategic responses to cyber attacks that cross network boundaries. We present an architecture that embodies these principles for attack management. The attack management system described engages a suite of detection tools for various networking domains, feeding real-time attack data to a comprehensive modeling, analysis and visualization subsystem. The resulting early warning system not only provides network administrators with a heads-up cockpit display of their entire network, it also supports guided response and predictive capabilities for multi-stage attacks in converged networks.

  9. Occupational health surveillance: a means to identify work-related risks.

    PubMed Central

    Froines, J R; Dellenbaugh, C A; Wegman, D H

    1986-01-01

    The lack of successful disease surveillance methods has resulted in few reliable estimates of workplace-related disease. Hazard surveillance--the ongoing assessment of chemical use and worker exposure to the chemicals--is presented as a way to supplement occupational disease surveillance. Existing OSHA (Occupational Safety and Health Administration) and NIOSH (National Institute for Occupational Health) data systems are adapted to this function to characterize the distribution and type of hazardous industry in Los Angeles County. A new method is developed for ranking potentially hazardous industries in the county using actual exposure measurements from federal OSHA compliance inspections. The strengths of the different systems are presented along with considerations of industrial employment and types of specific chemical exposures. Applications for information from hazard surveillance are discussed in terms of intervention, monitoring exposure control, planning, research, and as a complement to disease surveillance. PMID:3740331

  10. Identifying the best scenario for using schematic organizers as integration tools for alcohol-related information.

    PubMed

    Peel, J L; Dansereau, D F; Dees, S

    1993-01-01

    The goal of the present study was to examine scenarios for using two schematic organizers--schematic knowledge maps and conceptual matrices--in integrating episodic and semantic knowledge about alcohol. Seventy students from undergraduate general psychology classes participated for course credit. Participants were assigned to either a schematic organizer group or an essay writing group. These groups were subdivided further into two treatment sequences: episodic/semantic and semantic/episodic. The episodic activity required participants to complete materials using their own alcohol-related experiences, whereas the semantic activity required participants to annotate expert materials. Assessment measures used were consumer-satisfaction questionnaires and free-recall tests. While no preferences were established for any one scenario, the episodic activities were rated higher than the semantic activities regardless of integration sequence. The semantic/episodic integration scenario did produce higher recall scores for the expert information.

  11. How cooperatively breeding birds identify relatives and avoid incest: New insights into dispersal and kin recognition.

    PubMed

    Riehl, Christina; Stern, Caitlin A

    2015-12-01

    Cooperative breeding in birds typically occurs when offspring - usually males - delay dispersal from their natal group, remaining with the family to help rear younger kin. Sex-biased dispersal is thought to have evolved in order to reduce the risk of inbreeding, resulting in low relatedness between mates and the loss of indirect fitness benefits for the dispersing sex. In this review, we discuss several recent studies showing that dispersal patterns are more variable than previously thought, often leading to complex genetic structure within cooperative avian societies. These empirical findings accord with recent theoretical models suggesting that sex- biased dispersal is neither necessary, nor always sufficient, to prevent inbreeding. The ability to recognize relatives, primarily by learning individual or group-specific vocalizations, may play a more important role in incest avoidance than currently appreciated. © 2015 WILEY Periodicals, Inc.

  12. VEGF Polymorphisms Related to Higher Serum Levels of Protein Identify Patients with Hepatocellular Carcinoma

    PubMed Central

    Ferreira, Rafael Fernandes; Pinhel, Marcela Augusta de Souza; da Silva, Renato Ferreira; Fucuta, Patrícia da Silva; Souza, Dorotéia Rossi Silva

    2016-01-01

    Hepatocellular carcinoma (HCC) is the most common primary neoplasia of the liver. Major risk factors for hepatocellular carcinoma include chronic liver diseases, carcinogenic agents, and genetic alterations as well as vascular endothelial growth factor (VEGF) involved in angiogenesis process. The aim of this study was to evaluate the association of VEGF-A (C936T and A1154G) with HCC and cirrhosis, in addition to serum levels of VEGF, clinical profile, lifestyle habits, and comorbidities. A total of 346 individuals were studied: 102 with HCC (G1), 117 with cirrhosis (G2), and 127 controls (G3). Polymorphisms were analysed by PCR/RFLP and serum levels of VEGF by ELISA. Alpha error was set at 5%. The wild-type genotype of both polymorphisms prevailed (P > 0.05). In G1, 23% of the patients died, with no relation to genetic profile (P > 0.05). Increased VEGF level was observed in G1 and G3, related to the mutant allele of VEGF-C936T and VEGF-A1154G, respectively, and compared with the wild-type genotype (P = 0.0285; P = 0.0284, resp.) as well as G1 versus G2 and G3 for VEGF-C936T and G1 versus G2 for VEGF-A1154G (P < 0.05 for both). In conclusion, there is a relationship between mutant alleles of VEGF-C936T and VEGF-A1154G polymorphisms and higher VEGF level, making them potential markers for HCC. PMID:27660750

  13. B56δ-related protein phosphatase 2A dysfunction identified in patients with intellectual disability

    PubMed Central

    Houge, Gunnar; Haesen, Dorien; Vissers, Lisenka E.L.M.; Mehta, Sarju; Parker, Michael J.; Wright, Michael; Vogt, Julie; McKee, Shane; Tolmie, John L.; Cordeiro, Nuno; Kleefstra, Tjitske; Willemsen, Marjolein H.; Reijnders, Margot R.F.; Berland, Siren; Hayman, Eli; Lahat, Eli; Brilstra, Eva H.; van Gassen, Koen L.I.; Zonneveld-Huijssoon, Evelien; de Bie, Charlotte I.; Hoischen, Alexander; Eichler, Evan E.; Holdhus, Rita; Steen, Vidar M.; Døskeland, Stein Ove; Hurles, Matthew E.; FitzPatrick, David R.; Janssens, Veerle

    2015-01-01

    Here we report inherited dysregulation of protein phosphatase activity as a cause of intellectual disability (ID). De novo missense mutations in 2 subunits of serine/threonine (Ser/Thr) protein phosphatase 2A (PP2A) were identified in 16 individuals with mild to severe ID, long-lasting hypotonia, epileptic susceptibility, frontal bossing, mild hypertelorism, and downslanting palpebral fissures. PP2A comprises catalytic (C), scaffolding (A), and regulatory (B) subunits that determine subcellular anchoring, substrate specificity, and physiological function. Ten patients had mutations within a highly conserved acidic loop of the PPP2R5D-encoded B56δ regulatory subunit, with the same E198K mutation present in 6 individuals. Five patients had mutations in the PPP2R1A-encoded scaffolding Aα subunit, with the same R182W mutation in 3 individuals. Some Aα cases presented with large ventricles, causing macrocephaly and hydrocephalus suspicion, and all cases exhibited partial or complete corpus callosum agenesis. Functional evaluation revealed that mutant A and B subunits were stable and uncoupled from phosphatase activity. Mutant B56δ was A and C binding–deficient, while mutant Aα subunits bound B56δ well but were unable to bind C or bound a catalytically impaired C, suggesting a dominant-negative effect where mutant subunits hinder dephosphorylation of B56δ-anchored substrates. Moreover, mutant subunit overexpression resulted in hyperphosphorylation of GSK3β, a B56δ-regulated substrate. This effect was in line with clinical observations, supporting a correlation between the ID degree and biochemical disturbance. PMID:26168268

  14. Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists.

    PubMed

    Lerchenmueller, Marc J; Sorenson, Olav

    2016-01-01

    We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers-Principal Investigator (PI) IDs-that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity.

  15. Use of Restriction Fragment Length Polymorphism to Rapidly Identify Dermatophyte Species Related to Dermatophytosis

    PubMed Central

    Mohammadi, Rasoul; Abastabar, Mahdi; Mirhendi, Hossein; Badali, Hamid; Shadzi, Shahla; Chadeganipour, Mustafa; Pourfathi, Parinaz; Jalalizand, Niloufar; Haghani, Iman

    2015-01-01

    Background: Dermatophytes are a group of keratinophilic fungi worldwide, which can infect the skin, hair and nails of humans and animals. This genus includes several species that present different features of dermatophytosis. Although, laboratory diagnosis of dermatophytes is based on direct microscopy, biochemical tests and culture, these manners are expensive, time consuming and need skilled staff. Therefore, molecular methods like PCR-RFLP are the beneficial tools for identification, which are rapid and sensitive. Thus, dermatophyte species are able to generate characteristic band patterns on agarose gel electrophoresis using PCR-RFLP technique, which leads to successful identification at the species level within a 5-hour period. Objectives: The purpose of this study was to study inter- and intraspecific genomic variations for identification of clinically important dermatophyte species obtained from clinical specimens in Isfahan, Iran using PCR-RFLP. Materials and Methods: From March 2011 to August 2012, 135 clinical isolates were collected from infected patients at Isfahan, Iran. ITS1-5.8S-ITS2 region of rDNA was amplified using universal fungal primers. Subsequently, amplified products were digested by the MvaI restriction enzyme. Using discriminating band profiles on agarose gel, dermatophyte species were identified. However, DNA sequencing was used for unidentifiable strains. Results: The specimens were obtained from skin scrapings (70.3%), nail (24.4%) and hair (5.1%) clippings. Most patients were between 21 - 30 years and the ratio of male to female was 93/42. Trichophyton interdigitale was the commonest isolate (52.5%) in our findings, followed by Epidermophyton floccosum (24.4%), T. rubrum (16.2%), Microsporum canis (2.2%), T. erinacei (1.4%), T. violaceum (1.4%), T. tonsurans (0.7%) and M. gypseum (0.7%) based on PCR-RFLP. Conclusions: Combination of traditional methods and molecular techniques considerably improves identification of dermatophytes in

  16. Identifying obstacles to return to duty in severely injured combat-related servicemembers with amputation.

    PubMed

    Hurley, Richard K; Rivera, Jessica C; Wenke, Joseph C; Krueger, Chad A

    2015-01-01

    The capacity of servicemembers with amputation to return to duty after combat-related amputation and the associated disabilities remains largely unknown. The purpose of this study was to examine the disabling conditions and return to duty rates of servicemembers with amputation across all service branches following major limb amputations from September 2001 through July 2011. Pertinent medical information, military occupation status, return to duty designation, disabling conditions, and disability ratings for each servicemember were obtained from the Physical Evaluation Board Liaison Office (PEBLO). Across all service branches, 16 (2%) servicemembers were found fit for duty (Fit) and allowed to continue with their preinjury occupation. Another 103 (11%) were allowed to continue on Active Duty (COAD) in a less physically demanding role. More than half (554, 56%) were determined fully disabled (PEBLO rating > 75); the average disability rating was 73. COAD and Fit Army servicemembers had lower Injury Severity Scores than other servicemembers (17.4, p = 0.009 and 11.2, p < 0.001, respectively). Despite improvements in their care and rehabilitation, only 13% of all servicemembers with amputation are able to return to Active Duty and many have multiple disabling conditions that contribute to a very high level of disability.

  17. Identifying pain-related concerns in routine follow-up clinics following oral and oropharyngeal cancer.

    PubMed

    Rogers, Simon N; Cleator, Alexander J; Lowe, Derek; Ghazali, Naseem

    2012-08-10

    To describe clinical characteristics of head and neck cancer (HNC) patients with pain and those wishing to discuss pain concerns during consultation. Cross-sectional, questionnaire study using University of Washington Quality of Life, version 4 (UW-QOL) and the Patients Concerns Inventory (PCI) in disease-free, post-treatment HNC cohort. Significant pain on UW-QOL and indicating "Pain in head and neck" and "Pain elsewhere" on PCI. One hundred and seventy-seven patients completed UW-QOL and PCI. The prevalence of self-reported pain issues was 38% (67/177) comprising 25% (44/177) with significant problems despite medications and 13% (23/177) with lesser or no problems but wishing to discuss pain. Patients aged under 65 years and patients having treatment involving radiotherapy were more likely to have pain issues. Just over half, 55% (24/44) of patients with significant pain did not express a need to discuss this. Those with significant pain or others wanting to discuss pain in clinic had greater problems in physical and social-emotional functioning, reported suboptimal QOL, and also had more additional PCI items to discuss in clinic compared to those without significant pain and not wishing to discuss pain. Significant HNC-related pain is prevalent in the disease-free, posttreatment cohort. Onward referral to a specialist pain team may be beneficial. The UW-QOL and PCI package is a valuable tool that may routinely screen for significant pain in outpatient clinics.

  18. Case-only approach to identifying markers predicting treatment effects on the relative risk scale.

    PubMed

    Dai, James Y; Liang, C Jason; LeBlanc, Michael; Prentice, Ross L; Janes, Holly

    2017-09-28

    Retrospectively measuring markers on stored baseline samples from participants in a randomized controlled trial (RCT) may provide high quality evidence as to the value of the markers for treatment selection. Originally developed for approximating gene-environment interactions in the odds ratio scale, the case-only method has recently been advocated for assessing gene-treatment interactions on rare disease endpoints in randomized clinical trials. In this article, the case-only approach is shown to provide a consistent and efficient estimator of marker by treatment interactions and marker-specific treatment effects on the relative risk scale. The prohibitive rare-disease assumption is no longer needed, broadening the utility of the case-only approach. The case-only method is resource-efficient as markers only need to be measured in cases only. It eliminates the need to model the marker's main effect, and can be used with any parametric or nonparametric learning method. The utility of this approach is illustrated by an application to genetic data in the Women's Health Initiative (WHI) hormone therapy trial. © 2017, The International Biometric Society.

  19. Identifying Features of Fitness Landscapes and Relating Them to Problem Difficulty.

    PubMed

    Moser, I; Gheorghita, M; Aleti, A

    2016-02-29

    Complex combinatorial problems are most often optimised with heuristic solvers, which usually deliver acceptable results without any indication of the quality obtained. Recently, predictive diagnostic optimisation was proposed as a means of characterising the fitness landscape while optimising a combinatorial problem. The scalars produced by predictive diagnostic optimisation appear to describe the difficulty of the problem with relative reliability. In this study, we record more scalars that may be helpful in determining problem difficulty during the optimisation process and analyse these in combination with other well-known landscape descriptors by using exploratory factor analysis on four landscapes that arise from different search operators, applied to a varied set of quadratic assignment problem instances. Factors are designed to capture properties by combining the collinear variances of several variables. The extracted factors can be interpreted as the features of landscapes detected by the variables, but disappoint in their weak correlations with the result quality achieved by the optimiser, which we regard as the most reliable indicator of difficulty available. It appears that only the prediction error of predictive diagnostic optimisation has a strong correlation with the quality of the results produced, followed by a medium correlation of the fitness distance correlation of the local optima.

  20. Multiple actions of a molluscan cardioexcitatory neuropeptide and related peptides on identified Helix neurones.

    PubMed Central

    Cottrell, G A; Davies, N W; Green, K A

    1984-01-01

    The effects of the molluscan neuropeptide Phe-Met-Arg-Phe-NH2 (FMRF amide) and related peptides (Price & Greenberg, 1977) were tested on Helix aspersa neurones. Ionophoretic application of FMRFamide depolarized and excited some neurones, but hyperpolarized and inhibited others. In some neurones the sign of the response was dependent on the membrane potential. Two responses resulted from an increase in membrane conductance, a depolarizing response mediated mainly by an increase in Na+ ion permeability, and a hyperpolarizing response mediated by an increase in K+ ion permeability. In the C1 neurone a voltage-dependent response was observed, which only occurred when the neurone was depolarized from its resting level. This response was recorded as an inward current during voltage clamp and resulted from a decrease in K current(s), possibly Ca-activated K current. More than one response may occur in a single neurone. In the C1 neurone, the K-mediated hyperpolarization occurred as well as the voltage-dependent response, while the depolarization seen in the F2 neurone was a combination of an increase in Na conductance and an increase in K conductance. PMID:6097674

  1. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants.

    PubMed Central

    Guzmán, P; Ecker, J R

    1990-01-01

    Alterations in the response of dark-grown seedlings to ethylene (the "triple response") were used to isolate a collection of ethylene-related mutants in Arabidopsis thaliana. Mutants displaying a constitutive response (eto1) were found to produce at least 40 times more ethylene than the wild type. The morphological defects in etiolated eto1-1 seedlings reverted to wild type under conditions in which ethylene biosynthesis or ethylene action were inhibited. Mutants that failed to display the apical hook in the absence of ethylene (his1) exhibited reduced ethylene production. In the presence of exogenous ethylene, hypocotyl and root of etiolated his1-1 seedlings were inhibited in elongation but no apical hook was observed. Mutants that were insensitive to ethylene (ein1 and ein2) produced increased amounts of ethylene, displayed hormone insensitivity in both hypocotyl and root responses, and showed an apical hook. Each of the "triple response" mutants has an effect on the shape of the seedling and on the production of the hormone. These mutants should prove to be useful tools for dissecting the mode of ethylene action in plants. PMID:2152173

  2. Mentoring programs for medical students - a review of the PubMed literature 2000 - 2008

    PubMed Central

    2010-01-01

    Background Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. Methods A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. Results The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Conclusion Mentoring is obviously an important career advancement tool for medical students. In Europe

  3. Using event related potentials to identify a user's behavioural intention aroused by product form design.

    PubMed

    Ding, Yi; Guo, Fu; Zhang, Xuefeng; Qu, Qingxing; Liu, Weilin

    2016-07-01

    The capacity of product form to arouse user's behavioural intention plays a decisive role in further user experience, even in purchase decision, while traditional methods rarely give a fully understanding of user experience evoked by product form, especially the feeling of anticipated use of product. Behavioural intention aroused by product form designs has not yet been investigated electrophysiologically. Hence event related potentials (ERPs) were applied to explore the process of behavioural intention when users browsed different smart phone form designs with brand and price not taken into account for mainly studying the brain activity evoked by variety of product forms. Smart phone pictures with different anticipated user experience were displayed with equiprobability randomly. Participants were asked to click the left mouse button when certain picture gave them a feeling of behavioural intention to interact with. The brain signal of each participant was recorded by Curry 7.0. The results show that pictures with an ability to arouse participants' behavioural intention for further experience can evoke enhanced N300 and LPPs (late positive potentials) in central-parietal, parietal and occipital regions. The scalp topography shows that central-parietal, parietal and occipital regions are more activated. The results indicate that the discrepancy of ERPs can reflect the neural activities of behavioural intention formed or not. Moreover, amplitude of ERPs occurred in corresponding brain areas can be used to measure user experience. The exploring of neural correlated with behavioural intention provide an accurate measurement method of user's perception and help marketers to know which product can arouse users' behavioural intention, maybe taken as an evaluating indicator of product design.

  4. Identifying pain-related concerns in routine follow-up clinics following oral and oropharyngeal cancer

    PubMed Central

    Rogers, Simon N; Cleator, Alexander J; Lowe, Derek; Ghazali, Naseem

    2012-01-01

    AIM: To describe clinical characteristics of head and neck cancer (HNC) patients with pain and those wishing to discuss pain concerns during consultation. METHODS: Cross-sectional, questionnaire study using University of Washington Quality of Life, version 4 (UW-QOL) and the Patients Concerns Inventory (PCI) in disease-free, post-treatment HNC cohort. Significant pain on UW-QOL and indicating “Pain in head and neck” and “Pain elsewhere” on PCI. RESULTS: One hundred and seventy-seven patients completed UW-QOL and PCI. The prevalence of self-reported pain issues was 38% (67/177) comprising 25% (44/177) with significant problems despite medications and 13% (23/177) with lesser or no problems but wishing to discuss pain. Patients aged under 65 years and patients having treatment involving radiotherapy were more likely to have pain issues. Just over half, 55% (24/44) of patients with significant pain did not express a need to discuss this. Those with significant pain or others wanting to discuss pain in clinic had greater problems in physical and social-emotional functioning, reported suboptimal QOL, and also had more additional PCI items to discuss in clinic compared to those without significant pain and not wishing to discuss pain. CONCLUSION: Significant HNC-related pain is prevalent in the disease-free, posttreatment cohort. Onward referral to a specialist pain team may be beneficial. The UW-QOL and PCI package is a valuable tool that may routinely screen for significant pain in outpatient clinics. PMID:22905338

  5. Occipital artery vasculitis not identified as a mechanism of occipital neuralgia-related chronic migraine headaches.

    PubMed

    Ducic, Ivica; Felder, John M; Janis, Jeffrey E

    2011-10-01

    Recent evidence has shown that some cases of occipital neuralgia are attributable to musculofascial compression of the greater occipital nerve and improve with neurolysis. A mechanical interaction at the intersection of the nerve and the occipital artery may also be capable of producing neuralgia, although that mechanism remains one theoretical possibility among several. The authors evaluated the possibility of unrecognized vasculitis of the occipital artery as a potential mechanism of occipital neuralgia arising from the occipital artery/greater occipital nerve junction. Twenty-five patients with preoperatively documented bilateral occipital neuralgia-related chronic headaches underwent peripheral nerve surgery with decompression of the greater occipital nerve bilaterally, including the area of its intersection with the occipital artery. In 15 patients, a 2-cm segment of the occipital artery was excised and submitted for pathologic evaluation. All patients were evaluated intraoperatively for evidence of arterially mediated greater occipital nerve compression, and the configuration of the nerve-vessel intersection was noted. None of the 15 specimens submitted for pathologic evaluation showed vasculitis. Intraoperatively, all 50 sites examined showed an intimate physical association between the occipital artery and greater occipital nerve. Surgical specimens from this first in vivo study provided no histologic evidence of vasculitis as a cause of greater occipital nerve irritation at the occipital artery/greater occipital nerve junction in patients with chronic headaches caused by occipital neuralgia. Based on these findings, mechanical (and not primary inflammatory) irritation of the nerve by the occipital artery remains an important theoretical cause for otherwise idiopathic cases. The authors have adopted an operative technique that includes physical separation of the nerve-artery intersection (in addition to musculofascial neurolysis) for a more thorough

  6. Identifying mutation regions for closely related individuals without a known pedigree

    PubMed Central

    2012-01-01

    Background Linkage analysis is the first step in the search for a disease gene. Linkage studies have facilitated the identification of several hundred human genes that can harbor mutations leading to a disease phenotype. In this paper, we study a very important case, where the sampled individuals are closely related, but the pedigree is not given. This situation happens very often when the individuals share a common ancestor 6 or more generations ago. To our knowledge, no algorithm can give good results for this case. Results To solve this problem, we first developed some heuristic algorithms for haplotype inference without any given pedigree. We propose a model using the parsimony principle that can be viewed as an extension of the model first proposed by Dan Gusfield. Our heuristic algorithm uses Clark’s inference rule to infer haplotype segments. Conclusions We ran our program both on the simulated data and a set of real data from the phase II HapMap database. Experiments show that our program performs well. The recall value is from 90% to 99% in various cases. This implies that the program can report more than 90% of the true mutation regions. The value of precision varies from 29% to 90%. When the precision is 29%, the size of the reported regions is three times that of the true mutation region. This is still very useful for narrowing down the range of the disease gene location. Our program can complete the computation for all the tested cases, where there are about 110,000 SNPs on a chromosome, within 20 seconds. PMID:22731852

  7. A Teacher Attitude Inventory: Identifying Teacher Positions in Relation to Educational Issues and Decisions. Research and Development Memorandum No. 118.

    ERIC Educational Resources Information Center

    Whitmore, Joanne Rand

    This memorandum reports on the preliminary research using a 24-item inventory designed to measure teacher's positions in relation to education issues and teaching decisions. The instrument, whose development is reported, is intended to identify representatives of two dichotomous styles of teaching: traditional, teacher-centered teaching and…

  8. Development and Assessment of a Diagnostic Tool to Identify Organic Chemistry Students' Alternative Conceptions Related to Acid Strength

    ERIC Educational Resources Information Center

    McClary, LaKeisha M.; Bretz, Stacey Lowery

    2012-01-01

    The central goal of this study was to create a new diagnostic tool to identify organic chemistry students' alternative conceptions related to acid strength. Twenty years of research on secondary and college students' conceptions about acids and bases has shown that these important concepts are difficult for students to apply to qualitative problem…

  9. Development and Assessment of a Diagnostic Tool to Identify Organic Chemistry Students' Alternative Conceptions Related to Acid Strength

    ERIC Educational Resources Information Center

    McClary, LaKeisha M.; Bretz, Stacey Lowery

    2012-01-01

    The central goal of this study was to create a new diagnostic tool to identify organic chemistry students' alternative conceptions related to acid strength. Twenty years of research on secondary and college students' conceptions about acids and bases has shown that these important concepts are difficult for students to apply to qualitative problem…

  10. Assessing student pharmacists' ability to identify drug-related problems in patients within a patient-centered medical home.

    PubMed

    Armor, Becky L; Bulkley, Christina F; Truong, Teresa; Carter, Sandra M

    2014-02-12

    To quantify, describe, and categorize patient drug-related problems (DRPs) and recommendations identified by fourth-year (P4) student pharmacists during a live medication reconciliation activity within a patient-centered medical home (PCMH). Fourth-year student pharmacists conducted chart reviews, identified and documented DRPs, obtained live medication histories, and immediately provided findings and recommendations to the attending physicians. Documentation of DRPs and recommendations were analyzed retrospectively. Thirty-eight students completed 99 medication reconciliation sessions from June 2011 to October 2012 during their advanced pharmacy practice experience (APPE). The students obtained 676 patient medication histories and identified or intervened on 1308 DRPs. The most common DRPs reported were incomplete medication list and diagnostic/laboratory testing needed. Physicians accepted 1,018 (approximately 78%) recommendations. Student pharmacists successfully identified and reduced DRPs through a live medication reconciliation process within an academic-based PCMH model. Their medication history-taking skills improved and medication use was optimized.

  11. Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.

    PubMed

    Zaremba, Sam; Ramos-Santacruz, Mila; Hampton, Thomas; Shetty, Panna; Fedorko, Joel; Whitmore, Jon; Greene, John M; Perna, Nicole T; Glasner, Jeremy D; Plunkett, Guy; Shaker, Matthew; Pot, David

    2009-06-10

    The Enteropathogen Resource Integration Center (ERIC; http://www.ericbrc.org) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as Escherichia coli and Salmonella spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process. We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application. Our Text Mining application is available online on the ERIC website (http://www.ericbrc.org/portal/eric/articles). The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.

  12. PubMedAlertMe--standalone Windows-based PubMed SDI software application.

    PubMed

    Ma'ayan, Avi

    2008-05-01

    PubMedAlertMe is a Windows-based software system for automatically receiving e-mail alert messages about recent publications listed on PubMed. The e-mail messages contain links to newly available abstracts listed on PubMed describing publications that were selectively returned from a specified list of queries. Links are also provided to directly export citations to EndNote, and links are provided to directly forward articles to colleagues. The program is standalone. Thus, it does not require a remote mail server or user registration. PubMedAlertMe is free software, and can be downloaded from: http://amp.pharm.mssm.edu/PubMedAlertMe/PubMedAlertMe_setup.zip.

  13. Studying PubMed usages in the field for complex problem solving: Implications for tool design.

    PubMed

    Mirel, Barbara; Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2013-05-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists' behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists' problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users.

  14. What time-lag for a retraction search on PubMed?

    PubMed

    Decullier, Evelyne; Huot, Laure; Maisonneuve, Hervé

    2014-06-25

    To investigate fraud and errors, scientists have studied cohorts of retraction notices. These researches have been performed using a PubMed search on publication type "retraction of publication" which retrieves the notices of the retractions. We assessed the stability of the indexation of retraction notices over a 15-month period and what was the time-lag to get stability. A search on notices of retraction issued in 2008 was repeated every 3 months during 15 months from February 2011. The first search resulted in 237 notices of retraction. Throughout the study period, 14 discrepancies with the initial search were observed (6%). We found that the number of retraction notices became stable 35 months after the retraction. The time-lag observed in this study has to be taken into account when performing a PubMed search.

  15. PubMedAlertMe - Standalone Windows-based PubMed SDI Software Application

    PubMed Central

    Ma’ayan, Avi

    2008-01-01

    PubMedAlertMe is a Windows-based software system for automatically receiving e-mail alert messages about recent publications listed on PubMed. The e-mail messages contain links to newly available abstracts listed on PubMed describing publications that were selectively returned from a specified list of queries. Links are also provided to directly export citations to EndNote, and links are provided to directly forward articles to colleagues. The program is standalone. Thus, it does not require a remote mail server or user registration. PubMedAlertMe is free software, and can be downloaded from: http://amp.pharm.mssm.edu/PubMedAlertMe/PubMedAlertMe_setup.zip PMID:18402930

  16. Studying PubMed usages in the field for complex problem solving: Implications for tool design

    PubMed Central

    Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2012-01-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists’ behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists’ problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users. PMID:24376375

  17. Teaching PubMed in cyberspace: the development of a self-learning package.

    PubMed

    King, Samuel; Kaplan, Richard; MacDonald, Kathleen

    2008-01-01

    This article discusses the development of a series of online modules for learning the PubMed version of MEDLINE. Funded by a National Library of Medicine grant and targeted initially to physician assistants practicing in New Hampshire, the project is approved for CE credit nationally by the American Association of Physician Assistants. The development of the project is described, the tutorial modules are reviewed, and issues encountered with technology and human factors are discussed and evaluated.

  18. Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS

    PubMed Central

    2010-01-01

    Background Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. Results RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. Conclusions RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user’s feedback and efficiently processes the function to return relevant articles in real time. PMID:20406504

  19. Precision and negative predictive value of links between ClinicalTrials.gov and PubMed.

    PubMed

    Huser, Vojtech; Cimino, James J

    2012-01-01

    One of the goals of translational science is to shorten the time from discovery to clinical use. Clinical trial registries were established to increase transparency in completed and ongoing clinical trials, and they support linking trials with resulting publications. We set out to investigate precision and negative predictive value (NPV) of links between ClinicalTrials.gov (CT.gov) and PubMed. CT.gov has been established to increase transparency in clinical trials and the link to PubMed is crucial for supporting a number of important functions, including ascertaining publication bias. We drew a random sample of trials downloaded from CT.gov and performed manual review of retrieved publications. We characterize two types of links between trials and publications (NCT-link originating from MEDLINE and PMID-link originating from CT.gov).The link precision is different based on type (NCT-link: 100%; PMID-link: 63% to 96%). In trials with no linked publication, we were able to find publications 44% of the time (NPV=56%) by searching PubMed. This low NPV shows that there are potentially numerous publications that should have been formally linked with the trials. Our results indicate that existing trial registry and publisher policies may not be fully enforced. We suggest some automated methods for improving link quality.

  20. Increasing state public health professionals' proficiency in using PubMed

    PubMed Central

    Harwell, Todd S.; Law, Dionne Gesink; Ander, Jennifer L.; Helgerson, Steven D.

    2008-01-01

    Objective: The paper provides an overview of a strategy to increase utilization of online bibliographic databases by public health workers. Methods: A web-based survey of professional staff in the Montana Department of Public Health and Human Services was conducted to assess their use of and interest in training in online bibliographic databases. Based on the findings from the assessment, the department, in collaboration with the state university, provided brief ninety-minute training sessions for interested staff on the use of PubMed. Results: Seventy of 115 (61%) of staff completed the survey. Only 39% of staff reported using an online bibliographic database to conduct a literature search in the past year, and only 10% (n=7) reported having ever received any training in their use. Perceived proficiency with the use of PubMed was higher upon completion of the brief training. The majority of training participants (n=27) indicated that they were very likely to use PubMed in the next year to search the literature. Conclusions: A collaboratively designed training can increase public health workers' proficiency in and intentions of using online bibliographic databases. PMID:18379668

  1. Precision and Negative Predictive Value of Links between ClinicalTrials.gov and PubMed

    PubMed Central

    Huser, Vojtech; Cimino, James J.

    2012-01-01

    One of the goals of translational science is to shorten the time from discovery to clinical use. Clinical trial registries were established to increase transparency in completed and ongoing clinical trials, and they support linking trials with resulting publications. We set out to investigate precision and negative predictive value (NPV) of links between ClinicalTrials.gov (CT.gov) and PubMed. CT.gov has been established to increase transparency in clinical trials and the link to PubMed is crucial for supporting a number of important functions, including ascertaining publication bias. We drew a random sample of trials downloaded from CT.gov and performed manual review of retrieved publications. We characterize two types of links between trials and publications (NCT-link originating from MEDLINE and PMID-link originating from CT.gov).The link precision is different based on type (NCT-link: 100%; PMID-link: 63% to 96%). In trials with no linked publication, we were able to find publications 44% of the time (NPV=56%) by searching PubMed. This low NPV shows that there are potentially numerous publications that should have been formally linked with the trials. Our results indicate that existing trial registry and publisher policies may not be fully enforced. We suggest some automated methods for improving link quality. PMID:23304310

  2. Identifying Factors That May Influence Decision-Making Related to the Distribution of Patients During a Mass Casualty Incident.

    PubMed

    Hall, Trevor Nt; McDonald, Andrew; Peleg, Kobi

    2017-09-18

    We aimed to identify and seek agreement on factors that may influence decision-making related to the distribution of patients during a mass casualty incident. A qualitative thematic analysis of a literature review identified 56 unique factors related to the distribution of patients in a mass casualty incident. A modified Delphi study was conducted and used purposive sampling to identify peer reviewers that had either (1) a peer-reviewed publication within the area of disaster management or (2) disaster management experience. In round one, peer reviewers ranked the 56 factors and identified an additional 8 factors that resulted in 64 factors being ranked during the two-round Delphi study. The criteria for agreement were defined as a median score greater than or equal to 7 (on a 9-point Likert scale) and a percentage distribution of 75% or greater of ratings being in the highest tertile. Fifty-four disaster management peer reviewers, with hospital and prehospital practice settings most represented, assessed a total of 64 factors, of which 29 factors (45%) met the criteria for agreement. Agreement from this formative study suggests that certain factors are influential to decision-making related to the distribution of patients during a mass casualty incident. (Disaster Med Public Health Preparedness. 2017; page 1 of 8).

  3. Multivariate Modeling Identifies Neutrophil- and Th17-Related Factors as Differential Serum Biomarkers of Chronic Murine Colitis

    PubMed Central

    McBee, Megan E.; Zeng, Yu; Parry, Nicola; Nagler, Cathryn R.; Tannenbaum, Steven R.

    2010-01-01

    Background Diagnosis of chronic intestinal inflammation, which characterizes inflammatory bowel disease (IBD), along with prediction of disease state is hindered by the availability of predictive serum biomarker. Serum biomarkers predictive of disease state will improve trials for therapeutic intervention, and disease monitoring, particularly in genetically susceptible individuals. Chronic inflammation during IBD is considered distinct from infectious intestinal inflammation thereby requiring biomarkers to provide differential diagnosis. To address whether differential serum biomarkers could be identified in murine models of colitis, immunological profiles from both chronic spontaneous and acute infectious colitis were compared and predictive serum biomarkers identified via multivariate modeling. Methodology/Principal Findings Discriminatory multivariate modeling of 23 cytokines plus chlorotyrosine and nitrotyrosine (protein adducts from reactive nitrogen species and hypochlorite) in serum and tissue from two murine models of colitis was performed to identify disease-associated biomarkers. Acute C. rodentium-induced colitis in C57BL/6J mice and chronic spontaneous Helicobacter-dependent colitis in TLR4−/− x IL-10−/− mice were utilized for evaluation. Colon profiles of both colitis models were nearly identical with chemokines, neutrophil- and Th17-related factors highly associated with intestinal disease. In acute colitis, discriminatory disease-associated serum factors were not those identified in the colon. In contrast, the discriminatory predictive serum factors for chronic colitis were neutrophil- and Th17-related factors (KC, IL-12/23p40, IL-17, G-CSF, and chlorotyrosine) that were also elevated in colon tissue. Chronic colitis serum biomarkers were specific to chronic colitis as they were not discriminatory for acute colitis. Conclusions/Significance Immunological profiling revealed strikingly similar colon profiles, yet distinctly different serum

  4. Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)-variants in the spellings of drug names in PubMed: a database review.

    PubMed

    Ferner, Robin E; Aronson, Jeffrey K

    2016-12-14

     To examine how misspellings of drug names could impede searches for published literature.  Database review.  PubMed.  The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names-the international non-proprietary names, variant names-deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants-variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for "standard name[tw]" and "variant name[tw] NOT standard name[tw]."  The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in "in," "ine," or "micin" were commonly misspelt. Failing to search for hidden reference variants of "gentamicin," "amitriptyline," "mirtazapine," and "trazodone" would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, "No-el", was rare; variants of "X-miss" were rarer.  When performing searches, researchers should include misspellings of drug names among their search terms. Published by the BMJ Publishing Group Limited. For

  5. Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)—variants in the spellings of drug names in PubMed: a database review

    PubMed Central

    Aronson, Jeffrey K

    2016-01-01

    Objective To examine how misspellings of drug names could impede searches for published literature. Design Database review. Data source PubMed. Review methods The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names—the international non-proprietary names, variant names—deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants—variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for “standard name[tw]” and “variant name[tw] NOT standard name[tw].” Results The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in “in,” “ine,” or “micin” were commonly misspelt. Failing to search for hidden reference variants of “gentamicin,” “amitriptyline,” “mirtazapine,” and “trazodone” would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, “No-el”, was rare; variants of “X-miss” were rarer. Conclusion When performing searches, researchers should include

  6. Four Closely Related HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Identified in East China.

    PubMed

    Li, Fan; Li, Yuxueyun; Feng, Yi; Hu, Jing; Ruan, Yuhua; Xing, Hui; Shao, Yiming

    2017-07-01

    Five near full-length genomes of novel second-generation HIV-1 recombinant virus (JS150021, JS150029, JS150129, JS150132, and AH150183) were identified from five HIV-positive people in Jiangsu and Anhui province, east China. Phylogenic analyses showed that these five sequences are all composed of two well-established circulating recombinant forms (CRFs) CRF07_BC and CRF01_AE, grouped into four new discovered recombinant forms, which show several very similar but not identical recombinant breakpoints. The four recombinant forms are also identified to be a sort of family or related viruses, seems to be the results of different recombination events. The emergence of a serious new closely related CRF07_BC/CRF01_AE recombinant strain indicates the increasing complexity of sexual transmission of the HIV-1 epidemic in China.

  7. Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

    PubMed Central

    Yang, Tsun-Po; Pidsley, Ruth; Nisbet, James; Glass, Daniel; Mangino, Massimo; Zhai, Guangju; Zhang, Feng; Valdes, Ana; Shin, So-Youn; Dempster, Emma L.; Murray, Robin M.; Grundberg, Elin; Hedman, Asa K.; Nica, Alexandra; Small, Kerrin S.; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Mill, Jonathan; Spector, Tim D.; Deloukas, Panos

    2012-01-01

    Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype–phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a

  8. Denaturing HPLC-identified novel FBN1 mutations, polymorphisms, and sequence variants in Marfan syndrome and related connective tissue disorders.

    PubMed

    Liu, W O; Oefner, P J; Qian, C; Odom, R S; Francke, U

    Marfan syndrome (MFS), a common connective tissue disorder, is caused by fibrillin-1 (FBN1) mutations that are scattered throughout the gene and are largely unique to individual families. Mutation detection in this large gene of 65 exons is a considerable technical challenge. To develop an efficient method capable of identifying all possible mutations in this gene, we have explored the use of a novel denaturing high-performance liquid chromatography (DHPLC) system. This technique compares two or more chromosomes as a mixture of denatured and reannealed PCR amplicons. Under partially denaturing conditions, heteroduplexes can be separated from homoduplexes. A panel of 94 DNA samples from individuals with MFS or related connective tissue disorders was screened exon-by-exon by this method. A total of 66 unique heteroduplex profiles was identified. Sequencing of the amplicons detected 37 novel and two previously reported mutations, as well as 15 novel and 10 known polymorphisms or unique sequence variants that are probably of no clinical significance. Of the 34 mutations found in definitive MFS cases, 16 were identified in the 21 samples that had not been screened before (76% detection rate) and 17/40 (43%) were in samples previously screened by other mutation detection methods. In 32 individuals with MFS-related phenotypes, five FBN1 mutations were identified (16%). Our results demonstrate the power of the DHPLC method to detect FBN1 mutations. It should be applicable for mutation screening in any gene in a large population.

  9. Quantitative trait loci analysis of flowering time related traits identified in recombinant inbred lines of cowpea (Vigna unguiculata).

    PubMed

    Andargie, Mebeasealassie; Pasquet, Remy S; Muluvi, Geoffrey M; Timko, Michael P

    2013-05-01

    Flowering time is a major adaptive trait in plants and an important selection criterion in the breeding for genetic improvement of crop species. QTLs for the time of flower opening and days to flower were identified in a cross between a short duration domesticated cowpea (Vigna unguiculata (L.) Walp.) variety, 524B, and a relatively long duration wild accession, 219-01. A set of 159 F7 lines was grown under greenhouse conditions and scored for the flowering time associated phenotypes of time of flower opening and days to flower. Using a LOD threshold of 2.0, putative QTLs were identified and placed on a linkage map consisting of 202 SSR markers and four morphological loci. A total of five QTLs related to the time of flower opening were identified, accounting for 8.8%-29.8% of the phenotypic variation. Three QTLs for days to flower were detected, accounting for 5.7%-18.5% of the phenotypic variation. The major QTL of days to flower and time of flower opening were both mapped on linkage group 1. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for developing an efficient way to restrain the gene flow between the cultivated and wild plants.

  10. A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations.

    PubMed

    Wang, Wei; Haerian, Krystl; Salmasian, Hojjat; Harpaz, Rave; Chase, Herbert; Friedman, Carol

    2011-01-01

    Adverse drug events (ADEs) create a serious problem causing substantial harm to patients. An executable standardized knowledgebase of drug-ADE relations which is publicly available would be valuable so that it could be used for ADE detection. The literature is an important source that could be used to generate a knowledgebase of drug-ADE pairs. In this paper, we report on a method that automatically determines whether a specific adverse event (AE) is caused by a specific drug based on the content of PubMed citations. A drug-ADE classification method was initially developed to detect neutropenia based on a pre-selected set of drugs. This method was then applied to a different set of 76 drugs to determine if they caused neutropenia. For further proof of concept this method was applied to 48 drugs to determine whether they caused another AE, myocardial infarction. Results showed that AUROC was 0.93 and 0.86 respectively.

  11. Bibliometric analysis of the Korean Journal of Parasitology: measured from SCI, PubMed, Scopus, and Synapse databases.

    PubMed

    Lee, Choon Shil

    2009-10-01

    The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indices were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades.

  12. Bibliometric Analysis of the Korean Journal of Parasitology: Measured from SCI, PubMed, Scopus, and Synapse Databases

    PubMed Central

    2009-01-01

    The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indixes were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades. PMID:19885331

  13. The trend of indexed papers in PubMed covering different aspects of self-immolation.

    PubMed

    Rezaeian, Mohsen

    2014-01-01

    Self-immolation is a fatal and devastating method of committing suicide used around the world. The chief aim of the present article is to look at the trend of indexed papers in PubMed covering different aspects of self-immolation. PubMed search engine (http://www.ncbi.nlm.nih.gov) was searched by using six keywords i.e. "self-immolation", "self-inflicted burn", "self-burning", "self-incineration", "suicidal burns" and "suicide by burning". These keywords should appear either in the title or the abstract of the articles. The time frame was set as to retrieve papers expanding from early indexing time up to end of the year 2011. Based on the search strategy 132 papers were retrieved from these total numbers; 12 (9%) were categorized as review papers; 24 (18%) as case reports and the rest 96 (73%) were original studies. It seems that the number of papers increased during the years of investigations and the highest indexed papers i.e. 14 (10.6%) belonged to the year 2011. While most journals, published only one article the highest indexed papers i.e. 35 (26.5%) belonged to Burns. There was an increasing trend in the number of self-immolation articles indexed in PubMed since 1965. Three journals i.e. Burns, Journal of Burn Care and Rehabilitation and Journal of Forensic Sciences hosted for more than 37% of all those indexed articles. However, given the increasing trend of self-immolation still more studies are needed to shed light on the diverse aspects of this appalling human behavior.

  14. [Google and PubMed for physicians: how to find information without getting lost].

    PubMed

    Muñoz Núñez, C F; Sendra Portero, F

    2013-06-01

    Searching on Internet looking for clinically relevant medical information, used as a clinical decision aid tool, for self-learning or for research, is currently a common practice in Radiology. This task has been strengthened by the technological environment where radiologists work with direct access to information sources from the Workstation. The aim of this paper is to review the basic features of information searching tools in order to understand their functions and to optimize medical information searching on Internet. Google, Google Scholar and PubMed are reviewed as models for that purpose.

  15. PubMed, The New York Times and The Chicago Tribune as Tools for Teaching Genetics

    PubMed Central

    Strauss, Bernard S.

    2005-01-01

    An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. PMID:16143615

  16. Beyond PubMed: Searching the “Grey Literature” for Clinical Trial Results

    PubMed Central

    2014-01-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the “grey literature.” Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites. PMID:25337445

  17. Beyond PubMed: Searching the "Grey Literature" for Clinical Trial Results.

    PubMed

    Citrome, Leslie

    2014-07-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the "grey literature." Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites.

  18. Health-related quality of life among veterans in addictions treatment: identifying behavioral targets for future intervention

    PubMed Central

    Oppezzo, Marily A.; Michalek, Anne K.; Delucchi, Kevin; Baiocchi, Michael T. M.; Barnett, Paul G.

    2016-01-01

    Background US veterans report lower health-related quality of life (HRQoL) relative to the general population. Identifying behavioral factors related to HRQoL that are malleable to change may inform interventions to improve well-being in this vulnerable group. Purpose The current study sought to characterize HRQoL in a largely male sample of veterans in addictions treatment, both in relation to US norms and in association with five recommended health behavior practices: regularly exercising, managing stress, having good sleep hygiene, consuming fruits and vegetables, and being tobacco free. Methods We assessed HRQoL with 250 veterans in addictions treatment (96 % male, mean age 53, range 24–77) using scales from four validated measures. Data reduction methods identified two principal components reflecting physical and mental HRQoL. Model testing of HRQoL associations with health behaviors adjusted for relevant demographic and treatment-related covariates. Results Compared to US norms, the sample had lower HRQoL scores. Better psychological HRQoL was associated with higher subjective social standing, absence of pain or trauma, lower alcohol severity, and monotonically with the sum of health behaviors (all p < 0.05). Specifically, psychological HRQoL was associated with regular exercise, stress management, and sleep hygiene. Regular exercise also related to better physical HRQoL. The models explained >40 % of the variance in HRQoL. Conclusions Exercise, sleep hygiene, and stress management are strongly associated with HRQoL among veterans in addictions treatment. Future research is needed to test the effect of interventions for improving well-being in this high-risk group. PMID:26886926

  19. Identifying mismatches between institutional perceptions of water-related risk drivers and water management strategies in three river basin areas

    NASA Astrophysics Data System (ADS)

    Räsänen, Aleksi; Juhola, Sirkku; Monge Monge, Adrián; Käkönen, Mira; Kanninen, Markku; Nygren, Anja

    2017-07-01

    Water-related risks and vulnerabilities are driven by variety of stressors, including climate and land use change, as well as changes in socio-economic positions and political landscapes. Hence, water governance, which addresses risks and vulnerabilities, should target multiple stressors. We analyze the institutional perceptions of the drivers and strategies for managing water-related risks and vulnerabilities in three regionally important river basin areas located in Finland, Mexico, and Laos. Our analysis is based on data gathered through participatory workshops and complemented by qualitative content analysis of relevant policy documents. The identified drivers and proposed risk reduction strategies showed the multidimensionality and context-specificity of water-related risks and vulnerabilities across study areas. Most of the identified drivers were seen to increase risks, but some of the drivers were positive trends, and drivers also included also policy instruments that can both increase or decrease risks. Nevertheless, all perceived drivers were not addressed with suggested risk reduction strategies. In particular, most of the risk reduction strategies were incremental adjustments, although many of the drivers classified as most important were large-scale trends, such as climate change, land use changes and increase in foreign investments. We argue that there is a scale mismatch between the identified drivers and suggested strategies, which questions the opportunity to manage the drivers by single-scale incremental adjustments. Our study suggests that for more sustainable risk and vulnerability reduction, the root causes of water-related risks and vulnerabilities should be addressed through adaptive multi-scale governance that carefully considers the context-specificity and the multidimensionality of the associated drivers and stressors.

  20. Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

    PubMed Central

    Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J.

    2011-01-01

    The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing. PMID:21448266

  1. Finding complex biological relationships in recent PubMed articles using Bio-LDA.

    PubMed

    Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J

    2011-03-23

    The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.

  2. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments.

    PubMed

    Zhao, Min; Kong, Lei; Qu, Hong

    2014-02-25

    Although the intelligence quotient (IQ) is the most popular intelligence test in the world, little is known about the underlying biological mechanisms that lead to the differences in human. To improve our understanding of cognitive processes and identify potential biomarkers, we conducted a comprehensive investigation of 158 IQ-related genes selected from the literature. A genomic distribution analysis demonstrated that IQ-related genes were enriched in seven regions of chromosome 7 and the X chromosome. In addition, these genes were enriched in target lists of seven transcription factors and sixteen microRNAs. Using a network-based approach, we further reconstructed an IQ-related pathway from known human pathway interaction data. Based on this reconstructed pathway, we incorporated enriched drugs and described the importance of dopamine and norepinephrine systems in IQ-related biological process. These findings not only reveal several testable genes and processes related to IQ scores, but also have potential therapeutic implications for IQ-related mental disorders.

  3. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments

    PubMed Central

    Zhao, Min; Kong, Lei; Qu, Hong

    2014-01-01

    Although the intelligence quotient (IQ) is the most popular intelligence test in the world, little is known about the underlying biological mechanisms that lead to the differences in human. To improve our understanding of cognitive processes and identify potential biomarkers, we conducted a comprehensive investigation of 158 IQ-related genes selected from the literature. A genomic distribution analysis demonstrated that IQ-related genes were enriched in seven regions of chromosome 7 and the X chromosome. In addition, these genes were enriched in target lists of seven transcription factors and sixteen microRNAs. Using a network-based approach, we further reconstructed an IQ-related pathway from known human pathway interaction data. Based on this reconstructed pathway, we incorporated enriched drugs and described the importance of dopamine and norepinephrine systems in IQ-related biological process. These findings not only reveal several testable genes and processes related to IQ scores, but also have potential therapeutic implications for IQ-related mental disorders. PMID:24566931

  4. Identifying Grade/Stage-Related Active Modules in Human Co-regulatory Networks: A Case Study for Breast Cancer

    PubMed Central

    Feng, Chenchen; Li, Wan; Wang, Hong; Zhang, Liangcai; Jia, Xu; Miao, Zhengqiang; Qu, Xiaoli; Li, Weiguo; He, Weiming

    2012-01-01

    Abstract The histological grade/stage of tumor is widely acknowledged as an important clinical prognostic factor for cancer progression. Recent experimental studies have explored the following two topics at the molecular level: (1) whether or not gene expression levels vary by different degrees among different tumor grades/stages, and (2) whether some well-defined modules could distinguish one grade/stage from another. In this article, using breast cancer as an example, we investigated this topic and identified grade/stage-related active modules under the framework of a weighted network integrated from a human protein interaction network and a transcriptional regulatory network. Our results enabled us to draw the conclusion that the gene expression profile could provide more clues about tumor grade, but reveals less evidence about tumor stage. In addition, we found that our modular biomarker method had additional advantages in identifying some tumor grade/stage-related genes with slightly altered expression. According to our case study, the framework we introduced could be used for other cancers to identify their modules during grading or staging. PMID:23215806

  5. PubMed Informer: monitoring MEDLINE/PubMed through e-mail alerts, SMS, PDA downloads and RSS feeds.

    PubMed

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices.

  6. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  7. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    PubMed Central

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-01-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions. PMID:27185415

  8. Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease.

    PubMed

    Liu, Jing; Jing, Ling; Tu, Xilin

    2016-03-05

    The analysis of the potential molecule targets of coronary artery disease (CAD) is critical for understanding the molecular mechanisms of disease. However, studies of global microarray gene co-expression analysis of CAD still remain limited. Microarray data of CAD (GSE23561) were downloaded from Gene Expression Omnibus, including peripheral blood samples from CAD patients (n = 6) and controls (n = 9). Limma package in R was used to identify the differentially expressed genes (DEGs) between CAD and control samples. Using weighted gene co-expression network analysis (WGCNA) package in R, WGCNA was performed to identify significant modules in the network. Then, functional and pathway enrichment analyses were conducted for genes in the most significant module using DAVID software. Moreover, hub genes in the module were analyzed by isubpathwayminer package in R and GenCLiP 2.0 tool to identify the significant sub-pathways. Total 3711 DEGs and 21 modules for them were identified in CAD samples. The most significant module was associated with the pathways of hypertrophic cardiomyopathy and membrane related functions. In addition, the top 30 hub genes with high connectivity in the module were selected, and two genes (G6PD and S100A7) were taken as key molecules via sub-pathway screening and data mining. A module associated with hypertrophic cardiomyopathy pathway was detected in CAD samples. G6PD and S100A7 were the potential targets in CAD. Our finding might provide novel insight into the underlying molecular mechanism of CAD.

  9. Assessing Student Pharmacists’ Ability to Identify Drug-Related Problems in Patients Within a Patient-Centered Medical Home

    PubMed Central

    Bulkley, Christina F.; Truong, Teresa; Carter, Sandra M.

    2014-01-01

    Objective. To quantify, describe, and categorize patient drug-related problems (DRPs) and recommendations identified by fourth-year (P4) student pharmacists during a live medication reconciliation activity within a patient-centered medical home (PCMH). Methods. Fourth-year student pharmacists conducted chart reviews, identified and documented DRPs, obtained live medication histories, and immediately provided findings and recommendations to the attending physicians. Documentation of DRPs and recommendations were analyzed retrospectively. Results. Thirty-eight students completed 99 medication reconciliation sessions from June 2011 to October 2012 during their advanced pharmacy practice experience (APPE). The students obtained 676 patient medication histories and identified or intervened on 1308 DRPs. The most common DRPs reported were incomplete medication list and diagnostic/laboratory testing needed. Physicians accepted 1,018 (approximately 78%) recommendations. Conclusion. Student pharmacists successfully identified and reduced DRPs through a live medication reconciliation process within an academic-based PCMH model. Their medication history-taking skills improved and medication use was optimized. PMID:24558274

  10. Identifying the tobacco related free radicals by UPCC-QTOF-MS with radical trapping method in mainstream cigarette smoke.

    PubMed

    Wang, Ying; Liu, Misha; Zhu, Yingjing; Cheng, Kuan; Da Wu; Liu, Baizhan; Li, Fengting

    2016-11-01

    Tobacco related free radicals (TFRs) in the cigarette smoke are specific classes of hazardous compounds that merit concern. In this study, we developed a hybrid method to identify TFRs directly based on ultra-performance convergence chromatography with a quadrupole time-of-flight mass spectrometry (UPCC-QTOF MS) combined spin trapping technique. The short-lived TFRs were stabilized successfully in situ through spin trapping procedure and UPCC was applied to facilitate efficient separation of complex derivative products. Coupling of orthogonal partial least squares discriminant analysis (OPLS-DA), UPCC-QTOF MS system enabled us to identify specific potential TFRs with exact chemical formula. Moreover, computational stimulations have been carried out to evaluate the optimized stability of TFRs. This work is a successful demonstration for the application of an advanced hyphenated technique for separation of TFRs with short detection time (less than 7min) and high throughput. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Identifying Decision-Makers’ Science Needs for Adaptation to Climate-Related Impacts on Forest Ecosystem Services

    NASA Astrophysics Data System (ADS)

    Gordon, E.; Lukas, J.

    2009-12-01

    Through the Western Water Assessment RISA program, we are conducting a research project that will produce science synthesis information to help local, state, and federal decision-makers in Colorado and Wyoming develop adaptation strategies to deal with climate-related threats to forest ecosystem services, in particular bark beetle infestations and stand-replacing wildfires. We begin by using the problem orientation framework, a policy sciences methodology, to understand how decision-makers can most effectively address policy problems that threaten the attainment of socially accepted goals. By applying this framework to the challenges facing decision-makers, we more accurately identify specific areas where scientific research can improve decision-making. WWA researchers will next begin to connect decision-makers with relevant scientific literature and identify specific areas of future scientific research that will be most effective at addressing their needs.

  12. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.

    PubMed

    Okada, Yukinori; Sim, Xueling; Go, Min Jin; Wu, Jer-Yuarn; Gu, Dongfeng; Takeuchi, Fumihiko; Takahashi, Atsushi; Maeda, Shiro; Tsunoda, Tatsuhiko; Chen, Peng; Lim, Su-Chi; Wong, Tien-Yin; Liu, Jianjun; Young, Terri L; Aung, Tin; Seielstad, Mark; Teo, Yik-Ying; Kim, Young Jin; Lee, Jong-Young; Han, Bok-Ghee; Kang, Daehee; Chen, Chien-Hsiun; Tsai, Fuu-Jen; Chang, Li-Ching; Fann, S-J Cathy; Mei, Hao; Rao, Dabeeru C; Hixson, James E; Chen, Shufeng; Katsuya, Tomohiro; Isono, Masato; Ogihara, Toshio; Chambers, John C; Zhang, Weihua; Kooner, Jaspal S; Albrecht, Eva; Yamamoto, Kazuhiko; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki; Kato, Norihiro; He, Jiang; Chen, Yuan-Tsong; Cho, Yoon Shin; Tai, E-Shyong; Tanaka, Toshihiro

    2012-07-15

    Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

  13. Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

    PubMed Central

    Persoons, Antoine; Morin, Emmanuelle; Delaruelle, Christine; Payen, Thibaut; Halkett, Fabien; Frey, Pascal; De Mita, Stéphane; Duplessis, Sébastien

    2014-01-01

    Melampsora larici-populina is a fungal pathogen responsible for foliar rust disease on poplar trees, which causes damage to forest plantations worldwide, particularly in Northern Europe. The reference genome of the isolate 98AG31 was previously sequenced using a whole genome shotgun strategy, revealing a large genome of 101 megabases containing 16,399 predicted genes, which included secreted protein genes representing poplar rust candidate effectors. In the present study, the genomes of 15 isolates collected over the past 20 years throughout the French territory, representing distinct virulence profiles, were characterized by massively parallel sequencing to assess genetic variation in the poplar rust fungus. Comparison to the reference genome revealed striking structural variations. Analysis of coverage and sequencing depth identified large missing regions between isolates related to the mating type loci. More than 611,824 single-nucleotide polymorphism (SNP) positions were uncovered overall, indicating a remarkable level of polymorphism. Based on the accumulation of non-synonymous substitutions in coding sequences and the relative frequencies of synonymous and non-synonymous polymorphisms (i.e., PN/PS), we identify candidate genes that may be involved in fungal pathogenesis. Correlation between non-synonymous SNPs in genes encoding secreted proteins (SPs) and pathotypes of the studied isolates revealed candidate genes potentially related to virulences 1, 6, and 8 of the poplar rust fungus. PMID:25309551

  14. Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.).

    PubMed

    Hewitt, Seanna; Kilian, Benjamin; Hari, Ramyya; Koepke, Tyson; Sharpe, Richard; Dhingra, Amit

    2017-01-01

    Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.

  15. MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

    PubMed

    Theodosiou, T; Vizirianakis, I S; Angelis, L; Tsaftaris, A; Darzentas, N

    2011-12-01

    PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or productively utilized. The motivation behind this work was the discovery of unanticipated information through the appropriate ranking of MeSH term pairs and, indirectly, documents. Such information can be useful in guiding novel research and following promising trends. A web-based tool, called MeSHy, was developed implementing a mainly statistical algorithm. The algorithm takes into account the frequencies of occurrences, concurrences, and the semantic similarities of MeSH terms in retrieved PubMed documents to create MeSH term pairs. These are then scored and ranked, focusing on their unexpectedly frequent or infrequent occurrences. MeSHy presents results through an online interactive interface facilitating further manipulation through filtering and sorting. The results themselves include the MeSH term pairs, along with MeSH categories, the score, and document IDs, all of which are hyperlinked for convenience. To highlight the applicability of the tool, we report the findings of an expert in the pharmacology field on querying the molecularly-targeted drug imatinib and nutrition-related flavonoids. To the best of our knowledge, MeSHy is the first publicly available tool able to directly provide such a different perspective on the complex nature of published work. Implemented in Perl and served by Apache2 at http://bat.ina.certh.gr/tools/meshy/ with all major browsers supported. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Genome-Wide Temporal Expression Profiling in Caenorhabditis elegans Identifies a Core Gene Set Related to Long-Term Memory.

    PubMed

    Freytag, Virginie; Probst, Sabine; Hadziselimovic, Nils; Boglari, Csaba; Hauser, Yannick; Peter, Fabian; Gabor Fenyves, Bank; Milnik, Annette; Demougin, Philippe; Vukojevic, Vanja; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

    2017-07-12

    The identification of genes related to encoding, storage, and retrieval of memories is a major interest in neuroscience. In the current study, we analyzed the temporal gene expression changes in a neuronal mRNA pool during an olfactory long-term associative memory (LTAM) in Caenorhabditis elegans hermaphrodites. Here, we identified a core set of 712 (538 upregulated and 174 downregulated) genes that follows three distinct temporal peaks demonstrating multiple gene regulation waves in LTAM. Compared with the previously published positive LTAM gene set (Lakhina et al., 2015), 50% of the identified upregulated genes here overlap with the previous dataset, possibly representing stimulus-independent memory-related genes. On the other hand, the remaining genes were not previously identified in positive associative memory and may specifically regulate aversive LTAM. Our results suggest a multistep gene activation process during the formation and retrieval of long-term memory and define general memory-implicated genes as well as conditioning-type-dependent gene sets.SIGNIFICANCE STATEMENT The identification of genes regulating different steps of memory is of major interest in neuroscience. Identification of common memory genes across different learning paradigms and the temporal activation of the genes are poorly studied. Here, we investigated the temporal aspects of Caenorhabditis elegans gene expression changes using aversive olfactory associative long-term memory (LTAM) and identified three major gene activation waves. Like in previous studies, aversive LTAM is also CREB dependent, and CREB activity is necessary immediately after training. Finally, we define a list of memory paradigm-independent core gene sets as well as conditioning-dependent genes. Copyright © 2017 the authors 0270-6474/17/376661-12$15.00/0.

  17. Last drinks: A study of rural emergency department data collection to identify and target community alcohol-related violence.

    PubMed

    Miller, Peter; Droste, Nicolas; Baker, Tim; Gervis, Cathreena

    2015-06-01

    The present study summarises the methodology and findings of a pilot project designed to measure the sources and locations of alcohol-related harm by implementing anonymised 'last drinks' questions in the ED of a rural community. 'Last drinks' questions were added to computerised triage systems at South West Healthcare ED in rural Warrnambool, Victoria, from 1 November 2013 to 3 July 2014. For all injury presentations aged 15 years or older, attendees were asked whether alcohol was consumed in the 12 h prior to injury, how many standard drinks were consumed, where they purchased most of the alcohol and where they consumed the last alcoholic drink. From 3692 injury attendances, 10.8% (n = 399) reported consuming alcohol in the 12 h prior to injury. 'Last drinks' data collection was 100% complete for participants who reported alcohol use prior to injury. Approximately two-thirds (60.2%) of all alcohol-related presentations had purchased their alcohol at packaged liquor outlets. During high-alcohol hours, alcohol-related injuries accounted for 36.1% (n = 101) of all ED injury presentations, and in total 41.7% of alcohol-related attendances during these hours reported consuming last drinks at identifiable hotels, bars, nightclubs or restaurants, or identifiable public areas/events. This pilot demonstrates the feasibility and reliability of implementing sustainable 'last drinks' data collection methods in the ED, and the ability to effectively map the source of alcohol-related ED attendances in a rural community. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

  18. Feasibility of a self-administered survey to identify primary care patients at risk of medication-related problems.

    PubMed

    Makowsky, Mark J; Cave, Andrew J; Simpson, Scot H

    2014-01-01

    Pharmacists working in primary care clinics are well positioned to help optimize medication management of community-dwelling patients who are at high risk of experiencing medication-related problems. However, it is often difficult to identify these patients. Our objective was to test the feasibility of a self-administered patient survey, to facilitate identification of patients at high risk of medication-related problems in a family medicine clinic. We conducted a cross-sectional, paper-based survey at the University of Alberta Hospital Family Medicine Clinic in Edmonton, Alberta, which serves approximately 7,000 patients, with 25,000 consultations per year. Adult patients attending the clinic were invited to complete a ten-item questionnaire, adapted from previously validated surveys, while waiting to be seen by the physician. Outcomes of interest included: time to complete the questionnaire, staff feedback regarding impact on workflow, and the proportion of patients who reported three or more risk factors for medication-related problems. The questionnaire took less than 5 minutes to complete, according to the patient's report on the last page of the questionnaire. The median age (and interquartile range) of respondents was 57 (45-69) years; 59% were women; 47% reported being in very good or excellent health; 43 respondents of 100 had three or more risk factors, and met the definition for being at high risk of a medication-related problem. Distribution of a self-administered questionnaire did not disrupt patients, or the clinic workflow, and identified an important proportion of patients at high risk of medication-related problems.

  19. Using data sources beyond PubMed has a modest impact on the results of systematic reviews of therapeutic interventions.

    PubMed

    Halladay, Christopher W; Trikalinos, Thomas A; Schmid, Ian T; Schmid, Christopher H; Dahabreh, Issa J

    2015-09-01

    Searching multiple sources when conducting systematic reviews is considered good practice. We aimed to investigate the impact of using sources beyond PubMed in systematic reviews of therapeutic interventions. We randomly selected 50 Cochrane reviews that searched the PubMed (or MEDLINE) and EMBASE databases and included a meta-analysis of ≥10 studies. We checked whether each eligible record in each review (n = 2,700) was retrievable in PubMed and EMBASE. For the first-listed meta-analysis of ≥10 studies in each review, we examined whether excluding studies not found in PubMed affected results. A median of one record per review was indexed in EMBASE but not in PubMed; a median of four records per review was not indexed in PubMed or EMBASE. Meta-analyses included a median of 13.5 studies; a median of zero studies per meta-analysis was indexed in EMBASE but not in PubMed; a median of one study per meta-analysis was not indexed in PubMed or EMBASE. Meta-analysis using only PubMed-indexed vs. all available studies led to a different conclusion in a single case (on the basis of conventional criteria for statistical significance). In meta-regression analyses, effects in PubMed- vs. non-PubMed-indexed studies were statistically significantly different in a single data set. For systematic reviews of the effects of therapeutic interventions, gains from searching sources beyond PubMed, and from searching EMBASE in particular are modest. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Glomerular disease search filters for Pubmed, Ovid Medline, and Embase: a development and validation study.

    PubMed

    Hildebrand, Ainslie M; Iansavichus, Arthur V; Lee, Christopher W C; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Hladunewich, Michelle A; Clark, William F; Cattran, Daniel C; Garg, Amit X

    2012-06-06

    Tools to enhance physician searches of Medline and other bibliographic databases have potential to improve the application of new knowledge in patient care. This is particularly true for articles about glomerular disease, which are published across multiple disciplines and are often difficult to track down. Our objective was to develop and test search filters for PubMed, Ovid Medline, and Embase that allow physicians to search within a subset of the database to retrieve articles relevant to glomerular disease. We used a diagnostic test assessment framework with development and validation phases. We read a total of 22,992 full text articles for relevance and assigned them to the development or validation set to define the reference standard. We then used combinations of search terms to develop 997,298 unique glomerular disease filters. Outcome measures for each filter included sensitivity, specificity, precision, and accuracy. We selected optimal sensitive and specific search filters for each database and applied them to the validation set to test performance. High performance filters achieved at least 93.8% sensitivity and specificity in the development set. Filters optimized for sensitivity reached at least 96.7% sensitivity and filters optimized for specificity reached at least 98.4% specificity. Performance of these filters was consistent in the validation set and similar among all three databases. PubMed, Ovid Medline, and Embase can be filtered for articles relevant to glomerular disease in a reliable manner. These filters can now be used to facilitate physician searching.

  1. LitInspector: literature and signal transduction pathway mining in PubMed abstracts.

    PubMed

    Frisch, Matthias; Klocke, Bernward; Haltmeier, Manuela; Frech, Kornelie

    2009-07-01

    LitInspector is a literature search tool providing gene and signal transduction pathway mining within NCBI's PubMed database. The automatic gene recognition and color coding increases the readability of abstracts and significantly speeds up literature research. A main challenge in gene recognition is the resolution of homonyms and rejection of identical abbreviations used in a 'non-gene' context. LitInspector uses automatically generated and manually refined filtering lists for this purpose. The quality of the LitInspector results was assessed with a published dataset of 181 PubMed sentences. LitInspector achieved a precision of 96.8%, a recall of 86.6% and an F-measure of 91.4%. To further demonstrate the homonym resolution qualities, LitInspector was compared to three other literature search tools using some challenging examples. The homonym MIZ-1 (gene IDs 7709 and 9063) was correctly resolved in 87% of the abstracts by LitInspector, whereas the other tools achieved recognition rates between 35% and 67%. The LitInspector signal transduction pathway mining is based on a manually curated database of pathway names (e.g. wingless type), pathway components (e.g. WNT1, FZD1), and general pathway keywords (e.g. signaling cascade). The performance was checked for 10 randomly selected genes. Eighty-two per cent of the 38 predicted pathway associations were correct. LitInspector is freely available at http://www.litinspector.org/.

  2. Geography of Africa biomedical publications: An analysis of 1996–2005 PubMed papers

    PubMed Central

    Uthman, Olalekan A; Uthman, Mubashir B

    2007-01-01

    Background Scientific publications play an important role in scientific process providing a key linkage between knowledge production and use. Scientific publishing activity worldwide over the past decades shows that most countries in Africa have low levels of publication. We sought to examine trends and contribution of different Africa subregions and individual countries as represented by the articles indexed by PubMed between 1996 and 2005. Results Research production in Africa is highly skewed; South Africa, Egypt, and Nigeria make up a striking 60% of the total number of articles indexed by PubMed between 1996 and 2005. When adjusted for population size smaller countries, such as The Gambia, Gabon and Botswana, were more productive than Nigeria and Kenya. The Gambia and Eritrea had better records when total production was adjusted for gross domestic product. The contribution of Africa to global research production was persistently low through the period studied. Conclusion In this study, we found that most populous and rich countries (such as South Africa, Egypt, and Nigeria) have correspondingly higher research production; but smaller countries can be productive. We noted continuous increases and reassuring trends in the production of research articles from all African subregions during the period 1996 – 2005. However, contribution of Africa to global research production was limited. PMID:17927837

  3. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

    PubMed Central

    Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

  4. Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach

    PubMed Central

    Yuan, Fei; Zhou, You; Wang, Meng; Yang, Jing; Wu, Kai; Lu, Changhong; Kong, Xiangyin; Cai, Yu-Dong

    2015-01-01

    Prostate cancer is a type of cancer that occurs in the male prostate, a gland in the male reproductive system. Because prostate cancer cells may spread to other parts of the body and can influence human reproduction, understanding the mechanisms underlying this disease is critical for designing effective treatments. The identification of as many genes and chemicals related to prostate cancer as possible will enhance our understanding of this disease. In this study, we proposed a computational method to identify new candidate genes and chemicals based on currently known genes and chemicals related to prostate cancer by applying a shortest path approach in a hybrid network. The hybrid network was constructed according to information concerning chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions. Many of the obtained genes and chemicals are associated with prostate cancer. PMID:26504486

  5. Residential treatment for combat-related posttraumatic stress disorder: identifying trajectories of change and predictors of treatment response.

    PubMed

    Currier, Joseph M; Holland, Jason M; Drescher, Kent D

    2014-01-01

    Combat-related posttraumatic stress disorder (PTSD) can be a difficult condition to treat and has been associated with serious medical and economic issues among U.S. military veterans. Distinguishing between treatment responders vs. non-responders in this population has become an important public health priority. This study was conducted to identify pre-treatment characteristics of U.S. veterans with combat-related PTSD that might contribute to favorable and unfavorable responses to high value treatments for this condition. This study focused on 805 patients who completed a VHA PTSD residential program between 2000 and 2007. These patients completed the PTSD Clinical Checklist at pre-treatment, post-treatment, and a four-month follow-up assessment. Latent growth curve analysis (LCGA) was incorporated to determine trajectories of changes in PTSD across these assessments and whether several key clinical concerns for this population were associated with their treatment responses. LCGA indicated three distinct trajectories in PTSD outcomes and identified several clinical factors that were prospectively linked with changes in veterans' posttraumatic symptomatology. When compared to a group with high PTSD symptom severity that decreased over the program but relapsed at follow-up (41%), the near half (48.8%) of the sample with an improving trajectory had less combat exposure and superior physical/mental health. However, when compared to a minority (10.2%) with relatively low symptomatology that also remained somewhat stable, patients in the improving group were younger and also reported greater combat exposure, poorer physical/mental health status, and more problems with substance abuse before the start of treatment. Findings suggest that veterans are most likely to benefit from residential treatment in an intermediate range of symptoms and risk factors, including PTSD symptom severity, history of combat exposure, and comorbid issues with physical/mental health

  6. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

  7. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews

    PubMed Central

    2013-01-01

    Background The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. Methods The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. Results GS’ overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Conclusions Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to

  8. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

    PubMed

    Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

    2013-12-23

    The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be

  9. Development and Assessment of A Diagnostic Tool to Identify Organic Chemistry Students' Alternative Conceptions Related to Acid Strength

    NASA Astrophysics Data System (ADS)

    McClary, LaKeisha M.; Lowery Bretz, Stacey

    2012-10-01

    The central goal of this study was to create a new diagnostic tool to identify organic chemistry students' alternative conceptions related to acid strength. Twenty years of research on secondary and college students' conceptions about acids and bases has shown that these important concepts are difficult for students to apply to qualitative problem solving. Yet, few published studies document how students' prior knowledge of acids influences their understanding of acid strength in organic chemistry contexts. We developed a nine-item multiple-tier, multiple-choice concept inventory to identify alternative conceptions that organic chemistry students hold about acid strength, to determine the prevalence of these conceptions, and to determine how strongly these conceptions bias student reasoning. We identified two significant alternative conceptions that organic chemistry students hold about acid strength. Students who answered items incorrectly were more confident about their answers than peers who answered items correctly, suggesting that after one semester of organic chemistry, students do not know what they do not know. Implications for the teaching of acid strength are discussed.

  10. Human Plasma Metabolomics Study across All Stages of Age-Related Macular Degeneration Identifies Potential Lipid Biomarkers.

    PubMed

    Laíns, Inês; Kelly, Rachel S; Miller, John B; Silva, Rufino; Vavvas, Demetrios G; Kim, Ivana K; Murta, Joaquim N; Lasky-Su, Jessica; Miller, Joan W; Husain, Deeba

    2017-08-31

    To characterize the plasma metabolomic profile of patients with age-related macular degeneration (AMD) using mass spectrometry (MS). Cross-sectional observational study. We prospectively recruited participants with a diagnosis of AMD and a control group (>50 years of age) without any vitreoretinal disease. All participants underwent color fundus photography, used for AMD diagnosis and staging, according to the Age-Related Eye Disease Study classification scheme. Fasting blood samples were collected and plasma was analyzed by Metabolon, Inc. (Durham, NC), using ultrahigh-performance liquid chromatography (UPLC) and high-resolution MS. Metabolon's hardware and software were used to identify peaks and control quality. Principal component analysis and multivariate regression were performed to assess differences in the metabolomic profiles of AMD patients versus controls, while controlling for potential confounders. For biological interpretation, pathway enrichment analysis of significant metabolites was performed using MetaboAnalyst. The primary outcome measures were levels of plasma metabolites in participants with AMD compared with controls and among different AMD severity stages. We included 90 participants with AMD (30 with early AMD, 30 with intermediate AMD, and 30 with late AMD) and 30 controls. Using UPLC and MS, 878 biochemicals were identified. Multivariate logistic regression identified 87 metabolites with levels that differed significantly between AMD patients and controls. Most of these metabolites (82.8%; n = 72), including the most significant metabolites, belonged to the lipid pathways. Analysis of variance revealed that of the 87 metabolites, 48 (55.2%) also were significantly different across the different stages of AMD. A significant enrichment of the glycerophospholipids pathway was identified (P = 4.7 × 10(-9)) among these metabolites. Participants with AMD have altered plasma metabolomic profiles compared with controls. Our data suggest

  11. Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis.

    PubMed

    Wei, Jinfen; Liu, Baosuo; Fan, Sigang; Li, Haimei; Chen, Mingqiang; Zhang, Bo; Su, Jiaqi; Meng, Zihao; Yu, Dahui

    2017-03-01

    The pearl oyster Pinctada fucata is commonly cultured for marine pearls in China. To culture pearls, a mantle piece from a donor pearl oyster is grafted with a nucleus into a receptor. This transplanted mantle piece may be rejected by the immune system of the recipient oyster, thus reducing the success of transplantation. However, there have been limited studies about the oyster's immune defense against allograft. In this study, hemocyte transcriptome analysis was performed to detect the immune responses to allograft in P. fucata at 0 h and 48 h after a transplant. The sequencing reaction produced 92.5 million reads that were mapped against the reference genome sequences of P. fucata. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify all immune-related differentially expressed genes (DEGs). Compared with patterns at 0 h, a total of 798 DEGs were identified, including 410 up-regulated and 388 down-regulated genes at 48 h. The expression levels of interleukin receptor and toll-like receptor in hemocytes were increased significantly 48 h post-transplant, indicating that the oyster immune response was induced. Finally, altered levels of 18 randomly selected immune-related DEGs were confirmed by quantitative real-time PCR (qRT-PCR). Our results provide the basis for further analysis of the immune rejection of allotransplantation.

  12. The Animadora Project: identifying factors related to the promotion of physical activity among Mexican Americans with diabetes.

    PubMed

    Ingram, Maia; Ruiz, Maricruz; Mayorga, Maria Theresa; Rosales, Cecilia

    2009-01-01

    There is a dearth of information about factors related to physical activity among Mexican-Americans with diabetes. Self-efficacy and social support are associated with physical activity; however, little is known about their roles within different cultural groups. Focus groups were used to identify factors that motivated walking. Two Mexican-American communities located in Tucson, Arizona. Individuals who attended diabetes education. A community-based provider organized walking groups with people who previously attended diabetes classes. Walkers participated in focus groups exploring themes related to their experiences. Self-efficacy, social support, and collective efficacy. Grounded theory was used to analyze focus group results using two rounds of analysis; the first identified references to self-efficacy and social support, and the second added collective efficacy as a theoretic basis for walking. Among 43 eligible participants, 20 participated in focus groups. Social support was expressed as commitment and companionship. Walkers demonstrated a high level of self-efficacy for walking. Development of group identity/social cohesion was also a motivator to walk. Collective efficacy emerged as an applicable theoretic model encompassing these themes and their interrelationship. Collective efficacy, or the belief that the group can improve their lives through collective effort, is a viable theoretic construct in the development of physical activity interventions targeting Mexican-Americans with diabetes.

  13. The Animadora Project: Identifying factors related to the promotion of physical activity among Mexican Americans with diabetes

    PubMed Central

    Ingram, Maia; Ruis, Maricruz; Mayorga, Maria Theresa; Rosales, Cecilia

    2015-01-01

    Purpose There is a dearth of information about factors related to physical activity among Mexican Americans with diabetes. Self efficacy and social support are associated with physical activity, however little is known about their role within different cultural groups. Design Focus groups were used to identify factors that motivate walking. Setting Two Mexican American communities located in Tucson, Arizona. Subjects Individuals who attended diabetes education. Intervention A community-based provider organized walking groups with people who previously attended diabetes classes. Walkers participated in focus groups exploring themes related to their experience. Measures Self efficacy, social support, and collective efficacy. Grounded theory was used to analyze focus group results using two rounds of analysis; the first identifying references to self efficacy and social support and the second adding collective efficacy as a theoretical basis for walking. Results Among 43 eligible participants, 20 participated in focus groups. Social support was expressed as commitment and companionship. Walkers demonstrated a high level of self efficacy for walking. Development of group identity/social cohesion was also a motivator to walk. Collective efficacy emerged as an applicable theoretical model encompassing these themes and their interrelationship. Conclusion Collective efficacy, or the belief that the group can improve their lives through collective effort, is a viable theoretical construct in the development of physical activity interventions targeting Mexican Americans with diabetes. PMID:19601479

  14. Epigenomic Elements Analyses for Promoters Identify ESRRG as a New Susceptibility Gene for Obesity-related Traits

    PubMed Central

    Dong, Shan-Shan; Guo, Yan; Zhu, Dong-Li; Chen, Xiao-Feng; Wu, Xiao-Ming; Shen, Hui; Chen, Xiang-Ding; Tan, Li-Jun; Tian, Qing; Deng, Hong-Wen; Yang, Tie-Lin

    2016-01-01

    OBJECTIVES With ENCODE epigenomic data and results from published genome-wide association studies (GWASs), we aimed to find regulatory signatures of obesity genes and discover novel susceptibility genes. METHODS Obesity genes were obtained from public GWASs databases and their promoters were annotated based on the regulatory elements information. Significantly enriched or depleted epigenomic elements in the promoters of obesity genes were evaluated and all human genes were then prioritized according to the existence of the selected elements to predict new candidate genes. Top ranked genes were subsequently applied to validate their associations with obesity-related traits in three independent in-house GWASs samples. RESULTS We identified RAD21 and EZH2 as over-represented, STAT2 and IRF3 as depleted transcription factors. Histone modification of H3K9me3 and chromatin state segmentation of “poised promoter” and “repressed” were overrepresented. All genes were prioritized and we selected the top five genes for validation at population level. Combined results from the three GWASs samples, rs7522101 in ESRRG remained significantly associated with BMI after multiple testing corrections (P = 7.25 × 10−5). It was also associated with β-cell function (P = 1.99 × 10−3) and fasting glucose level (P < 0.05) in the meta-analyses of glucose and insulin-related traits consortium (MAGIC) dataset. CONCLUSIONS In summary, we identified epigenomic characteristics for obesity genes and suggested ESRRG as a novel obesity susceptibility gene. PMID:27113491

  15. PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed

    PubMed Central

    Zhang, Yucan; Sarkar, Indra Neil; Chen, Elizabeth S.

    2014-01-01

    The exponential growth of biomedical literature provides the opportunity to develop approaches for facilitating the identification of possible relationships between biomedical concepts. Indexing by Medical Subject Headings (MeSH) represent high-quality summaries of much of this literature that can be used to support hypothesis generation and knowledge discovery tasks using techniques such as association rule mining. Based on a survey of literature mining tools, a tool implemented using Ruby and R – PubMedMiner – was developed in this study for mining and visualizing MeSH-based associations for a set of MEDLINE articles. To demonstrate PubMedMiner’s functionality, a case study was conducted that focused on identifying and comparing comorbidities for asthma in children and adults. Relative to the tools surveyed, the initial results suggest that PubMedMiner provides complementary functionality for summarizing and comparing topics as well as identifying potentially new knowledge. PMID:25954472

  16. Drug-related problems identified during medication review before and after the introduction of a clinical decision support system.

    PubMed

    Verdoorn, S; Kwint, H F; Hoogland, P; Gussekloo, J; Bouvy, M L

    2017-10-02

    To facilitate the identification of drug-related problems (DRPs) during medication review, several tools have been developed. Explicit criteria, like Beers criteria or STOPP (Screening Tool of Older Peoples' Prescriptions) and START (Screening Tool to Alert doctors to Right Treatment) criteria, can easily be integrated into a clinical decision support system (CDSS). The aim of this study was to investigate the effect of adding a CDSS to medication review software on identifying and solving DRPs in daily pharmacy practice. Pre- to post-analysis of clinical medication reviews (CMRs) performed by 121 pharmacies in 2012 and 2013, before and after the introduction of CDSS into medication review software. Mean number of DRPs per patient, type of DRPs and their resolution rates were compared in the pharmacies pre- and post-CDSS using paired t tests. In total, 9151 DRPs were identified in 3100 patients pre-CDSS and 15 268 DRPs were identified in 4303 patients post-CDSS. The mean number of identified DRPs per patient (aggregated per pharmacy) was higher after the introduction of CDSS (3.2 vs 3.6 P < .01). The resolution rate was lower post-CDSS (50% vs 44%; P < .01), which overall resulted in 1.6 resolved DRPs per patient in both groups (P = .93). After the introduction of CDSS, 41% of DRPs were detected by the CDSS. The resolution rate of DRPs generated by CDSS was lower than of DRPs identified without the help of CDSS (29% vs 55%; P < .01). The two most prevalent DRP types were "Overtreatment" and "Suboptimal therapy" in both groups. The prevalence of "Overtreatment" was equal in both groups (mean DRPs per patient: 0.84 vs 0.77; P = .22), and "Suboptimal therapy" was more frequently identified post-CDSS (mean DRPs per patient: 0.54 vs 1.1; P < .01). The introduction of CDSS to medication review software generated additional DRPs with a lower resolution rate. Structural assessment including a patient interview elicited the most relevant DRPs. Further

  17. Capturing children and young people's perspectives to identify the content for a novel vision-related quality of life instrument.

    PubMed

    Rahi, Jugnoo S; Tadić, Valerie; Keeley, Sarah; Lewando-Hundt, Gillian

    2011-05-01

    To describe a child-centered approach to identifying content for a novel self-report questionnaire for assessing vision-related quality of life (QoL) of visually impaired (VI) or blind (BL) children and young people. Questionnaire development. A stratified random patient sample of children and young people who are VI/BL (visual acuity in the better eye Snellen <6/18; logarithm of the minimum angle of resolution <0.51) as the result of any visual disorder, but in the absence of any other significant impairment, aged 10 to 15 years (N=49); and a convenience school-based sample of children and young people who are VI/BL and aged 10 to 17 years (N=29). Individual interviews were conducted with a stratified random sample of 32 children and young people, aged 10 to 15 years, who were VI/BL. The interviews followed a topic guide based on vision-related issues identified from a focus group of affected children and young people, combined with a literature review and consultations with professionals. Collaborative qualitative thematic analysis was undertaken and used to derive draft items of the instrument, using the children's own language wherever possible. Items were reduced, rephrased, and refined through individual consultation, as well as an expert reference group of children and young people who were VI/BL, and supplemented by the research team's consensus. A draft 47-item instrument. A total of 874 potential questionnaire items were initially generated spanning the following domains: social relations, acceptance, and participation; independence and autonomy; psychological and emotional well-being; future-aspirations and fears; functioning-home, school, and leisure; and treatment of eye condition. This was eventually reduced to a 47-item instrument with each item presented as a vignette describing a QoL issue from an "illustrative" child's perspective. Thus, the responding child reports on how much he/she is presently like and how much he/she wishes to be like that

  18. Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels

    PubMed Central

    2017-01-01

    Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike’s information criterion (AICc) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis, the branchiopod water flea, Daphnia magna, normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus, which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei. The modeling approach presented here will be useful in selecting the most likely

  19. Quantitative Proteomic Analyses Identify ABA-Related Proteins and Signal Pathways in Maize Leaves under Drought Conditions.

    PubMed

    Zhao, Yulong; Wang, Yankai; Yang, Hao; Wang, Wei; Wu, Jianyu; Hu, Xiuli

    2016-01-01

    Drought stress is one of major factors resulting in maize yield loss. The roles of abscisic acid (ABA) have been widely studied in crops in response to drought stress. However, more attention is needed to identify key ABA-related proteins and also gain deeper molecular insights about drought stress in maize. Based on this need, the physiology and proteomics of the ABA-deficient maize mutant vp5 and its wild-type Vp5 under drought stress were examined and analyzed. Malondialdehyde content increased and quantum efficiency of photosystem II decreased under drought stress in both genotypes. However, the magnitude of the increase or decrease was significantly higher in vp5 than in Vp5. A total of 7051 proteins with overlapping expression patterns among three replicates in the two genotypes were identified by Multiplex run iTRAQ-based quantitative proteomic and liquid chromatography-tandem mass spectrometry methods, of which the expression of only 150 proteins (130 in Vp5, 27 in vp5) showed changes of at least 1.5-fold under drought stress. Among the 150 proteins, 67 and 60 proteins were up-regulated and down-regulated by drought stress in an ABA-dependent way, respectively. ABA was found to play active roles in regulating signaling pathways related to photosynthesis, oxidative phosphorylation (mainly related to ATP synthesis), and glutathione metabolism (involved in antioxidative reaction) in the maize response to drought stress. Our results provide an extensive dataset of ABA-dependent, drought-regulated proteins in maize plants, which may help to elucidate the underlying mechanisms of ABA-enhanced tolerance to drought stress in maize.

  20. Quantitative Proteomic Analyses Identify ABA-Related Proteins and Signal Pathways in Maize Leaves under Drought Conditions

    PubMed Central

    Zhao, Yulong; Wang, Yankai; Yang, Hao; Wang, Wei; Wu, Jianyu; Hu, Xiuli

    2016-01-01

    Drought stress is one of major factors resulting in maize yield loss. The roles of abscisic acid (ABA) have been widely studied in crops in response to drought stress. However, more attention is needed to identify key ABA-related proteins and also gain deeper molecular insights about drought stress in maize. Based on this need, the physiology and proteomics of the ABA-deficient maize mutant vp5 and its wild-type Vp5 under drought stress were examined and analyzed. Malondialdehyde content increased and quantum efficiency of photosystem II decreased under drought stress in both genotypes. However, the magnitude of the increase or decrease was significantly higher in vp5 than in Vp5. A total of 7051 proteins with overlapping expression patterns among three replicates in the two genotypes were identified by Multiplex run iTRAQ-based quantitative proteomic and liquid chromatography-tandem mass spectrometry methods, of which the expression of only 150 proteins (130 in Vp5, 27 in vp5) showed changes of at least 1.5-fold under drought stress. Among the 150 proteins, 67 and 60 proteins were up-regulated and down-regulated by drought stress in an ABA-dependent way, respectively. ABA was found to play active roles in regulating signaling pathways related to photosynthesis, oxidative phosphorylation (mainly related to ATP synthesis), and glutathione metabolism (involved in antioxidative reaction) in the maize response to drought stress. Our results provide an extensive dataset of ABA-dependent, drought-regulated proteins in maize plants, which may help to elucidate the underlying mechanisms of ABA-enhanced tolerance to drought stress in maize. PMID:28008332

  1. Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.

    PubMed

    Tao, Ying; Shi, Mang; Chommanard, Christina; Queen, Krista; Zhang, Jing; Markotter, Wanda; Kuzmin, Ivan V; Holmes, Edward C; Tong, Suxiang

    2017-03-01

    Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.

  2. Indexing of randomised controlled trials of physiotherapy interventions: a comparison of AMED, CENTRAL, CINAHL, EMBASE, hooked on evidence, PEDro, PsycINFO and PubMed.

    PubMed

    Moseley, Anne M; Sherrington, Catherine; Elkins, Mark R; Herbert, Robert D; Maher, Christopher G

    2009-09-01

    To compare the comprehensiveness of indexing the reports of randomised controlled trials of physiotherapy interventions by eight bibliographic databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO and PubMed). Audit of bibliographic databases. Two hundred and eighty-one reports of randomised controlled trials of physiotherapy interventions were identified by screening the reference lists of 30 relevant systematic reviews published in four consecutive issues of the Cochrane Database of Systematic Reviews (Issue 3, 2007 to Issue 2, 2008). AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO and PubMed were used to search for the trial reports. The number of trial reports indexed in each database was calculated. PEDro indexed 99% of the trial reports, CENTRAL indexed 98%, PubMed indexed 91%, EMBASE indexed 82%, CINAHL indexed 61%, Hooked on Evidence indexed 40%, AMED indexed 36% and PsycINFO indexed 17%. Most trial reports (92%) were indexed on four or more of the databases. One trial report was indexed on a single database (PEDro). Of the eight bibliographic databases examined, PEDro and CENTRAL provide the most comprehensive indexing of reports of randomised trials of physiotherapy interventions.

  3. Modeling Actions of PubMed Users with N-Gram Language Models.

    PubMed

    Lin, Jimmy; Wilbur, W John

    2008-09-12

    Transaction logs from online search engines are valuable for two reasons: First, they provide insight into human information-seeking behavior. Second, log data can be used to train user models, which can then be applied to improve retrieval systems. This article presents a study of logs from PubMed((R)), the public gateway to the MEDLINE((R)) database of bibliographic records from the medical and biomedical primary literature. Unlike most previous studies on general Web search, our work examines user activities with a highly-specialized search engine. We encode user actions as string sequences and model these sequences using n-gram language models. The models are evaluated in terms of perplexity and in a sequence prediction task. They help us better understand how PubMed users search for information and provide an enabler for improving users' search experience.

  4. Biomedicine's electronic publishing paradigm shift: copyright policy and PubMed Central.

    PubMed

    Markovitz, B P

    2000-01-01

    Biomedical publishing stands at a crossroads. The traditional print, peer-reviewed, subscription journal has served science well but is now being called into question. Because of spiraling print journal costs and the worldwide acceptance of the Internet as a valid publication medium, there is a compelling opportunity to re-examine our current paradigm and future options. This report illustrates the conflicts and restrictions inherent in the current publishing model and examines how the single act of permitting authors to retain copyright of their scholarly manuscripts may preserve the quality-control function of the current journal system while allowing PubMed Central, the Internet archiving system recently proposed by the director of the National Institutes of Health, to simplify and liberate access to the world's biomedical literature.

  5. An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge

    PubMed Central

    Xu, Yan; Wang, Yining; Liu, Tianren; Tsujii, Junichi; Chang, Eric I-Chao

    2013-01-01

    Objective To create an end-to-end system to identify temporal relation in discharge summaries for the 2012 i2b2 challenge. The challenge includes event extraction, timex extraction, and temporal relation identification. Design An end-to-end temporal relation system was developed. It includes three subsystems: an event extraction system (conditional random fields (CRF) name entity extraction and their corresponding attribute classifiers), a temporal extraction system (CRF name entity extraction, their corresponding attribute classifiers, and context-free grammar based normalization system), and a temporal relation system (10 multi-support vector machine (SVM) classifiers and a Markov logic networks inference system) using labeled sequential pattern mining, syntactic structures based on parse trees, and results from a coordination classifier. Micro-averaged precision (P), recall (R), averaged P&R (P&R), and F measure (F) were used to evaluate results. Results For event extraction, the system achieved 0.9415 (P), 0.8930 (R), 0.9166 (P&R), and 0.9166 (F). The accuracies of their type, polarity, and modality were 0.8574, 0.8585, and 0.8560, respectively. For timex extraction, the system achieved 0.8818, 0.9489, 0.9141, and 0.9141, respectively. The accuracies of their type, value, and modifier were 0.8929, 0.7170, and 0.8907, respectively. For temporal relation, the system achieved 0.6589, 0.7129, 0.6767, and 0.6849, respectively. For end-to-end temporal relation, it achieved 0.5904, 0.5944, 0.5921, and 0.5924, respectively. With the F measure used for evaluation, we were ranked first out of 14 competing teams (event extraction), first out of 14 teams (timex extraction), third out of 12 teams (temporal relation), and second out of seven teams (end-to-end temporal relation). Conclusions The system achieved encouraging results, demonstrating the feasibility of the tasks defined by the i2b2 organizers. The experiment result demonstrates that both global and local

  6. Glomerular disease search filters for Pubmed, Ovid Medline, and Embase: a development and validation study

    PubMed Central

    2012-01-01

    Background Tools to enhance physician searches of Medline and other bibliographic databases have potential to improve the application of new knowledge in patient care. This is particularly true for articles about glomerular disease, which are published across multiple disciplines and are often difficult to track down. Our objective was to develop and test search filters for PubMed, Ovid Medline, and Embase that allow physicians to search within a subset of the database to retrieve articles relevant to glomerular disease. Methods We used a diagnostic test assessment framework with development and validation phases. We read a total of 22,992 full text articles for relevance and assigned them to the development or validation set to define the reference standard. We then used combinations of search terms to develop 997,298 unique glomerular disease filters. Outcome measures for each filter included sensitivity, specificity, precision, and accuracy. We selected optimal sensitive and specific search filters for each database and applied them to the validation set to test performance. Results High performance filters achieved at least 93.8% sensitivity and specificity in the development set. Filters optimized for sensitivity reached at least 96.7% sensitivity and filters optimized for specificity reached at least 98.4% specificity. Performance of these filters was consistent in the validation set and similar among all three databases. Conclusions PubMed, Ovid Medline, and Embase can be filtered for articles relevant to glomerular disease in a reliable manner. These filters can now be used to facilitate physician searching. PMID:22672435

  7. Unraveling the complexity of the zoo community: identifying the variables related to conservation performance in zoological parks.

    PubMed

    Fàbregas, María C; Guillén-Salazar, Federico; Garcés-Narro, Carlos

    2012-01-01

    Zoological parks make up a highly heterogeneous community. Ranging from small collections at shopping malls to highly developed bioparks, their contribution to conservation is expected to vary enormously. Although several studies have focused on assessing such contribution, the parameters used frequently do not apply when considering more modest zoos. The goals of this study are to determine, within the wide range of zoos, which type tend to fulfill the conservation mission of modern zoos and to identify the variables associated to their conservation performance. We used the requirements demanded by the European Community Zoos Directive 1999/22/EC, relating to the keeping of wild animals in zoological parks, to assess conservation performance in 72% of officially registered Spanish zoos. Sampled zoos were classified into groups according to their common characteristics, and then the variables related to how they met each of the Directive's requirements in the groups were assessed. We found that private zoological parks with large zoological collections, located within metropolitan areas, and members of a zoo association tended to fulfill the requirements. Being a member of a zoo association was the variable that better explained fulfillment of the requirements among the evaluated zoos. Data revealed that zoos not meeting any requirement were few, although those meeting all of them were not frequent. The requirement related to adequate record keeping showed the lowest level of fulfillment. We discuss the implications of our results and propose measures of change in order to promote the contribution of zoos to biodiversity conservation.

  8. A global proteomic study identifies distinct pathological features of IgG4-related and primary sclerosing cholangitis.

    PubMed

    Zen, Yoh; Britton, David; Mitra, Vikram; Pike, Ian; Heaton, Nigel; Quaglia, Alberto

    2016-05-01

    This combined proteomic and histopathological study was aimed to compare tissue characteristics of immunoglobulin (Ig)G4-related sclerosing cholangitis (ISC) and primary sclerosing cholangitis (PSC) in a global, non-biased manner. Tissue proteomes and phosphorylomes of frozen large bile duct samples were analysed by a conventional liquid chromatography-tandem mass spectrometry (LC-MS/MS) protocol and additional phosphopeptide enrichment methods. The proteomic examination identified 23 373 peptides and 4870 proteins, including 4801 phosphopeptides and 1121 phosphoproteins. The expression profiles of phosphopeptides discriminated ISC from PSC more clearly than those of non-phosphopeptides. In the pathway analysis, ISC was found to have 11 more activated signal cascades, including three immunological pathways, all B cell- or immunoglobulin-related. On immunostaining, two immunological markers (FYN-binding protein and allograft inflammatory factor-1) up-regulated in ISC were expressed mainly in M2 macrophages, consistent with increased phagocytotic activity induced by the immunoglobulin (Ig)G-Fcγ receptor interaction. In contrast, PSC had two more activated signal pathways related to extracellular matrix (ECM) remodelling. Filamin-A involved in ECM remodelling was expressed aberrantly in injured bile ducts and associated cholangiocarcinomas in PSC, suggesting its possible roles in periductal fibrosis and carcinogenesis in PSC. This study suggested crucial roles of B cells and macrophages in ISC, and more dynamic ECM remodelling in PSC. © 2015 John Wiley & Sons Ltd.

  9. Identifying MRI markers to evaluate early treatment-related changes post-laser ablation for cancer pain management

    NASA Astrophysics Data System (ADS)

    Tiwari, Pallavi; Danish, Shabbar; Madabhushi, Anant

    2014-03-01

    by correcting for intensity drift in order to examine tissue-specific response, and (3) quantification of MRI maps via texture and intensity features to evaluate changes in MR markers pre- and post-LITT. A total of 78 texture features comprising of non-steerable and steerable gradient and second order statistical features were extracted from pre- and post-LITT MP-MRI on a per-voxel basis. Quantitative, voxel-wise comparison of the changes in MRI texture features between pre-, and post-LITT MRI indicate that (a) steerable and non-steerable gradient texture features were highly sensitive as well as specific in predicting subtle micro-architectural changes within and around the ablation zone pre- and post-LITT, (b) FLAIR was identified as the most sensitive MRI protocol in identifying early treatment changes yielding a normalized percentage change of 360% within the ablation zone relative to its pre-LITT value, and (c) GRE was identified as the most sensitive MRI protocol in quantifying changes outside the ablation zone post-LITT. Our preliminary results thus indicate great potential for non-invasive computerized MRI features in determining localized micro-architectural focal treatment related changes post-LITT.

  10. Identifying psychosocial stressors of well-being and factors related to substance use among Latino day laborers.

    PubMed

    Nalini Junko Negi

    2011-08-01

    Day labor is largely comprised of young Latino immigrant men, many of who are undocumented, and thus vulnerable to a myriad of workers' rights abuses. The difficult work and life conditions of this marginalized population may place them at heightened risk for mental health problems and substance use and abuse. However, factors related to Latino day laborers' well-being and substance misuse are largely unknown. This article utilizes ethnographic and focus group methodology to elucidate participant identified factors associated to well-being and substance use and abuse. This study has implications for informing public health and social service programming as it provides thick description regarding the context and circumstances associated to increased vulnerability to substance abuse and lack of well-being among this hard-to-reach population of Latino immigrants.

  11. Proteomic and genetic approaches to identifying defence-related proteins in rice challenged with the fungal pathogen Rhizoctonia solani.

    PubMed

    Lee, Joohyun; Bricker, Terry M; Lefevre, Michael; Pinson, Shannon R M; Oard, James H

    2006-09-01

    SUMMARY Sheath blight, caused by the fungus Rhizoctonia solani, is a major disease of rice world-wide, but little is known about the host response to infection. The objective of this study was to identify proteins and DNA markers in resistant and susceptible rice associated with response to infection by R. solani. Replicated two-dimensional polyacrylamide gel electrophoresis experiments were conducted to detect proteins differentially expressed under inoculated and non-inoculated conditions. Tandem mass spectra analysis using electrospray ionization quadrupole-time of flight mass spectrometry (ESI Q-TOF MS) was carried out for protein identification with the NCBI non-redundant protein database. Seven proteins were increased after inoculation in both susceptible and resistant plants. Six of the seven proteins were identified with presumed antifungal, photosynthetic and proteolytic activities. An additional 14 proteins were detected in the response of the resistant line. Eleven of the 14 proteins were identified with presumed functions relating to antifungal activity, signal transduction, energy metabolism, photosynthesis, molecular chaperone, proteolysis and antioxidation. The induction of 3-beta-hydroxysteroid dehydrogenase/isomerase was detected for the first time in resistant rice plants after pathogen challenge, suggesting a defensive role of this enzyme in rice against attack by R. solani. The chromosomal locations of four induced proteins were found to be in close physical proximity to genetic markers for sheath blight resistance in two genetic mapping populations. The proteomic and genetic results from this study indicate a complex response of rice to challenge by R. solani that involves simultaneous induction of proteins from multiple defence pathways.

  12. A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways.

    PubMed

    Olukolu, Bode A; Wang, Guan-Feng; Vontimitta, Vijay; Venkata, Bala P; Marla, Sandeep; Ji, Jiabing; Gachomo, Emma; Chu, Kevin; Negeri, Adisu; Benson, Jacqueline; Nelson, Rebecca; Bradbury, Peter; Nielsen, Dahlia; Holland, James B; Balint-Kurti, Peter J; Johal, Gurmukh

    2014-08-01

    Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene (Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants.

  13. Identifying consumer preferences for specific beef flavor characteristics in relation to cattle production and postmortem processing parameters.

    PubMed

    O'Quinn, T G; Woerner, D R; Engle, T E; Chapman, P L; Legako, J F; Brooks, J C; Belk, K E; Tatum, J D

    2016-02-01

    Sensory analysis of ground LL samples representing 12 beef product categories was conducted in 3 different regions of the U.S. to identify flavor preferences of beef consumers. Treatments characterized production-related flavor differences associated with USDA grade, cattle type, finishing diet, growth enhancement, and postmortem aging method. Consumers (N=307) rated cooked samples for 12 flavors and overall flavor desirability. Samples were analyzed to determine fatty acid content. Volatile compounds produced by cooking were extracted and quantified. Overall, consumers preferred beef that rated high for beefy/brothy, buttery/beef fat, and sweet flavors and disliked beef with fishy, livery, gamey, and sour flavors. Flavor attributes of samples higher in intramuscular fat with greater amounts of monounsaturated fatty acids and lesser proportions of saturated, odd-chain, omega-3, and trans fatty acids were preferred by consumers. Of the volatiles identified, diacetyl and acetoin were most closely correlated with desirable ratings for overall flavor and dimethyl sulfide was associated with an undesirable sour flavor. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Relation of microchannel structure identified by optical coherence tomography to plaque vulnerability in patients with coronary artery disease.

    PubMed

    Kitabata, Hironori; Tanaka, Atsushi; Kubo, Takashi; Takarada, Shigeho; Kashiwagi, Manabu; Tsujioka, Hiroto; Ikejima, Hideyuki; Kuroi, Akio; Kataiwa, Hideaki; Ishibashi, Kohei; Komukai, Kenichi; Tanimoto, Takashi; Ino, Yasushi; Hirata, Kumiko; Nakamura, Nobuo; Mizukoshi, Masato; Imanishi, Toshio; Akasaka, Takashi

    2010-06-15

    Increased neovascularization in atherosclerotic plaques is associated with plaque vulnerability. The high resolution of optical coherence tomography (OCT) might provide a chance to directly visualize plaque neovascularization in vivo. The aim of the present study was to investigate the relation between microchannels in culprit plaques identified by OCT and plaque vulnerability in patients with coronary artery disease. A total of 63 consecutive patients with coronary artery disease who had undergone both OCT and intravascular ultrasound before any interventions to examine culprit lesion morphologies were enrolled. Microchannel was defined as a no-signal tubuloluminal structure on the cross-sectional optical coherence tomographic image. Microchannels were found in 24 (38%) of the 63 patients. The patients were divided into 2 groups according to the presence or absence of microchannels. The frequency of plaque rupture tended to be greater in the microchannel group (50% vs 28%, p = 0.11). The thickness of the fibrous cap (median 60 vs 100 microm, p = 0.001) was significantly less in the patients with microchannels, and significant differences were found in the frequency of thin-cap fibroatheroma (54% vs 21%, p = 0.012) and positive remodeling (67% vs 36%, p = 0.02) between the 2 groups. The high-sensitivity C-reactive protein levels in the microchannel group was significantly greater than those in the no-microchannel group (median 0.27 vs 0.13 mg/dl, p = 0.015). Moreover, increased microchannel counts were associated with greater high-sensitivity C-reactive protein levels (p = 0.01). In conclusion, a significant relation was found between the presence of microchannels in plaques identified by OCT and plaque vulnerability in patients with coronary artery disease.

  15. Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer.

    PubMed

    Fang, Xiaocong; Netzer, Michael; Baumgartner, Christian; Bai, Chunxue; Wang, Xiangdong

    2013-02-01

    Cigarette smoking is the most demonstrated risk factor for the development of lung cancer, while the related genetic mechanisms are still unclear. The preprocessed microarray expression dataset was downloaded from Gene Expression Omnibus database. Samples were classified according to the disease state, stage and smoking state. A new computational strategy was applied for the identification and biological interpretation of new candidate genes in lung cancer and smoking by coupling a network-based approach with gene set enrichment analysis. Network analysis was performed by pair-wise comparison according to the disease states (tumor or normal), smoking states (current smokers or nonsmokers or former smokers), or the disease stage (stages I-IV). The most activated metabolic pathways were identified by gene set enrichment analysis. Panels of top ranked gene candidates in smoking or cancer development were identified, including genes involved in cell proliferation and drug metabolism like cytochrome P450 and WW domain containing transcription regulator 1. Semaphorin 5A and protein phosphatase 1F are the common genes represented as major hubs in both the smoking and cancer related network. Six pathways, e.g. cell cycle, DNA replication, RNA transport, protein processing in endoplasmic reticulum, vascular smooth muscle contraction and endocytosis were commonly involved in smoking and lung cancer when comparing the top ten selected pathways. New approach of bioinformatics for biomarker identification and validation can probe into deep genetic relationships between cigarette smoking and lung cancer. Our studies indicate that disease-specific network biomarkers, interaction between genes/proteins, or cross-talking of pathways provide more specific values for the development of precision therapies for lung. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Measures That Identify Prescription Medication Misuse, Abuse, and Related Events in Clinical Trials: ACTTION Critique and Recommended Considerations.

    PubMed

    Smith, Shannon M; Jones, Judith K; Katz, Nathaniel P; Roland, Carl L; Setnik, Beatrice; Trudeau, Jeremiah J; Wright, Stephen; Burke, Laurie B; Comer, Sandra D; Dart, Richard C; Dionne, Raymond; Haddox, J David; Jaffe, Jerome H; Kopecky, Ernest A; Martell, Bridget A; Montoya, Ivan D; Stanton, Marsha; Wasan, Ajay D; Turk, Dennis C; Dworkin, Robert H

    2017-05-04

    Accurate assessment of inappropriate medication use events (ie, misuse, abuse, and related events) occurring in clinical trials is an important component in evaluating a medication's abuse potential. A meeting was convened to review all instruments measuring such events in clinical trials according to previously published standardized terminology and definitions. Only 2 approaches have been reported that are specifically designed to identify and classify misuse, abuse, and related events occurring in clinical trials, rather than to measure an individual's risk of using a medication inappropriately: the Self-Reported Misuse, Abuse, and Diversion (SR-MAD) instrument and the Misuse, Abuse, and Diversion Drug Event Reporting System (MADDERS). The conceptual basis, strengths, and limitations of these methods are discussed. To our knowledge, MADDERS is the only system available to comprehensively evaluate inappropriate medication use events prospectively to determine the underlying intent. MADDERS can also be applied retrospectively to completed trial data. SR-MAD can be used prospectively; additional development may be required to standardize its implementation and fully appraise the intent of inappropriate use events. Additional research is needed to further demonstrate the validity and utility of MADDERS as well as SR-MAD. Identifying a medication's abuse potential requires assessing inappropriate medication use events in clinical trials on the basis of a standardized event classification system. The strengths and limitations of the 2 published methods designed to evaluate inappropriate medication use events are reviewed, with recommended considerations for further development and current implementation. Copyright © 2017 American Pain Society. Published by Elsevier Inc. All rights reserved.

  17. PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

    PubMed

    Vanhecke, Thomas E; Barnes, Michael A; Zimmerman, Janet; Shoichet, Sandor

    2007-09-01

    PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines.

  18. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives.

    PubMed

    Howard-Azzeh, Mohammad; Shamseer, Larissa; Schellhorn, Herb E; Gupta, Radhey S

    2014-11-01

    Detailed phylogenetic and comparative genomic analyses are reported on 140 genome sequenced cyanobacteria with the main focus on the heterocyst-differentiating cyanobacteria. In a phylogenetic tree for cyanobacteria based upon concatenated sequences for 32 conserved proteins, the available cyanobacteria formed 8-9 strongly supported clades at the highest level, which may correspond to the higher taxonomic clades of this phylum. One of these clades contained all heterocystous cyanobacteria; within this clade, the members exhibiting either true (Nostocales) or false (Stigonematales) branching of filaments were intermixed indicating that the division of the heterocysts-forming cyanobacteria into these two groups is not supported by phylogenetic considerations. However, in both the protein tree as well as in the 16S rRNA gene tree, the akinete-forming heterocystous cyanobacteria formed a distinct clade. Within this clade, the members which differentiate into hormogonia or those which lack this ability were also separated into distinct groups. A novel molecular signature identified in this work that is uniquely shared by the akinete-forming heterocystous cyanobacteria provides further evidence that the members of this group are specifically related and they shared a common ancestor exclusive of the other cyanobacteria. Detailed comparative analyses on protein sequences from the genomes of heterocystous cyanobacteria reported here have also identified eight conserved signature indels (CSIs) in proteins involved in a broad range of functions, and three conserved signature proteins, that are either uniquely or mainly found in all heterocysts-forming cyanobacteria, but generally not found in other cyanobacteria. These molecular markers provide novel means for the identification of heterocystous cyanobacteria, and they provide evidence of their monophyletic origin. Additionally, this work has also identified seven CSIs in other proteins which in addition to the heterocystous

  19. Greater body mass index is related to greater self-identified cold tolerance and greater insensible body mass loss.

    PubMed

    Jung, Dahee; Kim, Dami; Park, Joonhee; Lee, Joo Young

    2016-08-22

    Insensible body mass loss (IBL) from the human body continuously occurs, which is an important component in body heat exchange. The purpose of this study was to examine the relevance of IBL to anthropometric characteristics and self-identified thermal tolerance. A total of 289 healthy young Korean males were chosen and sorted into the following three groups: heat tolerable only (HTO, N = 79), cold tolerable only (CTO, N = 104), neither heat nor cold tolerable (NHC, N = 106). They weighed before and after a 30-min rest under lightly clothed condition at an air temperature of 23 ± 1 °C with a relative humidity 55 ± 5 %RH. (1) The IBL of 289 males had a mean of 90 ± 75 g h(-1) (48 ± 40 g h(-1) m(-2)); (2) No significant difference in IBL among the three groups were found; (3) Significant differences in body weight and body mass index (BMI) among three groups were found (P < 0.05), but insignificance was found for height (P = 0.726) or body surface area (P = 0.059); (4) CTO was approximately 4.1 kg heavier in body weight (P < 0.05) and higher in BMI (P < 0.01) than in HTO; (5) Only for the group CTO, IBL (g h(-1)) showed a positive relationship to BMI (P < 0.05, R (2) = 0.056), but there was no relationship between IBL and body surface area. For healthy young males within normal anthropometric ranges in Korea, IBL was positively related to BMI, and individuals with greater BMI showed greater self-identified cold tolerance, but no direct relationship was found between IBL and self-identified cold tolerance. This suggests that body physique (e.g., BMI) could be an explanatory factor between insensible body heat loss and subjective cognition on cold tolerance.

  20. Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.

    PubMed

    Kim, Sun; Yeganova, Lana; Wilbur, W John

    2016-10-01

    Medical Subject Headings (MeSH(®)) is a controlled vocabulary for indexing and searching biomedical literature. MeSH terms and subheadings are organized in a hierarchical structure and are used to indicate the topics of an article. Biologists can use either MeSH terms as queries or the MeSH interface provided in PubMed(®) for searching PubMed abstracts. However, these are rarely used, and there is no convenient way to link standardized MeSH terms to user queries. Here, we introduce a web interface which allows users to enter queries to find MeSH terms closely related to the queries. Our method relies on co-occurrence of text words and MeSH terms to find keywords that are related to each MeSH term. A query is then matched with the keywords for MeSH terms, and candidate MeSH terms are ranked based on their relatedness to the query. The experimental results show that our method achieves the best performance among several term extraction approaches in terms of topic coherence. Moreover, the interface can be effectively used to find full names of abbreviations and to disambiguate user queries. https://www.ncbi.nlm.nih.gov/IRET/MESHABLE/ CONTACT: sun.kim@nih.gov Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  1. Gendered discourses of youth sexualities--an exploration of PubMed articles on prevention of sexually transmissible infections.

    PubMed

    Johansson, Eva E; Alex, Lena; Christianson, Monica

    2014-10-01

    To explore how gender is addressed in medical articles on the prevention of sexually transmissible infections (STI) among adolescents. Sixtyone articles were retrieved from a PubMed search and scrutinized by qualitative content analysis. Most articles were affiliated with North American research institutions, but there were also reports from Europe, Africa, South America, and Asia. Gender turned up in the following four recurrent discourses: Gendered Receptiveness for Information, Stereotyped Heterosexual Expectations, Power Imbalance in Sexual Relations, and Gendered Prevention Approaches. Young women were described as knowledgeable, communicative, and responsible, but at risk because of feminine ideals and a lack of negotiating power. Men were described as less informed, more reluctant to discuss, and more risk taking due to masculine ideals and power dominance. Prevention approaches concerned how to postpone sex and/or tailor gender-sensitive programs for specific groups of young women and men. Researchers' own gender expectations might have a substantial impact on how sex and sexual health is considered in prevention research. To avoid reconstruction of current inequalities and stereotypes regarding sexual practices of young women and men, the impact of gender, the power structures in intimate relations, and the cultural context should be considered. Medical research on STI prevention could benefit from including a wider array of gender perspectives. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

    PubMed Central

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

  3. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site.

    PubMed

    Allentoft, M E; Heller, R; Holdaway, R N; Bunce, M

    2015-12-01

    By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.

  4. A novel outlier detection method for identifying torque-related transient patterns of in vivo muscle behavior.

    PubMed

    Sheng Han; Xin Chen; Sheng Zhong; Yongjin Zhou; Zhiguo Zhang

    2014-01-01

    This paper proposed a novel outlier detection method, named l1-regularized outlier isolation and regression (LOIRE), to examine torque-related transient patterns of in vivo muscle behavior from multimodal signals, including electromyography (EMG), mechanomyography (MMG) and ultrasonography (US), during isometric muscle contraction. Eight subjects performed isometric ramp contraction of knee up to 90% of the maximal voluntary contraction, and EMG, MMG and US were simultaneously recorded from the rectus femoris muscle. Five features, including two root mean square amplitudes from EMG and MMG, muscle cross sectional area, muscle thickness and width from US were extracted. Then, local polynomial regression was used to obtain the signal-to-torque relationships and their derivatives. By assuming the signal-to-torque functions are basically quadratic, the LOIRE method is applied to identify transient torque-related patterns of EMG, MMG and US features as outliers of the linear derivative-to-torque functions. The results show that the LOIRE method can effectively reveal transient patterns in the signal-to-torque relationships (for example, sudden changes around 20% MVC can be observed from all features), providing important information about in vivo muscle behavior.

  5. Using probability vs. nonprobability sampling to identify hard-to-access participants for health-related research: costs and contrasts.

    PubMed

    Feild, Lucy; Pruchno, Rachel A; Bewley, Jennifer; Lemay, Edward P; Levinsky, Norman G

    2006-08-01

    This article compares the recruitment costs and participant characteristics associated with the use of probability and nonprobability sampling strategies in a longitudinal study of older hemodialysis patients and their spouses. Contrasts were made of people who accrued to the study based on probability and nonprobability sampling strategies. Probability-based sampling was more time-efficient and cost-effective than nonprobability sampling. There were no significant differences between the respondents identified through probability and nonprobability sampling on age, gender, years married, education, work status, and professional job status. Respondents from the probability sample were more likely to be Protestant and less likely to be Catholic than those from the nonprobability sample. Respondents from the probability sample were more likely to be Black, whereas those from the nonprobability sample were more likely to be White. There are strengths and shortcomings associated with both nonprobability and probability sampling. Researchers need to consider representativeness and external validity issues when designing sampling and related recruitment plans for health-related research.

  6. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site

    PubMed Central

    Allentoft, M E; Heller, R; Holdaway, R N; Bunce, M

    2015-01-01

    By analysing ancient DNA (aDNA) from 74 14C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research. PMID:26039408

  7. A Heterogeneous Network Based Method for Identifying GBM-Related Genes by Integrating Multi-Dimensional Data.

    PubMed

    Chen Peng; Ao Li

    2017-01-01

    The emergence of multi-dimensional data offers opportunities for more comprehensive analysis of the molecular characteristics of human diseases and therefore improving diagnosis, treatment, and prevention. In this study, we proposed a heterogeneous network based method by integrating multi-dimensional data (HNMD) to identify GBM-related genes. The novelty of the method lies in that the multi-dimensional data of GBM from TCGA dataset that provide comprehensive information of genes, are combined with protein-protein interactions to construct a weighted heterogeneous network, which reflects both the general and disease-specific relationships between genes. In addition, a propagation algorithm with resistance is introduced to precisely score and rank GBM-related genes. The results of comprehensive performance evaluation show that the proposed method significantly outperforms the network based methods with single-dimensional data and other existing approaches. Subsequent analysis of the top ranked genes suggests they may be functionally implicated in GBM, which further corroborates the superiority of the proposed method. The source code and the results of HNMD can be downloaded from the following URL: http://bioinformatics.ustc.edu.cn/hnmd/ .

  8. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation.

    PubMed

    Yu, Li; Wang, Guo-Dong; Ruan, Jue; Chen, Yong-Bin; Yang, Cui-Ping; Cao, Xue; Wu, Hong; Liu, Yan-Hu; Du, Zheng-Lin; Wang, Xiao-Ping; Yang, Jing; Cheng, Shao-Chen; Zhong, Li; Wang, Lu; Wang, Xuan; Hu, Jing-Yang; Fang, Lu; Bai, Bing; Wang, Kai-Le; Yuan, Na; Wu, Shi-Fang; Li, Bao-Guo; Zhang, Jin-Guo; Yang, Ye-Qin; Zhang, Cheng-Lin; Long, Yong-Cheng; Li, Hai-Shu; Yang, Jing-Yuan; Irwin, David M; Ryder, Oliver A; Li, Ying; Wu, Chung-I; Zhang, Ya-Ping

    2016-08-01

    The snub-nosed monkey genus Rhinopithecus includes five closely related species distributed across altitudinal gradients from 800 to 4,500 m. Rhinopithecus bieti, Rhinopithecus roxellana, and Rhinopithecus strykeri inhabit high-altitude habitats, whereas Rhinopithecus brelichi and Rhinopithecus avunculus inhabit lowland regions. We report the de novo whole-genome sequence of R. bieti and genomic sequences for the four other species. Eight shared substitutions were found in six genes related to lung function, DNA repair, and angiogenesis in the high-altitude snub-nosed monkeys. Functional assays showed that the high-altitude variant of CDT1 (Ala537Val) renders cells more resistant to UV irradiation, and the high-altitude variants of RNASE4 (Asn89Lys and Thr128Ile) confer enhanced ability to induce endothelial tube formation in vitro. Genomic scans in the R. bieti and R. roxellana populations identified signatures of selection between and within populations at genes involved in functions relevant to high-altitude adaptation. These results provide valuable insights into the adaptation to high altitude in the snub-nosed monkeys.

  9. Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

    PubMed Central

    Righetti, Karima; Vu, Joseph Ly; Pelletier, Sandra; Vu, Benoit Ly; Glaab, Enrico; Lalanne, David; Pasha, Asher; Patel, Rohan V.; Provart, Nicholas J.; Verdier, Jerome; Leprince, Olivier

    2015-01-01

    Seed longevity, the maintenance of viability during storage, is a crucial factor for preservation of genetic resources and ensuring proper seedling establishment and high crop yield. We used a systems biology approach to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes from seed developmental time courses obtained in five growth environments, we generated a robust, stable coexpression network (MatNet), thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a coexpression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis of the maturation processes in M. truncatula and Arabidopsis thaliana seeds and mining Arabidopsis interaction databases revealed conserved connectivity for 87% of longevity module nodes between both species. Arabidopsis mutant screening for longevity and maturation phenotypes demonstrated high predictive power of the longevity cross-species network. Overrepresentation analysis of the network nodes indicated biological functions related to defense, light, and auxin. Characterization of defense-related wrky3 and nf-x1-like1 (nfxl1) transcription factor mutants demonstrated that these genes regulate some of the network nodes and exhibit impaired acquisition of longevity during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating the activation of defense against pathogens. PMID:26410298

  10. Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

    PubMed Central

    Smalheiser, Neil R; Zhou, Wei; Torvik, Vetle I

    2008-01-01

    Background PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection. Results In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles. Conclusion Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at [4]. Peer review and editorial matters for this article were handled by Aaron Cohen. PMID:18279519

  11. Identifying Factors for Optimal Development of Health-Related Websites: A Delphi Study Among Experts and Potential Future Users

    PubMed Central

    van Osch, Liesbeth; de Vries, Hein

    2012-01-01

    Background The Internet has become a popular medium for offering tailored and targeted health promotion programs to the general public. However, suboptimal levels of program use in the target population limit the public health impact of these programs. Optimizing program development is considered as one of the main processes to increase usage rates. Objective To distinguish factors potentially related to optimal development of health-related websites by involving both experts and potential users. By considering and incorporating the opinions of experts and potential users in the development process, involvement in the program is expected to increase, consequently resulting in increased appreciation, lower levels of attrition, and higher levels of sustained use. Methods We conducted a systematic three-round Delphi study through the Internet. Both national and international experts (from the fields of health promotion, health psychology, e-communication, and technical Web design) and potential users were invited via email to participate. During this study an extensive list of factors potentially related to optimal development of health-related websites was identified, by focusing on factors related to layout, general and risk information provision, questionnaire use, additional services, and ease of use. Furthermore, we assessed the extent to which experts and potential users agreed on the importance of these factors. Differences as well as similarities among experts and potentials users were deduced. Results In total, 20 of 62 contacted experts participated in the first round (32% response rate); 60 of 200 contacted experts (30% response rate) and 210 potential users (95% response rate) completed the second-round questionnaire, and 32 of 60 contacted experts completed the third round (53% response rate). Results revealed important factors consented upon by experts and potential users (eg, ease of use, clear structure, and detailed health information provision), as

  12. Using Satellite Maps and Related Spatial Data Sets to Identify Remaining Wild Areas of the Eastern US

    NASA Astrophysics Data System (ADS)

    Jantz, P.; Goetz, S. J.

    2005-12-01

    Roadless and wild areas of 12 states comprising the eastern United States were derived from a combination of satellite image data products (tree cover, urbanized areas, etc), a road network database, and related spatial data sets. These remote areas were defined as having greater than 60 percent tree cover of at least ~5000 acre (2000 ha) contiguous tracts situated more than 500m from any road. Detailed maps of the region were produced and then overlaid with information on existing parks, protected areas, easements, and state and national forest land boundaries. Statistics were tabulated on a regional and statewide basis, and are presented together with the derived map. A total of 1468 wild areas were mapped in the study area. Forty three percent of those were in areas offering some form of protected land disignation, but only 548 (37 percent) of the areas were at least 50 percent protected. Many of the areas identified as roadless wild lands not known to be currently protected in any form were, not surprisingly, located in the states of Maine and West Virginia. Other significant lands meeting the criteria were identified in New York and Tennessee and, to a lesser extent, Pennsylvania, Vermont and New Hampshire. This work forms, as far as we know, the first quantitative assessment across the region using consistent data sets and accepted national criteria for roadless areas. It underscores the urgent need for reserving some of the remaining wild lands to protect forest resources and biological diversity before exurban development encroaches of the last of these unique resource lands of the East. Our approach may also provide acceptable criteria for a national assessment, and results are discussed in this context.

  13. Use of amplified fragment length polymorphism to identify 42 Cladophialophora strains related to cerebral phaeohyphomycosis with in vitro antifungal susceptibility.

    PubMed

    Badali, Hamid; de Hoog, G Sybren; Curfs-Breuker, Ilse; Klaassen, Corné H W; Meis, Jacques F

    2010-07-01

    The amplified fragment length polymorphism technique has been applied to identify neurotropic chaetothyrialean black yeasts and relatives from clinical sources. Cladophialophora bantiana, C. emmonsii, C. arxii, C. devriesii, and C. modesta, previously identified on the basis of sequencing and phenotypic and physiological criteria, were confirmed by cluster analysis, demonstrating the clear separation of C. bantiana as a rather homogeneous group from the other species. C. bantiana is a neurotropic fungus causing cerebral abscesses with a mortality of up to 70%. Successful therapy consists of neurosurgical intervention and optimal antifungal therapy. Since the latter is not clearly defined in a large series, we tested the in vitro activities of eight antifungal drugs against clinical isolates of C. bantiana (n = 37), C. modesta (n = 2), C. arxii (n = 1), C. emmonsii (n = 1), and C. devriesii (n = 1), all of which had caused invasive infections. The resulting MIC(90)s for all neurotropic C. bantiana strains were as follows, in increasing order: posaconazole, 0.125 microg/ml; itraconazole, 0.125 microg/ml; isavuconazole, 0.5 microg/ml; amphotericin B, 1 microg/ml; voriconazole, 2 microg/ml; anidulafungin, 2 microg/ml; caspofungin, 4 microg/ml; and fluconazole, 64 microg/ml. On the basis of these in vitro results and the findings of previous clinical and animal studies, posaconazole seems to be a good alternative to the standard treatment, amphotericin B, for C. bantiana cerebral infections. The new agent isavuconazole, which is also available as an intravenous preparation, has adequate activity against C. bantiana.

  14. Using generalized additive modeling to empirically identify thresholds within the ITERS in relation to toddlers' cognitive development.

    PubMed

    Setodji, Claude Messan; Le, Vi-Nhuan; Schaack, Diana

    2013-04-01

    Research linking high-quality child care programs and children's cognitive development has contributed to the growing popularity of child care quality benchmarking efforts such as quality rating and improvement systems (QRIS). Consequently, there has been an increased interest in and a need for approaches to identifying thresholds, or cutpoints, in the child care quality measures used in these benchmarking efforts that differentiate between different levels of children's cognitive functioning. To date, research has provided little guidance to policymakers as to where these thresholds should be set. Using the Early Childhood Longitudinal Study, Birth Cohort (ECLS-B) data set, this study explores the use of generalized additive modeling (GAM) as a method of identifying thresholds on the Infant/Toddler Environment Rating Scale (ITERS) in relation to toddlers' performance on the Mental Development subscale of the Bayley Scales of Infant Development (the Bayley Mental Development Scale Short Form-Research Edition, or BMDSF-R). The present findings suggest that simple linear models do not always correctly depict the relationships between ITERS scores and BMDSF-R scores and that GAM-derived thresholds were more effective at differentiating among children's performance levels on the BMDSF-R. Additionally, the present findings suggest that there is a minimum threshold on the ITERS that must be exceeded before significant improvements in children's cognitive development can be expected. There may also be a ceiling threshold on the ITERS, such that beyond a certain level, only marginal increases in children's BMDSF-R scores are observed. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  15. Loci identified by genome-wide association studies influence different disease-related phenotypes in chronic obstructive pulmonary disease.

    PubMed

    Pillai, Sreekumar G; Kong, Xiangyang; Edwards, Lisa D; Cho, Michael H; Anderson, Wayne H; Coxson, Harvey O; Lomas, David A; Silverman, Edwin K

    2010-12-15

    Genome-wide association studies have shown significant associations between variants near hedgehog interacting protein HHIP, FAM13A, and cholinergic nicotinic acetylcholine receptor CHRNA3/5 with increased risk of chronic obstructive pulmonary disease (COPD) in smokers; however, the disease mechanisms behind these associations are not well understood. To identify the association between replicated loci and COPD-related phenotypes in well-characterized patient populations. The relationship between these three loci and COPD-related phenotypes was assessed in the Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-point (ECLIPSE) cohort. The results were validated in the family-based International COPD Genetics Network (ICGN). The CHRNA3/5 locus was significantly associated with pack-years of smoking (P = 0.002 and 3 × 10⁻⁴), emphysema assessed by a radiologist using high-resolution computed tomography (P = 2 × 10⁻⁴ and 4.8 × 10⁻⁵), and airflow obstruction (P = 0.004 and 1.8 × 10⁻⁵) in the ECLIPSE and ICGN populations, respectively. However, variants in the IREB2 gene were only significantly associated with FEV₁. The HHIP locus was not associated with smoking intensity but was associated with FEV₁/FVC (P = 1.9 × 10⁻⁴ and 0.004 in the ECLIPSE and ICGN populations). The HHIP locus was also associated with fat-free body mass (P = 0.007) and with both retrospectively (P = 0.015) and prospectively (P = 0.024) collected COPD exacerbations in the ECLIPSE cohort. Single-nucleotide polymorphisms in the FAM13A locus were associated with lung function. The CHRNA3/5 locus was associated with increased smoking intensity and emphysema in individuals with COPD, whereas the HHIP and FAM13A loci were not associated with smoking intensity. The HHIP locus was associated with the systemic components of COPD and with the frequency of COPD exacerbations. FAM13A locus was associated with lung function.

  16. The Case for High Resolution Extended 6-Loci HLA Typing for Identifying Related Donors in the Indian Subcontinent.

    PubMed

    Agarwal, Rajat Kumar; Kumari, Ankita; Sedai, Amit; Parmar, Lalith; Dhanya, Rakesh; Faulkner, Lawrence

    2017-09-01

    %) consanguinity was unknown. We identified 18 donors (6%; 13 siblings and 5 parents) who would have been considered a 12/12 match by LR HLA typing alone but were found not to match on extended HR typing. In this group, 11 donors (61%) were from consanguineous families, 3 donors (17%) had no reported consanguinity, and in 4 donors (22%) consanguinity was unknown. Outcome analysis showed that the actuarial proportion of patients with GVHD was 4% in the FT group compared with 16% in the ST group, with log-rank P = .1952. The ST group included 2 patients with grade III-IV acute GVHD and 1 patient each with moderate and severe chronic GVHD, whereas the FT group only 1 patient with grade III acute GVHD. We conclude that even in the context of related donors, the use of LR and/or 3-loci (A, B, and DRB1) HR HLA typing might result in a sizable risk of missing a clinically relevant mismatch, which may have an adverse impact on transplantation outcomes. In the Indian subcontinent, this observation is not limited to putatively compatible parents or consanguineous families; we recommend full 6-loci HR HLA typing even for matched related BMTs. Copyright © 2017 The American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

  17. Cupping Therapy May be Harmful for Eczema: A PubMed Search

    PubMed Central

    Hon, Kam Lun E.; Luk, David Chi Kong; Leong, Kin Fon; Leung, Alexander K. C.

    2013-01-01

    Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  “cupping,” “eczema,” and “atopic dermatitis,” only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families. PMID:24282650

  18. Making PubMed searching simple: learning to retrieve medical literature through interactive problem solving.

    PubMed

    Vincent, Beatriz; Vincent, Maurice; Ferreira, Carlos Gil

    2006-03-01

    Searching the literature has a direct, beneficial influence on patient care. The amount of medical scientific information has increased to a great extent, while the development of networking technologies has broadened access to online databases. Successful searches depend upon understanding technical librarianship concepts and the skills for mastering searching interfaces. From a problem-oriented approach, concepts like MEDLINE coverage, PubMed resources, Boolean logic, search strategies, and Web sources for full-text articles are introduced along seven online situations: locating a specific publication, answering a complex clinical question, finding information on a general subject, finding publications by a particular author, finding publications in a particular language, finding a specific publication type, and locating the full-text document. Oncologists should face the challenge of performing their own searches. Specific knowledge is mandatory to avoid frustrating, time-consuming work. The objective of this work is to present concepts, strategies, and skills required for medical literature retrieval, easing the incorporation of new and welcomed practices.

  19. PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.

    PubMed

    Goetz, Thomas; von der Lieth, Claus-Wilhelm

    2005-07-01

    Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder (www.glycosciences.de/tools/PubFinder) is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.

  20. Cupping Therapy May be Harmful for Eczema: A PubMed Search.

    PubMed

    Hon, Kam Lun E; Luk, David Chi Kong; Leong, Kin Fon; Leung, Alexander K C

    2013-01-01

    Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  "cupping," "eczema," and "atopic dermatitis," only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families.

  1. Evidence based palaeopathology: meta-analysis of Pubmed-listed scientific studies on pre-Columbian, South American mummies.

    PubMed

    Dageförde, K L; Vennemann, M; Rühli, F J

    2014-06-01

    The aim of this study was to review all Pubmed(®)-listed palaeopathological studies performed on pre-Columbian South American mummies. A total of 61 studies were found (1977-2005). Review criteria included e.g. method of examination, method of mummification, palaeopathological diagnoses and individual age of mummies as well as dating, which ranged from 7500 to 500 years BP, mainly (if reported) originating from the Chiribaya and Chinchorro cultures. The average age of the 99 individually reported mummies was about 25 years. Only six studies included computed tomography, thirteen studies used classical radiography as an examination method. Three studies analysed parasite related diseases, especially caused by Trypanosoma cruzi. Among all of the reported infectious diseases (n=9), there were seven studies presenting cases of tuberculosis. The results were also compared inter-culturally. In 61 studies (37 epidemiological and 24 case reports) more than 6400 mummified individuals were analysed. By contrast, meta-analytic data for ancient Egyptian mummies (Zweifel et al., 2009) included about 3000 analysed individuals in 131 studies (85 case reports and 46 epidemiological studies). In general, ancient Egyptian mummies were shown to be intentionally mummified, whereas the Pre-Columbian American mummies showed a great diversity of spontaneous mummification. However, ritualistic mummification methods were also practised (n=2). This study's results shall assist to improve evidence-based research in palaeopathology. Copyright © 2014 Elsevier GmbH. All rights reserved.

  2. Expression Analysis of Immune Related Genes Identified from the Coelomocytes of Sea Cucumber (Apostichopus japonicus) in Response to LPS Challenge

    PubMed Central

    Dong, Ying; Sun, Hongjuan; Zhou, Zunchun; Yang, Aifu; Chen, Zhong; Guan, Xiaoyan; Gao, Shan; Wang, Bai; Jiang, Bei; Jiang, Jingwei

    2014-01-01

    The sea cucumber (Apostichopus japonicus) occupies a basal position during the evolution of deuterostomes and is also an important aquaculture species. In order to identify more immune effectors, transcriptome sequencing of A. japonicus coelomocytes in response to lipopolysaccharide (LPS) challenge was performed using the Illumina HiSeq™ 2000 platform. One hundred and seven differentially expressed genes were selected and divided into four functional categories including pathogen recognition (25 genes), reorganization of cytoskeleton (27 genes), inflammation (41 genes) and apoptosis (14 genes). They were analyzed to elucidate the mechanisms of host-pathogen interactions and downstream signaling transduction. Quantitative real-time polymerase chain reactions (qRT-PCRs) of 10 representative genes validated the accuracy and reliability of RNA sequencing results with the correlation coefficients from 0.88 to 0.98 and p-value <0.05. Expression analysis of immune-related genes after LPS challenge will be useful in understanding the immune response mechanisms of A. japonicus against pathogen invasion and developing strategies for resistant markers selection. PMID:25421239

  3. Bactericidal activity identified in 2S Albumin from sesame seeds and in silico studies of structure-function relations.

    PubMed

    Maria-Neto, Simone; Honorato, Rodrigo V; Costa, Fábio T; Almeida, Renato G; Amaro, Daniel S; Oliveira, José T A; Vasconcelos, Ilka M; Franco, Octávio L

    2011-06-01

    Pathogenic bacteria constitute an important cause of hospital-acquired infections. However, the misuse of available bactericidal agents has led to the appearance of antibiotic-resistant strains. Thus, efforts to seek new antimicrobials with different action mechanisms would have an enormous impact. Here, a novel antimicrobial protein (SiAMP2) belonging to the 2S albumin family was isolated from Sesamum indicum kernels and evaluated against several bacteria and fungi. Furthermore, in silico analysis was conducted in order to identify conserved residues through other 2S albumin antimicrobial proteins (2S-AMPs). SiAMP2 specifically inhibited Klebsiella sp. Specific regions in the molecule surface where cationic (RR/RRRK) and hydrophobic (MEYWPR) residues are exposed and conserved were proposed as being involved in antimicrobial activity. This study reinforces the hypothesis that plant storage proteins might also play as pathogen protection providing an insight into the mechanism of action for this novel 2S-AMP and evolutionary relations between antimicrobial activity and 2S albumins.

  4. Genome-wide transcriptome analysis in the ovaries of two goats identifies differentially expressed genes related to fecundity.

    PubMed

    Miao, Xiangyang; Luo, Qingmiao; Qin, Xiaoyu

    2016-05-10

    The goats are widely kept as livestock throughout the world. Two excellent domestic breeds in China, the Laiwu Black and Jining Grey goats, have different fecundities and prolificacies. Although the goat genome sequences have been resolved recently, little is known about the gene regulations at the transcriptional level in goat. To understand the molecular and genetic mechanisms related to the fecundities and prolificacies, we performed genome-wide sequencing of the mRNAs from two breeds of goat using the next-generation RNA-Seq technology and used functional annotation to identify pathways of interest. Digital gene expression analysis showed 338 genes were up-regulated in the Jining Grey goats and 404 were up-regulated in the Laiwu Black goats. Quantitative real-time PCR verified the reliability of the RNA-Seq data. This study suggests that multiple genes responsible for various biological functions and signaling pathways are differentially expressed in the two different goat breeds, and these genes might be involved in the regulation of goat fecundity and prolificacy. Taken together, our study provides insight into the transcriptional regulation in the ovaries of 2 species of goats that might serve as a key resource for understanding goat fecundity, prolificacy and genetic diversity between species.

  5. Relating Science and Religion: An Ontology of Taxonomies and Development of a Research Tool for Identifying Individual Views

    NASA Astrophysics Data System (ADS)

    Yasri, Pratchayapong; Arthur, Shagufta; Smith, Mike U.; Mancy, Rebecca

    2013-10-01

    Understanding how individuals view the relationship between science and religion shows promise for explaining a range of aspects of teaching and learning in science. Several taxonomies, consisting of different views by which people relate science and religion, can be found in the philosophical literature. However, most of the science education literature uses these taxonomies selectively and with limited justification, hindering comparison between existing and future studies. The first aim of this paper is therefore to provide a comprehensive review of the different taxonomies described in the literature and to organise the different views according to their similarities and differences. The second aim of the paper is to present a new research tool developed on the basis of the findings of the literature review. This tool consists of a short questionnaire allowing educational researchers to identify the different viewpoints held by pre-service teachers, undergraduates majoring in biology and school learners. We present the tool itself and demonstrate its usefulness and versatility for future science education research based on three empirical studies covering a range of geographical areas, religious backgrounds, educational levels, age groups and genders.

  6. Identifying patients with poststroke mild cognitive impairment by pattern recognition of working memory load-related ERP.

    PubMed

    Li, Xiaoou; Yan, Yuning; Wei, Wenshi

    2013-01-01

    The early detection of subjects with probable cognitive deficits is crucial for effective appliance of treatment strategies. This paper explored a methodology used to discriminate between evoked related potential signals of stroke patients and their matched control subject