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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. All Information Is Not Equal: Using the Literature Databases PubMed and The Cochrane Library for Identifying the Evidence on Granulocyte Transfusion Therapy

    PubMed Central

    Metzendorf, Maria-Inti; Schulz, Manuela; Braun, Volker

    2014-01-01

    Summary To be able to take well-informed decisions or carry out sound research, clinicians and researchers alike require specific information seeking skills matching their respective information needs. Biomedical information is traditionally available via different literature databases. This article gives an introduction to two diverging sources, PubMed (23 million references) and The Cochrane Library (800,000 references), both of which offer sophisticated instruments for searching an increasing amount of medical publications of varied quality and ambition. Whereas PubMed as an unfiltered source of primary literature comprises all different kinds of publication types occurring in academic journals, The Cochrane Library is a pre-filtered source which offers access to either synthesized publication types or critically appraised and carefully selected references. A search approach has to be carried out deliberately and requires a good knowledge on the scope and features of the databases as well as on the ability to build a search strategy in a structured way. We present a specific and a sensitive search approach, making use of both databases within two application case scenarios in order to identify the evidence on granulocyte transfusions for infections in adult patients with neutropenia. PMID:25538539

  7. 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

  8. Identifying Adverse Drug Events by Relational Learning.

    PubMed

    Page, David; Costa, Vítor Santos; Natarajan, Sriraam; Barnard, Aubrey; Peissig, Peggy; Caldwell, Michael

    2012-07-01

    The pharmaceutical industry, consumer protection groups, users of medications and government oversight agencies are all strongly interested in identifying adverse reactions to drugs. While a clinical trial of a drug may use only a thousand patients, once a drug is released on the market it may be taken by millions of patients. As a result, in many cases adverse drug events (ADEs) are observed in the broader population that were not identified during clinical trials. Therefore, there is a need for continued, post-marketing surveillance of drugs to identify previously-unanticipated ADEs. This paper casts this problem as a reverse machine learning task, related to relational subgroup discovery and provides an initial evaluation of this approach based on experiments with an actual EMR/EHR and known adverse drug events. PMID:24955289

  9. PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.

    PubMed

    Ding, Jing; Hughes, Laron M; Berleant, Daniel; Fulmer, Andy W; Wurtele, Eve Syrkin

    2006-02-01

    MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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. PMID:24341067

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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. PMID:27242035

  2. 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. PMID:21553803

  3. 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. PMID:23442731

  4. 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.

  5. 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

  6. Identifying the information for the visual perception of relative phase.

    PubMed

    Wilson, Andrew D; Bingham, Geoffrey P

    2008-04-01

    The production and perception of coordinated rhythmic movement are very specifically structured. For production and perception, 0 degree mean relative phase is stable, 180 degrees is less stable, and no other state is stable without training. It has been hypothesized that perceptual stability characteristics underpin the movement stability characteristics, which has led to the development of a phase-driven oscillator model (e.g., Bingham, 2004a, 2004b). In the present study, a novel perturbation method was used to explore the identity of the perceptual information being used in rhythmic movement tasks. In the three conditions, relative position, relative speed, and frequency (variables motivated by the model) were selectively perturbed. Ten participants performed a judgment task to identify 0 degree or 180 degrees under these perturbation conditions, and 8 participants who had been trained to visually discriminate 90 degrees performed the task with perturbed 90 degrees displays. Discrimination of 0 degree and 180 degrees was unperturbed in 7 out of the 10 participants, but discrimination of 90 degrees was completely disrupted by the position perturbation and was made noisy by the frequency perturbation. We concluded that (1) the information used by most observers to perceive relative phase at 0 degree and 180 degrees was relative direction and (2) becoming an expert perceiver of 90 degrees entails learning a new variable composed of position and speed.

  7. 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

  8. 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

  9. The use of PubMed/Medline in psychiatry. 3: Searching PubMed.

    PubMed

    Theander, Sten S

    2006-01-01

    This paper is the third in a series of three, intended as a tutorial in the use of PubMed/Medline for an inexperienced user. The papers have the following contents: I--a description of NLM, Medline, PubMed and the system of Medical Subject Headings (MeSH), which form the basis for the indexing of scientific articles, books and other items at NLM. II--A description and a tutorial of the PubMed search window. III--The present article deals mainly with the searching for references in PubMed. Ways of restricting and concentrating the search are presented, and exercises are proposed. A reader may also find guidance for a search for medical books in the NLM Catalog, and in the use of tools like Related Articles, Bookshelf, and Index. With eating disorders as an example, more information is presented on the use of MeSH terms.

  10. 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. PMID:1933661

  11. 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.

  12. 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…

  13. 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

  14. Trends and topics in eye disease research in PubMed from 2010 to 2014

    PubMed Central

    Denion, Eric; Mortemousque, Bruno; Mouriaux, Fréderic

    2016-01-01

    Background: The purpose of this study is to provide a report on scientific production during the period 2010–2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. Methods: A PubMed search was carried out to extract articles related to eye diseases during the period 2010–2014. Data were downloaded and processed through developed PHP scripts for further analysis. Results: A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as “core journals” according to Braford’s law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Conclusions: Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010–2014 and allows us to better understand this field. PMID:26819840

  15. 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…

  16. Identifying novel resistance genes in rice wild relatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast and sheath blight are major fungal diseases of cultivated rice (Oryza sativa L. ) that limit Arkansas rough rice yields and market potential. Resistance to these diseases has been found in rice wild relatives (Oryza spp.) A collection of these wild relatives originating from outside the U...

  17. 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.

  18. 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. PMID:26004792

  19. 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.

  20. 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,…

  1. 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. PMID:27350512

  2. 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.

  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. 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

  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. NEMO: Extraction and normalization of organization names from PubMed affiliation strings

    PubMed Central

    Jonnalagadda, Siddhartha; Topham, Philip

    2010-01-01

    Background. We are witnessing an exponential increase in biomedical research citations in PubMed. However, translating biomedical discoveries into practical treatments is estimated to take around 17 years, according to the 2000 Yearbook of Medical Informatics, and much information is lost during this transition. Pharmaceutical companies spend huge sums to identify opinion leaders and centers of excellence. Conventional methods such as literature search, survey, observation, self-identification, expert opinion, and sociometry not only need much human effort, but are also noncomprehensive. Such huge delays and costs can be reduced by “connecting those who produce the knowledge with those who apply it”. A humble step in this direction is large scale discovery of persons and organizations involved in specific areas of research. This can be achieved by automatically extracting and disambiguating author names and affiliation strings retrieved through Medical Subject Heading (MeSH) terms and other keywords associated with articles in PubMed. In this study, we propose NEMO (Normalization Engine for Matching Organizations), a system for extracting organization names from the affiliation strings provided in PubMed abstracts, building a thesaurus (list of synonyms) of organization names, and subsequently normalizing them to a canonical organization name using the thesaurus. Results: We used a parsing process that involves multi-layered rule matching with multiple dictionaries. The normalization process involves clustering based on weighted local sequence alignment metrics to address synonymy at word level, and local learning based on finding connected components to address synonymy. The graphical user interface and java client library of NEMO are available at http://lnxnemo.sourceforge.net . Conclusion: NEMO is developed to associate each biomedical paper and its authors with a unique organization name and the geopolitical location of that organization. This system

  7. 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

  8. 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.

  9. 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/.

  10. 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.

  11. 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

    2016-01-01

    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

  12. 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

  13. The inclusion of an online journal in PubMed central - a difficult path.

    PubMed

    Grech, Victor

    2016-01-01

    The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database. PMID:27244254

  14. 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

  15. 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

  16. Use of Event-Related Potentials to Identify Language and Reading Skills

    ERIC Educational Resources Information Center

    Molfese, Victoria J.; Molfese, Dennis L.; Beswick, Jennifer L.; Jacobi-Vessels, Jill; Molfese, Peter J.; Molnar, Andrew E.; Wagner, Mary C.; Haines, Brittany L.

    2008-01-01

    The extent to which oral language and emergent literacy skills are influenced by event-related potential measures of phonological processing was examined. Results revealed that event-related potential responses identify differences in letter naming but not receptive language skills.

  17. 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

  18. Identifying and prioritizing disease-related genes based on the network topological features.

    PubMed

    Li, Zhan-Chao; Lai, Yan-Hua; Chen, Li-Li; Xie, Yun; Dai, Zong; Zou, Xiao-Yong

    2014-12-01

    Identifying and prioritizing disease-related genes are the most important steps for understanding the pathogenesis and discovering the therapeutic targets. The experimental examination of these genes is very expensive and laborious, and usually has a higher false positive rate. Therefore, it is highly desirable to develop computational methods for the identification and prioritization of disease-related genes. In this study, we develop a powerful method to identify and prioritize candidate disease genes. The novel network topological features with local and global information are proposed and adopted to characterize genes. The performance of these novel features is verified based on the 10-fold cross-validation test and leave-one-out cross-validation test. The proposed features are compared with the published features, and fused strategy is investigated by combining the current features with the published features. And, these combination features are also utilized to identify and prioritize Parkinson's disease-related genes. The results indicate that identified genes are highly related to some molecular process and biological function, which provides new clues for researching pathogenesis of Parkinson's disease. The source code of Matlab is freely available on request from the authors. PMID:25183318

  19. 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…

  20. Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways

    PubMed Central

    Modena, Brian D.; Tedrow, John R.; Milosevic, Jadranka; Bleecker, Eugene R.; Meyers, Deborah A.; Wu, Wei; Bar-Joseph, Ziv; Erzurum, Serpil C.; Gaston, Benjamin M.; Busse, William W.; Jarjour, Nizar N.; Kaminski, Naftali

    2014-01-01

    Rationale Although asthma is recognized as a heterogeneous disease associated with clinical phenotypes, the molecular basis of these phenotypes remains poorly understood. Although genomic studies have successfully broadened our understanding in diseases such as cancer, they have not been widely used in asthma studies. Objectives To link gene expression patterns to clinical asthma phenotypes. Methods We used a microarray platform to analyze bronchial airway epithelial cell gene expression in relation to the asthma biomarker fractional exhaled nitric oxide (FeNO) in 155 subjects with asthma and healthy control subjects from the Severe Asthma Research Program (SARP). Measurements and Main Results We first identified a diverse set of 549 genes whose expression correlated with FeNO. We used k-means to cluster the patient samples according to the expression of these genes, identifying five asthma clusters/phenotypes with distinct clinical, physiological, cellular, and gene transcription characteristics—termed “subject clusters” (SCs). To then investigate differences in gene expression between SCs, a total of 1,384 genes were identified that highly differentiated the SCs at an unadjusted P value < 10−6. Hierarchical clustering of these 1,384 genes identified nine gene clusters or “biclusters,” whose coexpression suggested biological characteristics unique to each SC. Although genes related to type 2 inflammation were present, novel pathways, including those related to neuronal function, WNT pathways, and actin cytoskeleton, were noted. Conclusions These findings show that bronchial epithelial cell gene expression, as related to the asthma biomarker FeNO, can identify distinct asthma phenotypes, while also suggesting the presence of underlying novel gene pathways relevant to these phenotypes. PMID:25338189

  1. 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

  2. [Identifying and solving drug-related problems in terms of the community pharmacist].

    PubMed

    Masaryková, Lucia; Fulmeková, Magdaléna; Lehocká, Lubica; Fazekaš, Tomáš

    2014-02-01

    The issue of drug related problems (DRPs) has been known and dealt with in many studies for a long time. It is primarily due to the fact that drug-related problems have the potential to increase patients morbidity and mortality in particular. The issue of identifying and solving drug-related problems in the area of pharmacotherapy by community pharmacists in the Slovak Republic, unlike in other European countries such as the Netherlands and the United Kingdom, is still at the beginning and gradually developing. The aim of the survey was to obtain information from pharmacy practice concerning the current state and possible solutions of potential risks of medicines in the form of drug-related problems of patients from community pharmacists point of view as well as to find out the role and status of community pharmacists in identifying and solving drug-related problems. A questionnaire survey using a sample of 237 respondents, its statistical processing and evaluation revealed the drug-related problems frequency met at their patients (the most common types of DRPs, their causes and subsequent intervention), as well as the opinions of community pharmacists on their current possibilities of (legislative, material, personnel, time) solving and risk-rating therapies for patients.

  3. 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

  4. 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.

  5. Cannabis-related hospitalizations: unexpected serious events identified through hospital databases

    PubMed Central

    Jouanjus, Emilie; Leymarie, Florence; Tubery, Marie; Lapeyre-Mestre, Maryse

    2011-01-01

    AIMS Cannabis is the most prevalent illicit drug used worldwide and can be responsible for serious health defects in users. However, the risk related to cannabis consumption is not well established. The present study aimed to assess cannabis-related adverse events leading to hospitalization, and to estimate the corresponding annual risk for consumers. METHODS Participants were patients admitted to the public hospitals in the Toulouse area (France) between January 2004 and December 2007 in relation to the use of cannabis. Reasons for admission and other occurring events were identified through hospital discharge summaries. We described all observed adverse events (AEs) and estimated their regional incidence on the basis of cannabis consumption data. RESULTS We included 200 patients, and identified a total of 619 adverse events (AEs), one of which was lethal. Psychiatric disorders involved 57.7% of patients and accounted for 18.2% of AEs. Most frequent outcomes were central and peripheral nervous system disorders (15.8% of AEs), acute intoxication (12.1%), respiratory system disorders (11.1%) and cardiovascular disorders (9.5%). We estimated that in 2007 the incidence of cannabis-related AEs in the Midi-Pyrenees region ranged from 1.2 per 1000 regular cannabis users (95% confidence interval (CI) 0.7, 1.6) to 3.2 (95% CI 2.5, 3.9). CONCLUSIONS Cannabis use is associated with complications, considered to be serious since they lead to hospitalization. Beyond the well-known and widely investigated psychiatric events, serious cerebro and cardiovascular complications have been identified. These findings contribute to improve the knowledge of cannabis-related adverse events. PMID:21204913

  6. Identifying aging-related genes in mouse hippocampus using gateway nodes

    PubMed Central

    2014-01-01

    Background High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph theoretic methodology can be applied to network models to increase efficiency and speed of analysis. In this project, we propose a network model that examines temporal data from mouse hippocampus at the transcriptional level via correlation of gene expression. Using this model, we formally define the concept of “gateway” nodes, loosely defined as nodes representing genes co-expressed in multiple states. We show that the proposed network model allows us to identify target genes implicated in hippocampal aging-related processes. Results By mining gateway genes related to hippocampal aging from networks made from gene expression in young and middle-aged mice, we provide a proof-of-concept of existence and importance of gateway nodes. Additionally, these results highlight how network analysis can act as a supplement to traditional statistical analysis of differentially expressed genes. Finally, we use the gateway nodes identified by our method as well as functional databases and literature to propose new targets for study of aging in the mouse hippocampus. Conclusions This research highlights the need for methods of temporal comparison using network models and provides a systems biology approach to extract information from correlation networks of gene expression. Our results identify a

  7. Exploring methods for identifying related patient safety events using structured and unstructured data.

    PubMed

    Fong, Allan; Hettinger, A Zachary; Ratwani, Raj M

    2015-12-01

    Most healthcare systems have implemented patient safety event reporting systems to identify safety hazards. Searching the safety event data to find related patient safety reports and identify trends is challenging given the complexity and quantity of these reports. Structured data elements selected by the event reporter may be inaccurate and the free-text narrative descriptions are difficult to analyze. In this paper we present and explore methods for utilizing both the unstructured free-text and structured data elements in safety event reports to identify and rank similar events. We evaluate the results of three different free-text search methods, including a unique topic modeling adaptation, and structured element weights, using a patient fall use case. The various search techniques and weight combinations tended to prioritize different aspects of the event reports leading to different search and ranking results. These search and prioritization methods have the potential to greatly improve patient safety officers, and other healthcare workers, understanding of which safety event reports are related.

  8. 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. PMID:25918679

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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'.

  15. 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

  16. 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.

  17. Identifying the relative priorities of subpopulations for containing infectious disease spread.

    PubMed

    Xia, Shang; Liu, Jiming; Cheung, William

    2013-01-01

    In response to the outbreak of an emerging infectious disease, e.g., H1N1 influenza, public health authorities will take timely and effective intervention measures to contain disease spread. However, due to the scarcity of required resources and the consequent social-economic impacts, interventions may be suggested to cover only certain subpopulations, e.g., immunizing vulnerable children and the elderly as well as closing schools or workplaces for social distancing. Here we are interested in addressing the question of how to identify the relative priorities of subpopulations for two measures of disease intervention, namely vaccination and contact reduction, especially when these measures are implemented together at the same time. We consider the measure of vaccination that immunizes susceptible individuals in different age subpopulations and the measure of contact reduction that cuts down individuals' effective contacts in different social settings, e.g., schools, households, workplaces, and general communities. In addition, we construct individuals' cross-age contact frequency matrix by inferring basic contact patterns respectively for different social settings from the socio-demographical census data. By doing so, we present a prioritization approach to identifying the target subpopulations that will lead to the greatest reduction in the number of disease transmissions. We calculate the relative priorities of subpopulations by considering the marginal effects of reducing the reproduction number for the cases of vaccine allocation by age and contact reduction by social setting. We examine the proposed approach by revisiting the real-world scenario of the 2009 Hong Kong H1N1 influenza epidemic and determine the relative priorities of subpopulations for age-specific vaccination and setting-specific contact reduction. We simulate the influenza-like disease spread under different settings of intervention. The results have shown that the proposed approach can improve

  18. 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

  19. 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.

  20. Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase.

    PubMed

    Berhane, Beniam T; Zong, Chenggong; Liem, David A; Huang, Aaron; Le, Steven; Edmondson, Ricky D; Jones, Richard C; Qiao, Xin; Whitelegge, Julian P; Ping, Peipei; Vondriska, Thomas M

    2005-08-01

    Proteomic profiling of accessible bodily fluids, such as plasma, has the potential to accelerate biomarker/biosignature development for human diseases. The HUPO Plasma Proteome Project pilot phase examined human plasma with distinct proteomic approaches across multiple laboratories worldwide. Through this effort, we confidently identified 3020 proteins, each requiring a minimum of two high-scoring MS/MS spectra. A critical step subsequent to protein identification is functional annotation, in particular with regard to organ systems and disease. Performing exhaustive literature searches, we have manually annotated a subset of these 3020 proteins that have cardiovascular-related functions on the basis of an existing body of published information. These cardiovascular-related proteins can be organized into eight groups: markers of inflammation and/or cardiovascular disease, vascular and coagulation, signaling, growth and differentiation, cytoskeletal, transcription factors, channels/receptors and heart failure and remodeling. In addition, analysis of the peptide per protein ratio for MS/MS identification reveals group-specific trends. These findings serve as a resource to interrogate the functions of plasma proteins, and moreover, the list of cardiovascular-related proteins in plasma constitutes a baseline proteomic blueprint for the future development of biosignatures for diseases such as myocardial ischemia and atherosclerosis. PMID:16052623

  1. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia

    PubMed Central

    van Uitert, Miranda; Moerland, Perry D.; Enquobahrie, Daniel A.; Laivuori, Hannele; van der Post, Joris A. M.; Ris-Stalpers, Carrie; Afink, Gijs B.

    2015-01-01

    Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite) and protein-protein associations (STRING). This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome). The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300) and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia. PMID:26171964

  2. Age-related changes in mesenchymal stem cells identified using a multi-omics approach.

    PubMed

    Peffers, M J; Collins, J; Fang, Y; Goljanek-Whysall, K; Rushton, M; Loughlin, J; Proctor, C; Clegg, P D

    2016-01-01

    Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based treatments for many clinical diseases and injuries. Ageing is associated with various altered cellular phenotypes coupled with a variety of transcriptional, epigenetic and translational changes. Furthermore, the regeneration potential of MSCs is reduced with increasing age and is correlated with changes in cellular functions. This study used a systems biology approach to investigate the transcriptomic (RNASeq), epigenetic (miRNASeq and DNA methylation) and protein alterations in ageing MSCs in order to understand the age-related functional and biological variations, which may affect their applications to regenerative medicine. We identified no change in expression of the cellular senescence markers. Alterations were evident at both the transcriptional and post-transcriptional level in a number of transcription factors. There was enrichment in genes involved in developmental disorders at mRNA and differential methylated loci (DML) level. Alterations in energy metabolism were apparent at the DML and protein level. The microRNA miR-199b-5p, whose expression was reduced in old MSCs, had predicted gene targets involved in energy metabolism and cell survival. Additionally, enrichment of DML and proteins in cell survival was evident. Enrichment in metabolic processes was revealed at the protein level and in genes identified as undergoing alternate splicing. Overall, an altered phenotype in MSC ageing at a number of levels implicated roles for inflamm-ageing and mitochondrial ageing. Identified changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients. PMID:26853623

  3. Applying the Fisher score to identify Alzheimer's disease-related genes.

    PubMed

    Yang, J; Liu, Y L; Feng, C S; Zhu, G Q

    2016-01-01

    Biologists and scientists can use the data from Alzheimer's disease (AD) gene expression microarrays to mine AD disease-related genes. Because of disadvantages such as small sample sizes, high dimensionality, and a high level of noise, it is difficult to obtain accurate and meaningful biological information from gene expression profiles. In this paper, we present a novel approach for utilizing AD microarray data to identify the morbigenous genes. The Fisher score, a classical feature selection method, is utilized to evaluate the importance of each gene. Genes with a large between-classes variance and small within-class variance are selected as candidate morbigenous genes. The results using an AD dataset show that the proposed approach is effective for gene selection. Satisfactory accuracy can be achieved by using only a small number of selected genes. PMID:27420981

  4. [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.

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

    PubMed

    Xiao, Ziya; Xue, Yuan; Yao, Chenling; 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

  6. New constituents related to 3-methyl-2,4-nonanedione identified in green tea.

    PubMed

    Naef, Regula; Jaquier, Alaini; Velluz, Alain; Maurer, Bruno

    2006-11-29

    The volatile constituents of two exquisite green tea varieties, Kiyosawa tea from Japan and Long Jing tea from China, were investigated in order to identify new compounds responsible for the characteristic flavor of a green tea brew. The extracts were prepared by solid-phase extraction using Oasis-HLB-cartridges. Besides the common compounds of green tea chemistry, the already described compounds 3-methyl-2,4-nonanedione (1) and 3-hydroxy-3-methyl-2,4-nonanedione (2), products of degradation of furan fatty acids, as well as three new compounds related to compound 1 were identified. These were 1-methyl-2-oxopropyl hexanoate (3), 1-methyl-2-oxoheptyl acetate (4) and 2-butyl-4,5-dimethyl-3(2H)-furanone (5). Their syntheses and spectroscopic data are reported. Compound 2 increases the sweet, creamy aroma and the characteristic mouthfeel of a green tea flavor, compounds 3 and 4 contribute to its floral, juicy notes and compound 5 exhibits an interesting sweet, buttery flavor.

  7. 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

  8. 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

  9. 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.

  10. 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. PMID:24376375

  11. 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

  12. 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. PMID:19042708

  13. Bibliometric analysis on retinoblastoma literatures in PubMed during 1929 to 2010

    PubMed Central

    Zhao, Zhi-Guang; Guo, Xue-Gang; Xu, Chang-Tai; Pan, Bo-Rong; Xu, Li-Xian

    2011-01-01

    AIM To determine the growth rule and tendency of retinoblastoma (Rb) literature, and to provide the basis for research of diagnosis, treatment and on Rb. METHODS Bibliometric analyses were carried out on Rb literatures which contain the descriptors of Rb in their titles or texts from 1929 to 2010 in PubMed database (www.ncbi.nlm.nih.gov/Pubmed). The biomedical journals referring to Rb by using bibliometric indicators were calculated. The principal bibliometric indicators, i.e., Price's and Bradford's laws to the increase or distribution of scientific literature, the participation index of languages and the journals were applied. By means of manual coding, Rb documents were classified according to documents studied and to statistical analysis. RESULTS During 1929-2010, there were 16162 literatures in the PubMed database including the word Rb. According to the literature type, it includes Review (n=2026), Randomized Controlled Trial (n=7), Practice guideline (n=3), meta-analysis (n=4), letter (n=215), editorial (n=98), clinical trial (n=115) and others (n=13694). By the statistical analysis, its equation is near power index (y=3.0477x2.6088, R2=0.9666). From 1929 to 2010, Rb literatures in English were primarily dominant (90.71%) and the amount of the literature in Chinese ranked the fourth (1.37%). By searching PubMed, 1420(8.8%) literatures covered were from 41 of 48 ophthalmological, and 406 (2.5%) literatures from 44 of 86 pediatrics journals that correlated with retinoblastoma (SCI-indexed). The data showed that the literatures of Rb were gradually increasing year by year and were approximate near power index during 1929-2010, and the document publishes published mainly in ophthalmological journals, and in English (90.71%), and showing that the study on Rb is a popular subject in the last half century. CONCLUSION The literatures of Rb are gradually increasing, mainly English in ophthalmologic journals. PMID:22553624

  14. 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.

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

    PubMed Central

    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. PMID:27367860

  16. 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

  17. 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. PMID:24361469

  18. 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.

  19. Sustained attention deficits in relation to psychometrically identified schizotypy: evaluating a potential endophenotypic marker.

    PubMed

    Gooding, Diane C; Matts, Christie W; Rollmann, Elizabeth A

    2006-02-15

    Sustained attention deficits have been posited as a potential endophenotypic marker of vulnerability to schizophrenia. Prior studies have indicated that schizophrenia patients, their first-degree relatives, and psychosis-prone individuals, identified on the basis of measures of positive schizotypy, have demonstrated sustained attention deficits. To date, there have been no published reports of sustained attention deficits in individuals with negative schizotypy, as measured by the revised Social Anhedonia Scale. In this study, we examined sustained attention, measured with the CPT-Identical Pairs version, in 160 individuals with elevated scores on the Chapman Perceptual Aberration and/or Magical Ideation Scales, 96 individuals with elevated scales on the Social Anhedonia Scale, and 137 controls. Both psychosis-prone groups performed more poorly than the controls in terms of discrimination ability, as measured by d', though the groups did not differ in terms of either their reaction time or overall response criterion (lnbeta). These results provide evidence that both positive and negative aspects of schizotypy are associated with sustained attention deficits, as measured by the Continuous Performance Test. The findings add to the converging evidence indicating that sustained attention deficits are a potential endophenotypic indicator of a schizophrenia diathesis.

  20. 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.

  1. Identifying psychiatric patients with serotonergic dysfunctions by event-related potentials.

    PubMed

    Hegerl, U; Juckel, G

    2000-04-01

    The increasing knowledge concerning anatomical structures and cellular processes underlying event-related potentials (ERP) as well as methodological advances in ERP data analysis (e.g. dipole source analysis) is beginning to bridge the gap between ERP and neurochemical aspects. Reliable indicators of the serotonin system are urgently needed because of its role in pathophysiology and as target of pharmacotherapeutic interventions in psychiatric disorders. Converging arguments from preclinical and clinical studies support the hypothesis that the loudness dependence of the auditory evoked N1/P2-response (LDAEP) is regulated by the level of central serotonergic neurotransmission. Dipole source analysis represents an important methodological advance in this context, because the two N1/P2-subcomponents, generated by the primary and secondary auditory cortex known to be differentially innervated by serotonergic fibres, can be separated. A pronounced LDAEP of primary auditory cortices is supposed to reflect low central serotonergic neurotransmission, and vice versa. LDAEP is a parameter with potential clinical value since subgroups of patients with a serotonergic dysfunction can be identified and can be treated more specifically. In depressed patients, a significant relationship between strong LDAEP, indicating low serotonergic function, and a favourable response to SSRI has been found. Additionally, there is evidence from several studies with patients with affective disorders that a strong LDAEP predicts favourable response to a preventive lithium treatment. PMID:12607207

  2. 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

  3. Electroretinogram analysis of relative spectral sensitivity in genetically identified dichromatic macaques

    PubMed Central

    Hanazawa, Akitoshi; Mikami, Akichika; Angelika, Puti Sulistyo; Takenaka, Osamu; Goto, Shunji; Onishi, Akishi; Koike, Satoshi; Yamamori, Tetsuo; Kato, Keichiro; Kondo, Aya; Suryobroto, Bambang; Farajallah, Achmad; Komatsu, Hidehiko

    2001-01-01

    The retinas of macaque monkeys usually contain three types of photopigment, providing them with trichromatic color vision homologous to that of humans. However, we recently used molecular genetic analysis to identify several macaques with a dichromatic genotype. The affected X chromosome of these animals contains a hybrid gene of long-wavelength-sensitive (L) and middle-wavelength-sensitive (M) photopigments instead of separate genes encoding L and M photopigments. The product of the hybrid gene exhibits a spectral sensitivity close to that of M photopigment; consequently, male monkeys carrying the hybrid gene are genetic protanopes, effectively lacking L photopigment. In the present study, we assessed retinal expression of L photopigment in monkeys carrying the hybrid gene. The relative sensitivities to middle-wavelength (green) and long-wavelength (red) light were measured by electroretinogram flicker photometry. We found the sensitivity to red light to be extremely low in protanopic male monkeys compared with monkeys with the normal genotype. In female heterozygotes, sensitivity to red light was intermediate between the genetic protanopes and normal monkeys. Decreased sensitivity to long wavelengths was thus consistent with genetic loss of L photopigment. PMID:11427736

  4. 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

    2016-01-01

    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

  5. 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.

  6. 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

  7. 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

  8. Identifying specific cues and contexts related to smoking craving for the development of effective virtual environments.

    PubMed

    García-Rodríguez, Olaya; Ferrer-García, Marta; Pericot-Valverde, Irene; Gutiérrez-Maldonado, José; Secades-Villa, Roberto; Carballo, José L

    2011-03-01

    Craving is considered the main variable associated with relapse after smoking cessation. Cue Exposure Therapy (CET) consists of controlled and repeated exposure to drug-related cues with the aim of extinguishing craving responses. Some virtual reality (VR) environments, such as virtual bars or parties, have previously shown their efficacy as tools for eliciting smoking craving. However, in order to adapt this technology to smoking cessation interventions, there is a need for more diverse environments that enhance the probability of generalization of extinction in real life. The main objective of this study was to identify frequent situations that produce smoking craving, as well as detecting specific craving cues in those contexts. Participants were 154 smokers who responded to an ad hoc self-administered inventory for assessing craving level in 12 different situations. Results showed that having a drink in a bar/pub at night, after having lunch/dinner in a restaurant and having a coffee in a cafe or after lunch/dinner at home were reported as the most craving-inducing scenarios. Some differences were found with regard to participants' gender, age, and number of cigarettes smoked per day. Females, younger people, and heavier smokers reported higher levels of craving in most situations. In general, the most widely cited specific cues across the contexts were people smoking, having a coffee, being with friends, and having finished eating. These results are discussed with a view to their consideration in the design of valid and reliable VR environments that could be used in the treatment of nicotine addicts who wish to give up smoking.

  9. 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

  10. 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. PMID:27417229

  11. 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

  12. 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.

  13. [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.

  14. 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

  15. Optimized search strategy for detecting scientifically strong studies on treatment through PubMed.

    PubMed

    Corrao, Salvatore; Colomba, Daniela; Argano, Christiano; Calvo, Luigi; Scaglione, Rosario; Licata, Giuseppe

    2012-06-01

    Our study was designed to optimize the search strategies based on the work of Haynes et al. for detecting randomized controlled trials (RCTs) through PubMed. In particular, we aimed to improve precision for broad and narrow searches on interventional studies. We used in addition to the string suggested by the Hedge Team the following: {NOT ((animals [mh] NOT humans [mh]) OR (review [pt] OR meta-analysis [pt]))} and tested its effectiveness. The search was carried out on a year's worth of articles from the PubMed database. We analyzed 35,590 bibliographic citations about four relevant major topics in internal medicine (hypertension, diabetes, heart failure, and hepatitis). Precision, percentage gain between the Hedge Team search strategies and the new one were computed and reported in the text. Moreover, a pooled analysis was carried out in terms of absolute precision difference. We observed better precision for both broad and narrow searches. However, effective gain resulted only for broad searches. In this case, bibliographic citation recall effectively reduced (-24 to -35 % retrieved citation with a gain of 32-54 %) without loss of information. The search strategy improved broad searches regarding each of the four considered topics. We think this new search strategy, based on a previous work of the Hedge team, could be a step forward and can save some time by researchers. PMID:22426813

  16. Improving efficacy of PubMed Clinical Queries for retrieving scientifically strong studies on treatment.

    PubMed

    Corrao, Salvatore; Colomba, Daniela; Arnone, Sabrina; Argano, Christiano; Di Chiara, Tiziana; Scaglione, Rosario; Licata, Giuseppe

    2006-01-01

    The authors evaluated the retrieval power of PubMed "Clinical Queries," narrow search string, about therapy in comparison with a modified search string to avoid possible retrieval bias. PubMed search strategy was compared to a slightly modified string that included the Britannic English term "randomised." The authors tested the two strings joined onto each of four terms concerning topics of broad interest: hypertension, hepatitis, diabetes, and heart failure. In particular, precision was computed for not-indexed citations. The added word "randomised" improved total citation retrieval in any case. Total retrieval gain for not-indexed citations ranged from 11.1% to 21.4%. A significant number of Randomized Controlled Trial(s) (RCT)s (9.1-18.2%) was retrieved for each of the selected topics. They were often recently published RCTs. The authors think that correction of the Clinical Queries filter (when they focus on therapy and use narrow searches) is necessary to avoid biased search results with loss of relevant and up-to-date scientifically sound information. PMID:16799123

  17. Identifying Differential Item Functioning Related to Student Socioeconomic Status and Investigating Sources Related to Classroom Opportunities to Learn

    ERIC Educational Resources Information Center

    Burkes, LaShona L.

    2009-01-01

    The current study identified socioeconomic status (SES) group differences in student performance on an eighth grade mathematics assessment derived from the Third/Trends in International Mathematics and Science Study (TIMSS) 2003. Differential item functioning (DIF) methodology was applied to examine SES group differences on item performance for…

  18. 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

  19. 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.

  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. 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…

  2. 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

  3. 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…

  4. 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…

  5. Identifying Gastric Cancer Related Genes Using the Shortest Path Algorithm and Protein-Protein Interaction Network

    PubMed Central

    Shi, Ying; Li, Li-Peng; Ren, Hui

    2014-01-01

    Gastric cancer, as one of the leading causes of cancer related deaths worldwide, causes about 800,000 deaths per year. Up to now, the mechanism underlying this disease is still not totally uncovered. Identification of related genes of this disease is an important step which can help to understand the mechanism underlying this disease, thereby designing effective treatments. In this study, some novel gastric cancer related genes were discovered based on the knowledge of known gastric cancer related ones. These genes were searched by applying the shortest path algorithm in protein-protein interaction network. The analysis results suggest that some of them are indeed involved in the biological process of gastric cancer, which indicates that they are the actual gastric cancer related genes with high probability. It is hopeful that the findings in this study may help promote the study of this disease and the methods can provide new insights to study various diseases. PMID:24729971

  6. 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.

  7. Modeling Actions of PubMed Users with N-Gram Language Models*

    PubMed Central

    Lin, Jimmy; Wilbur, W. John

    2008-01-01

    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®, the public gateway to the MEDLINE® 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. PMID:19684883

  8. 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.

  9. 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

    2016-07-01

    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.

  10. 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

    2016-07-01

    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. PMID:27346686

  11. 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

  12. Meta-analysis of age-related gene expression profiles identifies common signatures of aging

    PubMed Central

    de Magalhães, João Pedro; Curado, João; Church, George M.

    2009-01-01

    Motivation: Numerous microarray studies of aging have been conducted, yet given the noisy nature of gene expression changes with age, elucidating the transcriptional features of aging and how these relate to physiological, biochemical and pathological changes remains a critical problem. Results: We performed a meta-analysis of age-related gene expression profiles using 27 datasets from mice, rats and humans. Our results reveal several common signatures of aging, including 56 genes consistently overexpressed with age, the most significant of which was APOD, and 17 genes underexpressed with age. We characterized the biological processes associated with these signatures and found that age-related gene expression changes most notably involve an overexpression of inflammation and immune response genes and of genes associated with the lysosome. An underexpression of collagen genes and of genes associated with energy metabolism, particularly mitochondrial genes, as well as alterations in the expression of genes related to apoptosis, cell cycle and cellular senescence biomarkers, were also observed. By employing a new method that emphasizes sensitivity, our work further reveals previously unknown transcriptional changes with age in many genes, processes and functions. We suggest these molecular signatures reflect a combination of degenerative processes but also transcriptional responses to the process of aging. Overall, our results help to understand how transcriptional changes relate to the process of aging and could serve as targets for future studies. Availability: http://genomics.senescence.info/uarrays/signatures.html Contact: jp@senescence.info Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19189975

  13. 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.

  14. Using Research to Identify and Address Student Difficulties with Galilean and Special Relativity*

    NASA Astrophysics Data System (ADS)

    Vokos, Stamatis

    1998-04-01

    The Physics Education Group at the University of Washington has been engaged in an ongoing project in which research is used as a guide for the development of curriculum on Galilean and special relativity. Results from the analysis of student interviews, pretests and examinations form the basis for the design of instructional materials to supplement the lecture and textbook of a standard introductory course and an undergraduate course on relativity. Examples of specific student difficulties and instructional strategies to address them will be presented. * This work has been funded in part by NSF grants DUE 9354501 and 9727648, which include support from other Divisions of EHR and the Physics Division of MPS.

  15. 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.

  16. 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…

  17. 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

  18. Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms

    PubMed Central

    Kim, Sun; Yeganova, Lana; Wilbur, W. John

    2016-01-01

    Summary: 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. Availability and Implementation: https://www.ncbi.nlm.nih.gov/IRET/MESHABLE/ Contact: sun.kim@nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27288493

  19. 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

  20. Identifying the relation between trapping force of Laser Tweezers and Size of Microsphere particles

    NASA Astrophysics Data System (ADS)

    Diabre, Alexandra

    Optical trapping technique is the method in which micron and sub-micron particles can be studied. In this technique the laser pressure radiation creates the essential force to trap particles. This force depends on several parameters including the particles' indices of refraction, the specification of the beads surrounding environment and the characteristics of the implemented laser. On this work we present the outcome of the experiment we designed to analyze the trapping force. In this experiment we used micro sized beads with different indices of refraction, changed the viscosity of the surrounding environment of the beads and adjusted the power of the laser implemented. By analyzing the motion of the beads in several trials, the trapping force was estimated and its dependency to the parameters mentioned above was identified. Finally the outcomes of our experiment were compared with the theoretical reported results. This work was conducted under the supervision by Dr. Mitra Feizabadi.

  1. 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.

  2. 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

  3. A novel approach to identifying regulatory motifs in distantly related genomes

    PubMed Central

    Van Hellemont, Ruth; Monsieurs, Pieter; Thijs, Gert; De Moor, Bart; Van de Peer, Yves; Marchal, Kathleen

    2005-01-01

    Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic footprinting to distantly related organisms, we developed a two-step procedure that combines the advantages of sequence alignment and motif detection approaches. The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size. PMID:16420672

  4. 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. PMID:26146050

  5. 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

  6. Environmental Health Related Socio-Spatial Inequalities: Identifying "Hotspots" of Environmental Burdens and Social Vulnerability.

    PubMed

    Shrestha, Rehana; Flacke, Johannes; Martinez, Javier; van Maarseveen, Martin

    2016-01-01

    Differential exposure to multiple environmental burdens and benefits and their distribution across a population with varying vulnerability can contribute heavily to health inequalities. Particularly relevant are areas with high cumulative burdens and high social vulnerability termed as "hotspots". This paper develops an index-based approach to assess these multiple burdens and benefits in combination with vulnerability factors at detailed intra-urban level. The method is applied to the city of Dortmund, Germany. Using non-spatial and spatial methods we assessed inequalities and identified "hotspot" areas in the city. We found modest inequalities burdening higher vulnerable groups in Dortmund (CI = -0.020 at p < 0.05). At the detailed intra-urban level, however, inequalities showed strong geographical patterns. Large numbers of "hotspots" exist in the northern part of the city compared to the southern part. A holistic assessment, particularly at a detailed local level, considering both environmental burdens and benefits and their distribution across the population with the different vulnerability, is essential to inform environmental justice debates and to mobilize local stakeholders. Locating "hotspot" areas at this detailed spatial level can serve as a basis to develop interventions that target vulnerable groups to ensure a health conducive equal environment. PMID:27409625

  7. 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.

  8. Eye fixation-related potentials in free viewing identify encoding failures in change detection.

    PubMed

    Nikolaev, Andrey R; Nakatani, Chie; Plomp, Gijs; Jurica, Peter; van Leeuwen, Cees

    2011-06-01

    We considered the hypothesis that spontaneous dissociation between the direction of attention and eye movement causes encoding failure in change detection. We tested this hypothesis by analyzing eye fixation-related potentials (EFRP) at the encoding stage of a change blindness task; when participants freely inspect a scene containing an unmarked target region, in which a change will occur in a subsequent presentation. We measured EFRP amplitude prior to the execution of a saccade, depending on its starting or landing position relative to the target region. For those landings inside the target region, we found a difference in EFRP between correct detection and failure. Overall, correspondence between EFRP amplitude and the size of the saccade predicted successful detection of change; lack of correspondence was followed by change blindness. By contrast, saccade sizes and fixation durations around the target region were unrelated to subsequent change detection. Since correspondence between EFRP and eye movement indicates that overt attention was given to the target region, we concluded that overt attention is needed for successful encoding and that dissociation between eye movement and attention leads to change blindness.

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

    PubMed

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

    2016-04-01

    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

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

    PubMed

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

    2016-04-01

    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.

  11. Source investigation of personal particulates in relation to identify major routes of exposure among urban residentials

    NASA Astrophysics Data System (ADS)

    Gadkari, Neelima M.; Pervez, Shamsh

    Multiple 24-h average outdoor, indoor and personal respirable particulate matter (RPM) measurements were made in different urban residential colonies to determine major routes of personal exposure. The study area was Bhilai-Durg, District Durg, Chhattisgarh, India. About 100 residentials from each of two selected colonies have been surveyed for consent to participate in the study and for preparation of time-activity diary. On the basis of their time-activity diary, residentials have been categorized into three types: type-A, purely residential; type-B, residents who go out, and type-C, residence who go into work, specially in industrial area. A total of 28 adult participants (14 males and 14 females; mean age 40±15, range 21-61 years) were selected and monitored longitudinally during the summer (15 March-15 June) of 2004. Participants' residential indoor RPM level and also local ambient outdoor RPM levels were measured,and these are done simultaneous with personal monitoring. Residential indoor and ambient outdoors RPM monitoring sessions were throughout the year to obtain infiltration factor more precisely. To compare RPM levels with Indian National Ambient Air Quality Standards (NAAQS) of PM 10, simultaneous measurements of PM 10 were also done with the course of ambient outdoor RPM monitoring. RPM levels in indoors were higher compared to ambient outdoors. The annual average ratio RPM/PM 10 was found to vary significantly among residential sites due to variation in surroundings. Source contribution estimates (SCE) of personal exposure to RPM in selected 12 residences (six from each colony) have been investigated using chemical mass balance model CMB8. Ambient outdoors, residential indoors, soils and road-traffic borne RPM were identified as main routes and principal sources of personal RPM. Results of model output have shown that residential indoors and soil-borne RPM are the major routes of personal exposure.

  12. 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

  13. 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

  14. 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.

  15. 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. PMID:26577076

  16. 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.

  17. 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

  18. A Search Engine to Access PubMed Monolingual Subsets: Proof of Concept and Evaluation in French

    PubMed Central

    Schuers, Matthieu; Soualmia, Lina Fatima; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse; Darmoni, Stéfan Jacques

    2014-01-01

    Background PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. Objective The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). Methods To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. Results More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. Conclusions It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese. PMID:25448528

  19. Sex Disparity in Food Allergy: Evidence from the PubMed Database.

    PubMed

    Kelly, Caleb; Gangur, Venu

    2009-01-01

    Food allergies are potentially fatal immune-mediated disorders that are growing globally. The relationship between sex and food allergy remains incompletely understood. Here we tested the hypothesis that, should sex influence the clinical response to food allergens, this would be reflected by a sex disparity in published studies of food allergy. We performed a systematic search of the PubMed literature for IgE-mediated allergy to 11 allergenic foods of international regulatory importance. No date restriction was used and only articles in English were considered. Of the 4744 articles retrieved, 591 met the inclusion criteria representing 17528 subjects with food allergies. Whereas among children with food allergies, 64.35% were males and 35.65% were females (male/female ratio, 1.80), among adults 34.82% were males and 65.18% were females (male/female ratio, 0.53). Consequently, these data argue that there is need for further investigation to define the role of sex in the pathogenesis of food allergy.

  20. 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.

  1. 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. PMID:26995041

  2. 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…

  3. Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMed.

    PubMed

    Hooijmans, Carlijn R; Tillema, Alice; Leenaars, Marlies; Ritskes-Hoitinga, Merel

    2010-07-01

    Collecting and analysing all available literature before starting an animal experiment is important and it is indispensable when writing a systematic review (SR) of animal research. Writing such review prevents unnecessary duplication of animal studies and thus unnecessary animal use (Reduction). One of the factors currently impeding the production of 'high-quality' SRs in laboratory animal science is the fact that searching for all available literature concerning animal experimentation is rather difficult. In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies. This filter was compared with the method most frequently used, the PubMed Limit: Animals, and validated further by performing two PubMed topic searches. Our filter performs much better than the PubMed limit: it retrieves, on average, 7% more records. Other important advantages of our filter are that it also finds the most recent records and that it is easy to use. All in all, by using our search filter in PubMed, all available literature concerning animal studies on a specific topic can easily be found and assessed, which will help in increasing the scientific quality and thereby the ethical validity of animal experiments.

  4. Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

    PubMed Central

    Hu, Yang; Wu, Xiaoliang; Ma, Rui

    2016-01-01

    Many disease-related single nucleotide polymorphisms (SNPs) have been inferred from genome-wide association studies (GWAS) in recent years. Numerous studies have shown that some SNPs located in protein-coding regions are associated with numerous diseases by affecting gene expression. However, in noncoding regions, the mechanism of how SNPs contribute to disease susceptibility remains unclear. Enhancer elements are functional segments of DNA located in noncoding regions that play an important role in regulating gene expression. The SNPs located in enhancer elements may affect gene expression and lead to disease. We presented a method for identifying liver cancer-related enhancer SNPs through integrating GWAS and histone modification ChIP-seq data. We identified 22 liver cancer-related enhancer SNPs, 9 of which were regulatory SNPs involved in distal transcriptional regulation. The results highlight that these enhancer SNPs may play important roles in liver cancer. PMID:27429976

  5. Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data.

    PubMed

    Zhang, Tianjiao; Hu, Yang; Wu, Xiaoliang; Ma, Rui; Jiang, Qinghua; Wang, Yadong

    2016-01-01

    Many disease-related single nucleotide polymorphisms (SNPs) have been inferred from genome-wide association studies (GWAS) in recent years. Numerous studies have shown that some SNPs located in protein-coding regions are associated with numerous diseases by affecting gene expression. However, in noncoding regions, the mechanism of how SNPs contribute to disease susceptibility remains unclear. Enhancer elements are functional segments of DNA located in noncoding regions that play an important role in regulating gene expression. The SNPs located in enhancer elements may affect gene expression and lead to disease. We presented a method for identifying liver cancer-related enhancer SNPs through integrating GWAS and histone modification ChIP-seq data. We identified 22 liver cancer-related enhancer SNPs, 9 of which were regulatory SNPs involved in distal transcriptional regulation. The results highlight that these enhancer SNPs may play important roles in liver cancer. PMID:27429976

  6. 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.

  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. Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

    ERIC Educational Resources Information Center

    Hightower, Christy; Caldwell, Christy

    2010-01-01

    Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

  9. Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

    PubMed

    Davis, Philip M

    2013-07-01

    Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers. PMID:23554455

  10. Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

    PubMed

    Davis, Philip M

    2013-07-01

    Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

  11. 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

  12. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure.

    PubMed

    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

  13. 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

  14. 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.

  15. 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.

  16. 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. PMID:27591593

  17. 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

  18. Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors.

    PubMed

    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.

  19. 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

    2012-08-01

    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. PMID:22797727

  20. 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

  1. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer.

    PubMed

    Chen, Lei; Yang, Jing; 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

  2. 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

  3. Identifying cognitive preferences for attractive female faces: an event-related potential experiment using a study-test paradigm.

    PubMed

    Zhang, Yan; Kong, Fanchang; Chen, Hong; Jackson, Todd; Han, Li; Meng, Jing; Yang, Zhou; Gao, Jianguo; Najam ul Hasan, Abbasi

    2011-11-01

    In this experiment, sensitivity to female facial attractiveness was examined by comparing event-related potentials (ERPs) in response to attractive and unattractive female faces within a study-test paradigm. Fourteen heterosexual participants (age range 18-24 years, mean age 21.67 years) were required to judge 84 attractive and 84 unattractive face images as either "attractive" or "unattractive." They were then asked whether they had previously viewed each face in a recognition task in which 50% of the images were novel. Analyses indicated that attractive faces elicited more enhanced ERP amplitudes than did unattractive faces in judgment (N300 and P350-550 msec) and recognition (P160 and N250-400 msec and P400-700 msec) tasks on anterior locations. Moreover, longer reaction times and higher accuracy rate were observed in identifying attractive faces than unattractive faces. In sum, this research identified neural and behavioral bases related to cognitive preferences for judging and recognizing attractive female faces. Explanations for the results are that attractive female faces arouse more intense positive emotions in participants than do unattractive faces, and they also represent reproductive fitness and mating value from the evolutionary perspective.

  4. Quality of reporting of complex healthcare interventions and applicability of the CReDECI list - a survey of publications indexed in PubMed

    PubMed Central

    2013-01-01

    Background The development and evaluation of complex interventions in healthcare has obtained increased awareness. The Medical Research Council’s (MRC) framework for the development and evaluation of complex interventions and its update offers guidance for researchers covering the phases development, feasibility/piloting, and evaluation. Comprehensive reporting of complex interventions enhances transparency and is essential for researchers and policy-makers. Recently, a set of 16 criteria for reporting complex interventions in healthcare (CReDECI) was published. The aim of this study is to evaluate the reporting quality in publications of complex interventions adhering to either the first or the updated MRC framework, and to evaluate the applicability of CReDECI. Methods A systematic PubMed search was conducted. Two reviewers independently checked titles and abstracts for inclusion. Trials on complex interventions adhering to the MRC framework and including an evaluation study in English and German were included. For all included trials and for all publications which reported on phases prior to the evaluation study, related publications were identified via forward citation tracking. The quality of reporting was assessed independently by two reviewers using CReDECI. Inter-rater agreement and time needed to complete the assessment were determined. Results Twenty-six publications on eight trials were included. The number of publications per trial ranged from 1 to 6 (mean 3.25). The trials demonstrate a good reporting quality for the criteria referring to the development and feasibility/piloting. For the criteria addressing the introduction of the intervention and the evaluation, quality of reporting varied widely. Two trials fulfilled 7 and 8 items respectively, five trials fulfilled one to five items and one trial offered no information on any item. The mean number of items with differing ratings per trial was two. The time needed to rate a trial ranged from 30 to

  5. 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.

  6. Using Clinical Data, Hypothesis Generation Tools and PubMed Trends to Discover the Association between Diabetic Retinopathy and Antihypertensive Drugs

    SciTech Connect

    Senter, Katherine G; Sukumar, Sreenivas R; Patton, Robert M; Chaum, Ed

    2015-01-01

    Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), -blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from the biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and -blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking -blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of -blockers in the clinical data. We determined that clinical use of -blockers should be minimized in diabetic patients to prevent retinal damage.

  7. 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.

  8. 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.

  9. 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.

  10. A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

    PubMed Central

    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

    2014-01-01

    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. PMID:25166276

  11. A survey of scientific production and collaboration rate among of medical library and information sciences in ISI, scopus and Pubmed databases during 2001-2010

    PubMed Central

    Yousefy, Alireza; Malekahmadi, Parisa

    2013-01-01

    Background: Research is essential for development. In other words, scientific development of each country can be evaluated by researchers’ scientific production. Understanding and assessing the activities of researchers for planning and policy making is essential. The significance of collaboration in the production of scientific publications in today's complex world where technology is everything is very apparent. Scientists realized that in order to get their work wildly used and cited to by experts, they must collaborate. The collaboration among researchers results in the development of scientific knowledge and hence, attainment of wider information. The main objective of this research is to survey scientific production and collaboration rate in philosophy and theoretical bases of medical library and information sciences in ISI, SCOPUS, and Pubmed databases during 2001-2010. Materials and Methods: This is a descriptive survey and scientometrics methods were used for this research. Then data gathered via check list and analyzed by the SPSS software. Collaboration rate was calculated according to the formula. Results: Among the 294 related abstracts about philosophy, and theoretical bases of medical library and information science in ISI, SCOPUS, and Pubmed databases during 2001-2010, the year 2007 with 45 articles has the most and the year 2003 with 16 articles has the least number of related collaborative articles in this scope. “B. Hjorland” with eight collaborative articles had the most one among Library and Information Sciences (LIS) professionals in ISI, SCOPUS, and Pubmed. Journal of Documentation with 29 articles and 12 collaborative articles had the most related articles. Medical library and information science challenges with 150 articles had first place in number of articles. Results also show that the most elaborative country in terms of collaboration point of view and number of articles was US. “University of Washington” and

  12. 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.

  13. An evaluation of the API ZYM system as a means of identifying Haemophilus somnus and related taxa.

    PubMed Central

    Groom, S C; Hazlett, M J; Little, P B

    1986-01-01

    The commercially available API ZYM microbiological identification system was evaluated for the rapid identification of Haemophilus somnus. Eighty-seven isolates of the organism had API ZYM profiles which were characteristic. The API ZYM profiles demonstrate clear differences between H. somnus and other genera but suggest a close association to three related organisms. Enzyme activity of H. somnus isolates were similar to organisms identified as Histophilus ovis, Haemophilus agni and strains UQV of Actinobacillus actinoides and Actinobacillus seminis but was clearly different from isolates of Pasteurella haemolytica, Pasteurella multocida, Bordetella bronchiseptica and group EF4. The API ZYM system allowed more rapid identification of H. somnus than conventional biochemical tests and may be a useful adjunct to conventional methods used for identification of H. somnus isolates. The test did not reveal obvious differences between isolates from various anatomic locations. PMID:3530416

  14. Identifying Psychosocial Stressors of Well-Being and Factors Related to Substance Use Among Latino Day Laborers

    PubMed Central

    2012-01-01

    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. PMID:21107694

  15. 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. PMID:26560806

  16. 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

  17. 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

  18. Genetic Networks of Complex Disorders: from a Novel Search Engine for PubMed Article Database.

    PubMed

    Jung, Jae-Yoon; Wall, Dennis Paul

    2013-01-01

    Finding genetic risk factors of complex disorders may involve reviewing hundreds of genes or thousands of research articles iteratively, but few tools have been available to facilitate this procedure. In this work, we built a novel publication search engine that can identify target-disorder specific, genetics-oriented research articles and extract the genes with significant results. Preliminary test results showed that the output of this engine has better coverage in terms of genes or publications, than other existing applications. We consider it as an essential tool for understanding genetic networks of complex disorders.

  19. Identifying barriers to recovery from work related upper extremity disorders: use of a collaborative problem solving technique.

    PubMed

    Shaw, William S; Feuerstein, Michael; Miller, Virginia I; Wood, Patricia M

    2003-08-01

    Improving health and work outcomes for individuals with work related upper extremity disorders (WRUEDs) may require a broad assessment of potential return to work barriers by engaging workers in collaborative problem solving. In this study, half of all nurse case managers from a large workers' compensation system were randomly selected and invited to participate in a randomized, controlled trial of an integrated case management (ICM) approach for WRUEDs. The focus of ICM was problem solving skills training and workplace accommodation. Volunteer nurses attended a 2 day ICM training workshop including instruction in a 6 step process to engage clients in problem solving to overcome barriers to recovery. A chart review of WRUED case management reports (n = 70) during the following 2 years was conducted to extract case managers' reports of barriers to recovery and return to work. Case managers documented from 0 to 21 barriers per case (M = 6.24, SD = 4.02) within 5 domains: signs and symptoms (36%), work environment (27%), medical care (13%), functional limitations (12%), and coping (12%). Compared with case managers who did not receive the training (n = 67), workshop participants identified more barriers related to signs and symptoms, work environment, functional limitations, and coping (p < .05), but not to medical care. Problem solving skills training may help focus case management services on the most salient recovery factors affecting return to work. PMID:12934861

  20. 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. PMID:27399969

  1. Relative brain signature: a population-based feature extraction procedure to identify functional biomarkers in the brain of alcoholics

    PubMed Central

    Karamzadeh, Nader; Ardeshirpour, Yasaman; Kellman, Matthew; Chowdhry, Fatima; Anderson, Afrouz; Chorlian, David; Wegman, Edward; Gandjbakhche, Amir

    2015-01-01

    Background A novel feature extraction technique, Relative-Brain-Signature (RBS), which characterizes subjects' relationship to populations with distinctive neuronal activity, is presented. The proposed method transforms a set of Electroencephalography's (EEG) time series in high dimensional space to a space of fewer dimensions by projecting time series onto orthogonal subspaces. Methods We apply our technique to an EEG data set of 77 abstinent alcoholics and 43 control subjects. To characterize subjects' relationship to the alcoholic and control populations, one RBS vector with respect to the alcoholic and one with respect to the control population is constructed. We used the extracted RBS vectors to identify functional biomarkers over the brain of alcoholics. To achieve this goal, the classification algorithm was used to categorize subjects into alcoholics and controls, which resulted in 78% accuracy. Results and Conclusions Using the results of the classification, regions with distinctive functionality in alcoholic subjects are detected. These affected regions, with respect to their spatial extent, are frontal, anterior frontal, centro-parietal, parieto-occiptal, and occipital lobes. The distribution of these regions over the scalp indicates that the impact of the alcohol in the cerebral cortex of the alcoholics is spatially diffuse. Our finding suggests that these regions engage more of the right hemisphere relative to the left hemisphere of the alcoholics' brain. PMID:26221569

  2. 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. PMID:26039408

  3. 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.

  4. Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.

    PubMed

    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; Buitink, Julia

    2015-10-01

    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

  5. 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

  6. 450K Epigenome-Wide Scan Identifies Differential DNA Methylation in Newborns Related to Maternal Smoking during Pregnancy

    PubMed Central

    Joubert, Bonnie R.; Håberg, Siri E.; Nilsen, Roy M.; Wang, Xuting; Vollset, Stein E.; Murphy, Susan K.; Huang, Zhiqing; Hoyo, Cathrine; Midttun, Øivind; Cupul-Uicab, Lea A.; Ueland, Per M.; Wu, Michael C.; Nystad, Wenche; Bell, Douglas A.; Peddada, Shyamal D.

    2012-01-01

    Background: Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear. Objective: We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy. Methods: We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K). Results: We found differential DNA methylation at epigenome-wide statistical significance (p-value < 1.06 × 10–7) for 26 CpGs mapped to 10 genes. We replicated findings for CpGs in AHRR, CYP1A1, and GFI1 at strict Bonferroni-corrected statistical significance in a U.S. birth cohort. AHRR and CYP1A1 play a key role in the aryl hydrocarbon receptor signaling pathway, which mediates the detoxification of the components of tobacco smoke. GFI1 is involved in diverse developmental processes but has not previously been implicated in responses to tobacco smoke. Conclusions: We identified a set of genes with methylation changes present at birth in children whose mothers smoked during pregnancy. This is the first study of differential methylation across the genome in relation to maternal smoking during pregnancy using the 450K platform. Our findings implicate epigenetic mechanisms in the pathogenesis of the adverse health outcomes associated with this important in utero exposure. PMID:22851337

  7. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

    PubMed

    Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

    2013-04-15

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

  8. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

    PubMed Central

    2013-01-01

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms. Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources. PMID:23734562

  9. Pharmacy journal abstracts published in PubMed that abide by the CONsolidated Standards Of Reporting Trials (CONSORT) guidelines.

    PubMed

    Blair, Daniel A; Hughes, Peter J; Woolley, Thomas W

    2014-04-01

    The purpose of this research was to determine the proportion of abstracts in pharmacy journals that are prepared according to the CONsolidated Standards Of Reporting Trials (CONSORT) criteria for abstracts. Certain abstracts for randomized controlled clinical trials (RCTs) indexed in PubMed were eligible for inclusion, with the primary endpoint being median overall compliance to CONSORT recommendations for abstracts. A total of 63 RCT abstracts were included in the analysis, with only 56% of the recommended CONSORT items represented in the sample. It is recommended that pharmacy journals encourage authors to follow CONSORT recommendations for abstracts when submitting RCTs for publication.

  10. 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.

  11. Expression analysis of immune related genes identified from the coelomocytes of sea cucumber (Apostichopus japonicus) in response to LPS challenge.

    PubMed

    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.

  12. 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

  13. Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress

    PubMed Central

    Rayapuram, Channabasavangowda; Idänheimo, Niina; Hunter, Kerri; Kimura, Sachie; Merilo, Ebe; Vaattovaara, Aleksia; Oracz, Krystyna; Kaufholdt, David; Pallon, Andres; Anggoro, Damar Tri; Glów, Dawid; Lowe, Jennifer; Zhou, Ji; Mohammadi, Omid; Puukko, Tuomas; Albert, Andreas; Lang, Hans; Ernst, Dieter; Kollist, Hannes; Brosché, Mikael; Durner, Jörg; Borst, Jan Willem; Collinge, David B.; Karpiński, Stanisław; Lyngkjær, Michael F.; Robatzek, Silke; Wrzaczek, Michael; Kangasjärvi, Jaakko

    2015-01-01

    Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (DUF26) in their ectodomain. The CRKs form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. We conducted a large-scale phenotyping approach of a nearly complete crk T-DNA insertion line collection showing that CRKs control important aspects of plant development and stress adaptation in response to biotic and abiotic stimuli in a non-redundant fashion. In particular, the analysis of reactive oxygen species (ROS)-related stress responses, such as regulation of the stomatal aperture, suggests that CRKs participate in ROS/redox signalling and sensing. CRKs play general and fine-tuning roles in the regulation of stomatal closure induced by microbial and abiotic cues. Despite their great number and high similarity, large-scale phenotyping identified specific functions in diverse processes for many CRKs and indicated that CRK2 and CRK5 play predominant roles in growth regulation and stress adaptation, respectively. As a whole, the CRKs contribute to specificity in ROS signalling. Individual CRKs control distinct responses in an antagonistic fashion suggesting future potential for using CRKs in genetic approaches to improve plant performance and stress tolerance. PMID:26197346

  14. 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. PMID:26851539

  15. Activity of identified wrist-related pallidal neurons during step and ramp wrist movements in the monkey.

    PubMed

    Hamada, I; DeLong, M R; Mano, N

    1990-12-01

    1. The activity of globus pallidus (GP) neurons (n = 1,117) was studied in two monkeys to reexamine the relation of neuronal activity to movement type (slow vs. fast) while they performed both a visually guided step and ramp wrist tracking task. To select neurons specifically related to wrist movements, we employed both a somatosensory examination of individual body parts and a statistical analysis of the strength of temporal coupling of neuronal discharges to active wrist movement. 2. Neuronal responses to somatosensory stimulation were studied in 1,000 high-frequency GP neurons, of which 686 exhibited clear responses to manipulation of body parts. Of the latter, 336 responded to passive manipulation of forelimb joints and 58 selectively to passive flexion or extension of the wrist. 3. In the external segment of GP (GPe), most neurons responding to passive wrist movement were found to be clustered in four to five adjacent, closely positioned (separated by 200 microns) tracks in single coronal planes. The clusters were irregular in shape with a maximal width of 800-1,000 microns. Separate clusters of neurons responsive to passive wrist movement were identified in planes 3 mm apart in one monkey and in planes 500 microns apart in the other. Multiple clusters of neurons were also found for neurons responsive to joints other than the wrist. These findings suggest a more discrete and complex representation of individual joints in the primate GP than previously conceived. 4. During the performance of the wrist flexion and extension task, 92 neurons showed clear and consistent changes in activity. For these neurons we measured, with a statistical method on a trial-by-trial basis, the strength of temporal coupling between the onset of active wrist movement and the onset of change in neuronal discharge rate. Fifteen neurons showed changes in activity time-locked to the onset of active wrist movement. 5. Twelve pallidal neurons were classified as "wrist-related" based on

  16. Identifying Biotic Integrity and Water Chemistry Relations in Nonwadeable Rivers of Wisconsin: Toward the Development of Nutrient Criteria

    NASA Astrophysics Data System (ADS)

    Weigel, Brian M.; Robertson, Dale M.

    2007-10-01

    We sampled 41 sites on 34 nonwadeable rivers that represent the types of rivers in Wisconsin, and the kinds and intensities of nutrient and other anthropogenic stressors upon each river type. Sites covered much of United States Environmental Protection Agency national nutrient ecoregions VII—Mostly Glaciated Dairy Region, and VIII—Nutrient Poor, Largely Glaciated upper Midwest. Fish, macroinvertebrates, and three categories of environmental variables including nutrients, other water chemistry, and watershed features were collected using standard protocols. We summarized fish assemblages by index of biotic integrity (IBI) and its 10 component measures, and macroinvertebrates by 2 organic pollution tolerance and 12 proportional richness measures. All biotic and environmental variables represented a wide range of conditions, with biotic measures ranging from poor to excellent status, despite nutrient concentrations being consistently higher than reference concentrations reported for the regions. Regression tree analyses of nutrients on a suite of biotic measures identified breakpoints in total phosphorus (~0.06 mg/l) and total nitrogen (~0.64 mg/l) concentrations at which biotic assemblages were consistently impaired. Redundancy analyses (RDA) were used to identify the most important variables within each of the three environmental variable categories, which were then used to determine the relative influence of each variable category on the biota. Nutrient measures, suspended chlorophyll a, water clarity, and watershed land cover type (forest or row-crop agriculture) were the most important variables and they explained significant amounts of variation within the macroinvertebrate ( R 2 = 60.6%) and fish ( R 2 = 43.6%) assemblages. The environmental variables selected in the macroinvertebrate model were correlated to such an extent that partial RDA analyses could not attribute variation explained to individual environmental categories, assigning 89% of the

  17. Identifying biotic integrity and water chemistry relations in nonwadeable rivers of Wisconsin: toward the development of nutrient criteria.

    PubMed

    Weigel, Brian M; Robertson, Dale M

    2007-10-01

    We sampled 41 sites on 34 nonwadeable rivers that represent the types of rivers in Wisconsin, and the kinds and intensities of nutrient and other anthropogenic stressors upon each river type. Sites covered much of United States Environmental Protection Agency national nutrient ecoregions VII--Mostly Glaciated Dairy Region, and VIII--Nutrient Poor, Largely Glaciated upper Midwest. Fish, macroinvertebrates, and three categories of environmental variables including nutrients, other water chemistry, and watershed features were collected using standard protocols. We summarized fish assemblages by index of biotic integrity (IBI) and its 10 component measures, and macroinvertebrates by 2 organic pollution tolerance and 12 proportional richness measures. All biotic and environmental variables represented a wide range of conditions, with biotic measures ranging from poor to excellent status, despite nutrient concentrations being consistently higher than reference concentrations reported for the regions. Regression tree analyses of nutrients on a suite of biotic measures identified breakpoints in total phosphorus (approximately 0.06 mg/l) and total nitrogen (approximately 0.64 mg/l) concentrations at which biotic assemblages were consistently impaired. Redundancy analyses (RDA) were used to identify the most important variables within each of the three environmental variable categories, which were then used to determine the relative influence of each variable category on the biota. Nutrient measures, suspended chlorophyll a, water clarity, and watershed land cover type (forest or row-crop agriculture) were the most important variables and they explained significant amounts of variation within the macroinvertebrate (R(2) = 60.6%) and fish (R(2) = 43.6%) assemblages. The environmental variables selected in the macroinvertebrate model were correlated to such an extent that partial RDA analyses could not attribute variation explained to individual environmental categories

  18. Identifying biotic integrity and water chemistry relations in nonwadeable rivers of Wisconsin: Toward the development of nutrient criteria

    USGS Publications Warehouse

    Weigel, B.M.; Robertson, D.M.

    2007-01-01

    We sampled 41 sites on 34 nonwadeable rivers that represent the types of rivers in Wisconsin, and the kinds and intensities of nutrient and other anthropogenic stressors upon each river type. Sites covered much of United States Environmental Protection Agency national nutrient ecoregions VII-Mostly Glaciated Dairy Region, and VIII-Nutrient Poor, Largely Glaciated upper Midwest. Fish, macroinvertebrates, and three categories of environmental variables including nutrients, other water chemistry, and watershed features were collected using standard protocols. We summarized fish assemblages by index of biotic integrity (IBI) and its 10 component measures, and macroinvertebrates by 2 organic pollution tolerance and 12 proportional richness measures. All biotic and environmental variables represented a wide range of conditions, with biotic measures ranging from poor to excellent status, despite nutrient concentrations being consistently higher than reference concentrations reported for the regions. Regression tree analyses of nutrients on a suite of biotic measures identified breakpoints in total phosphorus (~0.06 mg/l) and total nitrogen (~0.64 mg/l) concentrations at which biotic assemblages were consistently impaired. Redundancy analyses (RDA) were used to identify the most important variables within each of the three environmental variable categories, which were then used to determine the relative influence of each variable category on the biota. Nutrient measures, suspended chlorophyll a, water clarity, and watershed land cover type (forest or row-crop agriculture) were the most important variables and they explained significant amounts of variation within the macroinvertebrate (R 2 = 60.6%) and fish (R 2 = 43.6%) assemblages. The environmental variables selected in the macroinvertebrate model were correlated to such an extent that partial RDA analyses could not attribute variation explained to individual environmental categories, assigning 89% of the explained

  19. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae).

    PubMed

    Wang, Fan-Hong; Lu, Jin-Mei; Wen, Jun; Ebihara, Atsushi; Li, De-Zhu

    2016-01-01

    DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure. PMID:27603700

  20. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae)

    PubMed Central

    Wen, Jun; Ebihara, Atsushi; Li, De-Zhu

    2016-01-01

    DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure. PMID:27603700

  1. Transcriptomic Analysis of a Tertiary Relict Plant, Extreme Xerophyte Reaumuria soongorica to Identify Genes Related to Drought Adaptation

    PubMed Central

    Zhao, Pengshan; Yin, Hengxia; Zhao, Xin; Xiao, Honglang; Li, Xinrong; Chen, Guoxiong; Ma, Xiao-Fei

    2013-01-01

    Background Reaumuria soongorica is an extreme xerophyte shrub widely distributed in the desert regions including sand dune, Gobi and marginal loess of central Asia which plays a crucial role to sustain and restore fragile desert ecosystems. However, due to the lacking of the genomic sequences, studies on R. soongorica had mainly limited in physiological responses to drought stress. Here, a deep transcriptomic sequencing of R. soongorica will facilitate molecular functional studies and pave the path to understand drought adaptation for a desert plant. Methodology/Principal Findings A total of 53,193,660 clean paired-end reads was generated from the Illumina HiSeq™ 2000 platform. By assembly with Trinity, we got 173,700 contigs and 77,647 unigenes with mean length of 677 bp and N50 of 1109 bp. Over 55% (43,054) unigenes were successfully annotated based on sequence similarity against public databases as well as Rfam and Pfam database. Local BLAST and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps were used to further exhausting seek for candidate genes related to drought adaptation and a set of 123 putative candidate genes were identified. Moreover, all the C4 photosynthesis genes existed and were active in R. soongorica, which has been regarded as a typical C3 plant. Conclusion/Significance The assembled unigenes in present work provide abundant genomic information for the functional assignments in an extreme xerophyte R. soongorica, and will help us exploit the genetic basis of how desert plants adapt to drought environment in the near future. PMID:23717523

  2. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae).

    PubMed

    Wang, Fan-Hong; Lu, Jin-Mei; Wen, Jun; Ebihara, Atsushi; Li, De-Zhu

    2016-01-01

    DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.

  3. Dual-task related gait changes after CSF tapping: a new way to identify idiopathic normal pressure hydrocephalus

    PubMed Central

    2013-01-01

    Background Gait disturbances found in patients with idiopathic normal pressure hydrocephalus (iNPH) are unspecific to the diagnosis and commonly occur in neurodegenerative or vascular conditions (iNPH-like conditions). This current retrospective pre-post intervention study aims to determine whether changes in quantitative gait parameters during dual task condition differed between iNPH and iNPH-like conditions before and after cerebrospinal fluid (CSF) tapping. Methods 49 patients assessed before and after CSF tapping were included in this study (27 with iNPH and 22 with iNPH-like conditions). Gait analysis during single and dual task conditions (walking and backward counting) was performed before and after a CSF spinal tap of 40 ml. Gait parameters were compared between iNPH and iNPH-like conditions patients. Logistic regressions were used to examine the association between iNPH and gait parameters. Results Improvements of step width (−9.03 (20.75)% for iNPH group; +0.28 (21.76)% for iNPH-like conditions group), stride length (+7.82 (20.71)% for iNPH group; -0.62 (19.22)% for iNPH-like conditions group), walking speed (+12.20 (29.79)% for iNPH group; +2.38 (32.50)% for iNPH-like conditions group) and stance duration (−1.23 (4.03)% for iNPH group; +0.49 (5.12)% for iNPH-like conditions group) during dual task, after CSF spinal tapping, were significant in patients with iNPH compared to patients with iNPH-like conditions. No between group difference was observed for the single walking task evaluation. The multiple logistic regression revealed that among these four gait parameters, only the improvement in step width was associated with the diagnosis of iNPH. Conclusion Dual-task related changes in spatio-temporal gait parameters before and after CSF tapping might be a novel and discriminative method of identifying iNPH patients from other similar conditions. PMID:24359487

  4. Torsional vestibulo-ocular reflex measurements for identifying otolith asymmetries possibly related to space motion sickness susceptibility

    NASA Astrophysics Data System (ADS)

    Peterka, Robert J.

    Recent studies by Diamond and Markham 1,2 have identified significant correlations between space motion sickness susceptibility and measures of disconjugate torsional eye movements recorded during parabolic flights. These results support an earlier proposal by von Baumgarten and Thümler 3 which hypothesized that an asymmetry of otolith function between the two ears is the cause of space motion sickness. It may be possible to devise experiments that can be performed in the 1 g environment on earth that could identify and quantify the presence of asymmetric otolith function. This paper summarizes the known physiological and anatomical properties of the otolith organs and the properties of the torsional vestibulo-ocular reflex which are relevant to the design of a stimulus to identify otolith asymmetries. A specific stimulus which takes advantage of these properties is proposed.

  5. Torsional vestibulo-ocular reflex measurements for identifying otolith asymmetries possibly related to space motion sickness susceptibility

    NASA Technical Reports Server (NTRS)

    Peterka, Robert J.

    1993-01-01

    Recent studies have identified significant correlations between space motion sickness susceptibility and measures of disconjugate torsional eye movements recorded during parabolic flights. These results support an earlier proposal which hypothesized that an asymmetry of otolith function between the two ears is the cause of space motion sickness. It may be possible to devise experiments that can be performed in the 1 g environment on earth that could identify and quantify the presence of asymmetric otolith function. This paper summarizes the known physiological and anatomical properties of the otolith organs and the properties of the torsional vestibulo-ocular reflex which are relevant to the design of a stimulus to identify otolith asymmetries. A specific stimulus which takes advantage of these properties is proposed.

  6. Torsional vestibulo-ocular reflex measurements for identifying otolith asymmetries possibly related to space motion sickness susceptibility

    NASA Technical Reports Server (NTRS)

    Peterka, R. J.

    1994-01-01

    Recent studies by Diamond and Markham have identified significant correlations between space motion sickness susceptibility and measures of disconjugate torsional eye movements recorded during parabolic flights. These results support an earlier proposal by von Baumgarten and Thumler which hypothesized that an asymmetry of otolith function between the two ears is the cause of space motion sickness. It may be possible to devise experiments that can be performed in the 1 g environment on earth that could identify and quantify the presence of asymmetric otolith function. This paper summarizes the known physiological and anatomical properties of the otolith organs and the properties of the torsional vestibulo-ocular reflex which are relevant to the design of a stimulus to identify otolith asymmetries. A specific stimulus which takes advantage of these properties is proposed.

  7. The Disruption of Celf6, a Gene Identified by Translational Profiling of Serotonergic Neurons, Results in Autism-Related Behaviors

    PubMed Central

    Dougherty, Joseph D.; Maloney, Susan E.; Wozniak, David F.; Rieger, Michael A.; Sonnenblick, Lisa; Coppola, Giovanni; Mahieu, Nathaniel G.; Zhang, Juliet; Cai, Jinlu; Patti, Gary J.; Abrahams, Brett S.; Geschwind, Daniel H.; Heintz, Nathaniel

    2013-01-01

    The immense molecular diversity of neurons challenges our ability to understand the genetic and cellular etiology of neuropsychiatric disorders. Leveraging knowledge from neurobiology may help parse the genetic complexity: identifying genes important for a circuit that mediates a particular symptom of a disease may help identify polymorphisms that contribute to risk for the disease as a whole. The serotonergic system has long been suspected in disorders that have symptoms of repetitive behaviors and resistance to change, including autism. We generated a bacTRAP mouse line to permit translational profiling of serotonergic neurons. From this, we identified several thousand serotonergic-cell expressed transcripts, of which 174 were highly enriched, including all known markers of these cells. Analysis of common variants near the corresponding genes in the AGRE collection implicated the RNA binding protein CELF6 in autism risk. Screening for rare variants in CELF6 identified an inherited premature stop codon in one of the probands. Subsequent disruption of Celf6 in mice resulted in animals exhibiting resistance to change and decreased ultrasonic vocalization as well as abnormal levels of serotonin in the brain. This work provides a reproducible and accurate method to profile serotonergic neurons under a variety of conditions and suggests a novel paradigm for gaining information on the etiology of psychiatric disorders. PMID:23407934

  8. Using Generalized Additive Modeling to Empirically Identify Thresholds within the ITERS in Relation to Toddlers' Cognitive Development

    ERIC Educational Resources Information Center

    Setodji, Claude Messan; Le, Vi-Nhuan; Schaack, Diana

    2013-01-01

    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,…

  9. ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae.

    PubMed

    Bossé, Janine T; Li, Yanwen; Fernandez Crespo, Roberto; Chaudhuri, Roy R; Rogers, Jon; Holden, Matthew T G; Maskell, Duncan J; Tucker, Alexander W; Wren, Brendan W; Rycroft, Andrew N; Langford, Paul R

    2016-01-01

    ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia. PMID:27379024

  10. ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae

    PubMed Central

    Bossé, Janine T.; Li, Yanwen; Fernandez Crespo, Roberto; Chaudhuri, Roy R.; Rogers, Jon; Holden, Matthew T. G.; Maskell, Duncan J.; Tucker, Alexander W.; Wren, Brendan W.; Rycroft, Andrew N.; Langford, Paul R.

    2016-01-01

    ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia. PMID:27379024

  11. High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.

    PubMed

    Sun, Celi; Molineros, Julio E; Looger, Loren L; Zhou, Xu-Jie; Kim, Kwangwoo; Okada, Yukinori; Ma, Jianyang; Qi, Yuan-Yuan; Kim-Howard, Xana; Motghare, Prasenjeet; Bhattarai, Krishna; Adler, Adam; Bang, So-Young; Lee, Hye-Soon; Kim, Tae-Hwan; Kang, Young Mo; Suh, Chang-Hee; Chung, Won Tae; Park, Yong-Beom; Choe, Jung-Yoon; Shim, Seung Cheol; Kochi, Yuta; Suzuki, Akari; Kubo, Michiaki; Sumida, Takayuki; Yamamoto, Kazuhiko; Lee, Shin-Seok; Kim, Young Jin; Han, Bok-Ghee; Dozmorov, Mikhail; Kaufman, Kenneth M; Wren, Jonathan D; Harley, John B; Shen, Nan; Chua, Kek Heng; Zhang, Hong; Bae, Sang-Cheol; Nath, Swapan K

    2016-03-01

    Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

  12. USE OF COMPETITIVE DNA HYBRIDIZATION TO IDENTIFY DIFFERENCES IN THE GENOMES OF TWO CLOSELY RELATED FECAL INDICATOR BACTERIA

    EPA Science Inventory

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expens...

  13. Comparative proteomic analysis of Streptococcus suis biofilms and planktonic cells that identified biofilm infection-related immunogenic proteins.

    PubMed

    Wang, Yang; Yi, Li; Wu, Zongfu; Shao, Jing; Liu, Guangjin; Fan, Hongjie; Zhang, Wei; Lu, Chengping

    2012-01-01

    Streptococcus suis (SS) is a zoonotic pathogen that causes severe disease symptoms in pigs and humans. Biofilms of SS bind to extracellular matrix proteins in both endothelial and epithelial cells and cause persistent infections. In this study, the differences in the protein expression profiles of SS grown either as planktonic cells or biofilms were identified using comparative proteomic analysis. The results revealed the existence of 13 proteins of varying amounts, among which six were upregulated and seven were downregulated in the Streptococcus biofilm compared with the planktonic controls. The convalescent serum from mini-pig, challenged with SS, was applied in a Western blot assay to visualize all proteins from the biofilm that were grown in vitro and separated by two-dimensional gel electrophoresis. A total of 10 immunoreactive protein spots corresponding to nine unique proteins were identified by MALDI-TOF/TOF-MS. Of these nine proteins, five (Manganese-dependent superoxide dismutase, UDP-N-acetylglucosamine 1-carboxyvinyltransferase, ornithine carbamoyltransferase, phosphoglycerate kinase, Hypothetical protein SSU05_0403) had no previously reported immunogenic properties in SS to our knowledge. The remaining four immunogenic proteins (glyceraldehyde-3-phosphate dehydrogenase, hemolysin, pyruvate dehydrogenase and DnaK) were identified under both planktonic and biofilm growth conditions. In conclusion, the protein expression pattern of SS, grown as biofilm, was different from the SS grown as planktonic cells. These five immunogenic proteins that were specific to SS biofilm cells may potentially be targeted as vaccine candidates to protect against SS biofilm infections. The four proteins common to both biofilm and planktonic cells can be targeted as vaccine candidates to protect against both biofilm and acute infections.

  14. Genome-wide association study with 1000 genomes imputation identifies signals for nine sex hormone-related phenotypes.

    PubMed

    Ruth, Katherine S; Campbell, Purdey J; Chew, Shelby; Lim, Ee Mun; Hadlow, Narelle; Stuckey, Bronwyn G A; Brown, Suzanne J; Feenstra, Bjarke; Joseph, John; Surdulescu, Gabriela L; Zheng, Hou Feng; Richards, J Brent; Murray, Anna; Spector, Tim D; Wilson, Scott G; Perry, John R B

    2016-02-01

    Genetic factors contribute strongly to sex hormone levels, yet knowledge of the regulatory mechanisms remains incomplete. Genome-wide association studies (GWAS) have identified only a small number of loci associated with sex hormone levels, with several reproductive hormones yet to be assessed. The aim of the study was to identify novel genetic variants contributing to the regulation of sex hormones. We performed GWAS using genotypes imputed from the 1000 Genomes reference panel. The study used genotype and phenotype data from a UK twin register. We included 2913 individuals (up to 294 males) from the Twins UK study, excluding individuals receiving hormone treatment. Phenotypes were standardised for age, sex, BMI, stage of menstrual cycle and menopausal status. We tested 7,879,351 autosomal SNPs for association with levels of dehydroepiandrosterone sulphate (DHEAS), oestradiol, free androgen index (FAI), follicle-stimulating hormone (FSH), luteinizing hormone (LH), prolactin, progesterone, sex hormone-binding globulin and testosterone. Eight independent genetic variants reached genome-wide significance (P<5 × 10(-8)), with minor allele frequencies of 1.3-23.9%. Novel signals included variants for progesterone (P=7.68 × 10(-12)), oestradiol (P=1.63 × 10(-8)) and FAI (P=1.50 × 10(-8)). A genetic variant near the FSHB gene was identified which influenced both FSH (P=1.74 × 10(-8)) and LH (P=3.94 × 10(-9)) levels. A separate locus on chromosome 7 was associated with both DHEAS (P=1.82 × 10(-14)) and progesterone (P=6.09 × 10(-14)). This study highlights loci that are relevant to reproductive function and suggests overlap in the genetic basis of hormone regulation.

  15. Comparative Proteomic Analysis of Streptococcus suis Biofilms and Planktonic Cells That Identified Biofilm Infection-Related Immunogenic Proteins

    PubMed Central

    Wang, Yang; Yi, Li; Wu, Zongfu; Shao, Jing; Liu, Guangjin; Fan, Hongjie; Zhang, Wei; Lu, Chengping

    2012-01-01

    Streptococcus suis (SS) is a zoonotic pathogen that causes severe disease symptoms in pigs and humans. Biofilms of SS bind to extracellular matrix proteins in both endothelial and epithelial cells and cause persistent infections. In this study, the differences in the protein expression profiles of SS grown either as planktonic cells or biofilms were identified using comparative proteomic analysis. The results revealed the existence of 13 proteins of varying amounts, among which six were upregulated and seven were downregulated in the Streptococcus biofilm compared with the planktonic controls. The convalescent serum from mini-pig, challenged with SS, was applied in a Western blot assay to visualize all proteins from the biofilm that were grown in vitro and separated by two-dimensional gel electrophoresis. A total of 10 immunoreactive protein spots corresponding to nine unique proteins were identified by MALDI-TOF/TOF-MS. Of these nine proteins, five (Manganese-dependent superoxide dismutase, UDP-N-acetylglucosamine 1-carboxyvinyltransferase, ornithine carbamoyltransferase, phosphoglycerate kinase, Hypothetical protein SSU05_0403) had no previously reported immunogenic properties in SS to our knowledge. The remaining four immunogenic proteins (glyceraldehyde-3-phosphate dehydrogenase, hemolysin, pyruvate dehydrogenase and DnaK) were identified under both planktonic and biofilm growth conditions. In conclusion, the protein expression pattern of SS, grown as biofilm, was different from the SS grown as planktonic cells. These five immunogenic proteins that were specific to SS biofilm cells may potentially be targeted as vaccine candidates to protect against SS biofilm infections. The four proteins common to both biofilm and planktonic cells can be targeted as vaccine candidates to protect against both biofilm and acute infections. PMID:22514606

  16. New insights into the pathogenesis of pseudoxanthoma elasticum and related soft tissue calcification disorders by identifying genetic interactions and modifiers

    PubMed Central

    Hendig, Doris; Knabbe, Cornelius; Götting, Christian

    2013-01-01

    Screening of the adenosine triphosphate binding cassette transporter protein subfamily C member 6 gene (ABCC6) in pseudoxanthoma elasticum (PXE) revealed a mutation detection rate of approximately 87%. Although 25% of the unidentified disease alleles underlie deletions/insertions, there remain several PXE patients with no clear genotype. The recent identification of PXE-related diseases and the high intra-familiar and inter-individual clinical variability of PXE led to the assumption that secondary genetic co-factors exist. Here, we summarize current knowledge of the genetics underlying PXE and PXE-related disorders based on human and animal studies. Furthermore, we discuss the role of genetic interactions and modifier genes in PXE and PXE-related diseases characterized by soft tissue calcification. PMID:23802012

  17. High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry

    PubMed Central

    Sun, Celi; Molineros, Julio E.; Looger, Loren L.; Zhou, Xu-jie; Kim, Kwangwoo; Okada, Yukinori; Ma, Jianyang; Qi, Yuan-yuan; Kim-Howard, Xana; Motghare, Prasenjeet; Bhattarai, Krishna; Adler, Adam; Bang, So-Young; Lee, Hye-Soon; Kim, Tae-Hwan; Kang, Young Mo; Suh, Chang-Hee; Chung, Won Tae; Park, Yong-Beom; Choe, Jung-Yoon; Shim, Seung Cheol; Kochi, Yuta; Suzuki, Akari; Kubo, Michiaki; Sumida, Takayuki; Yamamoto, Kazuhiko; Lee, Shin-Seok; Kim, Young Jin; Han, Bok-Ghee; Dozmorov, Mikhail; Kaufman, Kenneth M.; Wren, Jonathan D.; Harley, John B.; Shen, Nan; Chua, Kek Heng; Zhang, Hong; Bae, Sang-Cheol; Nath, Swapan K.

    2016-01-01

    Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,492 SLE cases and 12,675 controls from six East-Asian cohorts, to identify novel and better localize known SLE susceptibility loci. We identified 10 novel loci as well as 20 known loci with genome-wide significance. Among the novel loci, the most significant was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta=3.75×10−117, OR=2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We localized the most likely functional variants for each locus by analyzing epigenetic marks and gene regulation data. Ten putative variants are known to alter cis- or trans-gene expression. Enrichment analysis highlights the importance of these loci in B- and T-cell biology. Together with previously known loci, the explained heritability of SLE increases to 24%. Novel loci share functional and ontological characteristics with previously reported loci, and are possible drug targets for SLE therapeutics. PMID:26808113

  18. A Need for Better Studies to Identify Those Populations at Greatest Risk of a Pollutant-Related Health Effect

    EPA Science Inventory

    This invited editorial on a paper accepted for publication in the Journal of Pediatrics details scientific advances needed to improve the identification of those populations at greatest risk of a pollutant-related health effect with a primary focus on air pollution.

  19. Relating Science and Religion: An Ontology of Taxonomies and Development of a Research Tool for Identifying Individual Views

    ERIC Educational Resources Information Center

    Yasri, Pratchayapong; Arthur, Shagufta; Smith, Mike U.; Mancy, Rebecca

    2013-01-01

    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…

  20. Saccadic Eye Movement Task Identifies Cognitive Deficits in Children with Schizophrenia, but Not in Unaffected Child Relatives

    ERIC Educational Resources Information Center

    Ross, Randal G.; Heinlein, Shari; Zerbe, Gary O.; Radant, Allen

    2005-01-01

    Background: The delayed oculomotor response (DOR) task requires response inhibition followed by movement of gaze towards a known spatial location without a current stimulus. Abnormalities in response inhibition and in the spatial accuracy of the eye movement are found in individuals with schizophrenia and in many of their relatives, supporting the…

  1. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads.

    PubMed

    Takishita, Kiyotaka; Kolisko, Martin; Komatsuzaki, Hiroshi; Yabuki, Akinori; Inagaki, Yuji; Cepicka, Ivan; Smejkalová, Pavla; Silberman, Jeffrey D; Hashimoto, Tetsuo; Roger, Andrew J; Simpson, Alastair G B

    2012-05-01

    Diplomonads, retortamonads, and "Carpediemonas-like" organisms (CLOs) are a monophyletic group of protists that are microaerophilic/anaerobic and lack typical mitochondria. Most diplomonads and retortamonads are parasites, and the pathogen Giardia intestinalis is known to possess reduced mitochondrion-related organelles (mitosomes) that do not synthesize ATP. By contrast, free-living CLOs have larger organelles that superficially resemble some hydrogenosomes, organelles that in other protists are known to synthesize ATP anaerobically. This group represents an excellent system for studying the evolution of parasitism and anaerobic, mitochondrion-related organelles. Understanding these evolutionary transitions requires a well-resolved phylogeny of diplomonads, retortamonads and CLOs. Unfortunately, until now the deep relationships amongst these taxa were unresolved due to limited data for almost all of the CLO lineages. To address this, we assembled a dataset of up to six protein-coding genes that includes representatives from all six CLO lineages, and complements existing rRNA datasets. Multigene phylogenetic analyses place CLOs as well as the retortamonad Chilomastix as a paraphyletic basal assemblage to the lineage comprising diplomonads and the retortamonad Retortamonas. In particular, the CLO Dysnectes was shown to be the closest relative of the diplomonads + Retortamonas clade, with strong support. This phylogeny is consistent with a drastic degeneration of mitochondrion-related organelles during the evolution from a free-living organism resembling extant CLOs to a probable parasite/commensal common ancestor of diplomonads and Retortamonas.

  2. Long-term nursing care of elderly people: identifying ethically problematic experiences among patients, relatives and nurses in Finland.

    PubMed

    Teeri, Sari; Leino-Kilpi, Helena; Välimäki, Maritta

    2006-03-01

    The aim of this study was to explore ethically problematic situations in the long-term nursing care of elderly people. It was assumed that greater awareness of ethical problems in caring for elderly people helps to ensure ethically high standards of nursing care. To obtain a broad perspective on the current situation, the data for this study were collected among elderly patients, their relatives and nurses in one long-term care institution in Finland. The patients (n = 10) were interviewed, while the relatives, (n = 17) and nurses (n = 9) wrote an essay. Interpretation of the data was based on qualitative content analysis. Problematic experiences were divided into three categories concerning patients' psychological, physical and social integrity. In the case of psychological integrity, the problems were seen as being related to treatment, self-determination and obtaining information; for physical integrity, they were related to physical abuse and lack of individualized care; and for social integrity, to loneliness and social isolation. This study provided no information on the prevalence of ethical problems. However, it is clear from the results that patient integrity warrants more attention in the nursing care of elderly patients.

  3. Identifying relatively high-risk group of coronary artery calcification based on progression rate: statistical and machine learning methods.

    PubMed

    Kim, Ha-Young; Yoo, Sanghyun; Lee, Jihyun; Kam, Hye Jin; Woo, Kyoung-Gu; Choi, Yoon-Ho; Sung, Jidong; Kang, Mira

    2012-01-01

    Coronary artery calcification (CAC) score is an important predictor of coronary artery disease (CAD), which is the primary cause of death in advanced countries. Early prediction of high-risk of CAC based on progression rate enables people to prevent CAD from developing into severe symptoms and diseases. In this study, we developed various classifiers to identify patients in high risk of CAC using statistical and machine learning methods, and compared them with performance accuracy. For statistical approaches, linear regression based classifier and logistic regression model were developed. For machine learning approaches, we suggested three kinds of ensemble-based classifiers (best, top-k, and voting method) to deal with imbalanced distribution of our data set. Ensemble voting method outperformed all other methods including regression methods as AUC was 0.781. PMID:23366360

  4. A Fast and Cost-Effective Method for Identifying a Polymorphism of Interleukin 28B Related to Hepatitis C

    PubMed Central

    Ferreira, Camila da Silva; Abreu, Rodrigo Martins; da Silva, Marlone Cunha; Ferreira, Aline Siqueira; Nasser, Paulo Dominguez; Carrilho, Flair José; Ono, Suzane Kioko

    2013-01-01

    Approximately 170 million people are chronic carriers of hepatitis C virus (HCV). Patients with chronic hepatitis C are currently treated with pegylated interferon and ribavirin (PEG-IFN/RBV). A genome-wide association with PEG-IFN/RBV treatment response and a single nucleotide polymorphism (rs12979860) has been identified near the interleukin 28B gene that encodes interferon-λ-3. In this paper, we describe an innovative, fast, and low-cost multiplex polymerase chain reaction with confronting two-pair primers that detects the rs12979860 polymorphism. The assay is internally controlled and does not require the use of restriction endonucleases or special equipment. Moreover, the assay decreases costs, being about 40% cheaper than direct sequencing methods. PMID:24167602

  5. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

    PubMed

    Chasman, Daniel I; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Böger, Carsten A; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; O'Seaghdha, Conall M; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D; Gierman, Hinco J; Feitosa, Mary F; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Asa; Tönjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A; de Andrade, Mariza; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S; van Duijn, Cornelia M; Borecki, Ingrid B; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M; Kao, W H Linda; Fox, Caroline S; Köttgen, Anna

    2012-12-15

    In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

  6. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function

    PubMed Central

    Chasman, Daniel I.; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Böger, Carsten A.; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary F.; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid B.; Kardia, Sharon L.R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Kao, W.H. Linda; Fox, Caroline S.; Köttgen, Anna

    2012-01-01

    In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10−9) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10−4–2.2 × 10−7. Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general. PMID:22962313

  7. Identifying influential nodes in a wound healing-related network of biological processes using mean first-passage time

    NASA Astrophysics Data System (ADS)

    Arodz, Tomasz; Bonchev, Danail

    2015-02-01

    In this study we offer an approach to network physiology, which proceeds from transcriptomic data and uses gene ontology analysis to identify the biological processes most enriched in several critical time points of wound healing process (days 0, 3 and 7). The top-ranking differentially expressed genes for each process were used to build two networks: one with all proteins regulating the transcription of selected genes, and a second one involving the proteins from the signaling pathways that activate the transcription factors. The information from these networks is used to build a network of the most enriched processes with undirected links weighted proportionally to the count of shared genes between the pair of processes, and directed links weighted by the count of relationships connecting genes from one process to genes from the other. In analyzing the network thus built we used an approach based on random walks and accounting for the temporal aspects of the spread of a signal in the network (mean-first passage time, MFPT). The MFPT scores allowed identifying the top influential, as well as the top essential biological processes, which vary with the progress in the healing process. Thus, the most essential for day 0 was found to be the Wnt-receptor signaling pathway, well known for its crucial role in wound healing, while in day 3 this was the regulation of NF-kB cascade, essential for matrix remodeling in the wound healing process. The MFPT-based scores correctly reflected the pattern of the healing process dynamics to be highly concentrated around several processes between day 0 and day 3, and becoming more diffuse at day 7.

  8. Latinos and HIV/AIDS: Examining Factors Related to Disparity and Identifying Opportunities for Psychosocial Intervention Research

    PubMed Central

    Hendriksen, Ellen Setsuko; Collins, Erin Marie; Durán, Ron E.; Safren, Steven A.

    2013-01-01

    Latinos maintain an AIDS case rate more than 3 times higher than whites, a greater rate of progression to AIDS, and a higher rate of HIV/AIDS-related deaths. Three broad areas are reviewed related to these disparities: (1) relevant demographic, socioeconomic, and socio-cultural factors among Latinos; (2) drug abuse and mental health problems in Latinos relevant to HIV/AIDS outcomes; and (3) opportunities for psychosocial intervention. Latinos living with HIV are a rapidly growing group, are more severely impacted by HIV than whites, and confront unique challenges in coping with HIV/AIDS. A body of research suggests that depression, substance abuse, treatment adherence, health literacy, and access to healthcare may be fruitful targets for intervention research in this population. Though limited, the current literature suggests that psychosocial interventions that target these factors could help reduce HIV/AIDS disparities between Latinos and whites and could have important public health value. PMID:18498050

  9. Native fluorescence spectroscopy of blood plasma of rats with experimental diabetes: identifying fingerprints of glucose-related metabolic pathways

    NASA Astrophysics Data System (ADS)

    Shirshin, Evgeny; Cherkasova, Olga; Tikhonova, Tatiana; Berlovskaya, Elena; Priezzhev, Alexander; Fadeev, Victor

    2015-05-01

    We present the results of a native fluorescence spectroscopy study of blood plasma of rats with experimental diabetes. It was shown that the fluorescence emission band shape at 320 nm excitation is the most indicative of hyperglycemia in the blood plasma samples. We provide the interpretation of this fact based on the changes in reduced nicotinamide adenine dinucleotide phosphate concentration due to glucose-related metabolic pathways and protein fluorescent cross-linking formation following nonenzymatic glycation.

  10. The FIGS (focused identification of germplasm strategy) approach identifies traits related to drought adaptation in Vicia faba genetic resources.

    PubMed

    Khazaei, Hamid; Street, Kenneth; Bari, Abdallah; Mackay, Michael; Stoddard, Frederick L

    2013-01-01

    Efficient methods to explore plant agro-biodiversity for climate change adaptive traits are urgently required. The focused identification of germplasm strategy (FIGS) is one such approach. FIGS works on the premise that germplasm is likely to reflect the selection pressures of the environment in which it developed. Environmental parameters describing plant germplasm collection sites are used as selection criteria to improve the probability of uncovering useful variation. This study was designed to test the effectiveness of FIGS to search a large faba bean (Vicia faba L.) collection for traits related to drought adaptation. Two sets of faba bean accessions were created, one from moisture-limited environments, and the other from wetter sites. The two sets were grown under well watered conditions and leaf morpho-physiological traits related to plant water use were measured. Machine-learning algorithms split the accessions into two groups based on the evaluation data and the groups created by this process were compared to the original climate-based FIGS sets. The sets defined by trait data were in almost perfect agreement to the FIGS sets, demonstrating that ecotypic differentiation driven by moisture availability has occurred within the faba bean genepool. Leaflet and canopy temperature as well as relative water content contributed more than other traits to the discrimination between sets, indicating that their utility as drought-tolerance selection criteria for faba bean germplasm. This study supports the assertion that FIGS could be an effective tool to enhance the discovery of new genes for abiotic stress adaptation.

  11. Identifying selective visual attention biases related to fear of pain by tracking eye movements within a dot-probe paradigm.

    PubMed

    Yang, Zhou; Jackson, Todd; Gao, Xiao; Chen, Hong

    2012-08-01

    This research examined selective biases in visual attention related to fear of pain by tracking eye movements (EM) toward pain-related stimuli among the pain-fearful. EM of 21 young adults scoring high on a fear of pain measure (H-FOP) and 20 lower-scoring (L-FOP) control participants were measured during a dot-probe task that featured sensory pain-neutral, health catastrophe-neutral and neutral-neutral word pairs. Analyses indicated that the H-FOP group was more likely to direct immediate visual attention toward sensory pain and health catastrophe words than was the L-FOP group. The H-FOP group also had comparatively shorter first fixation latencies toward sensory pain and health catastrophe words. Conversely, groups did not differ on EM indices of attentional maintenance (i.e., first fixation duration, gaze duration, and average fixation duration) or reaction times to dot probes. Finally, both groups showed a cycle of disengagement followed by re-engagement toward sensory pain words relative to other word types. In sum, this research is the first to reveal biases toward pain stimuli during very early stages of visual information processing among the highly pain-fearful and highlights the utility of EM tracking as a means to evaluate visual attention as a dynamic process in the context of FOP. PMID:22717101

  12. Global Mapping of Gene/Protein Interactions in PubMed Abstracts: A Framework and an Experiment with P53 Interactions

    PubMed Central

    Li, Xin; Chen, Hsinchun; Huang, Zan; Su, Hua; Martinez, Jesse D.

    2007-01-01

    Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large body of biomedical literature is an important source of gene/protein interaction information. Recent advances in text mining tools have made it possible to automatically extract such documented interactions from free-text literature. In this paper, we propose a comprehensive framework for constructing and analyzing large-scale gene functional networks based on the gene/protein interactions extracted from biomedical literature repositories using text mining tools. Our proposed framework consists of analyses of the network topology, network topology-gene function relationship, and temporal network evolution to distill valuable information embedded in the gene functional interactions in literature. We demonstrate the application of the proposed framework using a testbed of P53-related PubMed abstracts, which shows that literature-based P53 networks exhibit small-world and scale-free properties. We also found that high degree genes in the literature-based networks have a high probability of appearing in the manually curated database and genes in the same pathway tend to form local clusters in our literature-based networks. Temporal analysis showed that genes interacting with many other genes tend to be involved in a large number of newly discovered interactions. PMID:17317333

  13. Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

    PubMed Central

    2013-01-01

    Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

  14. An experimental search strategy retrieves more precise results than PubMed and Google for questions about medical interventions

    PubMed Central

    Dylla, Daniel P.; Megison, Susan D.

    2015-01-01

    Objective. We compared the precision of a search strategy designed specifically to retrieve randomized controlled trials (RCTs) and systematic reviews of RCTs with search strategies designed for broader purposes. Methods. We designed an experimental search strategy that automatically revised searches up to five times by using increasingly restrictive queries as long at least 50 citations were retrieved. We compared the ability of the experimental and alternative strategies to retrieve studies relevant to 312 test questions. The primary outcome, search precision, was defined for each strategy as the proportion of relevant, high quality citations among the first 50 citations retrieved. Results. The experimental strategy had the highest median precision (5.5%; interquartile range [IQR]: 0%–12%) followed by the narrow strategy of the PubMed Clinical Queries (4.0%; IQR: 0%–10%). The experimental strategy found the most high quality citations (median 2; IQR: 0–6) and was the strategy most likely to find at least one high quality citation (73% of searches; 95% confidence interval 68%–78%). All comparisons were statistically significant. Conclusions. The experimental strategy performed the best in all outcomes although all strategies had low precision. PMID:25922798

  15. The prevalence of heat-related cardiorespiratory symptoms: the vulnerable groups identified from the National FINRISK 2007 Study

    NASA Astrophysics Data System (ADS)

    Näyhä, Simo; Rintamäki, Hannu; Donaldson, Gavin; Hassi, Juhani; Jousilahti, Pekka; Laatikainen, Tiina; Jaakkola, Jouni J. K.; Ikäheimo, Tiina M.

    2016-09-01

    The prevalence of heat-related cardiorespiratory symptoms among vulnerable groups is not well known. We therefore estimated the prevalence of heat-related cardiorespiratory symptoms among the Finnish population and their associations with social and individual vulnerability factors. The data came from the National FINRISK 2007 Study, in which 4007 men and women aged 25-74 answered questions on heat-related cardiorespiratory symptoms in the Oulu Cold and Heat Questionnaire 2007. Logistic regression was used to calculate odds ratios (ORs), their 95 % confidence intervals (CIs), and model-predicted prevalence figures. The prevalence of heat-related cardiorespiratory symptoms was 12 %. It increased with age, from 3 % at the age of 25 years to 28 % at the age of 75 years. The symptoms were associated with pre-existing lung (OR 3.93; CI 3.01-5.13) and cardiovascular diseases (OR 2.27; 1.78-2.89); being a pensioner (OR 2.91; 1.65-5.28), unemployed (OR 2.82; 1.47-5.48), or working in agriculture (OR 2.27; 1.14-4.46) compared with working in industry; having only basic vs academic education (OR 1.98; 1.31-3.05); being female (OR 1.94; 1.51-2.50); being heavy vs light alcohol consumer (OR 1.89; 1.02-3.32); undertaking hard vs light physical work (OR 1.48;1.06-2.07); and being inactive vs active in leisure time (OR 1.97; 1.39-2.81). The adjusted prevalence of symptoms showed a wide range of variation, from 3 to 61 % depending on sex, age, professional field, education, and pre-existing lung and cardiovascular diseases. In conclusion, heat-related cardiorespiratory symptoms are commonly perceived among people with pre-existing lung or cardiovascular disease, agricultural workers, unemployed, pensioners, and people having only basic education. This information is needed for any planning and targeting measures to reduce the burden of summer heat.

  16. Application of Satellite Remote Sensing to Identify Climatic and Anthropogenic Changes Related to Water and Health Conditions in Emerging Megacities

    NASA Astrophysics Data System (ADS)

    Akanda, A. S.; Serman, E. A.; Jutla, A.

    2014-12-01

    By 2050, more than 70% of the world's population is expected to be living in a city. In many of the urbanizing regions in Asia and Africa, most new development is taking place without adequate urban or regional planning, and a majority population is crowded into densely populated unplanned settlements, also known as slums. During the same period, precipitation and temperature patterns are likely to see significant changes in many of these regions while coastal megacities will have to accommodate sea-level rise in their ecosystems. The rapid increase in population is usually observed in fringes of the urban sprawl without adequate water or sanitation facilities or access to other municipal amenities (such as utilities, healthcare, and education). Collectively, these issues make the ever increasing slum dwellers in emerging megacities significantly vulnerable to a combination of climatic and anthropogenic threats. However, how the growth of unplanned urban and peri-urban sprawl and simultaneous change in climatic patterns have impacted public health in the emerging megacities remain largely unexplored due to lack of readily available and usable data. We employ a number of Remote Sensing products (GRACE, LANDSAT, MODIS) to bridge above knowledge gaps and to identify relevant hydrologic and anthropogenic changes in emerging megacities that are most vulnerable due to the climate-water-health nexus. We explore one of the largest and the fastest growing megacities in the world - Dhaka, Bangladesh - on identifying and investigating the changes in the water environment and growth of slum areas, and impact on water services and health outcomes. The hydroclimatology of South Asia is highly seasonal and the asymmetric availability of water affects vast areas of Bangladesh differently in space and time, exposing the population of Dhaka region to both droughts and floods and periodic spring-fall outbreaks of diarrheal diseases, such as cholera and rotavirus. This research

  17. Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley.

    PubMed

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions.

  18. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.

    PubMed

    Hinks, Anne; Cobb, Joanna; Marion, Miranda C; Prahalad, Sampath; Sudman, Marc; Bowes, John; Martin, Paul; Comeau, Mary E; Sajuthi, Satria; Andrews, Robert; Brown, Milton; Chen, Wei-Min; Concannon, Patrick; Deloukas, Panos; Edkins, Sarah; Eyre, Stephen; Gaffney, Patrick M; Guthery, Stephen L; Guthridge, Joel M; Hunt, Sarah E; James, Judith A; Keddache, Mehdi; Moser, Kathy L; Nigrovic, Peter A; Onengut-Gumuscu, Suna; Onslow, Mitchell L; Rosé, Carlos D; Rich, Stephen S; Steel, Kathryn J A; Wakeland, Edward K; Wallace, Carol A; Wedderburn, Lucy R; Woo, Patricia; Bohnsack, John F; Haas, Johannes Peter; Glass, David N; Langefeld, Carl D; Thomson, Wendy; Thompson, Susan D

    2013-06-01

    We used the Immunochip array to analyze 2,816 individuals with juvenile idiopathic arthritis (JIA), comprising the most common subtypes (oligoarticular and rheumatoid factor-negative polyarticular JIA), and 13,056 controls. We confirmed association of 3 known JIA risk loci (the human leukocyte antigen (HLA) region, PTPN22 and PTPN2) and identified 14 loci reaching genome-wide significance (P < 5 × 10(-8)) for the first time. Eleven additional new regions showed suggestive evidence of association with JIA (P < 1 × 10(-6)). Dense mapping of loci along with bioinformatics analysis refined the associations to one gene in each of eight regions, highlighting crucial pathways, including the interleukin (IL)-2 pathway, in JIA disease pathogenesis. The entire Immunochip content, the HLA region and the top 27 loci (P < 1 × 10(-6)) explain an estimated 18, 13 and 6% of the risk of JIA, respectively. In summary, this is the largest collection of JIA cases investigated so far and provides new insight into the genetic basis of this childhood autoimmune disease. PMID:23603761

  19. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis

    PubMed Central

    Hinks, Anne; Cobb, Joanna; Marion, Miranda C.; Prahalad, Sampath; Sudman, Marc; Bowes, John; Martin, Paul; Comeau, Mary E.; Sajuthi, Satria; Andrews, Robert; Brown, Milton; Chen, Wei-Min; Concannon, Patrick; Deloukas, Panos; Edkins, Sarah; Eyre, Stephen; Gaffney, Patrick M.; Guthery, Stephen L.; Guthridge, Joel M.; Hunt, Sarah E.; James, Judith A.; Keddache, Mehdi; Moser, Kathy L.; Nigrovic, Peter A.; Onengut-Gumuscu, Suna; Onslow, Mitchell L.; Rosé, Carlos D.; Rich, Stephen S.; Steel, Kathryn J.A.; Wakeland, Edward K.; Wallace, Carol A.; Wedderburn, Lucy R.; Woo, Patricia; Bohnsack, John F.; Haas, Johannes Peter; Glass, David N.; Langefeld, Carl D.; Thomson, Wendy; Thompson, Susan D.

    2013-01-01

    Analysis of the ImmunoChip single nucleotide polymorphism (SNP) array in 2816 individuals, comprising the most common subtypes (oligoarticular and RF negative polyarticular) of juvenile idiopathic arthritis (JIA) and 13056 controls strengthens the evidence for association to three known JIA-risk loci (HLA, PTPN22 and PTPN2) and has identified fourteen risk loci reaching genome-wide significance (p < 5 × 10-8) for the first time. Eleven additional novel regions showed suggestive evidence for association with JIA (p < 1 × 10-6). Dense-mapping of loci along with bioinformatic analysis has refined the association to one gene for eight regions, highlighting crucial pathways, including the IL-2 pathway, in JIA disease pathogenesis. The entire ImmunoChip loci, HLA region and the top 27 loci (p < 1 × 10-6) explain an estimated 18%, 13% and 6% risk of JIA, respectively. Analysis of the ImmunoChip dataset, the largest cohort of JIA cases investigated to date, provides new insight in understanding the genetic basis for this childhood autoimmune disease. PMID:23603761

  20. Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley.

    PubMed

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions. PMID:27585856

  1. Environmental Health Related Socio-Spatial Inequalities: Identifying “Hotspots” of Environmental Burdens and Social Vulnerability

    PubMed Central

    Shrestha, Rehana; Flacke, Johannes; Martinez, Javier; van Maarseveen, Martin

    2016-01-01

    Differential exposure to multiple environmental burdens and benefits and their distribution across a population with varying vulnerability can contribute heavily to health inequalities. Particularly relevant are areas with high cumulative burdens and high social vulnerability termed as “hotspots”. This paper develops an index-based approach to assess these multiple burdens and benefits in combination with vulnerability factors at detailed intra-urban level. The method is applied to the city of Dortmund, Germany. Using non-spatial and spatial methods we assessed inequalities and identified “hotspot” areas in the city. We found modest inequalities burdening higher vulnerable groups in Dortmund (CI = −0.020 at p < 0.05). At the detailed intra-urban level, however, inequalities showed strong geographical patterns. Large numbers of “hotspots” exist in the northern part of the city compared to the southern part. A holistic assessment, particularly at a detailed local level, considering both environmental burdens and benefits and their distribution across the population with the different vulnerability, is essential to inform environmental justice debates and to mobilize local stakeholders. Locating “hotspot” areas at this detailed spatial level can serve as a basis to develop interventions that target vulnerable groups to ensure a health conducive equal environment. PMID:27409625

  2. Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley

    PubMed Central

    Saade, Stephanie; Maurer, Andreas; Shahid, Mohammed; Oakey, Helena; Schmöckel, Sandra M.; Negrão, Sónia; Pillen, Klaus; Tester, Mark

    2016-01-01

    Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions. PMID:27585856

  3. Carboxylic acids in PM 2.5 over Pinus morrisonicola forest and related photoreaction mechanisms identified via Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Kuo, Su-Ching; Tsai, Ying I.; Tsai, Cheng-Hsien; Hsieh, Li-Ying

    2011-12-01

    The PM 2.5 aerosol from within an area of Pinus morrisonicola Hayata in Taiwan was collected and analyzed for its low molecular weight carboxylic acid (LMWCAs) content. Oxalic acid was the major LMWCA in the aerosol, followed by acetic, tartaric and maleic acids. This differs significantly from the LMWCA composition of PM 2.5 aerosol reported for a southern Taiwan suburban region (oxalic > succinic > malonic) [Atmospheric Environment 42, 6836-6850 (2008)]. P. morrisonicola Hayata emits oxalic, malic and formic acids and yet there was an abundance of maleic and tartaric acids in the PM 2.5 forest aerosol, indicating that tartaric acid is derived from the transformation of other P. morrisonicola Hayata emissions. Raman spectroscopy was applied and 28 species of LMWCAs and inorganic species were identified. The photochemical mechanisms of maleic and tartaric acids were studied and it was found that the abundant tartaric acid in forest aerosol is most probably the photochemical product from reactions of maleic acid. Furthermore, tartaric acid is photochemically transformed into formic acid and ultimately into CO 2.

  4. A genome-wide association study identifies susceptibility loci of silica-related pneumoconiosis in Han Chinese.

    PubMed

    Chu, Minjie; Ji, Xiaoming; Chen, Weihong; Zhang, Ruyang; Sun, Chongqi; Wang, Ting; Luo, Chen; Gong, Jianhang; Zhu, Meng; Fan, Jingjing; Hou, Zhiguo; Dai, Juncheng; Jin, Guangfu; Wu, Tangchun; Chen, Feng; Hu, Zhibin; Ni, Chunhui; Shen, Hongbing

    2014-12-01

    Pneumoconiosis is the most serious occupational disease in China and its leading cause is occupational silica exposure. Pneumoconiosis takes several years to develop depending on the exposure level of silica. However, individual variation in the susceptibility to pneumoconiosis has been observed among the subjects with similar exposure. We conducted a genome-wide screening with 710,999 single nucleotide polymorphisms (SNPs) in a cohort of 400 coal workers (202 cases and 198 exposed controls) for pneumoconiosis susceptible loci. Seven promising variants were evaluated in an independent cohort of 568 coal workers (323 cases and 245 exposed controls), followed by a second replication on 463 iron ore workers (167 cases and 296 exposed controls). By pooling all of the genome-wide association studies and replication stages together, we found a genome-wide significant (P < 5.0 × 10(-8)) association for rs73329476 (P = 1.74 × 10(-8), OR = 2.17, 95% CI = 1.66-2.85) and two additional replicated associations for rs4320486 (P < 0.05) and rs117626015 (P < 0.05) with combined P-values of 4.29 × 10(-6) and 5.05 × 10(-6), respectively. In addition, the risk allele T of rs73329476 was significantly associated with lower mRNA expression levels of carboxypeptidase M (CPM) in total cellular RNA from whole blood of 156 healthy individuals (P = 0.0252). The identified pneumoconiosis susceptibility loci may provide new insights into the pathogenesis of pneumoconiosis, and may also have some clinical utility for risk prediction for pneumoconiosis and high-risk population screening for workers with occupational silica exposure.

  5. Genomics and relative expression analysis identifies key genes associated with high female to male flower ratio in Jatropha curcas L.

    PubMed

    Gangwar, Manali; Sood, Hemant; Chauhan, Rajinder Singh

    2016-04-01

    Jatropha curcas, has been projected as a major source of biodiesel due to high seed oil content (42 %). A major roadblock for commercialization of Jatropha-based biodiesel is low seed yield per inflorescence, which is affected by low female to male flower ratio (1:25-30). Molecular dissection of female flower development by analyzing genes involved in phase transitions and floral organ development is, therefore, crucial for increasing seed yield. Expression analysis of 42 genes implicated in floral organ development and sex determination was done at six floral developmental stages of a J. curcas genotype (IC561235) with inherently higher female to male flower ratio (1:8-10). Relative expression analysis of these genes was done on low ratio genotype. Genes TFL1, SUP, AP1, CRY2, CUC2, CKX1, TAA1 and PIN1 were associated with reproductive phase transition. Further, genes CUC2, TAA1, CKX1 and PIN1 were associated with female flowering while SUP and CRY2 in female flower transition. Relative expression of these genes with respect to low female flower ratio genotype showed up to ~7 folds increase in transcript abundance of SUP, TAA1, CRY2 and CKX1 genes in intermediate buds but not a significant increase (~1.25 folds) in female flowers, thereby suggesting that these genes possibly play a significant role in increased transition towards female flowering by promoting abortion of male flower primordia. The outcome of study has implications in feedstock improvement of J. curcas through functional validation and eventual utilization of key genes associated with female flowering. PMID:26878857

  6. Genomics and relative expression analysis identifies key genes associated with high female to male flower ratio in Jatropha curcas L.

    PubMed

    Gangwar, Manali; Sood, Hemant; Chauhan, Rajinder Singh

    2016-04-01

    Jatropha curcas, has been projected as a major source of biodiesel due to high seed oil content (42 %). A major roadblock for commercialization of Jatropha-based biodiesel is low seed yield per inflorescence, which is affected by low female to male flower ratio (1:25-30). Molecular dissection of female flower development by analyzing genes involved in phase transitions and floral organ development is, therefore, crucial for increasing seed yield. Expression analysis of 42 genes implicated in floral organ development and sex determination was done at six floral developmental stages of a J. curcas genotype (IC561235) with inherently higher female to male flower ratio (1:8-10). Relative expression analysis of these genes was done on low ratio genotype. Genes TFL1, SUP, AP1, CRY2, CUC2, CKX1, TAA1 and PIN1 were associated with reproductive phase transition. Further, genes CUC2, TAA1, CKX1 and PIN1 were associated with female flowering while SUP and CRY2 in female flower transition. Relative expression of these genes with respect to low female flower ratio genotype showed up to ~7 folds increase in transcript abundance of SUP, TAA1, CRY2 and CKX1 genes in intermediate buds but not a significant increase (~1.25 folds) in female flowers, thereby suggesting that these genes possibly play a significant role in increased transition towards female flowering by promoting abortion of male flower primordia. The outcome of study has implications in feedstock improvement of J. curcas through functional validation and eventual utilization of key genes associated with female flowering.

  7. Core subjects at the end of primary school: identifying and explaining relative strengths of children with specific language impairment (SLI)

    PubMed Central

    Durkin, Kevin; Mok, Pearl L H; Conti-Ramsden, Gina

    2015-01-01

    Background In general, children with specific language impairment (SLI) tend to fall behind their typically developing (TD) peers in educational attainment. Less is known about how children with SLI fare in particular areas of the curriculum and what predicts their levels of performance. Aims To compare the distributions of performance of children with SLI in three core school subjects (English, Mathematics and Science); to test the possibility that performance would vary across the core subjects; and to examine the extent to which language impairment predicts performance. Methods & Procedures This study was conducted in England and reports historical data on educational attainments. Teacher assessment and test scores of 176 eleven-year-old children with SLI were examined in the three core subjects and compared with known national norms. Possible predictors of performance were measured, including language ability at ages 7 and 11, educational placement type, and performance IQ. Outcomes & Results Children with SLI, compared with national norms, were found to be at a disadvantage in core school subjects. Nevertheless, some children attained the levels expected of TD peers. Performance was poorest in English; relative strengths were indicated in Science and, to a lesser extent, in Mathematics. Language skills were significant predictors of performance in all three core subjects. PIQ was the strongest predictor for Mathematics. For Science, both early language skills at 7 years and PIQ made significant contributions. Conclusions & Implications Language impacts on the school performance of children with SLI, but differentially across subjects. English for these children is the most challenging of the core subjects, reflecting the high levels of language demand it incurs. Science is an area of relative strength and mathematics appears to be intermediate, arguably because some tasks in these subjects can be performed with less reliance on verbal processing. Many children

  8. Identifying the Source of High-Nitrate Ground Water Related to Artificial Recharge in a Desert Basin

    NASA Astrophysics Data System (ADS)

    Densmore, J. N.; Nishikawa, T.; Bohlke, J. K.; Martin, P.

    2002-12-01

    Ground water has been the sole source of water supply for the community of Yucca Valley in the Mojave Desert, California. Domestic wastewater from the community is treated using septic tanks. An imbalance between ground-water recharge and pumpage caused ground-water levels in the ground-water basin to decline by as much as 300 feet from the late 1940s through 1994. In response to this decline, the local water district, Hi-Desert Water District, began an artificial recharge program in February 1995 to replenish the ground water in the basin using imported surface water. The artificial recharge program resulted in water-level recovery of about 250 feet between February 1995 and December 2001; however, nitrate concentrations in some wells also increased from a background concentration of 10 mg/L as NO3 to more than the U.S. Environmental Protection Agency maximum contaminant level of 45 mg/L as NO3, limiting water use for some wells. The largest increase in nitrate concentrations occurred adjacent to the artificial recharge sites where the largest increase in water levels occurred even though the recharge water had low nitrate concentrations. The source of high nitrate concentrations observed in ground water during aquifer recovery was identified by compiling historical water-quality data; monitoring changes in water quality since artificial recharge began; and analyzing selected samples for major-ion chemistry, stable isotopes of H,O, and N, caffeine, and pharmaceuticals. The major-ions and H and O stable-isotope data indicate that ground-water samples that had the highest nitrate concentrations were mixtures of imported water and native ground water. Nitrate-to-chloride ratios, N isotopes and caffeine and pharmaceutical data indicate septic-tank seepage (septage) is the primary source of increases in nitrate concentration. The rapid rise in water levels entrained the large volume of high-nitrate septage stored in the unsaturated zone, resulting in the rapid increase

  9. Identifying a Network of Brain Regions Involved in Aversion-Related Processing: A Cross-Species Translational Investigation

    PubMed Central

    Hayes, Dave J.; Northoff, Georg

    2011-01-01

    The ability to detect and respond appropriately to aversive stimuli is essential for all organisms, from fruit flies to humans. This suggests the existence of a core neural network which mediates aversion-related processing. Human imaging studies on aversion have highlighted the involvement of various cortical regions, such as the prefrontal cortex, while animal studies have focused largely on subcortical regions like the periaqueductal gray and hypothalamus. However, whether and how these regions form a core neural network of aversion remains unclear. To help determine this, a translational cross-species investigation in humans (i.e., meta-analysis) and other animals (i.e., systematic review of functional neuroanatomy) was performed. Our results highlighted the recruitment of the anterior cingulate cortex, the anterior insula, and the amygdala as well as other subcortical (e.g., thalamus, midbrain) and cortical (e.g., orbitofrontal) regions in both animals and humans. Importantly, involvement of these regions remained independent of sensory modality. This study provides evidence for a core neural network mediating aversion in both animals and humans. This not only contributes to our understanding of the trans-species neural correlates of aversion but may also carry important implications for psychiatric disorders where abnormal aversive behavior can often be observed. PMID:22102836

  10. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.

    PubMed

    Tena, Juan J; González-Aguilera, Cristina; Fernández-Miñán, Ana; Vázquez-Marín, Javier; Parra-Acero, Helena; Cross, Joe W; Rigby, Peter W J; Carvajal, Jaime J; Wittbrodt, Joachim; Gómez-Skarmeta, José L; Martínez-Morales, Juan R

    2014-07-01

    The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer's formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115-200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan.

  11. Identifying social characteristics of health-related information seeker: a gender-specific approach for cancer survivors.

    PubMed

    Jung, Minsoo

    2015-01-01

    While health information-seeking behavior as an indicator of health communication of patients including cancer survivors has been researched, few studies have focused on how socioeconomic position and media use combine to influence health-related information seekers. This study examined social characteristics of health information-seeking behavior taking into account an individual's socioeconomic position and their media use in Korea, a developed country. The data for this study came from a survey of 1,010 respondents drawn from a nationally representative sample in the Republic of Korea. We conducted multivariate logistic regression analyses for gender-specific effects. We found that men who reported high household income were one and half times more likely to seek health information than those with low income status. We also found that women who performed Internet searches by computer at home were almost two times more likely to seek health information than those who did not. Similar results were found for men as well. Our analyses revealed that socioeconomic position and media use are associated with health information-seeking behavior by gender. Studies on information seekers may bring us more effective health promotion and relevant intervention for people with chronic conditions including cancer survivors. PMID:25773838

  12. Identifying social characteristics of health-related information seeker: a gender-specific approach for cancer survivors.

    PubMed

    Jung, Minsoo

    2015-01-01

    While health information-seeking behavior as an indicator of health communication of patients including cancer survivors has been researched, few studies have focused on how socioeconomic position and media use combine to influence health-related information seekers. This study examined social characteristics of health information-seeking behavior taking into account an individual's socioeconomic position and their media use in Korea, a developed country. The data for this study came from a survey of 1,010 respondents drawn from a nationally representative sample in the Republic of Korea. We conducted multivariate logistic regression analyses for gender-specific effects. We found that men who reported high household income were one and half times more likely to seek health information than those with low income status. We also found that women who performed Internet searches by computer at home were almost two times more likely to seek health information than those who did not. Similar results were found for men as well. Our analyses revealed that socioeconomic position and media use are associated with health information-seeking behavior by gender. Studies on information seekers may bring us more effective health promotion and relevant intervention for people with chronic conditions including cancer survivors.

  13. A predicted T4 secretion system and conserved DNA-repeats identified in a subset of related Arthrobacter plasmids.

    PubMed

    Mihăşan, Marius; Brandsch, Roderich

    2016-10-01

    BLAST analysis of pAO1 ORFs of Arthrobacter nicotinovorans revealed 12 ORFs, including the ORF of a transcriptional regulator, predicted to encode the components of a T4-secretion system involved in bacterial conjugation. These ORFs were conserved and showed synteny among 14 Arthrobacter plasmids. A DNA repeat of about 370 nucleotides was found to be present 5' to the pAO1 ORFs of DUF4192-, DprA- and ParB-like proteins. Similar repeats were present in identical positions on 12 additional Arthrobacter plasmids. The DNA repeats on a particular plasmid are highly identical duplications. The DNA repeats contain alternating GC and AT reach sequences, potential protein DNA-binding sites and purine reach stretches. The sequences end with 5'ATG.AAC3' which results in the amino terminal sequence methionine (M) and asparagine (N) for all predicted DprA, DUF4192 and ParB proteins. The presences of conserved ORFs of a T4-secretion system and of similar DNA repeats suggest that these Arthrobacter plasmids are related and evolved from a common ancestor. The functional significance of the DNA repeats in a coordinated common mechanism of regulation of expression of the dprA-(involved in natural competence), parB- (involved in plasmid partitioning) and duf4192- (unknown function in plasmid life cycle) genes remains to be established. PMID:27524651

  14. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

    PubMed Central

    Tena, Juan J.; González-Aguilera, Cristina; Fernández-Miñán, Ana; Vázquez-Marín, Javier; Parra-Acero, Helena; Cross, Joe W.; Rigby, Peter W.J.; Carvajal, Jaime J.; Wittbrodt, Joachim; Gómez-Skarmeta, José L.; Martínez-Morales, Juan R.

    2014-01-01

    The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer’s formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115–200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan. PMID:24709821

  15. Identifying Individual Risk Factors and Documenting the Pattern of Heat-Related Illness through Analyses of Hospitalization and Patterns of Household Cooling

    PubMed Central

    Schmeltz, Michael T.; Sembajwe, Grace; Marcotullio, Peter J.; Grassman, Jean A.; Himmelstein, David U.; Woolhandler, Stephanie

    2015-01-01

    Background As climate change increases the frequency and intensity of extreme heat events researchers and public health officials must work towards understanding the causes and outcomes of heat-related morbidity and mortality. While there have been many studies on both heat-related illness (HRI), there are fewer on heat-related morbidity than on heat-related mortality. Objective To identify individual and environmental risk factors for hospitalizations and document patterns of household cooling. Methods We performed a pooled cross-sectional analysis of secondary U.S. data, the Nationwide Inpatient Sample. Risk ratios were calculated from multivariable models to identify risk factors for hospitalizations. Hierarchical modeling was also employed to identify relationships between individual and hospital level predictors of hospitalizations. Patterns of air conditioning use were analyzed among the vulnerable populations identified. Results Hospitalizations due to HRI increased over the study period compared to all other hospitalizations. Populations at elevated risk for HRI hospitalization were blacks, males and all age groups above the age of 40. Those living in zip-codes in the lowest income quartile and the uninsured were also at an increased risk. Hospitalizations for HRI in rural and small urban clusters were elevated, compared to urban areas. Conclusions Risk factors for HRI include age greater than 40, male gender and hospitalization in rural areas or small urban clusters. Our analysis also revealed an increasing pattern of HRI hospitalizations over time and decreased association between common comorbidities and heat illnesses which may be indicative of underreporting. PMID:25742021

  16. A single predominantly expressed polymorphic immunoglobulin VH gene family, related to mammalian group, I, clan, II, is identified in cattle.

    PubMed

    Saini, S S; Hein, W R; Kaushik, A

    1997-06-01

    In order to understand the generation of antibody diversity in cattle, seven cDNAs, from heterohybridomas secreting bovine IgM and IgG1 antibodies, were cloned and structurally analyzed for rearranged bovine VDJ genes. All of the seven bovine VH genes, together with four available bovine VH gene sequences, shared a high nucleotide sequence homology (84.2-93.5%). Based upon the criteria of nucleic acid homology > or =80%, all of the bovine VH gene sequences isolated from the expressed antibody repertoire constitute a single VH gene family, which we have designated as bovine VH1 (Bov VH1). An analysis of 44 bovine IgM-secreting mouse x cattle heterohybridomas, originating from polyclonally-activated PBLs from bovine leukemia virus-infected cattle, revealed that all of these expressed Bov VH1 (100%) based upon DNA sequencing and Northern dot blot. The bovine VH genes showed highest DNA sequence similarity, ranging between 81.5 and 87.6%, with a single sheep VH gene family (related to human VH4) and are, thus, closest to the VH genes from another ruminant species. The Bov VH1 gene family is most homologous to the murine VH Q-52 (71.8-78%) and human VH4 (67.4-69.8%) gene families, which belong to mammalian group, I, clan, II, VH genes. The CDR3 length of rearranged bovine VDJ genes is characteristically long (15-23 amino acids). The bovine JH gene segments were most homologous to human JH4 (82.1-87.2%) and JH5 (84.6-89.7%) genes, suggesting the existence of at least two JH gene segments. An analysis of CDRs provides evidence that somatic hypermutations contribute significantly to the generation of antibody diversity in cattle. Southern blot analysis of BamH I, EcoR I and Hind III digested genomic DNA from four cattle breeds (Holstein, Jersey, Hereford and Charolais) revealed three RFLP patterns; the genomic complexity of Bov VH1 ranged between 13 and 15 genes. These observations provide evidence for polymorphism at the bovine Ig-VH locus, similar to that seen in mice

  17. Identifying duplicate content using statistically improbable phrases

    PubMed Central

    Errami, Mounir; Sun, Zhaohui; George, Angela C.; Long, Tara C.; Skinner, Michael A.; Wren, Jonathan D.; Garner, Harold R.

    2010-01-01

    Motivation: Document similarity metrics such as PubMed's ‘Find related articles’ feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. Results: When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Availability: Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/ Contact: merrami@collin.edu PMID:20472545

  18. Multiple Genes Related to Muscle Identified through a Joint Analysis of a Two-stage Genome-wide Association Study for Racing Performance of 1,156 Thoroughbreds

    PubMed Central

    Shin, Dong-Hyun; Lee, Jin Woo; Park, Jong-Eun; Choi, Ik-Young; Oh, Hee-Seok; Kim, Hyeon Jeong; Kim, Heebal

    2015-01-01

    Thoroughbred, a relatively recent horse breed, is best known for its use in horse racing. Although myostatin (MSTN) variants have been reported to be highly associated with horse racing performance, the trait is more likely to be polygenic in nature. The purpose of this study was to identify genetic variants strongly associated with racing performance by using estimated breeding value (EBV) for race time as a phenotype. We conducted a two-stage genome-wide association study to search for genetic variants associated with the EBV. In the first stage of genome-wide association study, a relatively large number of markers (~54,000 single-nucleotide polymorphisms, SNPs) were evaluated in a small number of samples (240 horses). In the second stage, a relatively small number of markers identified to have large effects (170 SNPs) were evaluated in a much larger number of samples (1,156 horses). We also validated the SNPs related to MSTN known to have large effects on racing performance and found significant associations in the stage two analysis, but not in stage one. We identified 28 significant SNPs related to 17 genes. Among these, six genes have a function related to myogenesis and five genes are involved in muscle maintenance. To our knowledge, these genes are newly reported for the genetic association with racing performance of Thoroughbreds. It complements a recent horse genome-wide association studies of racing performance that identified other SNPs and genes as the most significant variants. These results will help to expand our knowledge of the polygenic nature of racing performance in Thoroughbreds. PMID:25925054

  19. The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing.

    PubMed

    Tan, Christopher A; Topper, Scott; Ward Melver, Catherine; Stein, Jennifer; Reeder, Amanda; Arndt, Kelly; Das, Soma

    2014-04-01

    Primary autosomal recessive microcephaly (MCPH) is a genetically heterogeneous condition characterized by congenital microcephaly and intellectual disability. To date, 10 MCPH loci have been identified and due to the genetic heterogeneity of this condition, molecular testing for MCPH can be complicated. Our methods involved employing a next generation sequencing panel of MCPH-related genes allowing for the evaluation of multiple disease loci simultaneously. Next generation sequencing analysis of a 6 year old female with primary microcephaly identified novel compound heterozygous mutations (c.524_528del and c.4005-1G>A) in the CDK5RAP2 gene. A review of the published literature to date reveals that only three mutations have been previously reported in the CDK5RAP2 gene in the homozygous state in three Northern Pakistani and one Somali consanguineous MCPH families. Our patient represents the first non-consanguineous Caucasian individual to have been identified with CDK5RAP2-related MCPH. As only a handful of patients have been reported in the literature with CDK5RAP2-related MCPH, we anticipate the identification of individuals with CDK5RAP2 mutations from all ethnic backgrounds will continue. Our patient contributes to the ethnic and genotypic spectrum of CDK5RAP2-related MCPH and supports the occurrence of this genetic condition beyond that of consanguineous families of certain ethnic populations. Our results also highlight the utility of multi-gene sequencing panels to elucidate the etiology of genetically heterogeneous conditions. PMID:23726037

  20. A Review of Human Papillomavirus (HPV) Infection and HPV Vaccine-Related Attitudes and Sexual Behaviors among College-Aged Women in the United States

    ERIC Educational Resources Information Center

    Ratanasiripong, Nop T.

    2012-01-01

    Objective: To identify human papillomavirus (HPV) infection and HPV vaccine-related attitudes among college-aged women and the relationship between HPV vaccine uptake and subsequent sexual behaviors. Methods: PubMed, MEDLINE, CINAHL, and Google Scholar searches were performed from 2006, the date after the first HPV vaccine became available, to…

  1. Clinical use of meconium fatty acid ethyl esters for identifying children at risk for alcohol-related disabilities: the first reported case.

    PubMed

    Zelner, Irene; Shor, Sarit; Lynn, Hazel; Roukema, Henry; Lum, Lisa; Eisinga, Kirsten; Koren, Gideon

    2012-01-01

    Fatty acid ethyl esters (FAEEs) in meconium are validated biomarkers of heavy fetal alcohol exposure that may potentially be used clinically for identifying children at risk for alcohol-related disabilities. However, until now, FAEEs have been largely used anonymously in epidemiological studies, and by child protection authorities in need for verification of heavy alcohol use in pregnancy. Here we describe the first case of a neonate identified as part of a research study on a pilot neonatal screening program for prenatal alcohol exposure. The neonate's meconium tested high for FAEEs (52 nmol/g; positive cut-off ≥ 2 nmol/g), which prompted active follow-up of the infant's development, identifying early neurocognitive problems and allowing initiation of a remedial program. PMID:22247425

  2. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

    PubMed

    Sutton, Victoria R; Hauser, Susan E

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information.

  3. Comparison of the effects of pyrokinins and related peptides identified from arthropods on pupariation behaviour in flesh fly (Sarcophaga bullata) larvae (Diptera: Sarcophagidae).

    PubMed

    Zdárek, Jan; Verleyen, Peter; Mares, Michael; Dolecková, Lucie; Nachman, Ronald J

    2004-01-01

    Peptides from the pyrokinin/PBAN family and some structurally related compounds identified in various arthropods were tested for acceleration of puparial contraction in flesh fly larvae. Modifications of behavioural patterns of pupariation were further studied for the active compounds using a behavioural analysis based on the recording of changes in tension of the cuticle. Nine peptides belonging to the pyrokinin/PBAN family (Lem-PK, Pea-PK-5, Lom-PK II, Hez-PBAN, Bom-DH-I), identified in five different insect species, two pyrokinin peptides derived from the genome of Drosophila melanogaster (capa-3, and hugin), and two pyrokinins identified from the white shrimp Penaeus vannamei were very active in the pupariation assay, with threshold doses within the range of 0.1-5.0 pmol larva(-1). High activity was also detected for a related peptide ETH1 from Drosophila. All of these peptides share a C-terminal PRLamide, which is essential and sufficient for the activity. Interestingly, two other structurally related peptides from Drosophila--ETH2 and capa-1--which feature conservative changes (Ile and Val, respectively) at the C-terminal Leu position, were inactive within a physiological range of concentrations. It is clear that the receptor mediating the acceleration of puparial contraction behaviour is sensitive to the introduction of greater steric bulk at the C-terminal Leu position. The peptides that accelerated pupariation showed very similar patterns of muscular and cuticular activity.

  4. Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

    PubMed Central

    2014-01-01

    Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

  5. A systematic review of patient-related risk factors for catheter-related thrombosis.

    PubMed

    Leung, Amy; Heal, Clare; Perera, Marlon; Pretorius, Casper

    2015-10-01

    To identify patient-related risk factors for venous thrombosis in patients with central venous catheters (CVC) or peripherally inserted central catheters (PICC). We performed a systematic review of the literature assessing patient-related risk factors for thrombosis related to CVC or PICC. The databases PubMed, Ovid and the Cochrane library were searched for observational studies pertaining to patient-related risk factors for CVC and PICC-related thrombosis. The initial search through PubMed, Ovid and the Cochrane library yielded 516 results. After 71 duplicates were removed, 445 articles were assessed for eligibility based on title and abstract. Four hundred and eleven articles were then excluded and 33 full text articles were manually assessed for eligibility. Eight articles were eliminated as they did not contain content relevant to the review. Twenty-five studies were then selected to assess 20 risk factors. There were no consistent significant associations for catheter-related thrombosis across the twenty-five studies. Multiple studies identified age, malignancy, diabetes, obesity, chemotherapy, thrombophilia and a history of thrombosis as significant risk factors for catheter-related thrombosis. Inconsistent findings among studies make it difficult to establish which patient-related risk factors are associated with catheter-related thrombosis. Future studies could include larger sample sizes and more cases of catheter-related thrombosis to produce more significant results. Identification of patient-related risk factors could lead to early recognition of upper limb deep vein thrombosis in patients with catheters, thereby preventing complications.

  6. Fatigue-Related Gene Networks Identified in CD14+ Cells Isolated From HIV-Infected Patients—Part I: Research Findings

    PubMed Central

    Voss, Joachim G.; Dobra, Adrian; Morse, Caryn; Kovacs, Joseph A.; Danner, Robert L.; Munson, Peter J.; Logan, Carolea; Rangel, Zoila; Adelsberger, Joseph W.; McLaughlin, Mary; Adams, Larry D.; Raju, Raghavan; Dalakas, Marinos C.

    2016-01-01

    Purpose Human immunodeficiency virus (HIV)–related fatigue (HRF) is multicausal and potentially related to mitochondrial dysfunction caused by antiretroviral therapy with nucleoside reverse transcriptase inhibitors (NRTIs). Methodology The authors compared gene expression profiles of CD14+ cells of low versus high fatigued, NRTI-treated HIV patients to healthy controls (n = 5/group). The authors identified 32 genes predictive of low versus high fatigue and 33 genes predictive of healthy versus HIV infection. The authors constructed genetic networks to further elucidate the possible biological pathways in which these genes are involved. Relevance for nursing practice Genes including the actin cytoskeletal regulatory proteins Prokineticin 2 and Cofilin 2 along with mitochondrial inner membrane proteins are involved in multiple pathways and were predictors of fatigue status. Previously identified inflammatory and signaling genes were predictive of HIV status, clearly confirming our results and suggesting a possible further connection between mitochondrial function and HIV. Isolated CD14+ cells are easily accessible cells that could be used for further study of the connection between fatigue and mitochondrial function of HIV patients. Implication for Practice The findings from this pilot study take us one step closer to identifying biomarker targets for fatigue status and mitochondrial dysfunction. Specific biomarkers will be pertinent to the development of methodologies to diagnosis, monitor, and treat fatigue and mitochondrial dysfunction. PMID:23324479

  7. [Identifying residential areas with heat-related health risks. Sociodemographic and climate data mapping as a planning tool for targeted prevention strategies].

    PubMed

    Blättner, B; Heckenhahn, M; Georgy, S; Grewe, H A; Kupski, S

    2010-01-01

    Prognosticated heat waves in the context of climate change require appropriate strategies to prevent harmful health effects in the population. In a model project within the public health department of the Kassel region, elderly living in areas at risk of over-heating will be identified and advised. The localization of high-risk residential areas was part of the planning process. Through mapping of demographic and microclimate data and the characteristics of the material of the residential buildings, high-risk areas that require preventive measures as a top priority were identified. The prevention of heat-related mortality and morbidity by communal health authorities requires close cooperation with other administrative bodies, especially with town planning departments. Mapping demographic and microclimate data and the characteristics of the material of the residential buildings can facilitate the planning of preventive measures.

  8. The intolerance of uncertainty scale: measurement invariance, population heterogeneity, and its relation with worry among self-identifying White and Black respondents.

    PubMed

    Fergus, Thomas A; Wu, Kevin D

    2013-10-01

    Although it is understood that assessment tools require evaluation using diverse samples, such evaluations are relatively rare. There are obstacles to such work, but it remains important to pursue psychometric data in broad samples. As such, we evaluated measurement invariance and population heterogeneity of two versions of a widely used measure in the anxiety literature--the Intolerance of Uncertainty Scale (IUS)--among self-identifying White (N = 1,185) and Black (N = 301) students. Data from multiple-groups confirmatory factor analysis supported the equivalence of the equal form and factor loadings of both IUS versions in White and Black respondents. However, specific IUS items functioned differently in the two groups, with more IUS items appearing biased in the full-length relative to the short-form version. Correlations between IUS factors and worry were equivalent among White and Black respondents. We discuss the implications of these results for future research.

  9. A computer-based interview to identify HIV risk behaviors and to assess patient preferences for HIV-related health states.

    PubMed Central

    Sanders, G. D.; Owens, D. K.; Padian, N.; Cardinalli, A. B.; Sullivan, A. N.; Nease, R. F.

    1994-01-01

    We developed a computer-based utility assessment tool to assess the preferences of patients towards HIV-related health states and identify risk behaviors (both sexual and drug related) of the patient being interviewed. The reliability of the computer-based interview was assessed through comparison with person-to-person interviews. Our pilot study included 22 patients. Twelve of these patients were also interviewed by the research assistants in person-to-person interviews. The agreement between the person-to-person and computer-based interviews was excellent (3 discrepancies of 180 compared answers), and the majority of the patients preferred to use the computer to disclose sensitive information regarding risk behaviors. Our study suggests that assessment of patient preferences and risk factors can be performed reliably through a computer-based interview. PMID:7949919

  10. A Conserved BDNF, Glutamate- and GABA-Enriched Gene Module Related to Human Depression Identified by Coexpression Meta-Analysis and DNA Variant Genome-Wide Association Studies

    PubMed Central

    Chang, Lun-Ching; Jamain, Stephane; Lin, Chien-Wei; Rujescu, Dan; Tseng, George C.; Sibille, Etienne

    2014-01-01

    Large scale gene expression (transcriptome) analysis and genome-wide association studies (GWAS) for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD) and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases. In support of the superior discriminative power of this novel approach, we observed no significant enrichment for GWAS-related genes in coexpression modules extracted from single studies or in meta-modules using gene expression data from non-psychiatric control subjects. Genes in the identified module encode proteins implicated in neuronal signaling and structure, including glutamate metabotropic receptors (GRM1, GRM7), GABA receptors (GABRA2, GABRA4), and neurotrophic and development-related proteins [BDNF, reelin (RELN), Ephrin receptors (EPHA3, EPHA5)]. These results are consistent with the current understanding of molecular mechanisms of MDD and provide a set of putative interacting molecular partners, potentially reflecting components of a functional module across cells and biological pathways that are synchronously recruited in MDD, other brain disorders and MDD-related illnesses. Collectively, this study demonstrates the importance of integrating transcriptome data, gene coexpression modules

  11. Establishing Minimum Flow Requirements Based on Benthic Vegetation: What are Some Issues Related to Identifying Quantity of Inflow and Tools Used to Quantify Ecosystem Response?

    NASA Astrophysics Data System (ADS)

    Hunt, M. J.; Nuttle, W. K.; Cosby, B. J.; Marshall, F. E.

    2005-05-01

    Establishing minimum flow requirements in aquatic ecosystems is one way to stipulate controls on water withdrawals in a watershed. The basis of the determination is to identify the amount of flow needed to sustain a threshold ecological function. To develop minimum flow criteria an understanding of ecological response in relation to flow is essential. Several steps are needed including: (1) identification of important resources and ecological functions, (2) compilation of available information, (3) determination of historical conditions, (4) establishment of technical relationships between inflow and resources, and (5) identification of numeric criteria that reflect the threshold at which resources are harmed. The process is interdisciplinary requiring the integration of hydrologic and ecologic principles with quantitative assessments. The tools used quantify the ecological response and key questions related to how the quantity of flow influences the ecosystem are examined by comparing minimum flow determination in two different aquatic systems in South Florida. Each system is characterized by substantial hydrologic alteration. The first, the Caloosahatchee River is a riverine system, located on the southwest coast of Florida. The second, the Everglades- Florida Bay ecotone, is a wetland mangrove ecosystem, located on the southern tip of the Florida peninsula. In both cases freshwater submerged aquatic vegetation (Vallisneria americana or Ruppia maritima), located in areas of the saltwater- freshwater interface has been identified as a basis for minimum flow criteria. The integration of field studies, laboratory studies, and literature review was required. From this information we developed ecological modeling tools to quantify and predict plant growth in response to varying environmental variables. Coupled with hydrologic modeling tools questions relating to the quantity and timing of flow and ecological consequences in relation to normal variability are addressed.

  12. Identifying anti-cancer drug response related genes using an integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations

    PubMed Central

    Chen, Yunqin; Ma, Qin; Wei, Jia; Liu, Qi

    2016-01-01

    Background Clinical responses to anti-cancer therapies often only benefit a defined subset of patients. Predicting the best treatment strategy hinges on our ability to effectively translate genomic data into actionable information on drug responses. Results To achieve this goal, we compiled a comprehensive collection of baseline cancer genome data and drug response information derived from a large panel of cancer cell lines. This data set was applied to identify the signature genes relevant to drug sensitivity and their resistance by integrating CNVs and the gene expression of cell lines with in vitro drug responses. We presented an efficient in-silico pipeline for integrating heterogeneous cell line data sources with the simultaneous modeling of drug response values across all the drugs and cell lines. Potential signature genes correlated with drug response (sensitive or resistant) in different cancer types were identified. Using signature genes, our collaborative filtering-based drug response prediction model outperformed the 44 algorithms submitted to the DREAM competition on breast cancer cells. The functions of the identified drug response related signature genes were carefully analyzed at the pathway level and the synthetic lethality level. Furthermore, we validated these signature genes by applying them to the classification of the different subtypes of the TCGA tumor samples, and further uncovered their in vivo implications using clinical patient data. Conclusions Our work may have promise in translating genomic data into customized marker genes relevant to the response of specific drugs for a specific cancer type of individual patients. PMID:26824188

  13. Health-Related Quality of Life of Adolescent and Young Adult Survivors of Central Nervous System Tumors: Identifying Domains From a Survivor Perspective.

    PubMed

    Kuhlthau, Karen; Luff, Donna; Delahaye, Jennifer; Wong, Alicia; Yock, Torunn; Huang, Mary; Park, Elyse R

    2015-01-01

    This article uses qualitative methods to describe the domains of health-related quality of life (HRQoL) that adolescent and young adult (AYA) survivors of central nervous system (CNS) tumors identify as important. Survivors clearly attributed aspects of their current HRQoL to their disease or its treatment. We identified 7 key domains of AYA CNS tumor survivorship: physical health, social well-being, mental health, cognitive functioning, health behaviors, sexual and reproductive health, and support systems. Although most aspects of HRQoL that survivors discussed represented new challenges, there were several areas where survivors pointed out positive outcomes. There is a need for a HRQoL tool designed for this population of survivors, given their unique treatment and survivorship experience. Aspects of HRQoL related to cognition, sexual and reproductive health, health behaviors, and support systems are not typically included in generic HRQoL tools but should be assessed for this population. Developing HRQoL measurement instruments that capture the most significant aspects of HRQoL will improve the ability to track HRQoL in AYA CNS tumor survivors and in the long-term management of common sequelae from CNS tumors and their treatments.

  14. Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba).

    PubMed

    Ye, Manhong; Zhou, Bin; Wei, Shanshan; Ding, MengMeng; Lu, Xinghui; Shi, Xuehao; Ding, Jiatong; Yang, Shengmei; Wei, Wanhong

    2016-01-01

    Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)'s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs. PMID:27175015

  15. Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

    PubMed Central

    Ye, Manhong; Zhou, Bin; Wei, Shanshan; Ding, MengMeng; Lu, Xinghui; Shi, Xuehao; Ding, Jiatong; Yang, Shengmei; Wei, Wanhong

    2016-01-01

    Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs. PMID:27175015

  16. Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba).

    PubMed

    Ye, Manhong; Zhou, Bin; Wei, Shanshan; Ding, MengMeng; Lu, Xinghui; Shi, Xuehao; Ding, Jiatong; Yang, Shengmei; Wei, Wanhong

    2016-01-01

    Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)'s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.

  17. Identifying Quantitative In Vivo Multi-Parametric MRI Features For Treatment Related Changes after Laser Interstitial Thermal Therapy of Prostate Cancer

    PubMed Central

    Viswanath, Satish; Toth, Robert; Rusu, Mirabela; Sperling, Dan; Lepor, Herbert; Futterer, Jurgen; Madabhushi, Anant

    2014-01-01

    Laser interstitial thermal therapy (LITT) is a new therapeutic strategy being explored in prostate cancer (CaP), which involves focal ablation of organlocalized tumor via an interstitial laser fiber. While little is known about treatment-related changes following LITT, studying post-LITT changes via imaging is extremely significant for enabling early image-guided intervention and follow-up. In this work, we present the first attempt at examining focal treatment-related changes on a per-voxel basis via quantitative comparison of MRI features pre- and post-LITT, and hence identifying computerized MRI features that are highly sensitive as well as specific to post-LITT changes within the ablation zone in the prostate. A retrospective cohort of 5 patient datasets comprising both pre- and post-LITT T2-weighted (T2w) and diffusion-weighted (DWI) acquisitions was considered, where DWI MRI yielded an Apparent Diffusion Co-efficient (ADC) map. Our scheme involved (1) inter-protocol registration of T2w and ADC MRI, as well as inter-acquisition registration of pre- and post-LITT MRI, (2) quantitation of MRI parameters by correcting for intensity drift in order to examine tissuespecific response, and (3) quantification of the information captured by T2w MRI and ADC maps via texture and intensity features. Correction of parameter drift resulted in visually discernible improvements in highlighting tissue-specific response in different MRI features. Quantitative, voxel-wise comparison of the changes in different MRI features indicated that steerable and non-steerable gradient texture features, rather than the original T2w intensity and ADC values, were highly sensitive as well as specific in identifying changes within the ablation zone pre- and post-LITT. The highest ranked texture feature yielded a normalized percentage change of 186% within the ablation zone and 43% in a spatially distinct normal region, relative to its pre-LITT value. By comparison, both the original T2w

  18. Six DNA polymorphisms in the low density lipoprotein receptor gene: their genetic relationship and an example of their use for identifying affected relatives of patients with familial hypercholesterolaemia.

    PubMed Central

    Humphries, S; King-Underwood, L; Gudnason, V; Seed, M; Delattre, S; Clavey, V; Fruchart, J C

    1993-01-01

    We have determined the relative allele frequency and estimated linkage disequilibrium between six DNA polymorphisms of the low density lipoprotein (LDL) receptor gene. Polymorphisms were detected using the enzymes SfaNI, TaqI, StuI, HincII, AvaII, and NcoI after DNA amplification by the polymerase chain reaction. Strong linkage disequilibrium was detected between many of the pair wise comparisons in a sample of 60 patients heterozygous for familial hypercholesterolaemia (FH). Using the enzymes HincII, NcoI, and SfaNI, 85% of patients were heterozygous for at least one polymorphism and thus potentially informative for cosegregation studies. The polymorphisms were used to follow the inheritance of the defective allele of the LDL receptor gene in the relatives of a patient with FH. Assays of LDL receptor activity on lymphoblastoid cell lines from two members of the family was used to confirm that the proband, but not the hypercholesterolaemic brother, had a defect in the LDL receptor. In the family, none of the children had inherited the allele of the LDL receptor gene inferred to be defective. The problems associated with this cosegregation approach to identify relatives of patients with a clinical diagnosis of FH are discussed. PMID:8098067

  19. Eggplant and related species are promising genetic resources to dissect the plant immune response to Pseudomonas syringae and Xanthomonas euvesicatoria and to identify new resistance determinants.

    PubMed

    Clarke, Christopher R; Hayes, Byron W; Runde, Brendan J; Wicker, Emmanuel; Vinatzer, Boris A

    2014-10-01

    The apparent lack of durability of many resistance (R) genes highlights the need for the constant identification of new genetic sources of resistance for the breeding of new disease-resistant crop cultivars. To this end, we screened a collection of accessions of eggplant and close relatives for resistance against Pseudomonas syringae pv. tomato (Pto) and Xanthomonas euvesicatoria (Xeu), foliar plant pathogens of many solanaceous crops. Both pathogens caused substantial disease on most genotypes of eggplant and its relatives. Promisingly, however, some of the genotypes were fully or partially resistant to either of the pathogens, suggesting the presence of effective resistance determinants in these genotypes. Segregation of resistance to the growth of Xeu following infiltration in F2 progeny from a cross of a resistant and susceptible genotype suggests that resistance to Xeu is inherited as a multigenic trait. With regard to Pto, a mutant strain lacking all 28 functional type III secreted effectors, and a Pseudomonas fluorescens strain expressing a P. syringae type III secretion system (T3SS), both elicit a strong cell death response on most eggplant lines. Several genotypes thus appear to harbour a mechanism for the direct recognition of a component of the T3SS. Therefore, eggplant and its close relatives are promising resources to unravel novel aspects of plant immunity and to identify new candidate R genes that could be employed in other Solanaceae in which Xeu and Pto cause agriculturally relevant diseases.

  20. Sterylglucoside Catabolism in Cryptococcus neoformans with Endoglycoceramidase-related Protein 2 (EGCrP2), the First Steryl-β-glucosidase Identified in Fungi*

    PubMed Central

    Watanabe, Takashi; Ito, Tomoharu; Goda, Hatsumi M.; Ishibashi, Yohei; Miyamoto, Tomofumi; Ikeda, Kazutaka; Taguchi, Ryo; Okino, Nozomu; Ito, Makoto

    2015-01-01

    Cryptococcosis is an infectious disease caused by pathogenic fungi, such as Cryptococcus neoformans and Cryptococcus gattii. The ceramide structure (methyl-d18:2/h18:0) of C. neoformans glucosylceramide (GlcCer) is characteristic and strongly related to its pathogenicity. We recently identified endoglycoceramidase-related protein 1 (EGCrP1) as a glucocerebrosidase in C. neoformans and showed that it was involved in the quality control of GlcCer by eliminating immature GlcCer during the synthesis of GlcCer (Ishibashi, Y., Ikeda, K., Sakaguchi, K., Okino, N., Taguchi, R., and Ito, M. (2012) Quality control of fungus-specific glucosylceramide in Cryptococcus neoformans by endoglycoceramidase-related protein 1 (EGCrP1). J. Biol. Chem. 287, 368–381). We herein identified and characterized EGCrP2, a homologue of EGCrP1, as the enzyme responsible for sterylglucoside catabolism in C. neoformans. In contrast to EGCrP1, which is specific to GlcCer, EGCrP2 hydrolyzed various β-glucosides, including GlcCer, cholesteryl-β-glucoside, ergosteryl-β-glucoside, sitosteryl-β-glucoside, and para-nitrophenyl-β-glucoside, but not α-glucosides or β-galactosides, under acidic conditions. Disruption of the EGCrP2 gene (egcrp2) resulted in the accumulation of a glycolipid, the structure of which was determined following purification to ergosteryl-3β-glucoside, a major sterylglucoside in fungi, by mass spectrometric and two-dimensional nuclear magnetic resonance analyses. This glycolipid accumulated in vacuoles and EGCrP2 was detected in vacuole-enriched fraction. These results indicated that EGCrP2 was involved in the catabolism of ergosteryl-β-glucoside in the vacuoles of C. neoformans. Distinct growth arrest, a dysfunction in cell budding, and an abnormal vacuole morphology were detected in the egcrp2-disrupted mutants, suggesting that EGCrP2 may be a promising target for anti-cryptococcal drugs. EGCrP2, classified into glycohydrolase family 5, is the first steryl

  1. Trait Self-Control, Identified-Introjected Religiosity and Health-Related-Feelings in Healthy Muslims: A Structural Equation Model Analysis

    PubMed Central

    Briki, Walid; Chaouachi, Anis; Patrick, Thomas; Chamari, Karim

    2015-01-01

    Aim The present study attempted to test McCullough and Willoughby’s hypothesis that self-control mediates the relationships between religiosity and psychosocial outcomes. Specifically, this study examined whether trait self-control (TSC) mediates the relationship of identified-introjected religiosity with positive and negative health-related-feelings (HRF) in healthy Muslims. Methods Two hundred eleven French-speaking participants (116 females, 95 males; Mage = 28.15, SDage = 6.90) answered questionnaires. One hundred ninety participants were retained for the analyses because they reported to be healthy (105 females, 85 males; Mage = 27.72, SDage = 6.80). To examine the relationships between religiosity, TSC and HRF, two competing mediation models were tested using structural equation model analysis: While a starting model used TSC as mediator of the religiosity-HRF relationship, an alternative model used religiosity as mediator of the TSC-HRF relationship. Results The findings revealed that TSC mediated the relationship between identified religiosity and positive HRF, and that identified religiosity mediated the relationship between TSC and positive and negative HRF, thereby validating both models. Moreover, the comparison of both models showed that the starting model explained 13.211% of the variance (goodness of fit = 1.000), whereas the alternative model explained 6.877% of the variance (goodness of fit = 0.987). Conclusion These results show that the starting model is the most effective model to account for the relationships between religiosity, TSC, and HRF. Therefore, this study provides initial insights into how religiosity influences psychological health through TSC. Important practical implications for the religious education are suggested. PMID:25962179

  2. A genome-wide association study of posttraumatic stress disorder identifies the retinoid-related orphan receptor alpha (RORA) gene as a significant risk locus

    PubMed Central

    Logue, Mark W.; Baldwin, Clinton; Guffanti, Guia; Melista, Efi; Wolf, Erika J.; Reardon, Annemarie F.; Uddin, Monica; Wildman, Derek; Galea, Sandro; Koenen, Karestan C.; Miller, Mark W.

    2012-01-01

    We describe the results of the first genome-wide association study of PTSD performed using trauma-exposed white non-Hispanic participants from a cohort of veterans and their intimate partners (295 cases and 196 controls). Several SNPs yielded evidence of association. One SNP (rs8042149), located in the retinoid-related orphan receptor alpha gene (RORA), reached genome-wide significance. Nominally significant associations were observed for other RORA SNPs in two African American replication samples—one from the veteran cohort (43 cases and 41 controls) and another independent cohort (100 cases and 421 controls). However, only the associated SNP from the veteran African American replication sample survived gene-level multiple testing correction. RORA has been implicated in prior GWAS studies of psychiatric disorders and is known to play an important role in neuroprotection and other behaviorally-relevant processes. This study represents an important step towards identifying the genetic underpinnings of PTSD. PMID:22869035

  3. A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues

    PubMed Central

    Zhou, Xue-mei; Zhao, Peng; Wang, Wei; Zou, Jie; Cheng, Tian-he; Peng, Xiong-bo; Sun, Meng-xiang

    2015-01-01

    Autophagy is an evolutionarily conserved mechanism in both animals and plants, which has been shown to be involved in various essential developmental processes in plants. Nicotiana tabacum is considered to be an ideal model plant and has been widely used for the study of the roles of autophagy in the processes of plant development and in the response to various stresses. However, only a few autophagy-related genes (ATGs) have been identified in tobacco up to now. Here, we identified 30 ATGs belonging to 16 different groups in tobacco through a genome-wide survey. Comprehensive expression profile analysis reveals an abroad expression pattern of these ATGs, which could be detected in all tissues tested under normal growth conditions. Our series tests further reveal that majority of ATGs are sensitive and responsive to different stresses including nutrient starvation, plant hormones, heavy metal and other abiotic stresses, suggesting a central role of autophagy, likely as an effector, in plant response to various environmental cues. This work offers a detailed survey of all ATGs in tobacco and also suggests manifold functions of autophagy in both normal plant growth and plant response to environmental stresses. PMID:26205094

  4. A simple and reliable PCR-restriction fragment length polymorphism assay to identify Candida albicans and its closely related Candida dubliniensis

    PubMed Central

    Ge, Yi Ping; Wang, Le; Lu, Gui Xia; Shen, Yong Nian; Liu, Wei Da

    2012-01-01

    Candida dubliniensis is an emerging pathogen capable of causing superficial as well as systemic infections. Due to its close similarity to C. albcians, conventional methods based on phenotypic traits are not always reliable in identification of C. dubliniensis. In this study, we developed a PCR-restriction fragment length polymorphism (RFLP) assay to identify and discriminate between the two closely related species. The D1/D2 region of 28S rDNA was amplified by PCR and enzymatically digested by ApaI and BsiEI respectively. PCR products of both species were digested into two fragments by ApaI, but those of other yeast species were undigested. BsiEI cut the PCR products of C. albicans into two fragments but not those of C. dubliniensis. Thus two species were differentiated. We evaluated 10 reference strains representing 10 yeast species, among which C. albicans and C. dubliniensis were successfully identified. A total of 56 phenotypically characterized clinical isolates (42 C. albicans isolates and 14 C. dubliniensis isolates) were also investigated for intra-species variability. All tested isolates produced identical RFLP patterns to their respective reference strains except one initially misidentified isolate. Our method offers a simple, rapid and reliable molecular method for the identification of C. albicans and C. dubliniensis. PMID:24031901

  5. A simple and reliable PCR-restriction fragment length polymorphism assay to identify Candida albicans and its closely related Candida dubliniensis.

    PubMed

    Ge, Yi Ping; Wang, Le; Lu, Gui Xia; Shen, Yong Nian; Liu, Wei Da

    2012-07-01

    Candida dubliniensis is an emerging pathogen capable of causing superficial as well as systemic infections. Due to its close similarity to C. albcians, conventional methods based on phenotypic traits are not always reliable in identification of C. dubliniensis. In this study, we developed a PCR-restriction fragment length polymorphism (RFLP) assay to identify and discriminate between the two closely related species. The D1/D2 region of 28S rDNA was amplified by PCR and enzymatically digested by ApaI and BsiEI respectively. PCR products of both species were digested into two fragments by ApaI, but those of other yeast species were undigested. BsiEI cut the PCR products of C. albicans into two fragments but not those of C. dubliniensis. Thus two species were differentiated. We evaluated 10 reference strains representing 10 yeast species, among which C. albicans and C. dubliniensis were successfully identified. A total of 56 phenotypically characterized clinical isolates (42 C. albicans isolates and 14 C. dubliniensis isolates) were also investigated for intra-species variability. All tested isolates produced identical RFLP patterns to their respective reference strains except one initially misidentified isolate. Our method offers a simple, rapid and reliable molecular method for the identification of C. albicans and C. dubliniensis. PMID:24031901

  6. Pharmacist-Led Medication Reviews to Identify and Collaboratively Resolve Drug-Related Problems in Psychiatry – A Controlled, Clinical Trial

    PubMed Central

    Wolf, Carolin; Pauly, Anne; Mayr, Andreas; Grömer, Teja; Lenz, Bernd; Kornhuber, Johannes; Friedland, Kristina

    2015-01-01

    Aim of the study This prospective, controlled trial aimed to assess the effect of pharmacist-led medication reviews on the medication safety of psychiatric inpatients by the resolution of Drug-Related Problems (DRP). Both the therapy appropriateness measured with the Medication Appropriateness Index (MAI) and the number of unsolved DRP per patient were chosen as primary outcome measures. Methods Depending on their time of admission, 269 psychiatric patients that were admitted to a psychiatric university hospital were allocated in control (09/2012-03/2013) or intervention group (05/2013-12/2013). In both groups, DRP were identified by comprehensive medication reviews by clinical pharmacists at admission, during the hospital stay, and at discharge. In the intervention group, recommendations for identified DRP were compiled by the pharmacists and discussed with the therapeutic team. In the control group, recommendations were not provided except for serious or life threatening DRP. As a primary outcome measure, the changes in therapy appropriateness from admission to discharge as well as from admission to three months after discharge (follow-up) assessed with the MAI were compared between both groups. The second primary outcome was the number of unsolved DRP per patient after completing the study protocol. The DRP type, the relevance and the potential of drugs to cause DRP were also evaluated. Results The intervention led to a reduced MAI score by 1.4 points per patient (95% confidence interval [CI]: 0.8–2.0) at discharge and 1.3 points (95% CI: 0.7–1.9) at follow-up compared with controls. The number of unsolved DRP in the intervention group was 1.8 (95% CI: 1.5–2.1) less than in control. Conclusion The pharmaceutical medication reviews with interdisciplinary discussion of identified DRP appears to be a worthy strategy to improve medication safety in psychiatry as reflected by less unsolved DRP per patient and an enhanced appropriateness of therapy. The

  7. Trial-by-trial coupling between EEG and BOLD identifies networks related to alpha and theta EEG power increases during working memory maintenance.

    PubMed

    Scheeringa, René; Petersson, Karl Magnus; Oostenveld, Robert; Norris, David G; Hagoort, Peter; Bastiaansen, Marcel C M

    2009-02-01

    PET and fMRI experiments have previously shown that several brain regions in the frontal and parietal lobe are involved in working memory maintenance. MEG and EEG experiments have shown parametric increases with load for oscillatory activity in posterior alpha and frontal theta power. In the current study we investigated whether the areas found with fMRI can be associated with these alpha and theta effects by measuring simultaneous EEG and fMRI during a modified Sternberg task This allowed us to correlate EEG at the single trial level with the fMRI BOLD signal by forming a regressor based on single trial alpha and theta power estimates. We observed a right posterior, parametric alpha power increase, which was functionally related to decreases in BOLD in the primary visual cortex and in the posterior part of the right middle temporal gyrus. We relate this finding to the inhibition of neuronal activity that may interfere with WM maintenance. An observed parametric increase in frontal theta power was correlated to a decrease in BOLD in regions that together form the default mode network. We did not observe correlations between oscillatory EEG phenomena and BOLD in the traditional WM areas. In conclusion, the study shows that simultaneous EEG-fMRI recordings can be successfully used to identify the emergence of functional networks in the brain during the execution of a cognitive task.

  8. Label-free mass spectrometric analysis of the mdx-4cv diaphragm identifies the matricellular protein periostin as a potential factor involved in dystrophinopathy-related fibrosis.

    PubMed

    Holland, Ashling; Dowling, Paul; Meleady, Paula; Henry, Michael; Zweyer, Margit; Mundegar, Rustam R; Swandulla, Dieter; Ohlendieck, Kay

    2015-07-01

    Proteomic profiling plays a decisive role in the identification of novel biomarkers of muscular dystrophy and the elucidation of new pathobiochemical mechanisms that underlie progressive muscle wasting. Building on the findings of recent comparative analyses of tissue samples and body fluids from dystrophic animals and patients afflicted with Duchenne muscular dystrophy, we have used here label-free MS to study the severely dystrophic diaphragm from the not extensively characterized mdx-4cv mouse. This animal model of progressive muscle wasting exhibits less dystrophin-positive revertant fibers than the conventional mdx mouse, making it ideal for the future monitoring of experimental therapies. The pathoproteomic signature of the mdx-4cv diaphragm included a significant increase in the fibrosis marker collagen and related extracellular matrix proteins (asporin, decorin, dermatopontin, prolargin) and cytoskeletal proteins (desmin, filamin, obscurin, plectin, spectrin, tubulin, vimentin, vinculin), as well as decreases in proteins of ion homeostasis (parvalbumin) and the contractile apparatus (myosin-binding protein). Importantly, one of the most substantially increased proteins was identified as periostin, a matricellular component and apparent marker of fibrosis and tissue damage. Immunoblotting confirmed a considerable increase of periostin in the dystrophin-deficient diaphragm from both mdx and mdx-4cv mice, suggesting an involvement of this matricellular protein in dystrophinopathy-related fibrosis.

  9. Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein.

    PubMed

    Li, Hui; Zhang, Dan-feng; Lin, Xiang-min; Peng, Xuan-xian

    2015-06-01

    Antibiotic-resistant bacteria are a great threat to human health and food safety and there is an urgent need to understand the mechanisms of resistance for combating these bacteria. In the current study, comparative proteomic methodologies were applied to identify Escherichia coli K-12 outer membrane (OM) proteins related to kanamycin resistance. Mass spectrometry and western blotting results revealed that OM proteins TolC, Tsx and OstA were up-regulated, whereas MipA, OmpA, FadL and OmpW were down-regulated in kanamycin-resistant E. coli K-12 strain. Genetic deletion of tolC (ΔtolC-Km) led to a 2-fold decrease in the minimum inhibitory concentration (MIC) of kanamycin and deletion of mipA (ΔmipA-Km) resulted in a 4-fold increase in the MIC of kanamycin. Changes in the MICs for genetically modified strains could be completely recovered by gene complementation. Compared with the wild-type strain, the survival capability of ΔompA-Km was significantly increased and that of Δtsx-Km was significantly decreased. We further evaluated the role and expression of MipA in response to four other antibiotics including nalidixic acid, streptomycin, chloramphenicol and aureomycin, which suggested that MipA was a novel OM protein related to antibiotic resistance. PMID:25940639

  10. Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein.

    PubMed

    Li, Hui; Zhang, Dan-feng; Lin, Xiang-min; Peng, Xuan-xian

    2015-06-01

    Antibiotic-resistant bacteria are a great threat to human health and food safety and there is an urgent need to understand the mechanisms of resistance for combating these bacteria. In the current study, comparative proteomic methodologies were applied to identify Escherichia coli K-12 outer membrane (OM) proteins related to kanamycin resistance. Mass spectrometry and western blotting results revealed that OM proteins TolC, Tsx and OstA were up-regulated, whereas MipA, OmpA, FadL and OmpW were down-regulated in kanamycin-resistant E. coli K-12 strain. Genetic deletion of tolC (ΔtolC-Km) led to a 2-fold decrease in the minimum inhibitory concentration (MIC) of kanamycin and deletion of mipA (ΔmipA-Km) resulted in a 4-fold increase in the MIC of kanamycin. Changes in the MICs for genetically modified strains could be completely recovered by gene complementation. Compared with the wild-type strain, the survival capability of ΔompA-Km was significantly increased and that of Δtsx-Km was significantly decreased. We further evaluated the role and expression of MipA in response to four other antibiotics including nalidixic acid, streptomycin, chloramphenicol and aureomycin, which suggested that MipA was a novel OM protein related to antibiotic resistance.

  11. Molecular genetics of addiction and related heritable phenotypes: genome wide association approaches identify “connectivity constellation” and drug target genes with pleiotropic effects

    PubMed Central

    Uhl, George R; Drgon, Tomas; Johnson, Catherine; Li, Chuan-Yun; Contoreggi, Carlo; Hess, Judith; Naiman, Daniel; Liu, Qing-Rong

    2013-01-01

    Genome wide association (GWA) can elucidate molecular genetic bases for human individual differences in “complex” phenotypes that include vulnerability to addiction. Here, we review: a) evidence that supports polygenic models with (at least) modest heterogeneity for the genetic architectures of addiction and several related phenotypes; b) technical and ethical aspects of importance for understanding genome wide association data: genotyping in individual samples vs DNA pools, analytic approaches, power estimation and ethical issues in genotyping individuals with illegal behaviors; c) the samples and the data that shape our current understanding of the molecular genetics of individual differences in vulnerability to substance dependence and related phenotypes; d) overlaps between GWA datasets for dependence on different substances; e) overlaps between GWA data for addictions vs other heritable, brain-based phenotypes that include: i) bipolar disorder, ii) cognitive ability, iii) frontal lobe brain volume, iv) ability to successfully quit smoking, v) neuroticism and vi) Alzheimer’s disease. These convergent results identify potential targets for drugs that might modify addictions and play roles in these other phenotypes. They add to evidence that individual differences in the quality and quantity of brain connections make pleiotropic contributions to individual differences in vulnerability to addictions and to related brain disorders and phenotypes. A “connectivity constellation” of brain phenotypes and disorders appears to receive substantial pathogenic contributions from individual differences in a constellation of genes whose variants provide individual differences in the specification of brain connectivities during development and in adulthood. Heritable brain differences that underlie addiction vulnerability thus lie squarely in the midst of the repertoire of heritable brain differences that underlie vulnerability to other common brain disorders and

  12. Prediction of gene-based drug indications using compendia of public gene expression data and PubMed abstracts.

    PubMed

    Qabaja, Ala; Jarada, Tamer; Elsheikh, Abdallah; Alhajj, Reda

    2014-06-01

    The tremendous research effort on diseases and drug discovery has produced a huge amount of important biomedical information which is mostly hidden in the web. In addition, many databases have been created for the purpose of storing enormous amounts of information and high-throughput experiments related to drugs and diseases' effects on genes. Thus, developing an algorithm to integrate biological data from different sources forms one of the greatest challenges in the field of computational biology. Based on our belief that data integration would result in better understanding for the drug mode of action or the disease pathophysiology, we have developed a novel paradigm to integrate data from three major sources in order to predict novel therapeutic drug indications. Microarray data, biomedical text mining data, and gene interaction data have been all integrated to predict ranked lists of genes based on their relevance to a particular drug or disease molecular action. These ranked lists of genes have finally been used as a raw material for building a disease-drug connectivity map based on the enrichment between the up/down tags of a particular disease signature and the ranked lists of drugs. Using this paradigm, we have reported 13% sensitivity improvement in comparison with using microarray or text mining data independently. In addition, our paradigm is able to predict many clinically validated disease-drug associations that could not be captured using microarray or text mining data independently.

  13. Genome-wide DNA methylation identifies trophoblast invasion-related genes: Claudin-4 and Fucosyltransferase IV control mobility via altering matrix metalloproteinase activity.

    PubMed

    Hu, Yuxiang; Blair, John D; Yuen, Ryan K C; Robinson, Wendy P; von Dadelszen, Peter

    2015-05-01

    Previously we showed that extravillous cytotrophoblast (EVT) outgrowth and migration on a collagen gel explant model were affected by exposure to decidual natural killer cells (dNK). This study investigates the molecular causes behind this phenomenon. Genome wide DNA methylation of exposed and unexposed EVT was assessed using the Illumina Infinium HumanMethylation450 BeadChip array (450 K array). We identified 444 differentially methylated CpG loci in dNK-treated EVT compared with medium control (P < 0.05). The genes associated with these loci had critical biological roles in cellular development, cellular growth and proliferation, cell signaling, cellular assembly and organization by Ingenuity Pathway Analysis (IPA). Furthermore, 23 mobility-related genes were identified by IPA from dNK-treated EVT. Among these genes, CLDN4 (encoding claudin-4) and FUT4 (encoding fucosyltransferase IV) were chosen for follow-up studies because of their biological relevance from research on tumor cells. The results showed that the mRNA and protein expressions of both CLDN4 and FUT4 in dNK-treated EVT were significantly reduced compared with control (P < 0.01 for both CLDN4 and FUT4 mRNA expression; P < 0.001 for CLDN4 and P < 0.01 for FUT4 protein expression), and were inversely correlated with DNA methylation. Knocking down CLDN4 and FUT4 by small interfering RNA reduced trophoblast invasion, possibly through the altered matrix metalloproteinase (MMP)-2 and/or MMP-9 expression and activity. Taken together, dNK alter EVT mobility at least partially in association with an alteration of DNA methylation profile. Hypermethylation of CLDN4 and FUT4 reduces protein expression. CLDN4 and FUT4 are representative genes that participate in modulating trophoblast mobility. PMID:25697377

  14. Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits.

    PubMed

    Teumer, Alexander; Qi, Qibin; Nethander, Maria; Aschard, Hugues; Bandinelli, Stefania; Beekman, Marian; Berndt, Sonja I; Bidlingmaier, Martin; Broer, Linda; Cappola, Anne; Ceda, Gian Paolo; Chanock, Stephen; Chen, Ming-Huei; Chen, Tai C; Chen, Yii-Der Ida; Chung, Jonathan; Del Greco Miglianico, Fabiola; Eriksson, Joel; Ferrucci, Luigi; Friedrich, Nele; Gnewuch, Carsten; Goodarzi, Mark O; Grarup, Niels; Guo, Tingwei; Hammer, Elke; Hayes, Richard B; Hicks, Andrew A; Hofman, Albert; Houwing-Duistermaat, Jeanine J; Hu, Frank; Hunter, David J; Husemoen, Lise L; Isaacs, Aaron; Jacobs, Kevin B; Janssen, Joop A M J L; Jansson, John-Olov; Jehmlich, Nico; Johnson, Simon; Juul, Anders; Karlsson, Magnus; Kilpelainen, Tuomas O; Kovacs, Peter; Kraft, Peter; Li, Chao; Linneberg, Allan; Liu, Yongmei; Loos, Ruth J F; Lorentzon, Mattias; Lu, Yingchang; Maggio, Marcello; Magi, Reedik; Meigs, James; Mellström, Dan; Nauck, Matthias; Newman, Anne B; Pollak, Michael N; Pramstaller, Peter P; Prokopenko, Inga; Psaty, Bruce M; Reincke, Martin; Rimm, Eric B; Rotter, Jerome I; Saint Pierre, Aude; Schurmann, Claudia; Seshadri, Sudha; Sjögren, Klara; Slagboom, P Eline; Strickler, Howard D; Stumvoll, Michael; Suh, Yousin; Sun, Qi; Zhang, Cuilin; Svensson, Johan; Tanaka, Toshiko; Tare, Archana; Tönjes, Anke; Uh, Hae-Won; van Duijn, Cornelia M; van Heemst, Diana; Vandenput, Liesbeth; Vasan, Ramachandran S; Völker, Uwe; Willems, Sara M; Ohlsson, Claes; Wallaschofski, Henri; Kaplan, Robert C

    2016-10-01

    The growth hormone/insulin-like growth factor (IGF) axis can be manipulated in animal models to promote longevity, and IGF-related proteins including IGF-I and IGF-binding protein-3 (IGFBP-3) have also been implicated in risk of human diseases including cardiovascular diseases, diabetes, and cancer. Through genomewide association study of up to 30 884 adults of European ancestry from 21 studies, we confirmed and extended the list of previously identified loci associated with circulating IGF-I and IGFBP-3 concentrations (IGF1, IGFBP3, GCKR, TNS3, GHSR, FOXO3, ASXL2, NUBP2/IGFALS, SORCS2, and CELSR2). Significant sex interactions, which were characterized by different genotype-phenotype associations between men and women, were found only for associations of IGFBP-3 concentrations with SNPs at the loci IGFBP3 and SORCS2. Analyses of SNPs, gene expression, and protein levels suggested that interplay between IGFBP3 and genes within the NUBP2 locus (IGFALS and HAGH) may affect circulating IGF-I and IGFBP-3 concentrations. The IGF-I-decreasing allele of SNP rs934073, which is an eQTL of ASXL2, was associated with lower adiposity and higher likelihood of survival beyond 90 years. The known longevity-associated variant rs2153960 (FOXO3) was observed to be a genomewide significant SNP for IGF-I concentrations. Bioinformatics analysis suggested enrichment of putative regulatory elements among these IGF-I- and IGFBP-3-associated loci, particularly of rs646776 at CELSR2. In conclusion, this study identified several loci associated with circulating IGF-I and IGFBP-3 concentrations and provides clues to the potential role of the IGF axis in mediating effects of known (FOXO3) and novel (ASXL2) longevity-associated loci. PMID:27329260

  15. Genome-wide DNA methylation identifies trophoblast invasion-related genes: Claudin-4 and Fucosyltransferase IV control mobility via altering matrix metalloproteinase activity

    PubMed Central

    Hu, Yuxiang; Blair, John D.; Yuen, Ryan K.C.; Robinson, Wendy P.; von Dadelszen, Peter

    2015-01-01

    Previously we showed that extravillous cytotrophoblast (EVT) outgrowth and migration on a collagen gel explant model were affected by exposure to decidual natural killer cells (dNK). This study investigates the molecular causes behind this phenomenon. Genome wide DNA methylation of exposed and unexposed EVT was assessed using the Illumina Infinium HumanMethylation450 BeadChip array (450 K array). We identified 444 differentially methylated CpG loci in dNK-treated EVT compared with medium control (P < 0.05). The genes associated with these loci had critical biological roles in cellular development, cellular growth and proliferation, cell signaling, cellular assembly and organization by Ingenuity Pathway Analysis (IPA). Furthermore, 23 mobility-related genes were identified by IPA from dNK-treated EVT. Among these genes, CLDN4 (encoding claudin-4) and FUT4 (encoding fucosyltransferase IV) were chosen for follow-up studies because of their biological relevance from research on tumor cells. The results showed that the mRNA and protein expressions of both CLDN4 and FUT4 in dNK-treated EVT were significantly reduced compared with control (P < 0.01 for both CLDN4 and FUT4 mRNA expression; P < 0.001 for CLDN4 and P < 0.01 for FUT4 protein expression), and were inversely correlated with DNA methylation. Knocking down CLDN4 and FUT4 by small interfering RNA reduced trophoblast invasion, possibly through the altered matrix metalloproteinase (MMP)-2 and/or MMP-9 expression and activity. Taken together, dNK alter EVT mobility at least partially in association with an alteration of DNA methylation profile. Hypermethylation of CLDN4 and FUT4 reduces protein expression. CLDN4 and FUT4 are representative genes that participate in modulating trophoblast mobility. PMID:25697377

  16. Genome-wide DNA methylation identifies trophoblast invasion-related genes: Claudin-4 and Fucosyltransferase IV control mobility via altering matrix metalloproteinase activity.

    PubMed

    Hu, Yuxiang; Blair, John D; Yuen, Ryan K C; Robinson, Wendy P; von Dadelszen, Peter

    2015-05-01

    Previously we showed that extravillous cytotrophoblast (EVT) outgrowth and migration on a collagen gel explant model were affected by exposure to decidual natural killer cells (dNK). This study investigates the molecular causes behind this phenomenon. Genome wide DNA methylation of exposed and unexposed EVT was assessed using the Illumina Infinium HumanMethylation450 BeadChip array (450 K array). We identified 444 differentially methylated CpG loci in dNK-treated EVT compared with medium control (P < 0.05). The genes associated with these loci had critical biological roles in cellular development, cellular growth and proliferation, cell signaling, cellular assembly and organization by Ingenuity Pathway Analysis (IPA). Furthermore, 23 mobility-related genes were identified by IPA from dNK-treated EVT. Among these genes, CLDN4 (encoding claudin-4) and FUT4 (encoding fucosyltransferase IV) were chosen for follow-up studies because of their biological relevance from research on tumor cells. The results showed that the mRNA and protein expressions of both CLDN4 and FUT4 in dNK-treated EVT were significantly reduced compared with control (P < 0.01 for both CLDN4 and FUT4 mRNA expression; P < 0.001 for CLDN4 and P < 0.01 for FUT4 protein expression), and were inversely correlated with DNA methylation. Knocking down CLDN4 and FUT4 by small interfering RNA reduced trophoblast invasion, possibly through the altered matrix metalloproteinase (MMP)-2 and/or MMP-9 expression and activity. Taken together, dNK alter EVT mobility at least partially in association with an alteration of DNA methylation profile. Hypermethylation of CLDN4 and FUT4 reduces protein expression. CLDN4 and FUT4 are representative genes that participate in modulating trophoblast mobility.

  17. ALK1 signalling analysis identifies angiogenesis related genes and reveals disparity between TGF-β and constitutively active receptor induced gene expression

    PubMed Central

    Lux, Andreas; Salway, Fiona; Dressman, Holly K; Kröner-Lux, Gabriele; Hafner, Mathias; Day, Philip JR; Marchuk, Douglas A; Garland, John

    2006-01-01

    Background TGF-β1 is an important angiogenic factor involved in the different aspects of angiogenesis and vessel maintenance. TGF-β signalling is mediated by the TβRII/ALK5 receptor complex activating the Smad2/Smad3 pathway. In endothelial cells TGF-β utilizes a second type I receptor, ALK1, activating the Smad1/Smad5 pathway. Consequently, a perturbance of ALK1, ALK5 or TβRII activity leads to vascular defects. Mutations in ALK1 cause the vascular disorder hereditary hemorrhagic telangiectasia (HHT). Methods The identification of ALK1 and not ALK5 regulated genes in endothelial cells, might help to better understand the development of HHT. Therefore, the human microvascular endothelial cell line HMEC-1 was infected with a recombinant constitutively active ALK1 adenovirus, and gene expression was studied by using gene arrays and quantitative real-time PCR analysis. Results After 24 hours, 34 genes were identified to be up-regulated by ALK1 signalling. Analysing ALK1 regulated gene expression after 4 hours revealed 13 genes to be up- and 2 to be down-regulated. Several of these genes, including IL-8, ET-1, ID1, HPTPη and TEAD4 are reported to be involved in angiogenesis. Evaluation of ALK1 regulated gene expression in different human endothelial cell types was not in complete agreement. Further on, disparity between constitutively active ALK1 and TGF-β1 induced gene expression in HMEC-1 cells and primary HUVECs was observed. Conclusion Gene array analysis identified 49 genes to be regulated by ALK1 signalling and at least 14 genes are reported to be involved in angiogenesis. There was substantial agreement between the gene array and quantitative real-time PCR data. The angiogenesis related genes might be potential HHT modifier genes. In addition, the results suggest endothelial cell type specific ALK1 and TGF-β signalling. PMID:16594992

  18. A novel chemical footprinting approach identifies critical lysine residues involved in the binding of receptor-associated protein to cluster II of LDL receptor-related protein.

    PubMed

    Bloem, Esther; Ebberink, Eduard H T M; van den Biggelaar, Maartje; van der Zwaan, Carmen; Mertens, Koen; Meijer, Alexander B

    2015-05-15

    Tandem mass tags (TMTs) were utilized in a novel chemical footprinting approach to identify lysine residues that mediate the interaction of receptor-associated protein (RAP) with cluster II of LDL (low-density lipoprotein) receptor (LDLR)-related protein (LRP). The isolated RAP D3 domain was modified with TMT-126 and the D3 domain-cluster II complex with TMT-127. Nano-LC-MS analysis revealed reduced modification with TMT-127 of peptides including Lys(256), Lys(270) and Lys(305)-Lys(306) suggesting that these residues contribute to cluster II binding. This agrees with previous findings that Lys(256) and Lys(270) are critical for binding cluster II sub-domains [Fisher, Beglova and Blacklow (2006) Mol. Cell 22, 277-283]. Cluster II-binding studies utilizing D3 domain variants K(256)A, K(305)A and K(306)A now showed that Lys(306) contributes to cluster II binding as well. For full-length RAP, we observed that peptides including Lys(60), Lys(191), Lys(256), Lys(270) and Lys(305)-Lys(306) exhibited reduced modification with TMT in the RAP-cluster II complex. Notably, Lys(60) has previously been implicated to mediate D1 domain interaction with cluster II. Our results suggest that also Lys(191) of the D2 domain contributes to cluster II binding. Binding studies employing the RAP variants K(191)A, K(256)A, K(305)A and K(306)A, however, revealed a modest reduction in cluster II binding for the K(256)A variant only. This suggests that the other lysine residues can compensate for the absence of a single lysine residue for effective complex assembly. Collectively, novel insight has been obtained into the contribution of lysine residues of RAP to cluster II binding. In addition, we propose that TMTs can be utilized to identify lysine residues critical for protein complex formation. PMID:25728577

  19. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions.

    PubMed

    Oikkonen, J; Huang, Y; Onkamo, P; Ukkola-Vuoti, L; Raijas, P; Karma, K; Vieland, V J; Järvelä, I

    2015-02-01

    Humans have developed the perception, production and processing of sounds into the art of music. A genetic contribution to these skills of musical aptitude has long been suggested. We performed a genome-wide scan in 76 pedigrees (767 individuals) characterized for the ability to discriminate pitch (SP), duration (ST) and sound patterns (KMT), which are primary capacities for music perception. Using the Bayesian linkage and association approach implemented in program package KELVIN, especially designed for complex pedigrees, several single nucleotide polymorphisms (SNPs) near genes affecting the functions of the auditory pathway and neurocognitive processes were identified. The strongest association was found at 3q21.3 (rs9854612) with combined SP, ST and KMT test scores (COMB). This region is located a few dozen kilobases upstream of the GATA binding protein 2 (GATA2) gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. The highest probability of linkage was obtained for phenotype SP at 4p14, located next to the region harboring the protocadherin 7 gene, PCDH7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association. PCDH7 has been suggested to play a role in cochlear and amygdaloid complexes. Functional class analysis showed that inner ear and schizophrenia-related genes were enriched inside the linked regions. This study is the first to show the importance of auditory pathway genes in musical aptitude.

  20. Whole-exome and targeted sequencing identify ROBO1 and ROBO2 mutations as progression-related drivers in myelodysplastic syndromes

    PubMed Central

    Xu, Feng; Wu, Ling-Yun; Chang, Chun-Kang; He, Qi; Zhang, Zheng; Liu, Li; Shi, Wen-Hui; Guo, Juan; Zhu, Yang; Zhao, You-Shan; Gu, Shu-Cheng; Fei, Cheng-Ming; Wu, Dong; Zhou, Li-Yu; Su, Ji-Ying; Song, Lu-Xi; Xiao, Chao; Li, Xiao

    2015-01-01

    The progressive mechanism underlying myelodysplastic syndrome remains unknown. Here we identify ROBO1 and ROBO2 as novel progression-related somatic mutations using whole-exome and targeted sequencing in 6 of 16 (37.5%) paired MDS patients with disease progression. Further deep sequencing detects 20 (10.4%) patients with ROBO mutations in a cohort of 193 MDS patients. In addition, copy number loss and loss of heterogeneity (LOH) of ROBO1 and ROBO2 are frequently observed in patients with progression or carrying ROBO mutations. In in vitro experiments, overexpression of ROBO1 or ROBO2 produces anti-proliferative and pro-apoptotic effects in leukaemia cells. However, this effect was lost in ROBO mutants and ROBO-SLIT2 signalling is impaired. Multivariate analysis shows that ROBO mutations are independent factors for predicting poor survival. These findings demonstrate a novel contribution of ROBO mutations to the pathogenesis of MDS and highlight a key role for ROBO-SLIT2 signalling in MDS disease progression. PMID:26608094

  1. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions.

    PubMed

    Oikkonen, J; Huang, Y; Onkamo, P; Ukkola-Vuoti, L; Raijas, P; Karma, K; Vieland, V J; Järvelä, I

    2015-02-01

    Humans have developed the perception, production and processing of sounds into the art of music. A genetic contribution to these skills of musical aptitude has long been suggested. We performed a genome-wide scan in 76 pedigrees (767 individuals) characterized for the ability to discriminate pitch (SP), duration (ST) and sound patterns (KMT), which are primary capacities for music perception. Using the Bayesian linkage and association approach implemented in program package KELVIN, especially designed for complex pedigrees, several single nucleotide polymorphisms (SNPs) near genes affecting the functions of the auditory pathway and neurocognitive processes were identified. The strongest association was found at 3q21.3 (rs9854612) with combined SP, ST and KMT test scores (COMB). This region is located a few dozen kilobases upstream of the GATA binding protein 2 (GATA2) gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. The highest probability of linkage was obtained for phenotype SP at 4p14, located next to the region harboring the protocadherin 7 gene, PCDH7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association. PCDH7 has been suggested to play a role in cochlear and amygdaloid complexes. Functional class analysis showed that inner ear and schizophrenia-related genes were enriched inside the linked regions. This study is the first to show the importance of auditory pathway genes in musical aptitude. PMID:24614497

  2. Fatigue-Related Gene Networks Identified in CD14+ Cells Isolated From HIV-Infected Patients—Part II: Statistical Analysis

    PubMed Central

    Voss, Joachim G.; Dobra, Adrian; Morse, Caryn; Kovacs, Joseph A.; Raju, Raghavan; Danner, Robert L.; Munson, Peter J.; Logan, Carolea; Rangel, Zoila; Adelsberger, Joseph W.; McLaughlin, Mary; Adams, Larry D.; Dalakas, Marinos C.

    2012-01-01

    Purpose In limited samples of valuable biological tissues, univariate ranking methods of microarray analyses often fail to show significant differences among expression profiles. In order to allow for hypothesis generation, novel statistical modeling systems can be greatly beneficial. The authors applied new statistical approaches to solve the issue of limited experimental data to generate new hypotheses in CD14+ cells of patients with HIV-related fatigue (HRF) and healthy controls. Methodology We compared gene expression profiles of CD14+ cells of nucleoside reverse transcriptase inhibitor (NRTI)-treated HIV patients with low versus high fatigue to healthy controls (n = 5 each). With novel Bayesian modeling procedures, the authors identified 32 genes predictive of low versus high fatigue and 33 genes predictive of healthy versus HIV infection. Sparse association and liquid association networks further elucidated the possible biological pathways in which these genes are involved. Relevance for nursing practice Genetic networks developed in a comprehensive Bayesian framework from small sample sizes allow nursing researchers to design future research approaches to address such issues as HRF. Implication for practice The findings from this pilot study may take us one step closer to the development of useful biomarker targets for fatigue status. Specific and reliable tests are needed to diagnosis, monitor and treat fatigue and mitochondrial dysfunction. PMID:22084402

  3. Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study

    PubMed Central

    QU, LI-SHUAI; JIN, FEI; GUO, YAN-MEI; LIU, TAO-TAO; XUE, RU-YI; HUANG, XIAO-WU; XU, MIN; CHEN, TAO-YANG; NI, ZHENG-PING; SHEN, XI-ZHONG

    2016-01-01

    Previous studies have indicated that complex interactions among viral, environmental and genetic factors lead to hepatocellular carcinoma (HCC). To identify susceptibility alleles for hepatitis B virus (HBV)-related HCC, the present study conducted a pilot two-phase genome-wide association study (GWAS) in 660 Han Chinese individuals. In phase 1, a total of 500,447 single-nucleotide polymorphisms (SNPs) were genotyped in 50 HCC cases and 50 controls using Affymetrix GeneChip 500k Array Set. In phase 2, 1,152 SNPs were selected from phase 1 and genotyped in 282 cases and 278 controls using the Illumina GoldenGate platform. The prior probability of HCC in control subjects was assigned at 0.01, and false-positive report probability (FPRP) was utilized to evaluate the statistical significance. In phase 1, one SNP (rs2212522) showed a significant association with HCC (Pallele=5.23×10−8; ORallele=4.96; 95% CI, 2.72–9.03). In phase 2, among 27 SNPs with unadjusted Pallele<0.05, 9 SNPs were associated with HCC based on FPRP criteria (FPRP <0.20). The strongest statistical evidence for an association signal was with rs2120243 (combined ORallele=1.76; 95% CI, 1.39–2.22; P=2.00×10−6), which maps within the fourth intron of VEPH1. The second strongest statistical evidence for an association was identified for rs1350171 (combined ORallele=1.66; 95% CI, 1.33–2.07; P=6.48×10−6), which maps to the region downstream of the FZD4 gene. The other potential susceptibility genes included PCDH9, PRMT6, LHX1, KIF2B and L3MBTL4. In conclusion, this pilot two-phase GWAS provides the evidence for the existence of common susceptibility loci for HCC. These genes involved various signaling pathways, including those associated with transforming growth factor β, insulin/phosphoinositide 3 kinase, Wnt and epidermal growth factor receptor. These associations must be replicated and validated in larger studies. PMID:26870257

  4. Transcriptome Analysis Identifies Candidate Genes Related to Triacylglycerol and Pigment Biosynthesis and Photoperiodic Flowering in the Ornamental and Oil-Producing Plant, Camellia reticulata (Theaceae)

    PubMed Central

    Yao, Qiu-Yang; Huang, Hui; Tong, Yan; Xia, En-Hua; Gao, Li-Zhi

    2016-01-01

    Camellia reticulata, which is native to Southwest China, is famous for its ornamental flowers and high-quality seed oil. However, the lack of genomic information for this species has largely hampered our understanding of its key pathways related to oil production, photoperiodic flowering process and pigment biosynthesis. Here, we first sequenced and characterized the transcriptome of a diploid C. reticulata in an attempt to identify genes potentially involved in triacylglycerol biosynthesis (TAGBS), photoperiodic flowering, flavonoid biosynthesis (FlaBS), carotenoid biosynthesis (CrtBS) pathways. De novo assembly of the transcriptome provided a catalog of 141,460 unigenes with a total length of ~96.1 million nucleotides (Mnt) and an N50 of 1080 nt. Of them, 22,229 unigenes were defined as differentially expressed genes (DEGs) across five sequenced tissues. A large number of annotated genes in C. reticulata were found to have been duplicated, and differential expression patterns of these duplicated genes were commonly observed across tissues, such as the differential expression of SOC1_a, SOC1_b, and SOC1_c in the photoperiodic flowering pathway. Up-regulation of SAD_a and FATA genes and down-regulation of FAD2_a gene in the TAGBS pathway in seeds may be relevant to the ratio of monounsaturated fatty acid (MUFAs) to polyunsaturated fatty acid (PUFAs) in seed oil. MYBF1, a transcription regulator gene of the FlaBS pathway, was found with great sequence variation and alteration of expression patterns, probably resulting in functionally evolutionary differentiation in C. reticulata. MYBA1_a and some anthocyanin-specific biosynthetic genes in the FlaBS pathway were highly expressed in both flower buds and flowers, suggesting important roles of anthocyanin biosynthesis in flower development. Besides, a total of 40,823 expressed sequence tag simple sequence repeats (EST-SSRs) were identified in the C. reticulata transcriptome, providing valuable marker resources for

  5. Transcriptomics in Interferon-α-Treated Patients Identifies Inflammation-, Neuroplasticity- and Oxidative Stress-Related Signatures as Predictors and Correlates of Depression

    PubMed Central

    Hepgul, Nilay; Cattaneo, Annamaria; Agarwal, Kosh; Baraldi, Sara; Borsini, Alessandra; Bufalino, Chiara; Forton, Daniel M; Mondelli, Valeria; Nikkheslat, Naghmeh; Lopizzo, Nicola; Riva, Marco A; Russell, Alice; Hotopf, Matthew; Pariante, Carmine M

    2016-01-01

    Owing to the unique opportunity to assess individuals before and after they develop depression within a short timeframe, interferon-α (IFN-α) treatment for chronic hepatitis C virus (HCV) infection is an ideal model to identify molecular mechanisms relevant to major depression, especially in the context of enhanced inflammation. Fifty-eight patients were assessed prospectively, at baseline and monthly over 24 weeks of IFN-α treatment. New-onset cases of depression were determined using the Mini International Neuropsychiatric Interview (MINI). Whole-blood transcriptomic analyses were conducted to investigate the following: (1) baseline gene expression differences associated with future development of IFN-α-induced depression, before IFN-α, and (2) longitudinal gene expression changes from baseline to weeks 4 or 24 of IFN-α treatment, separately in those who did and did not develop depression. Transcriptomics data were analyzed using Partek Genomics Suite (1.4-fold, FDR adjusted p⩽0.05) and Ingenuity Pathway Analysis Software. Twenty patients (34%) developed IFN-α-induced depression. At baseline, 73 genes were differentially expressed in patients who later developed depression compared with those who did not. After 4 weeks of IFN-α treatment, 592 genes were modulated in the whole sample, representing primarily IFN-α-responsive genes. Substantially more genes were modulated only in patients who developed depression (n=506, compared with n=70 in patients who did not), with enrichment in inflammation-, neuroplasticity- and oxidative stress-related pathways. A similar picture was observed at week 24. Our data indicate that patients who develop IFN-α-induced depression have an increased biological sensitivity to IFN-α, as shown by larger gene expression changes, and specific signatures both as predictors and as correlates. PMID:27067128

  6. Identifying Early Paleozoic tectonic relations in a region affected by post-Taconian transcurrent faulting, an example from the PA-DE Piedmont

    SciTech Connect

    Alcock, J. . Dept. of Environmental Science); Wagner, M.E. . Geology); Srogi, L.A. . Dept. of Geology and Astronomy)

    1993-03-01

    Post-Taconian transcurrent faulting in the Appalachian Piedmont presents a significant problem to workers attempting to reconstruct the Early Paleozoic tectonic history. One solution to the problem is to identify blocks that lie between zones of transcurrent faulting and that retain the Early Paleozoic arrangement of litho-tectonic units. The authors propose that a comparison of metamorphic histories of different units can be used to recognize blocks of this type. The Wilmington Complex (WC) arc terrane, the pre-Taconian Laurentian margin rocks (LM) exposed in basement-cored massifs, and the Wissahickon Group metapelites (WS) that lie between them are three litho-tectonic units in the PA-DE Piedmont that comprise a block assembled in the Early Paleozoic. Evidence supporting this interpretation includes: (1) Metamorphic and lithologic differences across the WC-WS contact and detailed geologic mapping of the contact that suggest thrusting of the WC onto the WS; (2) A metamorphic gradient in the WS with highest grade, including spinel-cordierite migmatites, adjacent to the WC indicating that peak metamorphism of the WS resulted from heating by the WC; (3) A metamorphic discontinuity at the WS-LM contact, evidence for emplacement of the WS onto the LM after WS peak metamorphism; (4) A correlation of mineral assemblage in the Cockeysville Marble of the LM with distance from the WS indicating that peak metamorphism of the LM occurred after emplacement of the WS; and (5) Early Paleozoic lower intercept zircon ages for the LM that are interpreted to date Taconian regional metamorphism. Analysis of metamorphism and its timing relative to thrusting suggest that the WS was associated with the WC before the WS was emplaced onto the LM during the Taconian. It follows that these units form a block that has not been significantly disrupted by later transcurrent shear.

  7. Development and application of the Safe Performance Index as a risk-based methodology for identifying major hazard-related safety issues in underground coal mines

    NASA Astrophysics Data System (ADS)

    Kinilakodi, Harisha

    The underground coal mining industry has been under constant watch due to the high risk involved in its activities, and scrutiny increased because of the disasters that occurred in 2006-07. In the aftermath of the incidents, the U.S. Congress passed the Mine Improvement and New Emergency Response Act of 2006 (MINER Act), which strengthened the existing regulations and mandated new laws to address the various issues related to a safe working environment in the mines. Risk analysis in any form should be done on a regular basis to tackle the possibility of unwanted major hazard-related events such as explosions, outbursts, airbursts, inundations, spontaneous combustion, and roof fall instabilities. One of the responses by the Mine Safety and Health Administration (MSHA) in 2007 involved a new pattern of violations (POV) process to target mines with a poor safety performance, specifically to improve their safety. However, the 2010 disaster (worst in 40 years) gave an impression that the collective effort of the industry, federal/state agencies, and researchers to achieve the goal of zero fatalities and serious injuries has gone awry. The Safe Performance Index (SPI) methodology developed in this research is a straight-forward, effective, transparent, and reproducible approach that can help in identifying and addressing some of the existing issues while targeting (poor safety performance) mines which need help. It combines three injury and three citation measures that are scaled to have an equal mean (5.0) in a balanced way with proportionate weighting factors (0.05, 0.15, 0.30) and overall normalizing factor (15) into a mine safety performance evaluation tool. It can be used to assess the relative safety-related risk of mines, including by mine-size category. Using 2008 and 2009 data, comparisons were made of SPI-associated, normalized safety performance measures across mine-size categories, with emphasis on small-mine safety performance as compared to large- and

  8. Towards Identify Selective Antibacterial Peptides Based on Abstracts Meaning

    PubMed Central

    Barbosa-Santillán, Liliana I.; Sánchez-Escobar, Juan J.; Calixto-Romo, M. Angeles; Barbosa-Santillán, Luis F.

    2016-01-01

    We present an Identify Selective Antibacterial Peptides (ISAP) approach based on abstracts meaning. Laboratories and researchers have significantly increased the report of their discoveries related to antibacterial peptides in primary publications. It is important to find antibacterial peptides that have been reported in primary publications because they can produce antibiotics of different generations that attack and destroy the bacteria. Unfortunately, researchers used heterogeneous forms of natural language to describe their discoveries (sometimes without the sequence of the peptides). Thus, we propose that learning the words meaning instead of the antibacterial peptides sequence is possible to identify and predict antibacterial peptides reported in the PubMed engine. The ISAP approach consists of two stages: training and discovering. ISAP founds that the 35% of the abstracts sample had antibacterial peptides and we tested in the updated Antimicrobial Peptide Database 2 (APD2). ISAP predicted that 45% of the abstracts had antibacterial peptides. That is, ISAP found that 810 antibacterial peptides were not classified like that, so they are not reported in APD2. As a result, this new search tool would complement the APD2 with a set of peptides that are candidates to be antibacterial. Finally, 20% of the abstracts were not semantic related to APD2. PMID:27366202

  9. Towards Identify Selective Antibacterial Peptides Based on Abstracts Meaning.

    PubMed

    Barbosa-Santillán, Liliana I; Sánchez-Escobar, Juan J; Calixto-Romo, M Angeles; Barbosa-Santillán, Luis F

    2016-01-01

    We present an Identify Selective Antibacterial Peptides (ISAP) approach based on abstracts meaning. Laboratories and researchers have significantly increased the report of their discoveries related to antibacterial peptides in primary publications. It is important to find antibacterial peptides that have been reported in primary publications because they can produce antibiotics of different generations that attack and destroy the bacteria. Unfortunately, researchers used heterogeneous forms of natural language to describe their discoveries (sometimes without the sequence of the peptides). Thus, we propose that learning the words meaning instead of the antibacterial peptides sequence is possible to identify and predict antibacterial peptides reported in the PubMed engine. The ISAP approach consists of two stages: training and discovering. ISAP founds that the 35% of the abstracts sample had antibacterial peptides and we tested in the updated Antimicrobial Peptide Database 2 (APD2). ISAP predicted that 45% of the abstracts had antibacterial peptides. That is, ISAP found that 810 antibacterial peptides were not classified like that, so they are not reported in APD2. As a result, this new search tool would complement the APD2 with a set of peptides that are candidates to be antibacterial. Finally, 20% of the abstracts were not semantic related to APD2. PMID:27366202

  10. Phylogenetic analysis identifies a 'Candidatus Phytoplasma oryzae'-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India.

    PubMed

    Ramaswamy, Manimekalai; Nair, Smita; Soumya, V P; Thomas, George V

    2013-04-01

    Yellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for 'Candidatus Phytoplasma' species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3-1F7/7R2, 4Fwd/3Rev-4Fwd/5Rev and P1/P7-R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A blast search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of 'Candidatus Phytoplasma oryzae' and 97.8 % identity with that of 'Candidatus Phytoplasma cynodontis'. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a 'Candidatus Phytoplasma oryzae'-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI. PMID:22843718

  11. A Data Mining Project to Identify Cardiovascular Related Factors That May Contribute to Changes in Visual Acuity Within the US Astronaut Corps

    NASA Technical Reports Server (NTRS)

    Westby, Christian M.; Stein, Sydney P.; Platts, Steven H.

    2011-01-01

    Many of the cardiovascular-related adaptations that occur in the microgravity environment are due, in part, to a well-characterized cephalad-fluid shift that is evidenced by facial edema and decreased lower limb circumference. It is believed that most of these alterations occur as a compensatory response necessary to maintain a "normal" blood pressure and cardiac output while in space. However, data from both flight and analog research suggest that in some instances these microgravity-induced alterations may contribute to cardiovascular-related pathologies. Most concerning is the potential relation between the vision disturbances experienced by some long duration crewmembers and changes in cerebral blood flow and intra-ocular pressure. The purpose of this project was to identify cardiovascular measures that may potentially distinguish individuals at risk for visual disturbances after long duration space flight. Toward this goal, we constructed a dataset from Medical Operation tilt/stand test evaluations pre- (days L-15-L-5) and immediate post-flight (day R+0) on 20 (3 females, 17 males). We restricted our evaluation to only crewmembers who participated in both shuttle and space station missions. Data analysis was performed using both descriptive and analytical methods (Stata 11.2, College Station, TX) and are presented as means +/- 95% CI. Crewmembers averaged 5207 (3447 - 8934) flight hours across both long (MIR-23 through Expedition16) and short (STS-27 through STS-101) duration missions between 1988 and 2008. The mean age of the crew at the time of their most recent shuttle flight was 41 (34-44) compared to 47 (40-54) years during their time on station. In order to focus our analysis (we did not have codes to separate out subjects by symptomotology) , we performed a visual inspection of each cardiovascular measures captured during testing and plotted them against stand time, pre- to post-flight, and between mission duration. It was found that pulse pressure most

  12. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  13. Identifying, Defining, Coding, and Rating Nonverbal Behaviors That Appear to Be Related to Involvement: Project on Involvement Interim Report No. 2. Occasional Paper No. 12.

    ERIC Educational Resources Information Center

    Roderick, Jessie A.

    This document describes the process by which aspects of nonverbal communication that appear to be indicators of involvement were identified, described, classified, and rated. To facilitate this process, an Action Category System was developed through observation in the natural classroom setting and subsequent analyses of the recorded behavior…

  14. Serum profiling identifies novel muscle miRNA and cardiomyopathy-related miRNA biomarkers in Golden Retriever muscular dystrophy dogs and Duchenne muscular dystrophy patients.

    PubMed

    Jeanson-Leh, Laurence; Lameth, Julie; Krimi, Soraya; Buisset, Julien; Amor, Fatima; Le Guiner, Caroline; Barthélémy, Inès; Servais, Laurent; Blot, Stéphane; Voit, Thomas; Israeli, David

    2014-11-01

    Duchenne muscular dystrophy (DMD) is a fatal, X-linked neuromuscular disease that affects 1 boy in 3500 to 5000 boys. The golden retriever muscular dystrophy dog is the best clinically relevant DMD animal model. Here, we used a high-thoughput miRNA sequencing screening for identification of candidate serum miRNA biomarkers in golden retriever muscular dystrophy dogs. We confirmed the dysregulation of the previously described muscle miRNAs, miR-1, miR-133, miR-206, and miR-378, and identified a new candidate muscle miRNA, miR-95. We identified two other classes of dysregulated serum miRNAs in muscular dystrophy: miRNAs belonging to the largest known miRNA cluster that resides in the imprinting DLK1-DIO3 genomic region and miRNAs associated with cardiac disease, including miR-208a, miR-208b, and miR-499. No simple correlation was identified between serum levels of cardiac miRNAs and cardiac functional parameters in golden retriever muscular dystrophy dogs. Finally, we confirmed a dysregulation of miR-95, miR-208a, miR-208b, miR-499, and miR-539 in a small cohort of DMD patients. Given the interspecies conservation of miRNAs and preliminary data in DMD patients, these newly identified dysregulated miRNAs are strong candidate biomarkers for DMD patients.

  15. Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis.

    PubMed

    Moller-Levet, Carla S; Betts, Guy N J; Harris, Adrian L; Homer, Jarrod J; West, Catharine M L; Miller, Crispin J

    2009-11-01

    The identification of alternatively spliced transcript variants specific to particular biological processes in tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology, and associated splice variants may present new markers to help with planning treatment. A method was developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes with changes in expression across their loci, and a combination of the splicing index and a new metric based on the variation of reliability weighted fold changes to detect changes in the splicing patterns. The approach was validated on a cancer/normal sample dataset in which alternative splicing events had been confirmed using RT-PCR. We then analysed ten head and neck squamous cell carcinomas using exon arrays and identified differentially expressed splice variants in five samples with high versus five with low levels of hypoxia-associated genes. The analysis identified a splice variant of LAMA3 (Laminin alpha 3), LAMA3-A, known to be involved in tumour cell invasion and progression. The full-length transcript of the gene (LAMA3-B) did not appear to be hypoxia-associated. The results were confirmed using qualitative RT-PCR. In a series of 59 prospectively collected head and neck tumours, expression of LAMA3-A had prognostic significance whereas LAMA3-B did not. This work illustrates the potential for alternatively spliced transcripts to act as biomarkers of disease prognosis with improved specificity for particular tissues or conditions over assays which do not discriminate between splice variants. PMID:19936049

  16. New susceptibility and resistance HLA-DP alleles to HBV-related diseases identified by a trans-ethnic association study in Asia.

    PubMed

    Nishida, Nao; Sawai, Hiromi; Kashiwase, Koichi; Minami, Mutsuhiko; Sugiyama, Masaya; Seto, Wai-Kay; Yuen, Man-Fung; Posuwan, Nawarat; Poovorawan, Yong; Ahn, Sang Hoon; Han, Kwang-Hyub; Matsuura, Kentaro; Tanaka, Yasuhito; Kurosaki, Masayuki; Asahina, Yasuhiro; Izumi, Namiki; Kang, Jong-Hon; Hige, Shuhei; Ide, Tatsuya; Yamamoto, Kazuhide; Sakaida, Isao; Murawaki, Yoshikazu; Itoh, Yoshito; Tamori, Akihiro; Orito, Etsuro; Hiasa, Yoichi; Honda, Masao; Kaneko, Shuichi; Mita, Eiji; Suzuki, Kazuyuki; Hino, Keisuke; Tanaka, Eiji; Mochida, Satoshi; Watanabe, Masaaki; Eguchi, Yuichiro; Masaki, Naohiko; Murata, Kazumoto; Korenaga, Masaaki; Mawatari, Yoriko; Ohashi, Jun; Kawashima, Minae; Tokunaga, Katsushi; Mizokami, Masashi

    2014-01-01

    Previous studies have revealed the association between SNPs located on human leukocyte antigen (HLA) class II genes, including HLA-DP and HLA-DQ, and chronic hepatitis B virus (HBV) infection, mainly in Asian populations. HLA-DP alleles or haplotypes associated with chronic HBV infection or disease progression have not been fully identified in Asian populations. We performed trans-ethnic association analyses of HLA-DPA1, HLA-DPB1 alleles and haplotypes with hepatitis B virus infection and disease progression among Asian populations comprising Japanese, Korean, Hong Kong, and Thai subjects. To assess the association between HLA-DP and chronic HBV infection and disease progression, we conducted high-resolution (4-digit) HLA-DPA1 and HLA-DPB1 genotyping in a total of 3,167 samples, including HBV patients, HBV-resolved individuals and healthy controls. Trans-ethnic association analyses among Asian populations identified a new risk allele HLA-DPB1*09 ∶ 01 (P = 1.36 × 10(-6); OR= 1.97; 95% CI, 1.50-2.59) and a new protective allele DPB1*02 ∶ 01 (P = 5.22 × 10(-6); OR = 0.68; 95% CI, 0.58-0.81) to chronic HBV infection, in addition to the previously reported alleles. Moreover, DPB1*02 ∶ 01 was also associated with a decreased risk of disease progression in chronic HBV patients among Asian populations (P = 1.55 × 10(-7); OR = 0.50; 95% CI, 0.39-0.65). Trans-ethnic association analyses identified Asian-specific associations of HLA-DP alleles and haplotypes with HBV infection or disease progression. The present findings will serve as a base for future functional studies of HLA-DP molecules in order to understand the pathogenesis of HBV infection and the development of hepatocellular carcinoma. PMID:24520320

  17. Metabolomics in nutritional epidemiology: identifying metabolites associated with diet and quantifying their potential to uncover diet-disease relations in populations123

    PubMed Central

    Guertin, Kristin A; Moore, Steven C; Sampson, Joshua N; Huang, Wen-Yi; Xiao, Qian; Stolzenberg-Solomon, Rachael Z; Sinha, Rashmi; Cross, Amanda J

    2014-01-01

    Background: Metabolomics is an emerging field with the potential to advance nutritional epidemiology; however, it has not yet been applied to large cohort studies. Objectives: Our first aim was to identify metabolites that are biomarkers of usual dietary intake. Second, among serum metabolites correlated with diet, we evaluated metabolite reproducibility and required sample sizes to determine the potential for metabolomics in epidemiologic studies. Design: Baseline serum from 502 participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial was analyzed by using ultra-high-performance liquid-phase chromatography with tandem mass spectrometry and gas chromatography–mass spectrometry. Usual intakes of 36 dietary groups were estimated by using a food-frequency questionnaire. Dietary biomarkers were identified by using partial Pearson's correlations with Bonferroni correction for multiple comparisons. Intraclass correlation coefficients (ICCs) between samples collected 1 y apart in a subset of 30 individuals were calculated to evaluate intraindividual metabolite variability. Results: We detected 412 known metabolites. Citrus, green vegetables, red meat, shellfish, fish, peanuts, rice, butter, coffee, beer, liquor, total alcohol, and multivitamins were each correlated with at least one metabolite (P < 1.093 × 10−6; r = −0.312 to 0.398); in total, 39 dietary biomarkers were identified. Some correlations (citrus intake with stachydrine) replicated previous studies; others, such as peanuts and tryptophan betaine, were novel findings. Other strong associations included coffee (with trigonelline-N-methylnicotinate and quinate) and alcohol (with ethyl glucuronide). Intraindividual variability in metabolite levels (1-y ICCs) ranged from 0.27 to 0.89. Large, but attainable, sample sizes are required to detect associations between metabolites and disease in epidemiologic studies, further emphasizing the usefulness of metabolomics in nutritional

  18. Identifying Barriers, Perceptions and Motivations Related to Healthy Eating and Physical Activity among 6th to 8th Grade, Rural, Limited-Resource Adolescents

    ERIC Educational Resources Information Center

    Kumar, Janavi; Adhikari, Koushik; Li, Yijing; Lindshield, Erika; Muturi, Nancy; Kidd, Tandalayo

    2016-01-01

    Purpose: The purpose of this paper is to enable community members to discuss their perceptions of eating habits and physical activity in relation to sixth, seventh, and eighth graders, and reveal facilitators and barriers to healthy eating behavior and physical activity engagement. Design/methodology/approach: Nine focus groups, which included six…

  19. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    PubMed Central

    Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

  20. New Susceptibility and Resistance HLA-DP Alleles to HBV-Related Diseases Identified by a Trans-Ethnic Association Study in Asia

    PubMed Central

    Kashiwase, Koichi; Minami, Mutsuhiko; Sugiyama, Masaya; Seto, Wai-Kay; Yuen, Man-Fung; Posuwan, Nawarat; Poovorawan, Yong; Ahn, Sang Hoon; Han, Kwang-Hyub; Matsuura, Kentaro; Tanaka, Yasuhito; Kurosaki, Masayuki; Asahina, Yasuhiro; Izumi, Namiki; Kang, Jong-Hon; Hige, Shuhei; Ide, Tatsuya; Yamamoto, Kazuhide; Sakaida, Isao; Murawaki, Yoshikazu; Itoh, Yoshito; Tamori, Akihiro; Orito, Etsuro; Hiasa, Yoichi; Honda, Masao; Kaneko, Shuichi; Mita, Eiji; Suzuki, Kazuyuki; Hino, Keisuke; Tanaka, Eiji; Mochida, Satoshi; Watanabe, Masaaki; Eguchi, Yuichiro; Masaki, Naohiko; Murata, Kazumoto; Korenaga, Masaaki; Mawatari, Yoriko; Ohashi, Jun; Kawashima, Minae; Tokunaga, Katsushi; Mizokami, Masashi

    2014-01-01

    Previous studies have revealed the association between SNPs located on human leukocyte antigen (HLA) class II genes, including HLA-DP and HLA-DQ, and chronic hepatitis B virus (HBV) infection, mainly in Asian populations. HLA-DP alleles or haplotypes associated with chronic HBV infection or disease progression have not been fully identified in Asian populations. We performed trans-ethnic association analyses of HLA-DPA1, HLA-DPB1 alleles and haplotypes with hepatitis B virus infection and disease progression among Asian populations comprising Japanese, Korean, Hong Kong, and Thai subjects. To assess the association between HLA-DP and chronic HBV infection and disease progression, we conducted high-resolution (4-digit) HLA-DPA1 and HLA-DPB1 genotyping in a total of 3,167 samples, including HBV patients, HBV-resolved individuals and healthy controls. Trans-ethnic association analyses among Asian populations identified a new risk allele HLA-DPB1*09∶01 (P = 1.36×10−6; OR = 1.97; 95% CI, 1.50–2.59) and a new protective allele DPB1*02∶01 (P = 5.22×10−6; OR = 0.68; 95% CI, 0.58–0.81) to chronic HBV infection, in addition to the previously reported alleles. Moreover, DPB1*02∶01 was also associated with a decreased risk of disease progression in chronic HBV patients among Asian populations (P = 1.55×10−7; OR = 0.50; 95% CI, 0.39–0.65). Trans-ethnic association analyses identified Asian-specific associations of HLA-DP alleles and haplotypes with HBV infection or disease progression. The present findings will serve as a base for future functional studies of HLA-DP molecules in order to understand the pathogenesis of HBV infection and the development of hepatocellular carcinoma. PMID:24520320

  1. A Methodology for Validating Safety Heuristics Using Clinical Simulations: Identifying and Preventing Possible Technology-Induced Errors Related to Using Health Information Systems

    PubMed Central

    Borycki, Elizabeth; Kushniruk, Andre; Carvalho, Christopher

    2013-01-01

    Internationally, health information systems (HIS) safety has emerged as a significant concern for governments. Recently, research has emerged that has documented the ability of HIS to be implicated in the harm and death of patients. Researchers have attempted to develop methods that can be used to prevent or reduce technology-induced errors. Some researchers are developing methods that can be employed prior to systems release. These methods include the development of safety heuristics and clinical simulations. In this paper, we outline our methodology for developing safety heuristics specific to identifying the features or functions of a HIS user interface design that may lead to technology-induced errors. We follow this with a description of a methodological approach to validate these heuristics using clinical simulations. PMID:23606902

  2. Identifying patients with advanced chronic conditions for a progressive palliative care approach: a cross-sectional study of prognostic indicators related to end-of-life trajectories

    PubMed Central

    Amblàs-Novellas, J; Murray, S A; Espaulella, J; Martinez-Muñoz, M; Blay, C; Gómez-Batiste, X

    2016-01-01

    Objectives 2 innovative concepts have lately been developed to radically improve the care of patients with advanced chronic conditions (PACC): early identification of palliative care (PC) needs and the 3 end-of-life trajectories in chronic illnesses (acute, intermittent and gradual dwindling). It is not clear (1) what indicators work best for this early identification and (2) if specific clinical indicators exist for each of these trajectories. The objectives of this study are to explore these 2 issues. Setting 3 primary care services, an acute care hospital, an intermediate care centre and 4 nursing homes in a mixed urban–rural district in Barcelona, Spain. Participants 782 patients (61.5% women) with a positive NECPAL CCOMS-ICO test, indicating they might benefit from a PC approach. Outcome measures The characteristics and distribution of the indicators of the NECPAL CCOMS-ICO tool are analysed with respect to the 3 trajectories and have been arranged by domain (functional, nutritional and cognitive status, emotional problems, geriatric syndromes, social vulnerability and others) and according to their static (severity) and dynamic (progression) properties. Results The common indicators associated with early end-of-life identification are functional (44.3%) and nutritional (30.7%) progression, emotional distress (21.9%) and geriatric syndromes (15.7% delirium, 11.2% falls). The rest of the indicators showed differences in the associations per illness trajectories (p<0.05). 48.2% of the total cohort was identified as advanced frailty patients with no advanced disease criteria. Conclusions Dynamic indicators are present in the 3 trajectories and are especially useful to identify PACC for a progressive PC approach purpose. Most of the other indicators are typically associated with a specific trajectory. These findings can help clinicians improve the identification of patients for a palliative approach. PMID:27645556

  3. Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

    PubMed Central

    Mansfeldt, Cresten B.; Rowe, Annette R.; Heavner, Gretchen L. W.; Zinder, Stephen H.

    2014-01-01

    A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μM Cl−/h)- and fast (22.9 ± 9.6 μM Cl−/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). PMID

  4. An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins.

    PubMed

    Bernardo, Stella M; Allen, Christopher P; Waller, Anna; Young, Susan M; Oprea, Tudor; Sklar, Larry A; Lee, Samuel A

    2014-01-01

    Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new

  5. Development of a pluripotent stem cell derived neuronal model to identify chemically induced pathway perturbations in relation to neurotoxicity: Effects of CREB pathway inhibition

    SciTech Connect

    Pistollato, Francesca; Louisse, Jochem; Scelfo, Bibiana; Mennecozzi, Milena; Accordi, Benedetta; Basso, Giuseppe; Gaspar, John Antonydas; Zagoura, Dimitra; Barilari, Manuela; Palosaari, Taina; Sachinidis, Agapios; Bremer-Hoffmann, Susanne

    2014-10-15

    According to the advocated paradigm shift in toxicology, acquisition of knowledge on the mechanisms underlying the toxicity of chemicals, such as perturbations of biological pathways, is of primary interest. Pluripotent stem cells (PSCs), such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), offer a unique opportunity to derive physiologically relevant human cell types to measure molecular and cellular effects of such pathway modulations. Here we compared the neuronal differentiation propensity of hESCs and hiPSCs with the aim to develop novel hiPSC-based tools for measuring pathway perturbation in relation to molecular and cellular effects in vitro. Among other fundamental pathways, also, the cAMP responsive element binding protein (CREB) pathway was activated in our neuronal models and gave us the opportunity to study time-dependent effects elicited by chemical perturbations of the CREB pathway in relation to cellular effects. We show that the inhibition of the CREB pathway, using 2-naphthol-AS-E-phosphate (KG-501), induced an inhibition of neurite outgrowth and synaptogenesis, as well as a decrease of MAP2{sup +} neuronal cells. These data indicate that a CREB pathway inhibition can be related to molecular and cellular effects that may be relevant for neurotoxicity testing, and, thus, qualify the use of our hiPSC-derived neuronal model for studying chemical-induced neurotoxicity resulting from pathway perturbations. - Highlights: • HESCs derived neuronal cells serve as benchmark for iPSC based neuronal toxicity test development. • Comparisons between hESCs and hiPSCs demonstrated variability of the epigenetic state • CREB pathway modulation have been explored in relation to the neurotoxicant exposure KG-501 • hiPSC might be promising tools to translate theoretical AoPs into toxicological in vitro tests.

  6. A surface electromyography based objective method to identify patients with nonspecific chronic low back pain, presenting a flexion related movement control impairment.

    PubMed

    Van Damme, Benedicte; Stevens, Veerle; Perneel, Christiaan; Van Tiggelen, Damien; Neyens, Ellen; Duvigneaud, Nathalie; Moerman, Luc; Danneels, Lieven

    2014-12-01

    Movement control impairments (MCI) are often present in patients with non-specific chronic low back pain (NS-CLBP). Therefore, movement control exercises are widely used to rehabilitate patients. However, the objective assessment remains difficult. The purpose of this study was to develop a statistical model, based on logistic regression analysis, to differentiate patients with NS-CLBP presenting a flexion-related MCI from healthy subjects. This model is based on trunk muscle activation patterns measured by surface electromyography (sEMG), during movement control exercises. Sixty-three healthy male subjects and 36 male patients with a flexion-related MCI participated in this study. Muscle activity of the internal obliques, the external obliques, the lumbar multifidus and the thoracic part of the iliocostalis was registered. Ratios of deep stabilizing to superficial torque producing muscle activity were calculated to examine trunk muscle recruitment patterns during 6 different exercises. Logistic regression analyses were performed (1) to define the ratios and exercises that were most discriminating between patients and non-patients, (2) to make a predictive model. K-Fold cross-validation was used to assess the performance of the predictive model. This study demonstrated that sEMG trunk muscle recruitment patterns during movement control tests, allows differentiating NSCLBP patients with a flexion-related MCI from healthy subjects.

  7. Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora.

    PubMed

    Xiao, Bingbing; Niu, Xiaoxi; Han, Na; Wang, Ben; Du, Pengcheng; Na, Risu; Chen, Chen; Liao, Qinping

    2016-06-02

    Bacterial vaginosis (BV) is a highly prevalent disease in women, and increases the risk of pelvic inflammatory disease. It has been given wide attention because of the high recurrence rate. Traditional diagnostic methods based on microscope providing limited information on the vaginal microbiota increase the difficulty in tracing the development of the disease in bacteria resistance condition. In this study, we used deep-sequencing technology to observe dynamic variation of the vaginal microbiota at three major time points during treatment, at D0 (before treatment), D7 (stop using the antibiotics) and D30 (the 30-day follow-up visit). Sixty-five patients with BV were enrolled (48 were cured and 17 were not cured), and their bacterial composition of the vaginal microbiota was compared. Interestingly, we identified 9 patients might be recurrence. We also introduced a new measurement point of D7, although its microbiota were significantly inhabited by antibiotic and hard to be observed by traditional method. The vaginal microbiota in deep-sequencing-view present a strong correlation to the final outcome. Thus, coupled with detailed individual bioinformatics analysis and deep-sequencing technology, we may illustrate a more accurate map of vaginal microbial to BV patients, which provide a new opportunity to reduce the rate of recurrence of BV.

  8. Elevation in fibroblast growth factor 23 and its value for identifying subclinical atherosclerosis in first-degree relatives of patients with diabetes

    PubMed Central

    Hu, Xiang; Ma, Xiaojing; Luo, Yuqi; Xu, Yiting; Xiong, Qin; Pan, Xiaoping; Bao, Yuqian; Jia, Weiping

    2016-01-01

    Accumulating evidence supported an association between diabetes and fibroblast growth factor 23 (FGF23). The goal of the present study was to explore alteration in serum FGF23 levels and to assess its value for identifying subclinical atherosclerosis in normoglycemic individuals with a first-degree family history of diabetes (FHD). The study enrolled 312 subjects with a first-degree FHD and 1407 subjects without an FHD. Serum FGF23 levels were detected by a sandwich enzyme-linked immunosorbent assay. Serum FGF23 levels were much higher in subjects with a first-degree FHD than in those without an FHD (P = 0.006). A first-degree FHD was positively associated with serum FGF23 levels, independent of C-IMT and cardiovascular factors (both P < 0.05). In subjects with a first-degree FHD, only those with serum FGF23 levels in the upper quartile were more likely to have an increased C-IMT (odds ratio = 2.263, P < 0.05). As conclusions, a first-degree FHD contributes to the increased serum FGF23 levels independently. Subjects with a first-degree FHD need higher serum FGF23 levels to indicate subclinical atherosclerosis. The influence of a first-degree FHD on serum FGF23 levels should be considered to avoid overestimating the risk of cardiovascular disease in normoglycemic individuals with a first-degree FHD. PMID:27698482

  9. Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora

    PubMed Central

    Xiao, Bingbing; Niu, Xiaoxi; Han, Na; Wang, Ben; Du, Pengcheng; Na, Risu; Chen, Chen; Liao, Qinping

    2016-01-01

    Bacterial vaginosis (BV) is a highly prevalent disease in women, and increases the risk of pelvic inflammatory disease. It has been given wide attention because of the high recurrence rate. Traditional diagnostic methods based on microscope providing limited information on the vaginal microbiota increase the difficulty in tracing the development of the disease in bacteria resistance condition. In this study, we used deep-sequencing technology to observe dynamic variation of the vaginal microbiota at three major time points during treatment, at D0 (before treatment), D7 (stop using the antibiotics) and D30 (the 30-day follow-up visit). Sixty-five patients with BV were enrolled (48 were cured and 17 were not cured), and their bacterial composition of the vaginal microbiota was compared. Interestingly, we identified 9 patients might be recurrence. We also introduced a new measurement point of D7, although its microbiota were significantly inhabited by antibiotic and hard to be observed by traditional method. The vaginal microbiota in deep-sequencing-view present a strong correlation to the final outcome. Thus, coupled with detailed individual bioinformatics analysis and deep-sequencing technology, we may illustrate a more accurate map of vaginal microbial to BV patients, which provide a new opportunity to reduce the rate of recurrence of BV. PMID:27253522

  10. Metal impurities provide useful tracers for identifying exposures to airborne single-wall carbon nanotubes released from work-related processes

    NASA Astrophysics Data System (ADS)

    Rasmussen, Pat E.; Jayawardene, Innocent; Gardner, H. David; Chénier, Marc; Levesque, Christine; Niu, Jianjun

    2013-04-01

    This study investigated the use of metal impurities in single-wall carbon nanotubes (SWCNT) as potential tracers to distinguish engineered nanomaterials from background aerosols. TEM and SEM were used to characterize parent material and aerosolized agglomerates collected on PTFE filters using a cascade impactor. SEM image analysis indicated that the SWCNT agglomerates contained about 45% amorphous carbon and backscatter electron analysis indicated that metal impurities were concentrated within the amorphous carbon component. Two elements present as impurities (Y and Ni) were selected as appropriate tracers in this case as their concentrations were found to be highly elevated in the SWCNT parent material (% range) compared to ambient air particles (μg/g range), and background air concentrations were below detection limits for both elements. Bioaccessibility was also determined using physiologically-based extractions at pH conditions relevant to both ingestion and inhalation pathways. A portable wet electrostatic precipitation system effectively captured airborne Y and Ni released during sieving processes, in proportions similar to the bulk sample. These observations support the potential for catalysts and other metal impurities in carbon nanotubes to serve as tracers that uniquely identify emissions at source, after an initial analysis to select appropriate tracers.

  11. Molecular cloning of the CD3 eta subunit identifies a CD3 zeta-related product in thymus-derived cells.

    PubMed Central

    Jin, Y J; Clayton, L K; Howard, F D; Koyasu, S; Sieh, M; Steinbrich, R; Tarr, G E; Reinherz, E L

    1990-01-01

    The CD3 eta subunit of the T-cell antigen receptor forms a heterodimeric structure with the CD3 zeta subunit in thymus-derived lymphoid cells and is apparently involved in signal transduction through the receptor. Here we report the primary structure of murine CD3 eta as deduced from protein microsequencing and cDNA cloning. The mature protein is divided into three domains: a 9-amino acid extracellular segment, a 21-amino acid transmembrane segment including a negatively charged residue characteristic of CD3 subunits, and a 155-amino acid cytoplasmic tail. The NH2-terminal sequences of CD3 eta and CD3 zeta are identical through amino acid 122 of each mature protein but then diverge in the remainder of their respective COOH-terminal regions, consistent with alternatively spliced products of a common gene. The cytoplasmic domain of CD3 eta is 42 amino acids larger than that of CD3 zeta but lacks one of six potential tyrosine phosphorylation sites as well as a putative nucleotide binding site previously identified in CD3 zeta. These structural features presumably account for the difference between CD3 eta and CD3 zeta function and are consistent with the notion that CD3 eta may be an important component of a T-cell receptor isoform(s) during thymic development. Images PMID:2139725

  12. Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora.

    PubMed

    Xiao, Bingbing; Niu, Xiaoxi; Han, Na; Wang, Ben; Du, Pengcheng; Na, Risu; Chen, Chen; Liao, Qinping

    2016-01-01

    Bacterial vaginosis (BV) is a highly prevalent disease in women, and increases the risk of pelvic inflammatory disease. It has been given wide attention because of the high recurrence rate. Traditional diagnostic methods based on microscope providing limited information on the vaginal microbiota increase the difficulty in tracing the development of the disease in bacteria resistance condition. In this study, we used deep-sequencing technology to observe dynamic variation of the vaginal microbiota at three major time points during treatment, at D0 (before treatment), D7 (stop using the antibiotics) and D30 (the 30-day follow-up visit). Sixty-five patients with BV were enrolled (48 were cured and 17 were not cured), and their bacterial composition of the vaginal microbiota was compared. Interestingly, we identified 9 patients might be recurrence. We also introduced a new measurement point of D7, although its microbiota were significantly inhabited by antibiotic and hard to be observed by traditional method. The vaginal microbiota in deep-sequencing-view present a strong correlation to the final outcome. Thus, coupled with detailed individual bioinformatics analysis and deep-sequencing technology, we may illustrate a more accurate map of vaginal microbial to BV patients, which provide a new opportunity to reduce the rate of recurrence of BV. PMID:27253522

  13. Identifying panaxynol, a natural activator of nuclear factor erythroid-2 related factor 2 (Nrf2) from American ginseng as a suppressor of inflamed macrophage-induced cardiomyocyte hypertrophy

    PubMed Central

    Qu, Chen; Li, Bin; Lai, Yimu; Li, Hechu; Windust, Anthony; Hofseth, Lorne J.; Nagarkatti, Mitzi; Nagarkatti, Prakash; Wang, Xing Li; Tang, Dongqi; Janicki, Joseph S.; Tian, Xingsong; Cui, Taixing

    2015-01-01

    Ethnopharmacological relevance American ginseng is capable of ameliorating cardiac dysfunction and activating Nrf2, a master regulator of antioxidant defense, in the heart. This study was designed to isolate compounds from American ginseng and to determine those responsible for the Nrf2-mediated resolution of inflamed macrophage-induced cardiomyocyte hypertrophy. Materials and methods A standardized crude extract of American ginseng was supplied by the National Research Council of Canada, Institute for National Measurement Standards. A bioassay-based fractionization of American ginseng was performed to identify the putative substances which could activate Nrf2-mediated suppression of pro-inflammatory cytokine expression in macrophages and macrophage-mediated pro-hypertrophic growth in cardiomyocytes. Results A hexane fraction of an anti-inflammatory crude extract of American ginseng was found to be most effective in suppressing the inflammatory responses in macrophages. Preparative, reverse-phase HPLC and a comparative analysis by analytical scale LC–UV/MS revealed the hexane fraction contains predominantly C17 polyacetylenes and linolenic acid. Panaxynol, one of the major polyacetylenes, was found to be a potent Nrf2 activator. Panaxynol posttranscriptionally activated Nrf2 by inhibiting Kelch-like ECH-associated protein (Keap) 1-mediated degradation without affecting the binding of Keap1 and Nrf2. Moreover, panaxynol suppressed a selected set of cytokine expression via the activation of Nrf2 while minimally regulating nuclear factor-kappa B (NF-κB)-mediated cytokine expression in macrophages. It also dramatically inhibited the inflamed macrophage-mediated cardiomyocyte death and hypertrophy by activating Nrf2 in macrophages. Conclusions These results demonstrate that American ginseng-derived panaxynol is a specific Nrf2 activator and panaxynol-activated Nrf2 signaling is at least partly responsible for American ginseng-induced health benefit in the heart. PMID

  14. Open-Identity Sperm Donation: How Does Offering Donor-Identifying Information Relate to Donor-Conceived Offspring's Wishes and Needs?

    PubMed

    Ravelingien, An; Provoost, Veerle; Pennings, Guido

    2015-09-01

    Over the past years, a growing number of countries have legislated open-identity donation, in which donor-conceived offspring are given access to the donor's identity once the child has reached maturity. It is held that donor anonymity creates identity problems for such children similar to the "genealogical bewilderment" described within the adoption context. The study of the social and psychological effects of open-identity donation is still very much in its infancy, but what has been left unquestioned is whether (and to what extent) offering access to the donor's name and address is an adequate response to such effects. This study has two goals: First, we aim to provide a systematic review of the reasons why donor-conceived (DC) offspring want to know the identity of their sperm donor. Second, we examine to what extent the provision of donor-identifying information can satisfy the reasons mentioned. The most important motivations appear to be: (1) to avoid medical risks and consanguineous relationships; (2) to satisfy curiosity; (3) to learn more about the self or to complete one's identity; (4) to learn more about what kind of person the donor is (biographical information, why he donated, etc.); (5) to form a relationship with the donor and/or his family; and (6) to learn about one's ancestry/genealogy. Our analysis shows that for nearly all of these reasons access to the donor's identity is not necessary. In those cases where it is, moreover, donor identification is not sufficient. What is really needed is (extended) contact with the donor, rather than the mere provision of his name.

  15. Caenorhabditis elegans expressing the Saccharomyces cerevisiae NADH alternative dehydrogenase Ndi1p, as a tool to identify new genes involved in complex I related diseases

    PubMed Central

    Cossard, Raynald; Esposito, Michela; Sellem, Carole H.; Pitayu, Laras; Vasnier, Christelle; Delahodde, Agnès; Dassa, Emmanuel P.

    2015-01-01

    Isolated complex I deficiencies are one of the most commonly observed biochemical features in patients suffering from mitochondrial disorders. In the majority of these clinical cases the molecular bases of the diseases remain unknown suggesting the involvement of unidentified factors that are critical for complex I function. The Saccharomyces cerevisiae NDI1 gene, encoding the mitochondrial internal NADH dehydrogenase was previously shown to complement a complex I deficient strain in Caenorhabditis elegans with notable improvements in reproduction and whole organism respiration. These features indicate that Ndi1p can functionally integrate the respiratory chain, allowing complex I deficiency complementation. Taking into account the Ndi1p ability to bypass complex I, we evaluate the possibility to extend the range of defects/mutations causing complex I deficiencies that can be alleviated by NDI1 expression. We report here that NDI1 expressing animals unexpectedly exhibit a slightly shortened lifespan, a reduction in the progeny, and a depletion of the mitochondrial genome. However, Ndi1p is expressed and targeted to the mitochondria as a functional protein that confers rotenone resistance to those animals without affecting their respiration rate and ATP content. We show that the severe embryonic lethality level caused by the RNAi knockdowns of complex I structural subunit encoding genes (e.g., NDUFV1, NDUFS1, NDUFS6, NDUFS8, or GRIM-19 human orthologs) in wild type animals is significantly reduced in the Ndi1p expressing worm. All together these results open up the perspective to identify new genes involved in complex I function, assembly, or regulation by screening an RNAi library of genes leading to embryonic lethality that should be rescued by NDI1 expression. PMID:26124772

  16. Open-Identity Sperm Donation: How Does Offering Donor-Identifying Information Relate to Donor-Conceived Offspring's Wishes and Needs?

    PubMed

    Ravelingien, An; Provoost, Veerle; Pennings, Guido

    2015-09-01

    Over the past years, a growing number of countries have legislated open-identity donation, in which donor-conceived offspring are given access to the donor's identity once the child has reached maturity. It is held that donor anonymity creates identity problems for such children similar to the "genealogical bewilderment" described within the adoption context. The study of the social and psychological effects of open-identity donation is still very much in its infancy, but what has been left unquestioned is whether (and to what extent) offering access to the donor's name and address is an adequate response to such effects. This study has two goals: First, we aim to provide a systematic review of the reasons why donor-conceived (DC) offspring want to know the identity of their sperm donor. Second, we examine to what extent the provision of donor-identifying information can satisfy the reasons mentioned. The most important motivations appear to be: (1) to avoid medical risks and consanguineous relationships; (2) to satisfy curiosity; (3) to learn more about the self or to complete one's identity; (4) to learn more about what kind of person the donor is (biographical information, why he donated, etc.); (5) to form a relationship with the donor and/or his family; and (6) to learn about one's ancestry/genealogy. Our analysis shows that for nearly all of these reasons access to the donor's identity is not necessary. In those cases where it is, moreover, donor identification is not sufficient. What is really needed is (extended) contact with the donor, rather than the mere provision of his name. PMID:24996630

  17. Identifying quantitative trait loci and determining closely related stalk traits for rind penetrometer resistance in a high-oil maize population.

    PubMed

    Hu, Haixiao; Meng, Yujie; Wang, Hongwu; Liu, Hai; Chen, Shaojiang

    2012-05-01

    Stalk lodging in maize causes annual yield losses between 5 and 20% worldwide. Many studies have indicated that maize stalk strength significantly negatively correlates with lodging observed in the field. Rind penetrometer resistance (RPR) measurements can be used to effectively evaluate maize stalk strength, but little is known about the genetic basis of this parameter. The objective of this study was to explore a genetic model and detect quantitative trait loci (QTL) of RPR and determine relationships between RPR and other stalk traits, especially cell wall chemical components. RPR is quantitative trait in nature, and both additive and non-additive effects may be important to consider for the improvement of RPR. Nine additive-effect QTLs covering nine chromosomes, except chromosome 5, and one pair of epistatic QTLs were detected for RPR. CeSA11 involved in cellulose synthesis and colorless2 involved in lignin synthesis were identified as possible candidate genes for RPR. Internode diameter (InD), fresh weight of internode (FreW), dry weight of internode (DryW), fresh weight and dry weight as well as cell wall components per unit volume significantly positively correlated with RPR. The internode water content (InW) significantly negatively correlated with RPR. Notably, these traits significantly correlated with RPR, and the QTLs of these traits co-localized with those of RPR. The corresponding results obtained from correlation analysis and QTL mapping suggested the presence of pleitropism or linkage between genes and indicated that these different approaches may be used for cross authentication of relationships between different traits. PMID:22314785

  18. Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.

    PubMed

    Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

    2014-01-01

    The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We

  19. Nintendo related injuries and other problems: review

    PubMed Central

    Heineman, Erik; Pierie, Jean-Pierre E N; ten Cate Hoedemaker, Henk O

    2014-01-01

    Objective To identify all reported cases of injury and other problems caused by using a Nintendo video gaming system. Design Review. Data sources and review methods Search of PubMed and Embase in June 2014 for reports on injuries and other problems caused by using a Nintendo gaming system. Results Most of the 38 articles identified were case reports or case series. Injuries and problems ranged from neurological and psychological to surgical. Traditional controllers with buttons were associated with tendinitis of the extensor of the thumb. The joystick on the Nintendo 64 controller was linked to palmar ulceration. The motion sensitive Wii remote was associated with musculoskeletal problems and various traumas. Conclusions Most problems are mild and prevalence is low. The described injuries were related to the way the games are controlled, which varies according to the video game console. PMID:25515525

  20. Identifying factors related to Achilles tendon stress, strain, and stiffness before and after 6 months of growth in youth 10-14 years of age.

    PubMed

    Neugebauer, Jennifer M; Hawkins, David A

    2012-09-21

    The purposes of this study were (1) determine if youth peak Achilles tendon (AT) strain, peak AT stress, and AT stiffness, measured during an isometric plantar flexion, differed after six months (mos) of growth, and (2) determine if sex, physical activity level (Physical Activity Questionnaire (PAQ-C)), and/or growth rate (GR) were related to these properties. AT stress, strain, and stiffness were quantified in 20 boys (13.47±0.81 years) and 22 girls (11.18±0.82 years) at 2 times (0 and 6 mos). GR (change in height in 6 mos) was not significantly different between boys and girls (3.5±1.4 and 3.4±1.1cm/6 mos respectively). Peak AT strain and stiffness (mean 3.8±0.4% and 128.9±153.6N/mm, respectively) did not differ between testing sessions or sex. Peak AT stress (22.1±2.4 and 24.0±2.1MPa at 0 and 6 mos, respectively) did not differ between sex and increased significantly at 6 mos due to a significant decrease in AT cross-sectional area (40.6±1.3 and 38.1±1.6mm(2) at 0 and 6 mos, respectively) with no significant difference in peak AT force (882.3±93.9 and 900.3± 65.5N at 0 and 6 mos, respectively). Peak AT stress was significantly greater in subjects with greater PAQ-C scores (9.1% increase with 1 unit increase in PAQ-C score) and smaller in subjects with faster GRs (13.8% decrease with 1cm/6 mos increase in GR). These results indicate that of the AT mechanical properties quantified, none differed between sex, and only peak AT stress significantly differed after 6 months and was related to GR and physical activity.

  1. Gender-related traits in gay men, lesbian women, and heterosexual men and women: the virtual identify of homosexual-heterosexual diagnosticity and gender diagnosticity.

    PubMed

    Lippa, R A

    2000-10-01

    Three studies investigated the relationship between gender-related traits and sexual orientation. Study 1 showed that gay men and lesbians in an unselected sample of 721 college students differed from same-sex heterosexuals most strongly on gender diagnosticity (GD) measures, which assess male- versus female-typicality of interests (effect sizes of 2.70 for men and .96 for women) and least strongly on measures of instrumentality (I) and expressiveness (E). In Study 2, GD measures showed large differences between 95 gay and 136 heterosexual men (effect sizes of 1.61 and 1.83) and between 46 lesbian and 225 heterosexual women (effect sizes of .98 and 1.28), whereas I and E showed much smaller differences. In Study 3, GD showed large differences between 90 gay and 81 heterosexual men (effect sizes of 1.76 and 1.97) and between 82 lesbians and 108 heterosexual women (effect sizes 1.67 and 1.70). whereas I and E showed much smaller differences. Using data from Studies 2 and 3, "gay-heterosexual diagnosticity" measures were computed for men and "lesbian-heterosexual diagnosticity" measures for women, based on occupational and hobby preferences. These measures correlated very strongly with GD measures.

  2. USACE FUSRAP Maywood Team Identifies Challenges and Initiates Alternate Solutions Relating to the Radiochemical Analysis of Borosilicate Fiber Filters for Isotopes of Uranium and Thorium

    SciTech Connect

    Tucker, B.; Winters, M.; Hays, D.

    2008-07-01

    This presentation discusses the primary purposes of particulate radionuclide air monitoring at the US Army Corps of Engineers (USACE) Formerly Utilized Sites Remediation Program (FUSRAP) Maywood Superfund Site (FMSS), the challenges encountered by the team when standard radiochemistry analytical methods are attempted on borosilicate fiber filter samples, the surrogate evaluations used when sample specific isotopic analysis is unsuccessful, and current strategies for overcoming radiochemistry method deficiencies. Typical borosilicate fiber filter sample preparation procedures including tracer spike and digestion methods and their impact on uranium and thorium data quality are of particular interest. Analytes discussed include isotopic uranium (U-234, U-235, and U-238) and isotopic thorium (Th-228, Th-230, and Th-232). Efforts to obtain reproducible and defensible results also included discussions with commercial laboratory radiochemistry managers as well as industry experts. This presentation may benefit sites that use similar sample collection and analysis techniques, utilize data that may have unidentified method-related issues with diminished data quality, or have a similar isotopic signature. (authors)

  3. A Drosophila functional evaluation of candidates from human genome-wide association studies of type 2 diabetes and related metabolic traits identifies tissue-specific roles for dHHEX

    PubMed Central

    2013-01-01

    Background Genome-wide association studies (GWAS) identify regions of the genome that are associated with particular traits, but do not typically identify specific causative genetic elements. For example, while a large number of single nucleotide polymorphisms associated with type 2 diabetes (T2D) and related traits have been identified by human GWAS, only a few genes have functional evidence to support or to rule out a role in cellular metabolism or dietary interactions. Here, we use a recently developed Drosophila model in which high-sucrose feeding induces phenotypes similar to T2D to assess orthologs of human GWAS-identified candidate genes for risk of T2D and related traits. Results Disrupting orthologs of certain T2D candidate genes (HHEX, THADA, PPARG, KCNJ11) led to sucrose-dependent toxicity. Tissue-specific knockdown of the HHEX ortholog dHHEX (CG7056) directed metabolic defects and enhanced lethality; for example, fat-body-specific loss of dHHEX led to increased hemolymph glucose and reduced insulin sensitivity. Conclusion Candidate genes identified in human genetic studies of metabolic traits can be prioritized and functionally characterized using a simple Drosophila approach. To our knowledge, this is the first large-scale effort to study the functional interaction between GWAS-identified candidate genes and an environmental risk factor such as diet in a model organism system. PMID:23445342

  4. SNP screening of central MHC-identified HLA-DMB as a candidate susceptibility gene for HIV-related Kaposi's sarcoma.

    PubMed

    Aissani, B; Boehme, A K; Wiener, H W; Shrestha, S; Jacobson, L P; Kaslow, R A

    2014-09-01

    The major histocompatibility complex (MHC) region on chromosome 6p21.3 is suspected to host susceptibility loci for HIV-related Kaposi's sarcoma (HIV-KS). A nested case-control study in the Multicenter AIDS Cohort Study was designed to conduct fine genetic association mapping across central MHC. Individuals co-infected with HIV-1 and human herpes virus-8 who later developed KS were defined as cases (n=354) and were matched 1:1 with co-infected KS-free controls. We report data for new independent MHC class II and III susceptibility loci. In particular, class II HLA-DMB emerged as a strong candidate, with the intronic variant rs6902982 A>G associated with a fourfold increase of risk (odds ratio (OR)=4.09; 95% confidence interval (CI)=1.90-8.80; P=0.0003). A striking multiplicative effect on the estimated risk was associated with further carriage of two non-synonymous variants, rs1800453 A>G (Asp697Gly) and rs4148880 A>G (Ile393Val), in the linked TAP1 gene (OR=10.5; 95% CI=2.54-43.6; P=0.0012). The class III susceptibility variant is moderately associated with HIV-KS and lies within a 120-kb-long haplotype (OR=1.52; 95% CI=1.01-2.28; P=0.047) formed by rs7029 A>G (GPANK1 3' untranslated region), rs1065356 G>A (LY6G6C), rs3749953 A>G (MSH5-SAPCD1 read through) and rs707926 G>A (VARS). Our data suggest that antigen processing by MHC class II molecules is a target pathway in the pathogenesis of HIV-KS.

  5. Potential Susceptibility Mutations in C Gene for Hepatitis B-Related Hepatocellular Carcinoma Identified by a Two-Stage Study in Qidong, China

    PubMed Central

    Qu, Lishuai; Zhang, Haifeng; Liu, Jinxia; Liu, Taotao; Shen, Xizhong; Chen, Taoyang; Ni, Zhengpin; Lu, Cuihua

    2016-01-01

    A two stage study was conducted to explore new potential mutations in the full genome of hepatitis B virus (HBV) on the progression of hepatocellular carcinoma (HCC) in Qidong, China. In stage 1, full genomes of HBV were compared between 30 HCC cases and 30 controls. In stage 2, an independent case–control study including 100 HCC cases and 100 controls was enrolled to verify the relationship between hot-spot mutations and HCC development. Furthermore, a longitudinal study was conducted on 11 HCC cases with serial serum samples available before HCC diagnosis. A total of 10 mutations (including pre-S2 start codon mutation and pre-S deletion in pre-S gene, G1613A, C1653T, A1762T, and G1764A mutations in X gene, A2159G, A2189Y, G2203W, and C2288R mutations in C gene) showed an increased risk of HCC. In the validation study, pre-S deletion, C1653T, A1762T/G1764A, A2159G, A2189Y, G2203W, and C2288R mutations were associated with increased HCC risk in univariate analysis. Multivariate analysis indicated that pre-S deletion, A1762T/G1764A, A2159G, and A2189Y mutations were independently related with HCC development. Moreover, a significant biological gradient of HCC risk by number of mutations in the C gene was observed. Longitudinal observation demonstrated a gradual combination of the above mutations accumulated during the progression of HCC. PMID:27727182

  6. Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence.

    PubMed

    Zlojutro, Mark; Manz, Niklas; Rangaswamy, Madhavi; Xuei, Xiaoling; Flury-Wetherill, Leah; Koller, Daniel; Bierut, Laura J; Goate, Alison; Hesselbrock, Victor; Kuperman, Samuel; Nurnberger, John; Rice, John P; Schuckit, Marc A; Foroud, Tatiana; Edenberg, Howard J; Porjesz, Bernice; Almasy, Laura

    2011-01-01

    Event-related brain oscillations (EROs) represent highly heritable neuroelectrical correlates of human perception and cognitive performance that exhibit marked deficits in patients with various psychiatric disorders. We report the results of the first genome-wide association study (GWAS) of an ERO endophenotype-frontal theta ERO evoked by visual oddball targets during P300 response in 1,064 unrelated individuals drawn from a study of alcohol dependence. Forty-two SNPs of the Illumina HumanHap 1 M microarray were selected from the theta ERO GWAS for replication in family-based samples (N = 1,095), with four markers revealing nominally significant association. The most significant marker from the two-stage study is rs4907240 located within ARID protein 5A gene (ARID5A) on chromosome 2q11 (unadjusted, Fisher's combined P = 3.68 × 10⁻⁶). However, the most intriguing association to emerge is with rs7916403 in serotonin receptor gene HTR7 on chromosome 10q23 (combined P = 1.53 × 10⁻⁴), implicating the serotonergic system in the neurophysiological underpinnings of theta EROs. Moreover, promising SNPs were tested for association with diagnoses of alcohol dependence (DSM-IV), revealing a significant relationship with the HTR7 polymorphism among GWAS case-controls (P = 0.008). Significant recessive genetic effects were also detected for alcohol dependence in both case-control and family-based samples (P = 0.031 and 0.042, respectively), with the HTR7 risk allele corresponding to theta ERO reductions among homozygotes. These results suggest a role of the serotonergic system in the biological basis of alcohol dependence and underscore the utility of analyzing brain oscillations as a powerful approach to understanding complex genetic psychiatric disorders.

  7. BIOSPIDA: A Relational Database Translator for NCBI.

    PubMed

    Hagen, Matthew S; Lee, Eva K

    2010-01-01

    As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time. PMID:21347013

  8. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members. PMID:27331226

  9. Near Identifiability of Dynamical Systems

    NASA Technical Reports Server (NTRS)

    Hadaegh, F. Y.; Bekey, G. A.

    1987-01-01

    Concepts regarding approximate mathematical models treated rigorously. Paper presents new results in analysis of structural identifiability, equivalence, and near equivalence between mathematical models and physical processes they represent. Helps establish rigorous mathematical basis for concepts related to structural identifiability and equivalence revealing fundamental requirements, tacit assumptions, and sources of error. "Structural identifiability," as used by workers in this field, loosely translates as meaning ability to specify unique mathematical model and set of model parameters that accurately predict behavior of corresponding physical system.

  10. Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicing-related components with synMuv B activity

    PubMed Central

    Ceron, Julian; Rual, Jean-François; Chandra, Abha; Dupuy, Denis; Vidal, Marc; van den Heuvel, Sander

    2007-01-01

    Background The retinoblastoma tumor suppressor (Rb) acts in a conserved pathway that is deregulated in most human cancers. Inactivation of the single Rb-related gene in Caenorhabditis elegans, lin-35, has only limited effects on viability and fertility, yet causes changes in cell-fate and cell-cycle regulation when combined with inactivation of specific other genes. For instance, lin-35 Rb is a synthetic multivulva (synMuv) class B gene, which causes a multivulva phenotype when inactivated simultaneously with a class A or C synMuv gene. Results We used the ORFeome RNAi library to identify genes that interact with C. elegans lin-35 Rb and identified 57 genes that showed synthetic or enhanced RNAi phenotypes in lin-35 mutants as compared to rrf-3 and eri-1 RNAi hypersensitive mutants. Based on characterizations of a deletion allele, the synthetic lin-35 interactor zfp-2 was found to suppress RNAi and to cooperate with lin-35 Rb in somatic gonad development. Interestingly, ten splicing-related genes were found to function similar to lin-35 Rb, as synMuv B genes that prevent inappropriate vulval induction. Partial inactivation of specific spliceosome components revealed further similarities with lin-35 Rb functions in cell-cycle control, transgene expression and restricted expression of germline granules. Conclusion We identified an extensive series of candidate lin-35 Rb interacting genes and validated zfp-2 as a novel lin-35 synthetic lethal gene. In addition, we observed a novel role for a subset of splicing components in lin-35 Rb-controlled processes. Our data support novel hypotheses about possibilities for anti-cancer therapies and multilevel regulation of gene expression. PMID:17417969

  11. Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Quantitative Proteomic Analysis Identifies Galectin-1 as a Potential Biomarker for Predicting Sorafenib Resistance in Liver Cancer.

    PubMed

    Yeh, Chao-Chi; Hsu, Chih-Hung; Shao, Yu-Yun; Ho, Wen-Ching; Tsai, Mong-Hsun; Feng, Wen-Chi; Chow, Lu-Ping

    2015-06-01

    Sorafenib has become the standard therapy for patients with advanced hepatocellular carcinoma (HCC). Unfortunately, most patients eventually develop acquired resistance. Therefore, it is important to identify potential biomarkers that could predict the efficacy of sorafenib. To identify target proteins associated with the development of sorafenib resistance, we applied stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomic approach to analyze differences in protein expression levels between parental HuH-7 and sorafenib-acquired resistance HuH-7 (HuH-7(R)) cells in vitro, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) quantitative analysis of HuH-7 and HuH-7(R) tumors in vivo. In total, 2,450 quantified proteins were identified in common in SILAC and iTRAQ experiments, with 81 showing increased expression (>2.0-fold) with sorafenib resistance and 75 showing decreased expression (<0.5-fold). In silico analyses of these differentially expressed proteins predicted that 10 proteins were related to cancer with involvements in cell adhesion, migration, and invasion. Knockdown of one of these candidate proteins, galectin-1, decreased cell proliferation and metastasis in HuH-7(R) cells and restored sensitivity to sorafenib. We verified galectin-1 as a predictive marker of sorafenib resistance and a downstream target of the AKT/mTOR/HIF-1α signaling pathway. In addition, increased galectin-1 expression in HCC patients' serum was associated with poor tumor control and low response rate. We also found that a high serum galectin-1 level was an independent factor associated with poor progression-free survival and overall survival. In conclusion, these results suggest that galectin-1 is a possible biomarker for predicting the response of HCC patients to treatment with sorafenib. As such, it may assist in the stratification of HCC and help direct personalized therapy.

  12. Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Quantitative Proteomic Analysis Identifies Galectin-1 as a Potential Biomarker for Predicting Sorafenib Resistance in Liver Cancer*

    PubMed Central

    Yeh, Chao-Chi; Hsu, Chih-Hung; Shao, Yu-Yun; Ho, Wen-Ching; Tsai, Mong-Hsun; Feng, Wen-Chi; Chow, Lu-Ping

    2015-01-01

    Sorafenib has become the standard therapy for patients with advanced hepatocellular carcinoma (HCC). Unfortunately, most patients eventually develop acquired resistance. Therefore, it is important to identify potential biomarkers that could predict the efficacy of sorafenib. To identify target proteins associated with the development of sorafenib resistance, we applied stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomic approach to analyze differences in protein expression levels between parental HuH-7 and sorafenib-acquired resistance HuH-7 (HuH-7R) cells in vitro, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) quantitative analysis of HuH-7 and HuH-7R tumors in vivo. In total, 2,450 quantified proteins were identified in common in SILAC and iTRAQ experiments, with 81 showing increased expression (>2.0-fold) with sorafenib resistance and 75 showing decreased expression (<0.5-fold). In silico analyses of these differentially expressed proteins predicted that 10 proteins were related to cancer with involvements in cell adhesion, migration, and invasion. Knockdown of one of these candidate proteins, galectin-1, decreased cell proliferation and metastasis in HuH-7R cells and restored sensitivity to sorafenib. We verified galectin-1 as a predictive marker of sorafenib resistance and a downstream target of the AKT/mTOR/HIF-1α signaling pathway. In addition, increased galectin-1 expression in HCC patients' serum was associated with poor tumor control and low response rate. We also found that a high serum galectin-1 level was an independent factor associated with poor progression-free survival and overall survival. In conclusion, these results suggest that galectin-1 is a possible biomarker for predicting the response of HCC patients to treatment with sorafenib. As such, it may assist in the stratification of HCC and help direct personalized therapy. PMID:25850433

  13. Identifying Clients Predisposed To Failure

    ERIC Educational Resources Information Center

    Carnes, G. D.

    1973-01-01

    Studies are reviewed that report the prediction of rehabilitation failure from personality measures. Related research is discussed that suggest the dynamics underlying a key concept, the "hypochondriacally organized personality" which is identifiable from the Rorschach anatomy response percentage. (Author)

  14. Identifying and Describing the Impact of Cyclone, Storm and Flood Related Disasters on Treatment Management, Care and Exacerbations of Non-communicable Diseases and the Implications for Public Health

    PubMed Central

    Ryan, Benjamin; Franklin, Richard C.; Burkle, Frederick M.; Aitken, Peter; Smith, Erin; Watt, Kerrianne; Leggat, Peter

    2015-01-01

    Introduction: Over the last quarter of a century the frequency of natural disasters and the burden of non-communicable diseases (NCD) across the globe have been increasing. For individuals susceptible to, or chronically experiencing, NCDs this has become a significant risk. Disasters jeopardize access to essential treatment, care, equipment, water and food, which can result in an exacerbation of existing conditions or even preventable death. Consequently, there is a need to expand the public health focus of disaster management to include NCDs. To provide a platform for this to occur, this article presents the results from a systematic review that identifies and describes the impact of cyclone, flood and storm related disasters on those susceptible to, or experiencing, NCDs. The NCDs researched were: cardiovascular diseases; cancers; chronic respiratory diseases; and diabetes.   Methods: Four electronic publication databases were searched with a date limit of 31 December 2014. The data was analyzed through an aggregation of individual papers to create an overall data description. The data was then grouped by disease to describe the impact of a disaster on treatment management, exacerbation, and health care of people with NCDs. The PRISMA checklist was used to guide presentation of the research. Results:  The review identified 48 relevant articles. All studies represented developed country data. Disasters interrupt treatment management and overall care for people with NCDs, which results in an increased risk of exacerbation of their illness or even death. The interruption may be caused by a range of factors, such as damaged transport routes, reduced health services, loss of power and evacuations. The health impact varied according to the NCD. For people with chronic respiratory diseases, a disaster increases the risk of acute exacerbation. Meanwhile, for people with cancer, cardiovascular diseases and diabetes there is an increased risk of their illness

  15. Integrative review of factors related to the nursing diagnosis nausea during antineoplastic chemotherapy 1

    PubMed Central

    Moysés, Aline Maria Bonini; Durant, Lais Corsino; de Almeida, Ana Maria; Gozzo, Thais de Oliveira

    2016-01-01

    ABSTRACT Objective: to identify factors related to the nursing diagnosis nausea among cancer patients undergoing chemotherapy. Method: integrative review conducted in four electronic databases (PUBMED, EMBASE, CINAHL and LILACS) using the key words: neoplasia, antineoplastic agents and nausea. Results: only 30 out of 1,258 papers identified met the inclusion criteria. The most frequent related factors were: being younger than 50 years old, motion sickness, being a woman, emetogenic potential of the chemotherapy, anxiety, conditioned stimulus, and expecting nausea after treatment. Conclusion: this review's findings, coupled with the incidence of nausea among cancer patients undergoing chemotherapy, reveal an important difference between evidence found and that used by NANDA International, Inc. Even though it provides an appropriate definition of related factors, it does not mention chemotherapy, despite the various studies addressing the topic using different designs and presenting various objectives and outcomes. PMID:27737380

  16. Proteomic analysis identifies an NADPH oxidase 1 (Nox1)-mediated role for actin-related protein 2/3 complex subunit 2 (ARPC2) in promoting smooth muscle cell migration.

    PubMed

    Al Ghouleh, Imad; Rodríguez, Andrés; Pagano, Patrick J; Csányi, Gábor

    2013-01-01

    A variety of vascular pathologies, including hypertension, restenosis and atherosclerosis, are characterized by vascular smooth muscle cell (VSMC) hypertrophy and migration. NADPH oxidase 1 (Nox1) plays a pivotal role in these phenotypes via distinct downstream signaling. However, the mediators differentiating these distinct phenotypes and their precise role in vascular disease are still not clear. The present study was designed to identify novel targets of VSMC Nox1 signaling using 2D Differential In-Gel Electrophoresis and Mass Spectrometry (2D-DIGE/MS). VSMC treatment with scrambled (Scrmb) or Nox1 siRNA and incubation with the oxidant hydrogen peroxide (H2O2; 50 µM, 3 h) followed by 2D-DIGE/MS on cell lysates identified 10 target proteins. Among these proteins, actin-related protein 2/3 complex subunit 2 (ARPC2) with no previous link to Nox isozymes, H2O2, or other reactive oxygen species (ROS), was identified and postulated to play an intermediary role in VSMC migration. Western blot confirmed that Nox1 mediates H2O2-induced ARPC2 expression in VSMC. Treatment with a p38 MAPK inhibitor (SB203580) resulted in reduced ARPC2 expression in H2O2-treated VSMC. Additionally, wound-healing "scratch" assay confirmed that H2O2 stimulates VSMC migration via Nox1. Importantly, gene silencing of ARPC2 suppressed H2O2-stimulated VSMC migration. These results demonstrate for the first time that Nox1-mediated VSMC migration involves ARPC2 as a downstream signaling target. PMID:24152438

  17. Multiple Novel Loci, Including Those Related to Crohn’s Disease, Psoriasis and Inflammation, Identified in a Genome-Wide Association Study of Fibrinogen in 17,686 Women: the Women’s Genome Health Study

    PubMed Central

    Danik, Jacqueline S.; Pare, Guillaume; Chasman, Daniel I.; Zee, Robert Y.L.; Kwiatkowski, David J.; Parker, Alex; Miletich, Joseph P.; Ridker, Paul M

    2009-01-01

    Background Fibrinogen is a multifunctional circulating glycoprotein involved in wound-healing, thrombosis, platelet aggregation and inflammation, and elevated levels predict vascular disease. Despite evidence of such crucial biological functions and moderate heritability, comprehensive analysis of the influence of genetic variation on fibrinogen is not available. Methods and Results To address this issue, we undertook a genome-wide association study evaluating the potential relationships between 337,343 single nucleotide polymorphisms (SNPs) and plasma fibrinogen levels among 17,686 apparently healthy women participating in the Women’s Genome Health Study (WGHS). As C-reactive protein is also an inflammatory marker known to predict cardiovascular diseases, we compared the determinants of fibrinogen levels with those of C-reactive protein. Four novel loci were identified, in addition to the fibrinogen gene cluster, which were associated with fibrinogen levels at genome-wide levels of significance (range of P-values from 8.82×10-09 to 8.04×10-39). Two of the loci related to common chronic inflammatory diseases: the first, at locus 5q31.1 (SLC22A5, SLC22A4, IRF1) lies immediately adjacent to a locus linked to Crohn’s disease (P-value for lead SNP 1.24 × 10-12) and the second, at locus 17q25.1 (CD300LF, SLC9A3R1, NAT9) has been associated with psoriasis (P-value for lead SNP 7.72×10-11). A third locus at 1q21.3 (IL6R) lies within the interleukin 6 receptor gene, a critical component of the inflammatory cascade (P-value for lead SNP 1.80×10-11). A novel locus at 2q34 (CPS1) participates in the urea cycle (P-value 8.82×10-09). The majority of implicated SNPs showed little evidence of dual association with C-reactive protein levels. Conclusions An agnostic survey of the human genome identifies novel loci related to common chronic inflammatory diseases as genetic determinants of fibrinogen levels, in addition to loci that relate to the inflammatory cascade, the

  18. A translational systems biology approach in both animals and humans identifies a functionally related module of accumbal genes involved in the regulation of reward processing and binge drinking in males

    PubMed Central

    Stacey, David; Lourdusamy, Anbarasu; Ruggeri, Barbara; Maroteaux, Matthieu; Jia, Tianye; Cattrell, Anna; Nymberg, Charlotte; Banaschewski, Tobias; Bhattacharyya, Sohinee; Band, Hamid; Barker, Gareth; Bokde, Arun; Buchel, Christian; Carvalho, Fabiana; Conrod, Patricia; Desrivieres, Sylvane; Easton, Alanna; Fauth-Buehler, Mira; Fernandez-Medarde, Alberto; Flor, Herta; Frouin, Vincent; Gallinat, Jurgen; Garavanh, Hugh; Heinz, Andreas; Ittermann, Bernd; Lathrop, Mark; Lawrence, Claire; Loth, Eva; Mann, Karl; Martinot, Jean-Luc; Nees, Frauke; Paus, Tomas; Pausova, Zdenka; Rietschel, Marcella; Rotter, Andrea; Santos, Eugenio; Smolka, Michael; Sommer, Wolfgang; Mameli, Manuel; Spanagel, Rainer; Girault, Jean-Antoine; Mueller, Christian; Schumann, Gunter

    2016-01-01

    dopamine signalling or by the loss of Rasgrf2 function in the NAcc. Conclusion Taken together, our findings indicate that the accumbal M5 module, initially identified as being dysregulated in male Rasgrf2−/− mice, is also relevant for human alcohol-related phenotypes potentially through the modulation of reinforcement mechanisms in the NAcc. We therefore propose that the genes comprising this module represent important candidates for further elucidation within the context of alcohol-related phenotypes. PMID:26679926

  19. Circulating Endocannabinoids and the Polymorphism 385C>A in Fatty Acid Amide Hydrolase (FAAH) Gene May Identify the Obesity Phenotype Related to Cardiometabolic Risk: A Study Conducted in a Brazilian Population of Complex Interethnic Admixture.

    PubMed

    Martins, Cyro José de Moraes; Genelhu, Virginia; Pimentel, Marcia Mattos Gonçalves; Celoria, Bruno Miguel Jorge; Mangia, Rogerio Fabris; Aveta, Teresa; Silvestri, Cristoforo; Di Marzo, Vincenzo; Francischetti, Emilio Antonio

    2015-01-01

    The dysregulation of the endocannabinoid system is associated with cardiometabolic complications of obesity. Allelic variants in coding genes for this system components may contribute to differences in the susceptibility to obesity and related health hazards. These data have mostly been shown in Caucasian populations and in severely obese individuals. We investigated a multiethnic Brazilian population to study the relationships among the polymorphism 385C>A in an endocannabinoid degrading enzyme gene (FAAH), endocannabinoid levels and markers of cardiometabolic risk. Fasting plasma levels of endocannabinoids and congeners (anandamide, 2-arachidonoylglycerol, N-oleoylethanolamide and N-palmitoylethanolamide) were measured by liquid chromatography-mass spectrometry in 200 apparently healthy individuals of both genders with body mass indices from 22.5 ± 1.8 to 35.9 ± 5.5 kg/m2 (mean ± 1 SD) and ages between 18 and 60 years. All were evaluated for anthropometric parameters, blood pressure, metabolic variables, homeostatic model assessment of insulin resistance (HOMA-IR), adiponectin, leptin, C-reactive protein, and genotyping. The endocannabinoid levels increased as a function of obesity and insulin resistance. The homozygous genotype AA was associated with higher levels of anandamide and lower levels of adiponectin versus wild homozygous CC and heterozygotes combined. The levels of anandamide were independent and positively associated with the genotype AA position 385 of FAAH, C-reactive protein levels and body mass index. Our findings provide evidence for an endocannabinoid-related phenotype that may be identified by the combination of circulating anandamide levels with genotyping of the FAAH 385C>A; this phenotype is not exclusive to mono-ethnoracial populations nor to individuals with severe obesity.

  20. Identifiability, exchangeability and confounding revisited

    PubMed Central

    Greenland, Sander; Robins, James M

    2009-01-01

    In 1986 the International Journal of Epidemiology published "Identifiability, Exchangeability and Epidemiological Confounding". We review the article from the perspective of a quarter century after it was first drafted and relate it to subsequent developments on confounding, ignorability, and collapsibility. PMID:19732410

  1. The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant's on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates.

    PubMed

    Wibberg, Daniel; Szczepanowski, Rafael; Eikmeyer, Felix; Pühler, Alfred; Schlüter, Andreas

    2013-03-01

    The IncF antibiotic resistance and virulence plasmid pRSB225, isolated from an unknown bacterium released with the purified wastewater from a municipal sewage treatment plant into the environment has been analysed at the genomic level by pyrosequencing. The 164,550bp plasmid comprises 210 coding sequences (cds). It is composed of three replicons (RepFIA, RepFIB, and RepFII) and encodes further plasmid-specific functions for stable maintenance and inheritance and conjugative plasmid transfer. The plasmid is self-transmissible and shows a narrow host range limited to the family Enterobacteriaceae. The accessory modules of the plasmid mainly comprise genes conferring resistance to ampicillin (bla(TEM-1b)), chloramphenicol (catA1), erythromycin (mphA), kanamycin and neomycin (aphA1), streptomycin (strAB), sulphonamides (sul2), tetracycline (tetA(B)) and trimethoprim (dfrA14), as well as mercuric ions (mer genes). In addition, putative virulence-associated genes coding for iron uptake (iutA/iucABCD, sitABCD, and a putative high-affinity Fe²⁺ uptake system) and for a toxin/antitoxin system (vagCD) were identified on the plasmid. All antibiotic and heavy metal resistance genes are located either on class 1 (Tn10-remnant, Tn4352B) and class 2 transposons (Tn2-remnant, Tn21, Tn402-remnant) or a class 1 integron, whereas almost all putative virulence genes are associated with IS elements (IS1, IS26), indicating that transposition and/or recombination events were responsible for acquisition of the accessory pRSB225 modules. Particular modules of plasmid pRSB225 are related to corresponding segments of different virulence plasmids harboured by pathogenic Escherichia coli strains. Moreover, pRSB225 modules were also detected in entero-aggregative-haemorrhagic E. coli (EAHEC) draft genome sequences suggesting that IncF plasmids related to pRSB225 mediated gene transfer into pathogenic E. coli derivatives. PMID:23212116

  2. Network Topology Analysis of Post-Mortem Brain Microarrays Identifies More Alzheimer’s Related Genes and MicroRNAs and Points to Novel Routes for Fighting with the Disease

    PubMed Central

    Chandrasekaran, Sreedevi; Bonchev, Danail

    2016-01-01

    Network-based approaches are powerful and beneficial tools to study complex systems in their entirety, elucidating the essential factors that turn the multitude of individual elements into a functional system. In this study we used critical network topology descriptors and guilt-by-association rule to explore and understand the significant molecular players, drug targets and underlying biological mechanisms of Alzheimer’s disease. Analyzing two post-mortem brain gene microarrays (GSE4757 and GSE28146) with Pathway Studio software package we constructed and analyzed a set of protein-protein interaction, as well as miRNA-target networks. In a 4-step procedure the expression datasets were normalized using Robust Multi-array Average approach, while the modulation of gene expression by the disease was statistically evaluated by the empirical Bayes method from the limma Bioconductor package. Representative set of 214 seed-genes (p<0.01) common for the three brain sections of the two microarrays was thus created. The Pathway Studio analysis of the networks built identified 15 new potential AD-related genes and 17 novel AD-involved microRNAs. Using KEGG pathways relevant in Alzheimer’s disease we built an integrated mechanistic network from the interactions between the overlapping genes in these pathways. Routes of possible disease initiation process were thus revealed through the CD4, DCN, and IL8 extracellular ligands. DAVID and IPA enrichment analysis uncovered a number of deregulated biological processes and pathways including neuron projection/differentiation, aging, oxidative stress, chemokine/ neurotrophin signaling, long-term potentiation and others. The findings in this study offer information of interest for subsequent experimental studies. PMID:26784894

  3. Dendrogeomorphic approaches for identifying the probable occurrence of debris flows and related torrential processes in steep headwater catchments: The Hrubý Jeseník Mountains, Czech Republic

    NASA Astrophysics Data System (ADS)

    Tichavský, Radek; Šilhán, Karel

    2015-10-01

    Culminating parts of mid-mountain ranges in Central Europe are interwoven by a network of high-gradient streams. These parts, together with the surrounding slopes, form a coupling system in which hazardous geomorphic processes, such as landslides, debris flows or flash floods, can occur. In the case of the Hrubý Jeseník Mountains (Eastern Sudetes, Czech Republic), we present an evaluation of the debris flows and related torrential processes in the high-gradient streams of the selected catchment based on dendrogeomorphic methods. In addition to the classical dendrogeomorphic approaches we refined the procedure of identifying certain and probable events using new weighted indexes for event reconstruction. Additionally, because of the steep narrow channels without a characteristic accumulation cone, a new spatial approach is defined based on the spacing of disturbed trees for each event (random distribution or clustering) and location of disturbed trees in an individual section of the valley floor. Using Kernel Density analysis for each event and calculating the particular grids in ArcGIS software, we are able to describe the spatial reach and probable nature of an event (debris flow or hyperconcentrated flow). Dendrogeomorphic analysis of 397 sampled trees (predominantly coniferous trees) revealed 24 torrential events (15 certain, nine probable) since 1928 with peaks in 1991, 1997 and 2010 according to index values. In addition, the spatial distribution of disturbed trees (grouped in clusters) in these years indicates debris flow events in the upper parts of the catchment. It seems that new dendrogeomorphic approaches should be valuable in remote, steep headwater catchments where several types of processes affect the valley floors.

  4. Helping You Identify Quality Laboratory Services

    MedlinePlus

    Helping You Identify Quality Laboratory Services Selecting quality health care services for yourself, a relative or friend requires special thought and attention. The Joint Commission has prepared ...

  5. Job-Related Stressors of Classical Instrumental Musicians: A Systematic Qualitative Review.

    PubMed

    Vervainioti, A; Alexopoulos, E C

    2015-12-01

    Epidemiological studies among performing artists have found elevated stress levels and health effects, but scarcely the full range of stressors has been reported. We review here the existing literature on job-related stressors of classical instrumental musicians (orchestra musicians). PubMed, Google Scholar and JSTOR databases were screened for relevant papers indexed up to August 2012. A total of 122 papers was initially identified which, after exclusion of duplicates and those not meeting eligibility criteria, yielded 67 articles for final analysis. We identified seven categories of stressors affecting musicians in their everyday working lives: public exposure, personal hazards, repertoire, competition, job context, injury/illness, and criticism, but with interrelated assigned factors. The proposed categories provide a framework for future comprehensive research on the impact and management of musician stressors. PMID:26614973

  6. Job-Related Stressors of Classical Instrumental Musicians: A Systematic Qualitative Review.

    PubMed

    Vervainioti, A; Alexopoulos, E C

    2015-12-01

    Epidemiological studies among performing artists have found elevated stress levels and health effects, but scarcely the full range of stressors has been reported. We review here the existing literature on job-related stressors of classical instrumental musicians (orchestra musicians). PubMed, Google Scholar and JSTOR databases were screened for relevant papers indexed up to August 2012. A total of 122 papers was initially identified which, after exclusion of duplicates and those not meeting eligibility criteria, yielded 67 articles for final analysis. We identified seven categories of stressors affecting musicians in their everyday working lives: public exposure, personal hazards, repertoire, competition, job context, injury/illness, and criticism, but with interrelated assigned factors. The proposed categories provide a framework for future comprehensive research on the impact and management of musician stressors.

  7. Identifying maternal risk factors associated with Fetal Alcohol Spectrum Disorders: a systematic review.

    PubMed

    Esper, Larissa Horta; Furtado, Erikson Felipe

    2014-10-01

    To identify the demographic, psychological, and social maternal risk factors associated with the development of Fetal Alcohol Spectrum Disorders (FASD). A bibliographic search was conducted in PubMed, SciELO, Lilacs, Web of Knowledge, and PsycINFO. The Newcastle-Ottawa Quality Assessment Scale (NOS) was used to evaluate the quality of the studies with case-control design. Articles were selected based on their relevance and presentation of data related to statistical comparisons of at least one or more demographic, psychological, or social maternal risk factors for FASD. 738 references were identified, of which 15 met the criteria to be included in the present review. Mothers of FASD children tend to: be older at the time of birth of the affected child, present lower educational level, have other family relatives with alcohol abuse, have other children with FASD, present a pattern of little prenatal care and a distinguishing pattern of alcohol consumption (alcohol use before and during pregnancy, failure to reduce alcohol use during pregnancy, and frequent episodes of binge drinking). Application of the NOS scale of methodological quality indicated that 8 studies (53 %) met the criterion for selection, 4 (27 %) were suitable for the criterion for comparability and only 4 studies were suitable for the exposition criterion. Mothers of FASD children have a distinctive pattern of drinking and accumulate several social risk factors. Maternal age at birth of the child seems to accentuate the risk. There are, however, few controlled studies that are adequate according to the NOS requirements for methodological quality. Fewer are based on the verification of a theoretical model. Clinicians should be aware of the relevance of preventive assessment of FASD risk mothers.

  8. Metal alloy identifier

    DOEpatents

    Riley, William D.; Brown, Jr., Robert D.

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  9. Identifying and Managing Risk.

    ERIC Educational Resources Information Center

    Abraham, Janice M.

    1999-01-01

    The role of the college or university chief financial officer in institutional risk management is (1) to identify risk (physical, casualty, fiscal, business, reputational, workplace safety, legal liability, employment practices, general liability), (2) to develop a campus plan to reduce and control risk, (3) to transfer risk, and (4) to track and…

  10. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    PubMed

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-01

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  11. Identifying Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Hargraves, Paul E.

    Until recently, anyone who needed to accurately identify marine phytoplankton had one of four choices: use the outdated Englishlanguage volumes by E. E. Cupp and N. I. Hendey plus the more recent book by J. Dodge, acquire a working knowledge of German and use the old volumes by Schiller and Hustedt, spend huge amounts of time in an exceedingly well-equipped marine science library trying in vain to keep up with the rapidly evolving field of phytoplankton systematics and taxonomy, or track down one of the rarest of endangered species—a phytoplankton taxonomist—and beg for help.To these unfortunate choices is added one considerably more hopeful: Identifying Marine Phytoplankton. This volume, which has seven contributing authors, contains most of the taxonomic groups that make up the planktonic autotrophs and some heterotrophs of the seas, coasts, and estuaries of the world (missing are cyanobacteria and some of the picoplankton groups).

  12. On identified predictive control

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  13. Identifying conical singularities

    SciTech Connect

    Oliveira-Neto, G. |

    1996-09-01

    A method based upon the concept of holonomy of a metric space{endash}time ({ital M},{ital g}), in order to identify the presence of conical singularities in {ital M} is proposed. The validity and usefulness of this so-called holonomy method is proven by applying it to a set of four-dimensional space{endash}times and one three-dimensional space{endash}time. The holonomy method predictions are confirmed by the comparison with the predictions obtained after coordinate transformations which take the metrics {ital g}, to a new basis where the global properties of conical singularities are explicitly seen. {copyright} {ital 1996 American Institute of Physics.}

  14. Transcriptional regulators transforming growth factor-β1 and estrogen-related receptor-α identified as putative mediators of calf rumen epithelial tissue development and function during weaning.

    PubMed

    Connor, E E; Baldwin, R L; Walker, M P; Ellis, S E; Li, C; Kahl, S; Chung, H; Li, R W

    2014-07-01

    Molecular mechanisms regulating rumen epithelial development remain largely unknown. To identify gene networks and regulatory factors controlling rumen development, Holstein bull calves (n=18) were fed milk replacer only (MRO) until 42 d of age. Three calves each were euthanized at 14 and 42 d of age for tissue collection to represent preweaning, and the remaining calves were provided diets of either milk replacer + orchard grass hay (MH; n=6) to initiate weaning without development of rumen papillae, or milk replacer + calf starter (MG; n=6) to initiate weaning and development of rumen papillae. At 56 and 70 d of age, 3 calves from the MH and MG groups were euthanized for collection of rumen epithelium. Total RNA and protein were extracted for microarray analysis and to validate detected changes in selected protein expression, respectively. As expected, calves fed MRO had no rumen papillae and development of papillae was greater in MG versus MH calves. Differentially expressed genes between the MRO diet at d 42 (preweaning) versus the MG or MH diets at d 56 (during weaning) were identified using permutation analysis of differential expression. Expression of 345 and 519 transcripts was uniquely responsive to MG and MH feeding, respectively. Ingenuity Pathway Analysis (Qiagen, Redwood City, CA) indicated that the top-ranked biological function affected by the MG diet was the cell cycle, and TFGB1, FBOX01, and PPARA were identified as key transcriptional regulators of genes responsive to the MG diet and associated with development of rumen papillae. Increased expressions of TGFB1 mRNA and protein in response to the MG diet were confirmed by subsequent analyses. The top-ranking biological function affected by the MH diet was energy production. Receptors for IGF-1 and insulin, ESRRA, and PPARD were identified by ingenuity pathway analysis as transcriptional regulators of genes responsive to the MH diet. Further analysis of TGFB1 and ESRRA mRNA expression in rumen

  15. Transcriptional regulators transforming growth factor-β1 and estrogen-related receptor-α identified as putative mediators of calf rumen epithelial tissue development and function during weaning.

    PubMed

    Connor, E E; Baldwin, R L; Walker, M P; Ellis, S E; Li, C; Kahl, S; Chung, H; Li, R W

    2014-07-01

    Molecular mechanisms regulating rumen epithelial development remain largely unknown. To identify gene networks and regulatory factors controlling rumen development, Holstein bull calves (n=18) were fed milk replacer only (MRO) until 42 d of age. Three calves each were euthanized at 14 and 42 d of age for tissue collection to represent preweaning, and the remaining calves were provided diets of either milk replacer + orchard grass hay (MH; n=6) to initiate weaning without development of rumen papillae, or milk replacer + calf starter (MG; n=6) to initiate weaning and development of rumen papillae. At 56 and 70 d of age, 3 calves from the MH and MG groups were euthanized for collection of rumen epithelium. Total RNA and protein were extracted for microarray analysis and to validate detected changes in selected protein expression, respectively. As expected, calves fed MRO had no rumen papillae and development of papillae was greater in MG versus MH calves. Differentially expressed genes between the MRO diet at d 42 (preweaning) versus the MG or MH diets at d 56 (during weaning) were identified using permutation analysis of differential expression. Expression of 345 and 519 transcripts was uniquely responsive to MG and MH feeding, respectively. Ingenuity Pathway Analysis (Qiagen, Redwood City, CA) indicated that the top-ranked biological function affected by the MG diet was the cell cycle, and TFGB1, FBOX01, and PPARA were identified as key transcriptional regulators of genes responsive to the MG diet and associated with development of rumen papillae. Increased expressions of TGFB1 mRNA and protein in response to the MG diet were confirmed by subsequent analyses. The top-ranking biological function affected by the MH diet was energy production. Receptors for IGF-1 and insulin, ESRRA, and PPARD were identified by ingenuity pathway analysis as transcriptional regulators of genes responsive to the MH diet. Further analysis of TGFB1 and ESRRA mRNA expression in rumen

  16. Obesity Educational Interventions in U.S. Medical Schools: A Systematic Review and Identified Gaps

    PubMed Central

    Vitolins, Mara Z.; Crandall, Sonia; Miller, Davis; Ip, Eddie; Marion, Gail; Spangler, John G.

    2013-01-01

    Objective Obesity is the second leading cause of preventable death in the U.S. However, physicians feel poorly trained to address the obesity epidemic. This review examines effective training methods for overweight and obesity intervention in undergraduate medical education. Data Sources Using indexing terms related to overweight, obesity and medical student education, we conducted a literature searched PubMed PsychInfo, Cochrane and ERIC for relevant articles in English. References from articles identified were also reviewed to located additional articles. Review Methods We included all studies that incorporated processor outcome evaluations of obesity educational interventions for US medical students. Of an initial 168 citations, 40 abstracts were retrieved; 11 studies were found to be pertinent to medical student obesity education, but only 5 included intervention and evaluation elements. Quality criteria for inclusion consisted of explicit evaluation of the educational methods used. Data extraction identified participants (e.g., year of medical students), interventions, evaluations and results. Results These five studies successfully used a variety of teaching methods including hands on training, didactic lectures, role playing and standardized patient interaction to increase medical students’ knowledge, attitudes and skills regarding overweight and obesity intervention. Two studies addressed medical student bias towards overweight and obese patients. No studies addressed health disparities in the epidemiology and bias of obesity. Conclusions Despite the commonly cited “obesity epidemic,” there are very few published studies that report the effectiveness of medical school obesity educational programs. Gaps still exist within undergraduate medical education including specific training that addresses obesity and long-term studies showing that such training is retained. PMID:22775792

  17. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  18. A systematic review on skin complications of bone-anchored hearing aids in relation to surgical techniques.

    PubMed

    Mohamad, Shwan; Khan, Imran; Hey, S Y; Hussain, S S Musheer

    2016-03-01

    A systematic review to study the skin complications associated with the bone-anchored hearing aid in relation to surgical techniques. The following databases have been searched: MEDLINE, EMBASE, the Cochrane Library , Google scholar and the PubMed. The literature search date was from January 1977 until November 2013. Randomised controlled trials and retrospective studies were included. Initial search identified 420 publications. Thirty articles met the inclusion criteria of this review. The most common surgical techniques identified were full-thickness skin graft, Dermatome and linear incision techniques. The result shows that dermatome technique is associated with higher rate of skin complications when compared to linear incision and skin graft techniques. Based on the available literature, the use of a linear incision technique appears to be associated with lower skin complications; however, there is limited data available supporting this. Higher quality studies would allow a more reliable comparison between the surgical techniques.

  19. Extreme water-related weather events and waterborne disease.

    PubMed

    Cann, K F; Thomas, D Rh; Salmon, R L; Wyn-Jones, A P; Kay, D

    2013-04-01

    Global climate change is expected to affect the frequency, intensity and duration of extreme water-related weather events such as excessive precipitation, floods, and drought. We conducted a systematic review to examine waterborne outbreaks following such events and explored their distribution between the different types of extreme water-related weather events. Four medical and meteorological databases (Medline, Embase, GeoRef, PubMed) and a global electronic reporting system (ProMED) were searched, from 1910 to 2010. Eighty-seven waterborne outbreaks involving extreme water-related weather events were identified and included, alongside 235 ProMED reports. Heavy rainfall and flooding were the most common events preceding outbreaks associated with extreme weather and were reported in 55·2% and 52·9% of accounts, respectively. The most common pathogens reported in these outbreaks were Vibrio spp. (21·6%) and Leptospira spp. (12·7%). Outbreaks following extreme water-related weather events were often the result of contamination of the drinking-water supply (53·7%). Differences in reporting of outbreaks were seen between the scientific literature and ProMED. Extreme water-related weather events represent a risk to public health in both developed and developing countries, but impact will be disproportionate and likely to compound existing health disparities.

  20. A Metabolomics Study of Retrospective Forensic Data from Whole Blood Samples of Humans Exposed to 3,4-Methylenedioxymethamphetamine: A New Approach for Identifying Drug Metabolites and Changes in Metabolism Related to Drug Consumption.

    PubMed

    Nielsen, Kirstine L; Telving, Rasmus; Andreasen, Mette F; Hasselstrøm, Jørgen B; Johannsen, Mogens

    2016-02-01

    The illicit drug 3,4-methylenedioxymethamphetamine (MDMA) has profound physiological cerebral, cardiac, and hepatic effects that are reflected in the blood. Screening of blood for MDMA and other narcotics are routinely performed in forensics analysis using ultra-performance liquid chromatography with high-resolution time-of-flight mass spectrometry (UPLC-HR-TOFMS). The aim of this study was to investigate whether such UPLC-HR-TOFMS data collected over a two-year period could be used for untargeted metabolomics to determine MDMA metabolites as well as endogenous changes related to drug response and toxicology. Whole blood samples from living Danish drivers' positive for MDMA in different concentrations were compared to negative control samples using various statistical methods. The untargeted identification of known MDMA metabolites was used to validate the methods. The results further revealed changes of several acylcarnitines, adenosine monophosphate, adenosine, inosine, thiomorpholine 3-carboxylate, tryptophan, S-adenosyl-l-homocysteine (SAH), and lysophospatidylcholine (lysoPC) species in response to MDMA. These endogenous metabolites could be implicated in an increased energy demand and mechanisms related to the serotonergic syndrome as well as drug induced neurotoxicity. The findings showed that it was possible to extract meaningful results from retrospective UPLC-HR-TOFMS screening data for metabolic profiling in relation to drug metabolism, endogenous physiological effects, and toxicology. PMID:26705142

  1. Identifying Adolescent Sleep Problems

    PubMed Central

    Short, Michelle A.; Gradisar, Michael; Gill, Jason; Camfferman, Danny

    2013-01-01

    Objectives To examine the efficacy of self-report and parental report of adolescent sleep problems and compare these findings to the incidence of adolescents who fulfill clinical criteria for a sleep problem. Sleep and daytime functioning factors that predict adolescents’ self-identification of a sleep problem will also be examined. Method 308 adolescents (aged 13–17 years) from eight socioeconomically diverse South Australian high schools participated in this study. Participants completed a survey battery during class time, followed by a 7-day Sleep Diary and the Flinders Fatigue Scale completed on the final day of the study. Parents completed a Sleep, Medical, Education and Family History Survey. Results The percentage of adolescents fulfilling one or more of the criteria for a sleep problem was inordinately high at 66%. Adolescent self-reporting a sleep problem was significantly lower than the adolescents who had one or more of the clinical criteria for a sleep problem (23.1% vs. 66.6%; χ2 = 17.46, p<.001). Parental report of their adolescent having a sleep problem was significantly lower than adolescent self-report (14.3% vs. 21.1%, p<.001). Adolescents who reported unrefreshing sleep were 4.81 times more likely to report a sleep problem. For every hour that bedtime was delayed, the odds of self-reporting a sleep problem increased by 1.91 times, while each additional 10 minutes taken to fall asleep increased the odds 1.40 times. Conclusion While many adolescents were found to have sleep patterns indicative of a sleep problem, only a third of this number self-identify having a sleep problem, while only a sixth of this number are indicated by parental report. This study highlights important features to target in future sleep education and intervention strategies for both adolescents and parents. PMID:24086501

  2. Identifying Nearby Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Rathborne, J. M.; Shah, R. Y., Jackson, J. M.; Bania, T. M.; Clemens, D. P.; Johnson, A. M.; Flynn, E.; Bonaventura, N.; Simon, R.; Meyer, M. H.

    2004-12-01

    Recent molecular surveys, such as the BU-FCRAO Galactic Ring Survey, are revealing the complex structure and dynamics of clouds within the Galactic plane. Yet, difficulties often remain in separating molecular clouds along a line of sight. Identification of nearby clouds is facilitated through the combination of molecular datasets and extinction maps. Star counts at optical and infrared (IR) wavelengths indirectly trace extinction, and when morphologically similar to molecular emission, unambiguously reveal nearby clouds. Here we present the methodology and data used to separate and determine the relative distance to two molecular clouds along the same line of sight (GRSMC 45.60+0.30 and GRSMC 45.46+0.05). We use a combination of optical and near-IR star count maps (derived from the US Naval Observatory and 2MASS catalogs, respectively) and molecular data from the BU-FCRAO Galactic Ring Survey.

  3. Epidemiological aspects of rheumatoid arthritis patients affected by oral bisphosphonate-related osteonecrosis of the jaws

    PubMed Central

    2012-01-01

    This literature review aims to evaluate the epidemiologic profile of patients with rheumatoid arthritis (RA) that developed a bisphosphonate-related osteonecrosis that affect the jaws (BRONJ), including demographic aspects, as well as clinical and therapeutic issues. A search of PUBMED/MEDLINE, Scopus, and Cochrane databases from January 2003 to September 2011 was conducted with the objective of identifying publications that contained case reports regarding oral BRONJ in RA patients. Patients with RA who develop oral BRONJ are usually women above 60 years taking steroids and long-term alendronate. Most of them have osteoporosis, and lesions, triggered by dental procedures, are usually detected at stage II in the mandible. Although there is no accepted treatment protocol, these patients seem to have better outcomes with conservative approaches that include antibiotic therapy, chlorhexidine, and drug discontinuation. PMID:22376948

  4. Meteor fireball sounds identified

    NASA Technical Reports Server (NTRS)

    Keay, Colin

    1992-01-01

    Sounds heard simultaneously with the flight of large meteor fireballs are electrical in origin. Confirmation that Extra/Very Low Frequency (ELF/VLF) electromagnetic radiation is produced by the fireball was obtained by Japanese researchers. Although the generation mechanism is not fully understood, studies of the Meteorite Observation and Recovery Project (MORP) and other fireball data indicate that interaction with the atmosphere is definitely responsible and the cut-off magnitude of -9 found for sustained electrophonic sounds is supported by theory. Brief bursts of ELF/VLF radiation may accompany flares or explosions of smaller fireballs, producing transient sounds near favorably placed observers. Laboratory studies show that mundane physical objects can respond to electrical excitation and produce audible sounds. Reports of electrophonic sounds should no longer be discarded. A catalog of over 300 reports relating to electrophonic phenomena associated with meteor fireballs, aurorae, and lightning was assembled. Many other reports have been cataloged in Russian. These may assist the full solution of the similar long-standing and contentious mystery of audible auroral displays.

  5. Repetitive titin epitopes with a 42 nm spacing coincide in relative position with known A band striations also identified by major myosin-associated proteins. An immunoelectron-microscopical study on myofibrils.

    PubMed

    Fürst, D O; Nave, R; Osborn, M; Weber, K

    1989-09-01

    A direct titin-thick filament interaction in certain regions of the A band is suggested by results using four new monoclonal antibodies specific for titin in immunoelectron microscopy. Antibodies T30, T31 and T32 identify quasi-repeats in the titin molecule characterized by a 42-43 nm repeat spacing. These stripes seem to coincide with striations established by others on negatively stained cryosections of the A band. Antibodies T30 and T32 recognize epitopes matching five or two of the seven striations per half sacromere known to harbor both the myosin-associated C-protein and an 86K (K = 10(3) Mr) protein. Antibody T31 labels two stripes in the P zone, which correspond to the two positions where decoration is seen with 86K protein, but not with C-protein. The single titin epitope defined by antibody T33 is located 55 nm prior to the center of the M band. This position seems to coincide with the M7 striation defined by others on negatively stained A bands. The T33 epitope position proves that the titin molecule, which is known to be anchored at the Z line, also penetrates into the complex architecture of the M band. The titin epitopes described here enable us to begin to correlate known ultrastructural aspects of the interior part of the A band with the disposition of the titin molecule in the sarcomere. They raise the question of whether there is a regular interaction pattern between titin and the thick filaments.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Genome-wide screen identifies Escherichia coli TCA cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA

    PubMed Central

    Gonidakis, Stavros; Finkel, Steven E.; Longo, Valter D.

    2010-01-01

    Summary Single-gene mutants with extended lifespan have been described in several model organisms. We performed a genome-wide screen for long-lived mutants in Escherichia coli which revealed strains lacking TCA cycle-related genes that exhibit longer stationary phase survival and increased resistance to heat stress compared to wild-type. Extended lifespan in the sdhA mutant, lacking subunit A of succinate dehydrogenase, is associated with reduced production of superoxide and increased stress resistance. On the other hand, the longer lifespan of the lipoic acid synthase mutant (lipA) is associated with reduced oxygen consumption and requires the acetate-producing enzyme pyruvate oxidase, as well as acetyl-CoA synthetase, the enzyme that converts extracellular acetate to acetyl-CoA. The hypoxia-inducible transcription factor ArcA, acting independently of acetate metabolism, is also required for maximum lifespan extension in the lipA and lpdA mutants, indicating that these mutations promote entry into a mode normally associated with a low-oxygen environment. Since analogous changes from respiration to fermentation have been observed in long-lived Saccharomyces cerevisiae and Caenorhabditis elegans strains, such metabolic alterations may represent an evolutionarily conserved strategy to extend lifespan. PMID:20707865

  7. Identified EM Earthquake Precursors

    NASA Astrophysics Data System (ADS)

    Jones, Kenneth, II; Saxton, Patrick

    2014-05-01

    Many attempts have been made to determine a sound forecasting method regarding earthquakes and warn the public in turn. Presently, the animal kingdom leads the precursor list alluding to a transmission related source. By applying the animal-based model to an electromagnetic (EM) wave model, various hypotheses were formed, but the most interesting one required the use of a magnetometer with a differing design and geometry. To date, numerous, high-end magnetometers have been in use in close proximity to fault zones for potential earthquake forecasting; however, something is still amiss. The problem still resides with what exactly is forecastable and the investigating direction of EM. After a number of custom rock experiments, two hypotheses were formed which could answer the EM wave model. The first hypothesis concerned a sufficient and continuous electron movement either by surface or penetrative flow, and the second regarded a novel approach to radio transmission. Electron flow along fracture surfaces was determined to be inadequate in creating strong EM fields, because rock has a very high electrical resistance making it a high quality insulator. Penetrative flow could not be corroborated as well, because it was discovered that rock was absorbing and confining electrons to a very thin skin depth. Radio wave transmission and detection worked with every single test administered. This hypothesis was reviewed for propagating, long-wave generation with sufficient amplitude, and the capability of penetrating solid rock. Additionally, fracture spaces, either air or ion-filled, can facilitate this concept from great depths and allow for surficial detection. A few propagating precursor signals have been detected in the field occurring with associated phases using custom-built loop antennae. Field testing was conducted in Southern California from 2006-2011, and outside the NE Texas town of Timpson in February, 2013. The antennae have mobility and observations were noted for

  8. 31P MR Spectroscopy and Computational Modeling Identify a Direct Relation between Pi Content of an Alkaline Compartment in Resting Muscle and Phosphocreatine Resynthesis Kinetics in Active Muscle in Humans

    PubMed Central

    van Oorschot, Joep W. M.; Schmitz, Joep P. J.; Webb, Andrew; Nicolay, Klaas; Jeneson, Jeroen A. L.; Kan, Hermien E.

    2013-01-01

    The assessment of mitochondrial properties in skeletal muscle is important in clinical research, for instance in the study of diabetes. The gold standard to measure mitochondrial capacity non-invasively is the phosphocreatine (PCr) recovery rate after exercise, measured by 31P Magnetic Resonance spectroscopy (31P MRS). Here, we sought to expand the evidence base for an alternative method to assess mitochondrial properties which uses 31P MRS measurement of the Pi content of an alkaline compartment attributed to mitochondria (Pi2; as opposed to cytosolic Pi (Pi1)) in resting muscle at high magnetic field. Specifically, the PCr recovery rate in human quadriceps muscle was compared with the signal intensity of the Pi2 peak in subjects with varying mitochondrial content of the quadriceps muscle as a result of athletic training, and the results were entered into a mechanistic computational model of mitochondrial metabolism in muscle to test if the empirical relation between Pi2/Pi1 ratio and the PCr recovery was consistent with theory. Localized 31P spectra were obtained at 7T from resting vastus lateralis muscle to measure the intensity of the Pi2 peak. In the endurance trained athletes a Pi2/Pi1 ratio of 0.07 ± 0.01 was found, compared to a significantly lower (p<0.05) Pi2/Pi1 ratio of 0.03 ± 0.01 in the normally active group. Next, PCr recovery kinetics after in magnet bicycle exercise were measured at 1.5T. For the endurance trained athletes, a time constant τPCr 12 ± 3 s was found, compared to 24 ± 5s in normally active subjects. Without any parameter optimization the computational model prediction matched the experimental data well (r2 of 0.75). Taken together, these results suggest that the Pi2 resonance in resting human skeletal muscle observed at 7T provides a quantitative MR-based functional measure of mitochondrial density. PMID:24098796

  9. A search strategy to identify studies on the prognosis of work disability: a diagnostic test framework

    PubMed Central

    Kok, Rob; Verbeek, Jos A H M; Faber, Babs; van Dijk, Frank J H; Hoving, Jan L

    2015-01-01

    Objective Searching the medical literature for evidence on prognosis is an important aspect of evidence-based disability evaluation. To facilitate this, we aimed to develop and evaluate a comprehensive and efficient search strategy in PubMed, to be used by either researchers or practitioners and that will identify articles on the prognosis of work disability. Methods We used a diagnostic test analytic framework. First, we created a reference set of 225 articles on the prognosis of work disability by screening a total of 65 692 titles and abstracts from10 journals in the period 2000–2009. Included studies had a minimum follow-up of 6 months, participants in the age of 18–64 with a minimum sick leave of 4 weeks or longer or having serious activity limitations in 50% of the cases and outcome measures that reflect impairments, activity limitations or participation restrictions. Using text mining methods, we extracted search terms from the reference set and, according to sensitivity and relative frequency, we combined these into search strings. Results Both the research and the practice search filter outperformed existing filters in occupational health, all combined with the Yale-prognostic filter. The Work Disability Prognosis filter for Research showed a comprehensiveness of 90% (95% CI 86 to 94) and efficiency expressed more user-friendly as Number Needed to Read=20 (95% CI 17 to 34). Conclusions The Work Disability Prognosis filter will help practitioners and researchers who want to find prognostic evidence in the area of work disability evaluation. However, further refining of this filter is possible and needed, especially for the practitioner for whom efficiency is especially important. PMID:25991444

  10. Identifying barriers to billing compliance.

    PubMed

    Lorence, Daniel P; Ibrahim, Ibrahim Awad

    2003-01-01

    Programs designed toward the control of health care fraud are leading to increasingly aggressive enforcement and prosecutorial efforts by federal regulators, related to over-reimbursement for service providers. Greater penalties for fraudulent practices have been touted as an effective deterrent to practices that encourage, or fail to prevent, incorrect claims for reimbursement. In such a context, this study sought to examine the extent of compliance management barriers through a national survey of all accredited US health information managers, examining likely barriers to payment of health care claims. Using data from a series of surveys on the stated compliance actions of more than 16,000 health care managers, we find that the publication and dissemination of compliance enforcement regulations had a significant effect on the reduction of fraud. Results further suggest that significant non-adoption of proper billing compliance measures continues to occur, despite the existence of counter-fraud prosecution risk designed to enforce proper compliance. Finally, we identify benchmarks of compliance management and show how they vary across demographic, practice setting, and market characteristics. We find significant variation in influence across practice settings and managed care markets. While greater publicity related to proper billing procedures generally leads to greater compliance awareness, this trend may have created pockets of "institutional non-compliance," which result in an increase in the prevalence of non-compliant management actions. As a more general proposition, we find that it is not sufficient to consider compliance actions independent of institutional or industry-wide influences. PMID:12967244

  11. TRAINING ERRORS AND RUNNING RELATED INJURIES: A SYSTEMATIC REVIEW

    PubMed Central

    Buist, Ida; Sørensen, Henrik; Lind, Martin; Rasmussen, Sten

    2012-01-01

    Purpose: The purpose of this systematic review was to examine the link between training characteristics (volume, duration, frequency, and intensity) and running related injuries. Methods: A systematic search was performed in PubMed, Web of Science, Embase, and SportDiscus. Studies were included if they examined novice, recreational, or elite runners between the ages of 18 and 65. Exposure variables were training characteristics defined as volume, distance or mileage, time or duration, frequency, intensity, speed or pace, or similar terms. The outcome of interest was Running Related Injuries (RRI) in general or specific RRI in the lower extremity or lower back. Methodological quality was evaluated using quality assessment tools of 11 to 16 items. Results: After examining 4561 titles and abstracts, 63 articles were identified as potentially relevant. Finally, nine retrospective cohort studies, 13 prospective cohort studies, six case-control studies, and three randomized controlled trials were included. The mean quality score was 44.1%. Conflicting results were reported on the relationships between volume, duration, intensity, and frequency and RRI. Conclusion: It was not possible to identify which training errors were related to running related injuries. Still, well supported data on which training errors relate to or cause running related injuries is highly important for determining proper prevention strategies. If methodological limitations in measuring training variables can be resolved, more work can be conducted to define training and the interactions between different training variables, create several hypotheses, test the hypotheses in a large scale prospective study, and explore cause and effect relationships in randomized controlled trials. Level of evidence: 2a PMID:22389869

  12. Laxative Related Primary Hyperphosphatemic Tumoral Calcinosis Identified by Bone Scintigraphy.

    PubMed

    Asokendaran, Marcus; Lenzo, Nat Patrick

    2016-09-01

    We describe a case of a 40-year-old female patient presenting with tumor calcinosis where hypertrophic pulmonary osteoarthropathy (HPOA) was suspected given her extensive history of malignancy. Plain X-rays did not show reveal the typical periarticular calcification but did show appearances consistent with HPOA. Bone scintigraphy with (99m)Tc-methylene diphosphonate (MDP) is a sensitive investigation in the detection of hypertrophic osteoarthopathy but did not show findings characteristics of HPOA like bilateral symmetrical increased uptake of the radiopharmaceutical along the cortical margins of the long bones. The final diagnosis of tumor calcinosis was only made after low dose computerized tomography chest showed a moderated sized amorphous calcified cluster in the apical segment of the right upper lobe consistent. In conclusion, bone scintigraphy continues to be a useful investigation for both common and rare conditions like tumor calcinosis. The unusual three phase bone scan finding of diffuse activity throughout both lung fields, which turned to out to be tumoral calcinosis is highlighted in this case. PMID:27651742

  13. Multiplex PCR Method for Identifying Recombinant Vaccine-Related Polioviruses

    PubMed Central

    Kilpatrick, David R.; Ching, Karen; Iber, Jane; Campagnoli, Ray; Freeman, Christopher J.; Mishrik, Nada; Liu, Hong-Mei; Pallansch, Mark A.; Kew, Olen M.

    2004-01-01

    The recent discovery of recombinant circulating vaccine-derived poliovirus (recombinant cVDPV) has highlighted the need for enhanced global poliovirus surveillance to assure timely detection of any future cVDPV outbreaks. Six pairs of Sabin strain-specific recombinant primers were designed to permit rapid screening for VDPV recombinants by PCR. PMID:15365031

  14. Laxative Related Primary Hyperphosphatemic Tumoral Calcinosis Identified by Bone Scintigraphy

    PubMed Central

    Asokendaran, Marcus; Lenzo, Nat Patrick

    2016-01-01

    We describe a case of a 40-year-old female patient presenting with tumor calcinosis where hypertrophic pulmonary osteoarthropathy (HPOA) was suspected given her extensive history of malignancy. Plain X-rays did not show reveal the typical periarticular calcification but did show appearances consistent with HPOA. Bone scintigraphy with 99mTc-methylene diphosphonate (MDP) is a sensitive investigation in the detection of hypertrophic osteoarthopathy but did not show findings characteristics of HPOA like bilateral symmetrical increased uptake of the radiopharmaceutical along the cortical margins of the long bones. The final diagnosis of tumor calcinosis was only made after low dose computerized tomography chest showed a moderated sized amorphous calcified cluster in the apical segment of the right upper lobe consistent. In conclusion, bone scintigraphy continues to be a useful investigation for both common and rare conditions like tumor calcinosis. The unusual three phase bone scan finding of diffuse activity throughout both lung fields, which turned to out to be tumoral calcinosis is highlighted in this case. PMID:27651742

  15. Laxative Related Primary Hyperphosphatemic Tumoral Calcinosis Identified by Bone Scintigraphy

    PubMed Central

    Asokendaran, Marcus; Lenzo, Nat Patrick

    2016-01-01

    We describe a case of a 40-year-old female patient presenting with tumor calcinosis where hypertrophic pulmonary osteoarthropathy (HPOA) was suspected given her extensive history of malignancy. Plain X-rays did not show reveal the typical periarticular calcification but did show appearances consistent with HPOA. Bone scintigraphy with 99mTc-methylene diphosphonate (MDP) is a sensitive investigation in the detection of hypertrophic osteoarthopathy but did not show findings characteristics of HPOA like bilateral symmetrical increased uptake of the radiopharmaceutical along the cortical margins of the long bones. The final diagnosis of tumor calcinosis was only made after low dose computerized tomography chest showed a moderated sized amorphous calcified cluster in the apical segment of the right upper lobe consistent. In conclusion, bone scintigraphy continues to be a useful investigation for both common and rare conditions like tumor calcinosis. The unusual three phase bone scan finding of diffuse activity throughout both lung fields, which turned to out to be tumoral calcinosis is highlighted in this case.

  16. Sports-related injuries in athletes with disabilities.

    PubMed

    Fagher, K; Lexell, J

    2014-10-01

    The number of athletes with disabilities participating in organized sports and the popularity of the Paralympic Games is steadily increasing around the world. Despite this growing interest and the fact that participation in sports places the athlete at risk for injury, there are few studies concerning injury patterns, risk factors, and prevention strategies of injuries in disabled athletes. In this systematic literature search and critical review, we summarize current knowledge of the epidemiology of sports-related injuries in disabled athletes and describe their characteristics, incidence, prevalence, and prevention strategies. The outcomes of interest were any injury, either an acute trauma or an overuse event. PubMed, EMBASE, CINAHL, and Google Scholar were systematically searched and 25 of 605 identified studies met the inclusion criteria. Lower extremity injuries were more common in walking athletes, whereas upper extremity injuries were more prevalent in wheelchair athletes. The methodologies and populations varied widely between the studies. Few studies were sports or disability specific, which makes it difficult to determine specific risk factors, and few studies reported injury severity and prevention of injuries. Further longitudinal, systematic sports and disability specific studies are needed in order to identify and prevent injuries in athletes with disabilities.

  17. Isolated myocardial bridging and exercise-related cardiac events.

    PubMed

    Gowd, B M P; Thompson, P D

    2014-12-01

    Myocardial bridging, which is defined as cardiac muscle overlying a part of a coronary artery, is the most common congenital coronary artery anomaly. Myocardial bridging is usually benign, but has been associated with exercise-related cardiac events. Guidelines for athletic participation in these patients are primarily based on reports from the general population with myocardial bridging. We performed a systematic literature search of PubMed, Ovid and Google Scholar for articles addressing exercise-related cardiac events associated with myocardial bridging. We identified 69 cases of which only 35 were well defined. We conclude that there are insufficient data to form definitive guidelines as to how physically active individuals with myocardial bridging should be managed. Prudence suggests that management should be individualized for those with possible symptoms. Beta adrenergic blockade is recommended as initial medical therapy. Surgery should be restricted to those with continued symptoms despite beta blocker therapy. There is no evidence that asymptomatic individuals without clinical evidence of ischemia should be restricted from vigorous activity. PMID:25144435

  18. Stochastic control system parameter identifiability

    NASA Technical Reports Server (NTRS)

    Lee, C. H.; Herget, C. J.

    1975-01-01

    The parameter identification problem of general discrete time, nonlinear, multiple input/multiple output dynamic systems with Gaussian white distributed measurement errors is considered. The knowledge of the system parameterization was assumed to be known. Concepts of local parameter identifiability and local constrained maximum likelihood parameter identifiability were established. A set of sufficient conditions for the existence of a region of parameter identifiability was derived. A computation procedure employing interval arithmetic was provided for finding the regions of parameter identifiability. If the vector of the true parameters is locally constrained maximum likelihood (CML) identifiable, then with probability one, the vector of true parameters is a unique maximal point of the maximum likelihood function in the region of parameter identifiability and the constrained maximum likelihood estimation sequence will converge to the vector of true parameters.

  19. Identifying the Culturally Different Gifted Student.

    ERIC Educational Resources Information Center

    Chambers, Jack A.; Barron, Frank

    The study was designed to provide a relatively simple method of identifying gifted Mexican-American elementary school children, using as Ss approximately 298 Mexican-Americans (in grades 3-6) from both urban and rural schools. Ss were rated by present and former teachers on traits found to be characteristic of highly creative and talented…

  20. Identifying Ethical Hypernorms for Accounting Educators

    ERIC Educational Resources Information Center

    Siegel, Philip H.; Mintz, Steven; Naser-Tavakolian, Mohsen; O'Shaughnessy, John

    2012-01-01

    Accounting educators have a unique role in academe because students learn about codes of ethics that will guide their actions as professionals. We identify hypernorms related to internal auditing educators that reflect unethical behaviors believed to be universally unacceptable by that community. We then compare the results to a prior survey of…

  1. Identifying signs of intimate partner violence.

    PubMed

    Ali, Parveen; McGarry, Julie; Dhingra, Katie

    2016-02-01

    Intimate partner violence is a major public health and social problem that affects people everywhere. Nurses can play an important role in identifying victims who present to healthcare settings with domestic abuse-related health issues. Evidence suggests that most women who present to emergency departments have experienced domestic abuse at some point in their lives, but that only 5% are identified by healthcare professionals. To identify and respond to victims effectively, emergency nurses must understand domestic abuse and its associated complexities. This article provides an overview of these issues, including the different types of abuse, and their prevalence, causes and effects on health. The article also explores how emergency nurses can identify and manage the effects of violence at work. PMID:26853673

  2. Health-related quality of life in atrial fibrillation patients over 65 years: A review.

    PubMed

    Zhang, Ling; Gallagher, Robyn; Neubeck, Lis

    2015-08-01

    Atrial fibrillation is the most common sustained cardiac arrhythmia affecting 1-2% of the population; the prevalence of atrial fibrillation increases with ageing. The condition is associated with high morbidity and mortality, as well as reduced health-related quality of life, particularly in older people. A PubMed, CINAHL, EMBASE and CENTRAL search (January 2003 to April 2013) was conducted using the search terms atrial fibrillation, quality of life, health-related quality of life, older, aged, and over 65 years. In total, 572 papers were identified of which 15 were eligible, including three observational studies, five descriptive comparative studies and seven randomized control trials. Older atrial fibrillation patients (≥65 years) were significantly impaired in their health-related quality of life in both physical and mental domains compared to the general population or patients with sinus rhythm. Increasing age, being female or having severe symptoms resulted in poorer health-related quality of life particularly in the physical domain. The review also found that the current treatment of AF including rate and rhythm control strategies improved some aspects of health-related quality of life in atrial fibrillation patients but no specific strategy had a superior effect.

  3. A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes

    PubMed Central

    Zhao, Min; Liu, Yining; Huang, Fuda; Qu, Hong

    2016-01-01

    Colorectal cancer (CRC) is a cancer of growing incidence that associates with a high mortality rate worldwide. There is a poor understanding of the heterogeneity of CRC with regard to causative genetic mutations and gene regulatory mechanisms. Previous studies have identified several susceptibility genes in small-scale experiments. However, the information has not been comprehensively and systematically compiled and interpreted. In this study, we constructed the gbCRC, the first literature-based gene resource for investigating CRC-related human genes. The features of our database include: (i) manual curation of experimentally-verified genes reported in the literature; (ii) comprehensive integration of five reliable data sources; and (iii) pre-computed regulatory patterns involving transcription factors, microRNAs and long non-coding RNAs. In total, 2067 genes associating with 2819 PubMed abstracts were compiled. Comprehensive functional annotations associated with all the genes, including gene expression profiles, homologous genes in other model species, protein-protein interactions, somatic mutations, and potential methylation sites. These comprehensive annotations and this pre-computed regulatory information highlighted the importance of the gbCRC with regard to the unexplored regulatory network of CRC. This information is available in a plain text format that is free to download. PMID:27477450

  4. A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes.

    PubMed

    Zhao, Min; Liu, Yining; Huang, Fuda; Qu, Hong

    2016-01-01

    Colorectal cancer (CRC) is a cancer of growing incidence that associates with a high mortality rate worldwide. There is a poor understanding of the heterogeneity of CRC with regard to causative genetic mutations and gene regulatory mechanisms. Previous studies have identified several susceptibility genes in small-scale experiments. However, the information has not been comprehensively and systematically compiled and interpreted. In this study, we constructed the gbCRC, the first literature-based gene resource for investigating CRC-related human genes. The features of our database include: (i) manual curation of experimentally-verified genes reported in the literature; (ii) comprehensive integration of five reliable data sources; and (iii) pre-computed regulatory patterns involving transcription factors, microRNAs and long non-coding RNAs. In total, 2067 genes associating with 2819 PubMed abstracts were compiled. Comprehensive functional annotations associated with all the genes, including gene expression profiles, homologous genes in other model species, protein-protein interactions, somatic mutations, and potential methylation sites. These comprehensive annotations and this pre-computed regulatory information highlighted the importance of the gbCRC with regard to the unexplored regulatory network of CRC. This information is available in a plain text format that is free to download. PMID:27477450

  5. Identifying Occupationally Specific Affective Behaviors.

    ERIC Educational Resources Information Center

    Pucel, David J.

    1993-01-01

    Data from two groups of cosmetology instructors (n=15) and two groups of machinist instructors (n=17) validated the Occupational Affective Behavior Analysis instrument as capable of identifying affective behaviors viewed as important to success in a given occupation. (SK)

  6. Health-Related Quality of Life (HRQoL) in Idiopathic Inflammatory Myopathy: A Systematic Review

    PubMed Central

    Regardt, Malin; Wojcik, Sophie

    2016-01-01

    Health-related quality of life (HRQoL) is a research priority in chronic diseases. We undertook a systematic review (registration #CRD42015024939) to identify, appraise and synthesize the evidence relating to HRQoL in idiopathic inflammatory myopathies (IIM). A comprehensive search was conducted in August 2015 using CINAHL, EMBase and Pubmed to identify studies reporting original data on HRQoL in IIM using generic HRQoL instruments. Characteristics of samples and results from selected studies were extracted and appraised using a standardized approach. Qualitative synthesis of the results was performed. Ten studies including a total of 654 IIM subjects were included in this systematic review. HRQoL was significantly impaired in all subsets of IIM compared with the general population. Disease activity, disease damage and chronic disease course were associated with poorer HRQoL. Insufficient or conflicting results were found in associations between clinical features, treatment, disease duration and mood or illness perception, and HRQoL in IIM. This study suggests that HRQoL is impaired in IIM. However, due to the paucity and heterogeneity of the evidence to date, robust estimates are lacking and significant knowledge gaps persist. There is a need for studies that systematically investigate the correlates and trajectory of HRQoL in IIM. PMID:27504827

  7. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base. PMID:23615061

  8. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base.

  9. An unsupervised text mining method for relation extraction from biomedical literature.

    PubMed

    Quan, Changqin; Wang, Meng; Ren, Fuji

    2014-01-01

    The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein-protein interactions extraction, and (2) Gene-suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene-suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method.

  10. MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline

    PubMed Central

    Kim, Jung-jae; Pȩzik, Piotr; Rebholz-Schuhmann, Dietrich

    2008-01-01

    Summary: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however, have limitations when applied for the task of seeking textual evidence of relations between given concepts. The limitations are mainly due to the problem that the search engines do not effectively deal with multi-term queries which may imply semantic relations between the terms. To address this problem, we present MedEvi, a novel search engine that imposes positional restriction on occurrences matching multi-term queries, based on the observation that terms with semantic relations which are explicitly stated in text are not found too far from each other. MedEvi further identifies additional keywords of biological and statistical significance from local context of matching occurrences in order to help users reformulate their queries for better results. Availability: http://www.ebi.ac.uk/tc-test/textmining/medevi/ Contact: kim@ebi.ac.uk PMID:18400773

  11. Scientometric methods for identifying emerging technologies

    DOEpatents

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2015-11-03

    Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

  12. "Geriatricizing" Hospitalists: Identifying Educational Opportunities

    ERIC Educational Resources Information Center

    Friedman, Susan M.; Gillespie, Suzanne M.; Medina-Walpole, Annette M.; Caprio, Thomas V.; Karuza, Jurgis; McCann, Robert M.

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in…

  13. Identifying Intellectually Superior Black Children.

    ERIC Educational Resources Information Center

    Ryan, Judith S.

    1983-01-01

    The effectiveness of several methods used to identify intellectually superior black children was evaluated. Findings suggest that less commonly used identification methods, such as parents' opinion and the Leiter International Performance Scale, may point out these children more accurately than do traditional measures. (Author/PP)

  14. Identifying the Gifted Child Humorist.

    ERIC Educational Resources Information Center

    Fern, Tami L.

    1991-01-01

    This study attempted to identify gifted child humorists among 1,204 children in grades 3-6. Final identification of 13 gifted child humorists was determined through application of such criteria as funniness, originality, and exemplary performance or product. The influence of intelligence, development, social factors, sex differences, family…

  15. Identifying Innovative Agricultural Education Programs

    ERIC Educational Resources Information Center

    Rayfield, John; Murphy, Tim; Briers, Gary; Lewis, Lauren

    2012-01-01

    Researchers identified innovative agricultural education programs across the United States. A Delphi study was conducted with the teachers in innovative programs. According to the teachers, innovative programs in 2020 will use hands-on activities and will be run by highly motivated teachers. The purpose of innovative programs in the future will be…

  16. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, V.A.; Ward, M.B.

    1991-03-26

    A finely detailed diffraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the diffraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figures.

  17. Identifying glass compositions in fly ash

    NASA Astrophysics Data System (ADS)

    Aughenbaugh, Katherine; Stutzman, Paul; Juenger, Maria

    2016-01-01

    In this study, four Class F fly ashes were studied with a scanning electron microscope; the glassy phases were identified and their compositions quantified using point compositional analysis with k-means clustering and multispectral image analysis. The results showed that while the bulk oxide contents of the fly ashes were different, the four fly ashes had somewhat similar glassy phase compositions. Aluminosilicate glasses (AS), calcium aluminosilicate glasses (CAS), a mixed glass, and, in one case, a high iron glass were identified in the fly ashes. Quartz and iron crystalline phases were identified in each fly ash as well. The compositions of the three main glasses identified, AS, CAS, and mixed glass, were relatively similar in each ash. The amounts of each glass were varied by fly ash, with the highest calcium fly ash containing the most of calcium-containing glass. Some of the glasses were identified as intermixed in individual particles, particularly the calcium-containing glasses. Finally, the smallest particles in the fly ashes, with the most surface area available to react in alkaline solution, such as when mixed with portland cement or in alkali-activated fly ash, were not different in composition than the large particles, with each of the glasses represented. The method used in the study may be applied to a fly ash of interest for use as a cementing material in order to understand its potential for reactivity.

  18. [Identifying victims of a disaster].

    PubMed

    de Boer, Hans H; Kloosterman, Ate D; de Bruijn, Arie G; Maat, George J R

    2014-01-01

    Identifying the victims of a disaster is important for the next of kin, to issue a death certificate and, if necessary, for forensic investigations. In the Netherlands victims are identified by the Dutch disaster victim identification team, which is part of the national forensic investigation team ('Landelijk Team Forensische Opsporing'). Ante-mortem data are collected during the identification process; these include the victim's specific medical characteristics and the DNA profile of the victim and their family members. The victim's own doctor can play an important role in the ante-mortem investigation because of his or her knowledge of their personal medical details, and of the possible availability of samples for establishing a DNA profile. The ante-mortem data are then compared with post-mortem data. For a definitive identification at least 1 primary identification characteristic has to be established from the physical remains - dermatoglyphics, the DNA profile or the dental status.

  19. Identifying and managing problem drinkers.

    PubMed Central

    Kahan, M.

    1996-01-01

    Problem drinking is far more common than severe alcohol dependence and is associated with considerable morbidity and health care costs. Whereas patients with alcohol dependence respond best to intensive treatment, one or more brief sessions of physician advice and counseling reduces alcohol consumption among problem drinkers. The two most useful tools to identify problem drinkers are the CAGE and the drinking problem question. PMID:8653034

  20. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  1. Identifying Topics in Microblogs Using Wikipedia

    PubMed Central

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  2. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail.

  3. Identifying new targets in leukemogenesis using computational approaches.

    PubMed

    Jayaraman, Archana; Jamil, Kaiser; Khan, Haseeb A

    2015-09-01

    There is a need to identify novel targets in Acute Lymphoblastic Leukemia (ALL), a hematopoietic cancer affecting children, to improve our understanding of disease biology and that can be used for developing new therapeutics. Hence, the aim of our study was to find new genes as targets using in silico studies; for this we retrieved the top 10% overexpressed genes from Oncomine public domain microarray expression database; 530 overexpressed genes were short-listed from Oncomine database. Then, using prioritization tools such as ENDEAVOUR, DIR and TOPPGene online tools, we found fifty-four genes common to the three prioritization tools which formed our candidate leukemogenic genes for this study. As per the protocol we selected thirty training genes from PubMed. The prioritized and training genes were then used to construct STRING functional association network, which was further analyzed using cytoHubba hub analysis tool to investigate new genes which could form drug targets in leukemia. Analysis of the STRING protein network built from these prioritized and training genes led to identification of two hub genes, SMAD2 and CDK9, which were not implicated in leukemogenesis earlier. Filtering out from several hundred genes in the network we also found MEN1, HDAC1 and LCK genes, which re-emphasized the important role of these genes in leukemogenesis. This is the first report on these five additional signature genes in leukemogenesis. We propose these as new targets for developing novel therapeutics and also as biomarkers in leukemogenesis, which could be important for prognosis and diagnosis.

  4. Systematic review of employer-sponsored wellness strategies and their economic and health-related outcomes.

    PubMed

    Kaspin, Lisa C; Gorman, Kathleen M; Miller, Ross M

    2013-02-01

    This review determines the characteristics and health-related and economic outcomes of employer-sponsored wellness programs and identifies possible reasons for their success. PubMed, ABI/Inform, and Business Source Premier databases, and Corporate Wellness Magazine were searched. English-language articles published from 2005 to 2011 that reported characteristics of employer-sponsored wellness programs and their impact on health-related and economic outcomes among US employees were accepted. Data were abstracted, synthesized, and interpreted. Twenty references were accepted. Wellness interventions were classified into health assessments, lifestyle management, and behavioral health. Improved economic outcomes were reported (health care costs, return on investment, absenteeism, productivity, workers' compensation, utilization) as well as decreased health risks. Programs associated with favorable outcomes had several characteristics in common. First, the corporate culture encouraged wellness to improve employees' lives, not only to reduce costs. Second, employees and leadership were strongly motivated to support the wellness programs and to improve their health in general. Third, employees were motivated by a participation-friendly corporate policy and physical environment. Fourth, successful programs adapted to the changing needs of the employees. Fifth, community health organizations provided support, education, and treatment. Sixth, successful wellness programs utilized technology to facilitate health risk assessments and wellness education. Improved health-related and economic outcomes were associated with employer-sponsored wellness programs. Companies with successful programs tended to include wellness as part of their corporate culture and supported employee participation in several key ways.

  5. Systematic review of employer-sponsored wellness strategies and their economic and health-related outcomes.

    PubMed

    Kaspin, Lisa C; Gorman, Kathleen M; Miller, Ross M

    2013-02-01

    This review determines the characteristics and health-related and economic outcomes of employer-sponsored wellness programs and identifies possible reasons for their success. PubMed, ABI/Inform, and Business Source Premier databases, and Corporate Wellness Magazine were searched. English-language articles published from 2005 to 2011 that reported characteristics of employer-sponsored wellness programs and their impact on health-related and economic outcomes among US employees were accepted. Data were abstracted, synthesized, and interpreted. Twenty references were accepted. Wellness interventions were classified into health assessments, lifestyle management, and behavioral health. Improved economic outcomes were reported (health care costs, return on investment, absenteeism, productivity, workers' compensation, utilization) as well as decreased health risks. Programs associated with favorable outcomes had several characteristics in common. First, the corporate culture encouraged wellness to improve employees' lives, not only to reduce costs. Second, employees and leadership were strongly motivated to support the wellness programs and to improve their health in general. Third, employees were motivated by a participation-friendly corporate policy and physical environment. Fourth, successful programs adapted to the changing needs of the employees. Fifth, community health organizations provided support, education, and treatment. Sixth, successful wellness programs utilized technology to facilitate health risk assessments and wellness education. Improved health-related and economic outcomes were associated with employer-sponsored wellness programs. Companies with successful programs tended to include wellness as part of their corporate culture and supported employee participation in several key ways. PMID:23113636

  6. Differential Adverse Event Profiles Associated with BCG as a Preventive Tuberculosis Vaccine or Therapeutic Bladder Cancer Vaccine Identified by Comparative Ontology-Based VAERS and Literature Meta-Analysis

    PubMed Central

    Xie, Jiangan; Codd, Christopher; Mo, Kevin; He, Yongqun

    2016-01-01

    M. bovis strain Bacillus Calmette–Guérin (BCG) has been the only licensed live attenuated vaccine against tuberculosis (TB) for nearly one century and has also been approved as a therapeutic vaccine for bladder cancer treatment since 1990. During its long time usage, different adverse events (AEs) have been reported. However, the AEs associated with the BCG preventive TB vaccine and therapeutic cancer vaccine have not been systematically compared. In this study, we systematically collected various BCG AE data mined from the US VAERS database and PubMed literature reports, identified statistically significant BCG-associated AEs, and ontologically classified and compared these AEs related to these two types of BCG vaccine. From 397 VAERS BCG AE case reports, we identified 64 AEs statistically significantly associated with the BCG TB vaccine and 14 AEs with the BCG cancer vaccine. Our meta-analysis of 41 peer-reviewed journal reports identified 48 AEs associated with the BCG TB vaccine and 43 AEs associated with the BCG cancer vaccine. Among all identified AEs from VAERS and literature reports, 25 AEs belong to serious AEs. The Ontology of Adverse Events (OAE)-based ontological hierarchical analysis indicated that the AEs associated with the BCG TB vaccine were enriched in immune system (e.g., lymphadenopathy and lymphadenitis), skin (e.g., skin ulceration and cyanosis), and respiratory system (e.g., cough and pneumonia); in contrast, the AEs associated with the BCG cancer vaccine mainly occurred in the urinary system (e.g., dysuria, pollakiuria, and hematuria). With these distinct AE profiles detected, this study also discovered three AEs (i.e., chills, pneumonia, and C-reactive protein increased) shared by the BCG TB vaccine and bladder cancer vaccine. Furthermore, our deep investigation of 24 BCG-associated death cases from VAERS identified the important effects of age, vaccine co-administration, and immunosuppressive status on the final BCG-associated death

  7. Identifying Network Perturbation in Cancer

    PubMed Central

    Logsdon, Benjamin A.; Gentles, Andrew J.; Lee, Su-In

    2016-01-01

    We present a computational framework, called DISCERN (DIfferential SparsE Regulatory Network), to identify informative topological changes in gene-regulator dependence networks inferred on the basis of mRNA expression datasets within distinct biological states. DISCERN takes two expression datasets as input: an expression dataset of diseased tissues from patients with a disease of interest and another expression dataset from matching normal tissues. DISCERN estimates the extent to which each gene is perturbed—having distinct regulator connectivity in the inferred gene-regulator dependencies between the disease and normal conditions. This approach has distinct advantages over existing methods. First, DISCERN infers conditional dependencies between candidate regulators and genes, where conditional dependence relationships discriminate the evidence for direct interactions from indirect interactions more precisely than pairwise correlation. Second, DISCERN uses a new likelihood-based scoring function to alleviate concerns about accuracy of the specific edges inferred in a particular network. DISCERN identifies perturbed genes more accurately in synthetic data than existing methods to identify perturbed genes between distinct states. In expression datasets from patients with acute myeloid leukemia (AML), breast cancer and lung cancer, genes with high DISCERN scores in each cancer are enriched for known tumor drivers, genes associated with the biological processes known to be important in the disease, and genes associated with patient prognosis, in the respective cancer. Finally, we show that DISCERN can uncover potential mechanisms underlying network perturbation by explaining observed epigenomic activity patterns in cancer and normal tissue types more accurately than alternative methods, based on the available epigenomic data from the ENCODE project. PMID:27145341

  8. Energy Contribution and Nutrient Composition of Breakfast and Their Relations to Overweight in Free-living Individuals: A Systematic Review.

    PubMed

    Rosato, Valentina; Edefonti, Valeria; Parpinel, Maria; Milani, Gregorio Paolo; Mazzocchi, Alessandra; Decarli, Adriano; Agostoni, Carlo; Ferraroni, Monica

    2016-05-01

    Previous systematic reviews on the relation between overweight or obesity and breakfast focused on the frequency of consumption and only partially accounted for breakfast nutritional profiles. Given the central role of these factors, we conducted a systematic review of the literature on this putative relation, with a specific focus on breakfast energy intake and/or breakfast composition. Among the 814 articles identified from the literature search in PubMed, 19, mostly cross-sectional, studies met the inclusion criteria (i.e., studies providing a quantitative estimate of the relation between any measure of weight, overweight, and obesity and breakfast energy intake or breakfast macronutrient composition). We excluded studies in subjects with acquired metabolic disorders, such as diabetes or impaired glucose tolerance. Of the 16 studies that evaluated the amount of energy intake at breakfast, 4 found that a lower energy intake at breakfast was significantly associated with obesity in children, adolescents, and adults, whereas 2 partially overlapping studies found that a higher energy intake was significantly associated with a higher body mass index in children. Of the 8 studies investigating breakfast composition, 3 suggested that a breakfast characterized by a higher amount of carbohydrates and a lower amount of fat is significantly related to normal weight in adults, whereas the others reported mixed results. In conclusion, there is some evidence that a lower energy intake at breakfast is related to obesity, although the studies are few and heterogeneous. Studies on the nutrient composition of breakfast have shown inconsistent results.

  9. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R.M.; Grand, J.B.; Fondell, T.F.; Miller, David A.

    2006-01-01

    We used cameras and artificial eggs to identify nest predators of dusky Canada goose Branta canadensis occidentalis nests during 1997-2000. Cameras were set up at 195 occupied goose nests and 60 artificial nests. We placed wooden eggs and domestic goose eggs that were emptied and then filled with wax or foam in an additional 263 natural goose nests to identify predators from marks in the artificial eggs. All techniques had limitations, but each correctly identified predators and estimated their relative importance. Nests with cameras had higher rates of abandonment than natural nests, especially during laying. Abandonment rates were reduced by deploying artificial eggs late in laying and reducing time at nests. Predation rates for nests with cameras were slightly lower than for nests without cameras. Wax-filled artificial eggs caused mortality of embryos in natural nests, but were better for identifying predator marks at artificial nests. Use of foam-filled artificial eggs in natural nests was the most cost effective means of monitoring nest predation. ?? Wildlife Biology (2006).

  10. Odor recognition: familiarity, identifiability, and encoding consistency.

    PubMed

    Rabin, M D; Cain, W S

    1984-04-01

    The investigation examined the association between the perceived identity of odorous stimuli and the ability to recognize the previous occurrence of them. The stimuli comprised 20 relatively familiar odorous objects such as chocolate, leather, popcorn, and soy sauce. Participants rated the familiarity of the odors and sought to identify them. At various intervals up to 7 days after initial inspection, the participants sought to recognize the odors among sets of distractor odors that included such items as soap, cloves, pipe tobacco, and so on. The recognition response entailed a confidence rating as to whether or not an item had appeared in the original set. At the time of testing, the participants also sought to identify the stimuli again. The results upheld previous findings of excellent initial recognition memory for environmentally relevant odors and slow forgetting. The results also uncovered, for the first time, a strong association between recognition memory and identifiability, rated familiarity, and the ability to use an odor label consistently at inspection and subsequent testing. Encodability seems to enhance rather than to permit recognizability. Even items identified incorrectly or inconsistently were recognized at levels above chance.

  11. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental.

  12. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental. PMID:20628167

  13. A scoping study to identify opportunities to advance the ethical implementation and scale-up of HIV treatment as prevention: priorities for empirical research

    PubMed Central

    2014-01-01

    Background Despite the evidence showing the promise of HIV treatment as prevention (TasP) in reducing HIV incidence, a variety of ethical questions surrounding the implementation and “scaling up” of TasP have been articulated by a variety of stakeholders including scientists, community activists and government officials. Given the high profile and potential promise of TasP in combatting the global HIV epidemic, an explicit and transparent research priority-setting process is critical to inform ongoing ethical discussions pertaining to TasP. Methods We drew on the Arksey and O’Malley framework for conducting scoping review studies as well as systematic approaches to identifying empirical and theoretical gaps within ethical discussions pertaining to population-level intervention implementation and scale up. We searched the health science database PubMed to identify relevant peer-reviewed articles on ethical and implementation issues pertaining to TasP. We included English language articles that were published after 2009 (i.e., after the emergence of causal evidence within this field) by using search terms related to TasP. Given the tendency for much of the criticism and support of TasP to occur outside the peer-reviewed literature, we also included grey literature in order to provide a more exhaustive representation of how the ethical discussions pertaining to TasP have and are currently taking place. To identify the grey literature, we systematically searched a set of search engines, databases, and related webpages for keywords pertaining to TasP. Results Three dominant themes emerged in our analysis with respect to the ethical questions pertaining to TasP implementation and scale-up: (a) balancing individual- and population-level interests; (b) power relations within clinical practice and competing resource demands within health care systems; (c) effectiveness considerations and socio-structural contexts of HIV treatment experiences within broader

  14. Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years

    PubMed Central

    Keim, Paul; Grunow, Roland; Vipond, Richard; Grass, Gregor; Hoffmaster, Alex; Birdsell, Dawn N.; Klee, Silke R.; Pullan, Steven; Antwerpen, Markus; Bayer, Brittany N.; Latham, Jennie; Wiggins, Kristin; Hepp, Crystal; Pearson, Talima; Brooks, Tim; Sahl, Jason; Wagner, David M.

    2015-01-01

    Government of Germany. This work was supported by funds from the German Ministry of Defense (Sonderforschungsprojekt 25Z1-S-431,214). Support for sequencing was also obtained from Illumina, Inc. These sources had no role in the data generation or interpretation, and had not role in the manuscript preparation. Panel 1: Research in Context Systematic Review We searched PubMed for any article published before Jun. 17, 2015, with the terms “Bacillus anthracis” and “heroin”, or “injectional anthrax”. Other than our previously published work (Price et al., 2012), we found no other relevant studies on elucidating the global phylogenetic relationships of B. anthracis strains associated with injectional anthrax caused by recreational heroin consumption of spore-contaminated drug. There were, however, publically available genome sequences of two strains involved (Price et al., 2012, Grunow et al., 2013) and the draft genome sequence of Bacillus anthracis UR-1, isolated from a German heroin user (Ruckert et al., 2012) with only limited information on the genotyping of closely related strains (Price et al., 2012, Grunow et al., 2013). Lay Person Interpretation Injectional anthrax has been plaguing heroin drug users across Europe for more than 10 years. In order to better understand this outbreak, we assessed genomic relationships of all available injectional anthrax strains from four countries spanning a > 12 year period. Very few differences were identified using genome-based analysis, but these differentiated the isolates into two distinct clusters. This strongly supports a hypothesis of at least two separate anthrax spore contamination events perhaps during the drug production processes. Identification of two events would not have been possible from standard epidemiological analysis. These comprehensive data will be invaluable for classifying future injectional anthrax isolates and for future geographic attribution. PMID:26870786

  15. Guidelines for identifying suspect/counterfeit material

    SciTech Connect

    1995-09-01

    These guidelines are intended to assist users of products in identifying: substandard, misrepresented, or fraudulently marked items. The guidelines provide information about such topics as: precautions, inspection and testing, dispositioning identified items, installed inspection and reporting suspect/counterfeit materials. These guidelines apply to users who are developing procurement documents, product acceptance/verification methods, company procedures, work instructions, etc. The intent of these SM guidelines in relation to the Quality Assurance Program Description (QAPD) and implementing company Management Control Procedures is not to substitute or replace existing requirements, as defined in either the QAPD or company implementing instructions (Management Control Procedures). Instead, the guidelines are intended to provide a consolidated source of information addressing the issue of Suspect/Counterfeit materials. These guidelines provide an extensive suspect component listing and suspect indications listing. Users can quickly check their suspect items against the list of manufacturers products (i.e., type, LD. number, and nameplate information) by consulting either of these listings.

  16. [Interface between bioethics and international relations].

    PubMed

    Manchola-Castillo, Camilo; Garrafa, Volnei

    2016-08-01

    Recently, bioethics and international relations have gotten closer to one an other, probably as a result of the motivation of bioethics to intervene in global affairs. However, this relationship has only been on the practical level.This study's objective, through a literature review, is to highlight the huge potential that the epistemologies of both areas have to build a more fruitful dialogue. 18 articles relating both areas were retrieved from databases Scopus, Web of Science, Bireme and PubMed. The articles were then grouped in three categories of analysis: bioethics and global health; international organizations and bioethics; and international relations and bioethics. This study concludes that an epistemological approaching between these areas is desirable and proposes the establishment of two new areas of study: international relations in health and international relations from the South, drawing upon the conceptual basis developed by Latin-American bioethics. PMID:27599082

  17. "Geriatricizing" hospitalists: identifying educational opportunities.

    PubMed

    Friedman, Susan M; Gillespie, Suzanne M; Medina-Walpole, Annette M; Caprio, Thomas V; Karuza, Jurgis; McCann, Robert M

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in caring for hospitalized older adults, targeting areas previously defined as central to taking care of older hospitalized patients. Overall, geriatricians had more confidence and more knowledge in caring for older hospitalized adults. The areas in which hospitalists expressed the least confidence were in caring for patients with dementia, self-care issues, and care planning. Geriatricians reported more routine medication reviews, functional and cognitive assessments, and fall evaluations. Geriatricians and hospitalists differ in their approach to older adults. Where these differences reflect lack of knowledge or experience, they set the stage for developing curricula to help narrow these gaps. PMID:23971409

  18. Important caves to be identified

    NASA Astrophysics Data System (ADS)

    Criteria to identify significant caves on federal land are being developed by the Interior Department's Bureau of Land Management and the Agriculture Department's Forest Service under requirements of the Federal Cave Resources Protection Act of 1988. The departments gave advance notice of proposed rulemaking March 3 and invited suggestions and comments from the public for 30 days.The law requires protection, to the extent practical, of significant caves on lands administered by the Secretaries of Agriculture and Interior and includes authority to issue and revoke permits for collection and removal of cave resources and special provisions for regulation of cave resources on Indian lands. Final regulations must be published by August 18, 1989.

  19. Identifying vulnerable surface water utilities

    SciTech Connect

    Clark, R.M.; Grayman, W.M.; Males, R.M.; Kilgore, R.

    1989-01-01

    Although industrial discharges from point sources are regulated by the Federal Water Pollution Control Acts, National Pollutant Discharge Elimination System (NPDES), some toxic pollutants continue to be discharged into surface waters. Frequently these same surface waters are major sources of drinking water. The Safe Drinking Water Act Amendments have specified a large number of new contaminant levels, (MCLs) at the microgram per liter level. It is possible that many water utilities finding that these new MCLs are violated will seek to identify upstream dischargers and request that regulatory agencies force them to install discharge controls rather than pay for expensive water treatment processes. The study reported in the paper documents the development of a data base management system and a water quality modeling approach that allows drinking water utilities to assess the impact of these upstream discharges on raw water quality. The report makes recommendations to USEPA for modifying its NPDES procedures.

  20. Identifying methamphetamine exposure in children

    PubMed Central

    Castaneto, Marisol S.; Barnes, Allan J.; Scheidweiler, Karl B.; Schaffer, Michael; Rogers, Kristen K.; Stewart, Deborah; Huestis, Marilyn A.

    2013-01-01

    Introduction Methamphetamine (MAMP) use, distribution and manufacture remain a serious public health and safety problem in the United States, and children environmentally exposed to MAMP face a myriad of developmental, social and health risks, including severe abuse and neglect necessitating child protection involvement. It is recommended that drug-endangered children receive medical evaluation and care with documentation of overall physical and mental conditions and have urine drug testing.1 The primary aim of this study was to determine the best biological matrix to detect MAMP, amphetamine (AMP), methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA) and methylenedioxyethylamphetamine (MDEA) in environmentally exposed children. Method 91 children, environmentally exposed to household MAMP intake, were medically evaluated at the Child and Adolescent Abuse Resource and Evaluation (CAARE) Diagnostic and Treatment Center at the University of California, Davis (UCD) Children's Hospital. MAMP, AMP, MDMA, MDA and MDEA were quantified in urine and oral fluid (OF) by gas chromatography mass spectrometry (GCMS) and in hair by liquid chromatography tandem mass spectrometry (LCMSMS). Results Overall drug detection rates in OF, urine and hair were 6.9%, 22.1% and 77.8%, respectively. Seventy children (79%) tested positive for 1 or more drugs in 1 or more matrices. MAMP was the primary analyte detected in all 3 biological matrices. All positive OF (n=5) and 18 of 19 positive urine specimens also had a positive hair test. Conclusion Hair analysis offered a more sensitive tool for identifying MAMP, AMP and MDMA environmental exposure in children than urine or OF testing. A negative urine, or hair test does not exclude the possibility of drug exposure, but hair testing provided the greatest sensitivity for identifying drug-exposed children. PMID:24263642

  1. Characteristics of binge eating disorder in relation to diagnostic criteria.

    PubMed

    Wilfley, Denise E; Citrome, Leslie; Herman, Barry K

    2016-01-01

    The objective of this review was to examine the evidentiary basis for binge eating disorder (BED) with reference to the Diagnostic and Statistical Manual of Mental Disorders - Fifth Edition (DSM-5) diagnostic criteria for BED. A PubMed search restricted to titles and abstracts of English-language reviews, meta-analyses, clinical trials, randomized controlled trials, journal articles, and letters using human participants was conducted on August 7, 2015, using keywords that included "binge eating disorder," DSM-5, DSM-IV, guilt, shame, embarrassment, quantity, psychological, behavior, and "shape and weight concerns." Of the 257 retrieved publications, 60 publications were considered relevant to discussions related to DSM-5 diagnostic criteria and were included in the current review, and 20 additional references were also included on the basis of the authors' knowledge and/or on a review of the reference lists from relevant articles obtained through the literature search. Evidence supports the duration/frequency criterion for BED and the primary importance of loss of control and marked distress in identifying individuals with BED. Although overvaluation of shape/weight is not a diagnostic criterion, its relationship to the severity of BED psychopathology may identify a unique subset of individuals with BED. Additionally, individuals with BED often exhibit a clinical profile consisting of psychiatric (eg, mood, obsessive-compulsive, and impulsive disorders) and medical (eg, gastrointestinal symptoms, metabolic syndrome, and type 2 diabetes) comorbidities and behavioral profiles (eg, overconsumption of calories outside of a binge eating episode and emotional eating). Future revisions of the BED diagnostic criteria should consider the inclusion of BED subtypes, perhaps based on the overvaluation of shape/weight, and an evidence-based reassessment of severity criteria. PMID:27621631

  2. Characteristics of binge eating disorder in relation to diagnostic criteria

    PubMed Central

    Wilfley, Denise E; Citrome, Leslie; Herman, Barry K

    2016-01-01

    The objective of this review was to examine the evidentiary basis for binge eating disorder (BED) with reference to the Diagnostic and Statistical Manual of Mental Disorders – Fifth Edition (DSM-5) diagnostic criteria for BED. A PubMed search restricted to titles and abstracts of English-language reviews, meta-analyses, clinical trials, randomized controlled trials, journal articles, and letters using human participants was conducted on August 7, 2015, using keywords that included “binge eating disorder,” DSM-5, DSM-IV, guilt, shame, embarrassment, quantity, psychological, behavior, and “shape and weight concerns.” Of the 257 retrieved publications, 60 publications were considered relevant to discussions related to DSM-5 diagnostic criteria and were included in the current review, and 20 additional references were also included on the basis of the authors’ knowledge and/or on a review of the reference lists from relevant articles obtained through the literature search. Evidence supports the duration/frequency criterion for BED and the primary importance of loss of control and marked distress in identifying individuals with BED. Although overvaluation of shape/weight is not a diagnostic criterion, its relationship to the severity of BED psychopathology may identify a unique subset of individuals with BED. Additionally, individuals with BED often exhibit a clinical profile consisting of psychiatric (eg, mood, obsessive–compulsive, and impulsive disorders) and medical (eg, gastrointestinal symptoms, metabolic syndrome, and type 2 diabetes) comorbidities and behavioral profiles (eg, overconsumption of calories outside of a binge eating episode and emotional eating). Future revisions of the BED diagnostic criteria should consider the inclusion of BED subtypes, perhaps based on the overvaluation of shape/weight, and an evidence-based reassessment of severity criteria. PMID:27621631

  3. Prevalence of musculoskeletal disorders and related occupational causative factors among electricity linemen: A narrative review.

    PubMed

    Padmanathan, Vinothini; Joseph, Leonard; Omar, Baharudin; Nawawi, Roslizawati

    2016-01-01

    Occupational tasks of linemen are highly associated with the development of work related musculoskeletal disorders (WRMDs). Although linemen are prone to develop WRMDs, there is paucity of information on the prevalence of WRMDs and related occupational causative factors. Therefore, the present review was conducted to report on the prevalence of WRMDs and to outline causative risk factors within occupational tasks in the lineman profession. Literature search was conducted in various databases such as Scopus, PubMed and ScienceDirect for articles published between 1996-2013. The articles were analyzed, selected and retrieved based on predetermined objectives, inclusion criteria and Medical Subject Headings (MeSH). In the review process only articles published in English were considered. The review identified moderate to high prevalence of WRMDs among the linemen population. Back and shoulder regions were highly affected compared to the other body regions. The review also reported occupational tasks such as bar installation, insulator fixation and manual handling of tools as high risk tasks that lead to the development of WRMDs. In addition, occupational tools such as ladders, manual cutters and manual presses were also identified as a potential ergonomic hazard. In conclusion, the current review identified that WRMDs are common in the back and shoulder regions among linemen. Also, a number of occupational risk factors were identified to be associated with WRMDs among the linemen. Hence, future research on prevention and intervention studies concerning lineman profession population in order to develop a good job practice are recommended. Int J Occup Med Environ Health 2016;29(5):725-734.

  4. Prevalence of musculoskeletal disorders and related occupational causative factors among electricity linemen: A narrative review.

    PubMed

    Padmanathan, Vinothini; Joseph, Leonard; Omar, Baharudin; Nawawi, Roslizawati

    2016-01-01

    Occupational tasks of linemen are highly associated with the development of work related musculoskeletal disorders (WRMDs). Although linemen are prone to develop WRMDs, there is paucity of information on the prevalence of WRMDs and related occupational causative factors. Therefore, the present review was conducted to report on the prevalence of WRMDs and to outline causative risk factors within occupational tasks in the lineman profession. Literature search was conducted in various databases such as Scopus, PubMed and ScienceDirect for articles published between 1996-2013. The articles were analyzed, selected and retrieved based on predetermined objectives, inclusion criteria and Medical Subject Headings (MeSH). In the review process only articles published in English were considered. The review identified moderate to high prevalence of WRMDs among the linemen population. Back and shoulder regions were highly affected compared to the other body regions. The review also reported occupational tasks such as bar installation, insulator fixation and manual handling of tools as high risk tasks that lead to the development of WRMDs. In addition, occupational tools such as ladders, manual cutters and manual presses were also identified as a potential ergonomic hazard. In conclusion, the current review identified that WRMDs are common in the back and shoulder regions among linemen. Also, a number of occupational risk factors were identified to be associated with WRMDs among the linemen. Hence, future research on prevention and intervention studies concerning lineman profession population in order to develop a good job practice are recommended. Int J Occup Med Environ Health 2016;29(5):725-734. PMID:27518883

  5. Preventing and managing aberrant drug-related behavior in primary care: systematic review of outcomes evidence.

    PubMed

    Argoff, Charles E; Kahan, Meldon; Sellers, Edward M

    2014-01-01

    Several strategies for preventing, identifying, and responding to aberrant opioid-related behaviors are recommended in pain management guidelines. This systematic review evaluated data supporting basic strategies for addressing aberrant opioid-related behaviors. Risk reduction strategies were identified via a review of available guidelines. Systematic literature searches of PubMed (May 1, 2007-January 18, 2013) identified articles with evidence relevant to nine basic strategies. Reference lists from relevant articles were reviewed for additional references of interest. Levels of evidence for articles identified were graded on a four-point scale (strongest evidence = level 1; weakest evidence = level 4) using Oxford Centre for Evidence-Based Medicine Levels of Evidence criteria. Weak to moderate evidence supports the value of thorough patient assessment, risk-screening tools, controlled-substance agreements, careful dose titration, opioid dose ceilings, compliance monitoring, and adherence to practice guidelines. Moderate to strong evidence suggests that prescribing tamper-resistant opioids may help prevent misuse but may also have the unintended consequence of prompting a migration of users to other marketed opioids, heroin, or other substances. Similarly, preliminary evidence suggests that although recent regulatory and legal efforts may reduce misuse, they also impose barriers to the legitimate treatment of pain. Despite an absence of consistent, strong supporting evidence, clinicians are advised to use each of the available risk-mitigation strategies in combination in an attempt to minimize the risk of abuse in opioid treatment patients. Physicians must critically evaluate their opioid prescribing and not only increase their efforts to prevent substance abuse but also not compromise pain management in patients who benefit from it.