WorldWideScience

Sample records for research identified specific

  1. Identifying specific interstellar polycyclic aromatic hydrocarbons

    International Nuclear Information System (INIS)

    Mulas, Giacomo; Malloci, Giuliano; Porceddu, Ignazio

    2005-01-01

    Interstellar Polycyclic Aromatic Hydrocarbons (PAHs) have been thought to be ubiquitous for more than twenty years, yet no single species in this class has been identified in the Interstellar Medium (ISM) to date. The unprecedented sensitivity and resolution of present Infrared Space Observatory (ISO) and forthcoming Herschel observations in the far infrared spectral range will offer a unique way out of this embarrassing impasse

  2. NIH Researchers Identify OCD Risk Gene

    Science.gov (United States)

    ... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

  3. Water resources management in Tanzania: identifying research ...

    African Journals Online (AJOL)

    This paper aims at identifying research gaps and needs and recommendations for a research agenda on water resources management in Tanzania. We reviewed published literature on water resources management in Tanzania in order to highlight what is currently known, and to identify knowledge gaps, and suggest ...

  4. Development of technical specifications for research reactors

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    This standard identifies and establishes the content of technical specifications for research reactors. Areas addressed are: definitions, safety limits, limiting safety system settings, limiting conditions for operation, surveillance requirements, design features and administrative controls. Sufficient detail is incorporated so that applicable specifications can be derived or extracted

  5. Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities.

    Science.gov (United States)

    Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B; Papamarkou, Theodore; Huber, Kilian V M; Mutz, Cornelia; Toretsky, Jeffrey A; Bennett, Keiryn L; Olsen, Jesper V; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio

    2017-01-01

    Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR. ©2016 American Association for Cancer Research.

  6. Identifying subgroups of CERME affect research papers

    OpenAIRE

    Hannula, Markku S.; Garcia Moreno-Esteva, Enrique

    2017-01-01

    Research in mathematics related affect uses a variety of theoretical frameworks. Three different dimensions have been suggested as significant to characterize concepts in this area: (1) emotional, motivational, and cognitive aspects of affect, (2) state and trait aspects of affect, and (3) physiological, psychological, and sociological level of theorizing affect. In this study, we used the information in reference lists and graph theory to identify Graph Communities (coherent clusters) of res...

  7. Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

    DEFF Research Database (Denmark)

    Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

    2017-01-01

    Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

  8. Research on minimum sound specifications for hybrid and electric vehicles

    Science.gov (United States)

    2012-06-30

    This report documents research by the National Highway Traffic Safety Administration (NHTSA) to identify ways : to develop sound specifications for electric and hybrid vehicles. The research was conducted to support activities : related to the implem...

  9. Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

    DEFF Research Database (Denmark)

    Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

    2017-01-01

    Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

  10. Identifying the Gender Dimension in Research Content

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, D.; Lalonde, B.St.L.; Tippett, C.; Archambault, E.; Callaert, J.; Mantouvalou, K.; Arora, L.

    2016-07-01

    Globally, there is an increasing interest in integrating the gender dimension in research content (GDRC). As a first step towards monitoring progress in this area, a new indicator measuring the proportion of a country’s scientific publications integrating a gender dimension in their subject matter was developed for the European Commission’s She Figures 2015 publication. This indicator is based on a keyword-based query covering both sex-related terms (biological characteristics of both women and men) and gender-related terms (social/cultural factors of both women and men). The final GDRC dataset consisted of some 212,600 distinct publications including a gender dimension in their research content. Findings suggest that integrating a gender dimension into research content is relatively rare. Unsurprisingly, it was less common for scientific articles in the fields of agricultural sciences, engineering and technology, and natural sciences to do so, and more common in the social sciences. (Author)

  11. Identifying and addressing specific student difficulties in advanced thermal physics

    Science.gov (United States)

    Smith, Trevor I.

    As part of an ongoing multi-university research study on student understanding of concepts in thermal physics at the upper division, I identified several student difficulties with topics related to heat engines (especially the Carnot cycle), as well as difficulties related to the Boltzmann factor. In an effort to address these difficulties, I developed two guided-inquiry worksheet activities (a.k.a. tutorials) for use in advanced undergraduate thermal physics courses. Both tutorials seek to improve student understanding of the utility and physical background of a particular mathematical expression. One tutorial focuses on a derivation of Carnot's theorem regarding the limit on thermodynamic efficiency, starting from the Second Law of Thermodynamics. The other tutorial helps students gain an appreciation for the origin of the Boltzmann factor and when it is applicable; focusing on the physical justification of its mathematical derivation, with emphasis on the connections between probability, multiplicity, entropy, and energy. Student understanding of the use and physical implications of Carnot's theorem and the Boltzmann factor was assessed using written surveys both before and after tutorial instruction within the advanced thermal physics courses at the University of Maine and at other institutions. Classroom tutorial sessions at the University of Maine were videotaped to allow in-depth scrutiny of student successes and failures following tutorial prompts. I also interviewed students on various topics related to the Boltzmann factor to gain a more complete picture of their understanding and inform tutorial revisions. Results from several implementations of my tutorials at the University of Maine indicate that students did not have a robust understanding of these physical principles after lectures alone, and that they gain a better understanding of relevant topics after tutorial instruction; Fisher's exact tests yield statistically significant improvement at the

  12. Technical specifications: Health Physics Research Reactor

    International Nuclear Information System (INIS)

    1986-03-01

    These technical specifications define the key limitations that must be observed for safe operation of the Health Physics Research Reactor (HPRR) and an envelope of operation within which there is assurance that these limits will not be exceeded

  13. Technical specifications: Health Physics Research Reactor

    International Nuclear Information System (INIS)

    1979-02-01

    The technical specifications define the key limitations that must be observed for safe operation of the Health Physics Research Reactor (HPRR) and an envelope of operation within which there is assurance that these limits will not be exceeded. The specifications were written to satisfy the requirements of the Department of Energy (DOE) Manual Chapter 0540, September 1, 1972

  14. Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar.

    Science.gov (United States)

    Ko, Jae-Heung; Kim, Hyun-Tae; Hwang, Ildoo; Han, Kyung-Hwan

    2012-06-01

    Plant biotechnology offers a means to create novel phenotypes. However, commercial application of biotechnology in crop improvement programmes is severely hindered by the lack of utility promoters (or freedom to operate the existing ones) that can drive gene expression in a tissue-specific or temporally controlled manner. Woody biomass is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, developing xylem (DX)-specific modification of the feedstock is highly desirable. To develop utility promoters that can drive transgene expression in a DX-specific manner, we used the Affymetrix Poplar Genome Arrays to obtain tissue-type-specific transcriptomes from poplar stems. Subsequent bioinformatics analysis identified 37 transcripts that are specifically or strongly expressed in DX cells of poplar. After further confirmation of their DX-specific expression using semi-quantitative PCR, we selected four genes (DX5, DX8, DX11 and DX15) for in vivo confirmation of their tissue-specific expression in transgenic poplars. The promoter regions of the selected DX genes were isolated and fused to a β-glucuronidase (GUS)-reported gene in a binary vector. This construct was used to produce transgenic poplars via Agrobacterium-mediated transformation. The GUS expression patterns of the resulting transgenic plants showed that these promoters were active in the xylem cells at early seedling growth and had strongest expression in the developing xylem cells at later growth stages of poplar. We conclude that these DX promoters can be used as a utility promoter for DX-specific biomass engineering. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  15. Research Priorities for Fertility and Conception Research as Identified by Multidisciplinary Health Care Practitioners and Researchers

    Directory of Open Access Journals (Sweden)

    Lisa J. Moran

    2016-01-01

    Full Text Available The Robinson Research Institute of the University of Adelaide convened a multidisciplinary group of n = 33 clinicians, researchers and representatives of government organisations on the 2 October 2014 for a workshop entitled “Promoting fertility and healthy conception. How do we generate greater reproductive health awareness?” The key aim of the workshop was to assess the body of knowledge that informs clinical practice and government policy, and to identify questions and additional information needed by health practitioners and government representatives working in the field of reproductive health and to frame future research and policy. The workshop identified topics that fell mostly into three categories: lifestyle-related, societal and biological factors. The lifestyle topics included nutrition and diet, exercise, obesity, shift work and other factors deemed to be modifiable at the level of the individual. The societal topics included discussions of matters that are structural, and resistant to change by individuals, including specific ethical issues, social disadvantage, government and educational policies. The biological factors are intrinsic physical states of the individual, and included many factors where there is a dense body of scientific knowledge which may not be readily accessible in less academic language. This workshop thus provided an opportunity to identify further actions that could be undertaken to meet the needs of diverse organisations and groups of professionals with an interest in human fertility. Since so many factors in our social and biological environment can impact fertility and preconception health, it is imperative to involve many disciplines or levels of government or societal organisations that have not traditionally been involved in this area.

  16. Helping Practitioners and Researchers Identify and Use Education Research Literature

    Science.gov (United States)

    Wilson, Kristy J.; Brame, Cynthia J.

    2018-01-01

    Evidence-based teaching practices are being encouraged to increase student skills and understanding in the sciences. Finding, interpreting, and applying education literature to a specific context are barriers to adopting these evidence-based practices. Here, we introduce a new feature, "Evidence-Based Teaching Guides." This feature…

  17. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

    Science.gov (United States)

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  18. Utilization of genomic signatures to identify phenotype-specific drugs.

    Directory of Open Access Journals (Sweden)

    Seiichi Mori

    2009-08-01

    Full Text Available Genetic and genomic studies highlight the substantial complexity and heterogeneity of human cancers and emphasize the general lack of therapeutics that can match this complexity. With the goal of expanding opportunities for drug discovery, we describe an approach that makes use of a phenotype-based screen combined with the use of multiple cancer cell lines. In particular, we have used the NCI-60 cancer cell line panel that includes drug sensitivity measures for over 40,000 compounds assayed on 59 independent cells lines. Targets are cancer-relevant phenotypes represented as gene expression signatures that are used to identify cells within the NCI-60 panel reflecting the signature phenotype and then connect to compounds that are selectively active against those cells. As a proof-of-concept, we show that this strategy effectively identifies compounds with selectivity to the RAS or PI3K pathways. We have then extended this strategy to identify compounds that have activity towards cells exhibiting the basal phenotype of breast cancer, a clinically-important breast cancer characterized as ER-, PR-, and Her2- that lacks viable therapeutic options. One of these compounds, Simvastatin, has previously been shown to inhibit breast cancer cell growth in vitro and importantly, has been associated with a reduction in ER-, PR- breast cancer in a clinical study. We suggest that this approach provides a novel strategy towards identification of therapeutic agents based on clinically relevant phenotypes that can augment the conventional strategies of target-based screens.

  19. What do medical students understand by research and research skills? Identifying research opportunities within undergraduate projects.

    Science.gov (United States)

    Murdoch-Eaton, Deborah; Drewery, Sarah; Elton, Sarah; Emmerson, Catherine; Marshall, Michelle; Smith, John A; Stark, Patsy; Whittle, Sue

    2010-01-01

    Undergraduate research exposure leads to increased recruitment into academic medicine, enhanced employability and improved postgraduate research productivity. Uptake of undergraduate research opportunities is reported to be disappointing, and little is known about how students perceive research. To investigate opportunities for undergraduate participation in research, recognition of such opportunities, and associated skills development. A mixed method approach, incorporating student focus and study groups, and documentary analysis at five UK medical schools. Undergraduates recognised the benefits of acquiring research skills, but identified practical difficulties and disadvantages of participating. Analysis of 905 projects in four main research skill areas - (1) research methods; (2) information gathering; (3) critical analysis and review; (4) data processing - indicated 52% of projects provided opportunities for students to develop one or more skills, only 13% offered development in all areas. In 17%, project descriptions provided insufficient information to determine opportunities. Supplied with information from a representative sample of projects (n = 80), there was little consensus in identifying skills among students or between students and researchers. Consensus improved dramatically following guidance on how to identify skills. Undergraduates recognise the benefits of research experience but need a realistic understanding of the research process. Opportunities for research skill development may not be obvious. Undergraduates require training to recognise the skills required for research and enhanced transparency in potential project outcomes.

  20. Identifying and Researching Market Opportunities for New High Technology Products.

    Science.gov (United States)

    Dunstan, Peter

    Using a product called the synchro-pulse welder as a case study example, this paper discusses the activities of CSIRO (Commonwealth Scientific and Industrial Research Organisation) in identifying and marketing new high-technology products. A general discussion of CSIRO's market research plans includes two goals to be attained within the next 5…

  1. Investigations regarding the lowering of specific intellectual property risks identified in the production process

    Directory of Open Access Journals (Sweden)

    Pakocs Ramona

    2017-01-01

    Full Text Available The main purpose of this research is to decrease the emergence of specific intellectual property risks within the production process as well as increasing risk management performance of IP by preventing them. In order to achieve this, previous studies regarding the main specific intellectual property risks from industrial companies were analyzed together with their managerial methods as well as the possibility of reducing their emergence. As a result of the research conducted were identified five types of intellectual property risks that have a high potential of emergence in the production process, namely: the risk of production of goods in violation of IP rights; the know-how, production knowledge and trade secret disclosure risk; the technological risk of unprotected utility models; the technological risk of unprotected integrated circuits topographies and finally the risk of product counterfeit. In order to achieve the main purpose of our investigation, we have proposed new formulas for estimating the specific intellectual property risks identified in the production process. Their purpose was to minimalize the risk’s negative effects on industrial companies and to increase the managerial performance from the intellectual property domain through a new type of management appropriately named: intellectual property management. The research is finalized with a case study regarding the lapse of rights of a patented invention. Based on a case analysis, it was proved that the exploitation of an invention without a contract represents a counterfeit.

  2. Review panel comments on geomedia specific research

    International Nuclear Information System (INIS)

    Heath, C.A.

    1984-01-01

    This includes remarks made by three panel members concerning geomedia-specific repository relevant research. The scientific work in the materials area has progressed significantly. Investigators are showing a better understanding of the importance of groundwater compositions. Significant attention is being paid to the importance of colloids and complexing agents. Good planning seems to be in evidence in the Nevada program. Much cooperation and planning in the materials program is needed. Requirements concerning the performance of waste management systems were included. Other topics discussed at the symposium were interactive testing of waste forms, canister materials, and repository rock. Characterization of the chemical and physical environment in the near-field was considered by several speakers. These papers and discussions were part of the Seventh International Symposium on the Scientific Ban's for Nuclear Waste Management

  3. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.

    Directory of Open Access Journals (Sweden)

    Dunja Knapp

    Full Text Available Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

  4. Research Note Identifying key grazing indicators to monitor trends in ...

    African Journals Online (AJOL)

    Research Note Identifying key grazing indicators to monitor trends in the veld condition of Lambert's Bay Strandveld, South Africa. ... from which a minimum number of species necessary to monitor trends in the condition of the veld were determined, making it user-friendly for land-users, extension officers and others. The key ...

  5. Researchers Develop Method to Identify Sparticles in Big Bang Conditions

    CERN Multimedia

    2008-01-01

    Three Northeastern University researchers have proposed a new approach for the highly anticipated discovery of supersymmetric particles, often called sparticles. The methodology, which was published in the December 21 issue of the Physical Review Letters, is based on identifying the hierarchical mass patterns of sparticles, which are assumed to exist in a new class of particle physics theories beyond the Standard Model.

  6. Radioactivity and United Kingdom estuaries: an overview identifying research priorities

    International Nuclear Information System (INIS)

    Hamilton, E.I.; Clifton, R.J.; Stevens, H.E.

    1985-05-01

    The report consists of the results of an evaluation of research priorities for the environmental radioactivity of estuaries, (and near shore waters) of the United Kingdom. The format of this report is:(i) general conclusions for the future requirements for research in the field of environmental radioactivity; (ii) an overview of some specific recommendations for research; and (iii) an appendix in which a comprehensive evaluation of the research priorities for specific areas of research are given. On the basis that man is the prime target for concern and protection, special attention has been given to the environment in the vicinity of the British Nuclear Fuels (BNFL) reprocessing plant at Sellafield, Cumbria, which is the source of major releases of a variety of radionuclides into the natural environment. Subjects covered in the Appendix are: site factors; pathways to man; source term; hot particles; terrestrial inputs; surveys and monitoring; analysis; organics; field versus laboratory data; biology; bioaccumulation factors; some bioaccumulators of radioactivity; bioturbation; bacteria; genetics; natural change; sediment; resuspension; surfaces; Ksub(d) factors; pore liquids; diagenesis and the ageing processes; airborne transport of radionuclides; models; natural radioactivity; public opinion; recreation; the ICRP; the ALARA principle; decommissioning of nuclear power stations; identification of research requirements; environmental radioactivity - the national effort. (U.K.)

  7. ASPECTS REGARDING NEUROMARKETING SPECIFIC RESEARCH METHODS

    Directory of Open Access Journals (Sweden)

    MIRELA-CRISTINA VOICU

    2012-05-01

    Full Text Available Information is one of the most important resources that a company must posses. Some informations are hidden deep in the black box - the mind of the consumer. Neuromarketing helps us find what is inside of the black box without troubling the consumer with questions that he doesn’t want to answer or that he can’t answer. Today because of an extensive research in mapping cortical and subcortical activity in association with behaviors and thoughts, the confidence in neurological data is growing. Thanks to discoveries in perceptual sciences we can identify the parts of the brain that are responsible for the phenomena that we experience daily. For all those interested in information obtained through neuromarketing techniques it becomes evident that there are corresponding neural substrates of consumer decision making process and these substrates can be observed, measured, and possibly manipulated. The following paper reveals some important aspects of the use of neuromarketing in studying consumer behavior by presenting the concepts, methods and techniques used under this sophisticated name, the limitations and advantages of using neuromarketing techniques and the importance of this type of information in decision making process at a company level.

  8. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.

    Science.gov (United States)

    Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O'Connor, Timothy D; Abecasis, Gonçalo R; Wojcik, Genevieve L; Gignoux, Christopher R; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E; Bustamante, Carlos; Beaty, Terri H; Mathias, Rasika A; Barnes, Kathleen C; Qin, Zhaohui S

    2017-04-21

    A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

  9. Top IS research on quality of transaction standards: a structured literature review to identify a research gap

    OpenAIRE

    Folmer, E.J.A.; Berends, W.; Oude Luttighuis, P.; Hillegersberg, J. van

    2009-01-01

    This paper contains the results of a systematic literature review executed to determine the coverage of transaction standards in top information systems (IS) and management journals. Specifically, it aims to identify a research gap with respect to this topic. The top 25 journals are thoroughly searched and the selected publications are classified in order to make grounded statements. A moderate amount of literature found specifically aims at transaction standards. Hardly any research is found...

  10. Identifying Industry-Specific Components of Product Liability Response System Using Delphi-AHP Method

    Directory of Open Access Journals (Sweden)

    Seo JunHyeok

    2016-12-01

    Full Text Available PL (product liability response system is an enterprise-wide system that prevents company’s financial loss due to PL-related accidents. Existing researches on PL response system are mainly focused on preventive and/or defense strategies for the companies. Also, it is obvious that each industry has their original characteristics related on PL issues. It means industry-specific characteristics should be considered to adopt PL response strategies. Thus, this paper aims to discuss industry-specific PL response system and their components. Based on prior researches, we tried to reveal the possibility of its application to manufacturing companies of existing PL response strategies using Delphi method with PL experts. Based on first round results, we tried to classify existing PL strategies of manufacturing companies into several categories. To validate our suggestion for essential components of PL response system, second round Delphi method are applied. Analytic hierarchy process (AHP technique will be applied to identify a prioritized list of each components and strategies. Existing PL response strategies could be categorized with six components – strategy, technology, investment, training, awareness, and organization. Among six components, Technology – it represents the technology needed for improving the safety of all products – is the most important components to prepare PL accidents. The limitation of this paper is on the size of survey and variety of examples. However, the future study will enhance the potential of the proposed method. Regardless of rich research efforts to identify PL response strategies, there is no effort to categorize these strategies and prioritized them. Well-coordinated and actionable PL response strategies and their priorities could help small-and-medium sized enterprise (SME to develop their own PL response system with their limited resources.

  11. Identifying research priorities for effective retention strategies in clinical trials.

    Science.gov (United States)

    Kearney, Anna; Daykin, Anne; Shaw, Alison R G; Lane, Athene J; Blazeby, Jane M; Clarke, Mike; Williamson, Paula; Gamble, Carrol

    2017-08-31

    The failure to retain patients or collect primary-outcome data is a common challenge for trials and reduces the statistical power and potentially introduces bias into the analysis. Identifying strategies to minimise missing data was the second highest methodological research priority in a Delphi survey of the Directors of UK Clinical Trial Units (CTUs) and is important to minimise waste in research. Our aim was to assess the current retention practices within the UK and priorities for future research to evaluate the effectiveness of strategies to reduce attrition. Seventy-five chief investigators of NIHR Health Technology Assessment (HTA)-funded trials starting between 2009 and 2012 were surveyed to elicit their awareness about causes of missing data within their trial and recommended practices for improving retention. Forty-seven CTUs registered within the UKCRC network were surveyed separately to identify approaches and strategies being used to mitigate missing data across trials. Responses from the current practice surveys were used to inform a subsequent two-round Delphi survey with registered CTUs. A consensus list of retention research strategies was produced and ranked by priority. Fifty out of seventy-five (67%) chief investigators and 33/47 (70%) registered CTUs completed the current practice surveys. Seventy-eight percent of trialists were aware of retention challenges and implemented strategies at trial design. Patient-initiated withdrawal was the most common cause of missing data. Registered CTUs routinely used newsletters, timeline of participant visits, and telephone reminders to mitigate missing data. Whilst 36 out of 59 strategies presented had been formally or informally evaluated, some frequently used strategies, such as site initiation training, have had no research to inform practice. Thirty-five registered CTUs (74%) participated in the Delphi survey. Research into the effectiveness of site initiation training, frequency of patient contact

  12. Identifying multiple submissions in Internet research: preserving data integrity.

    Science.gov (United States)

    Bowen, Anne M; Daniel, Candice M; Williams, Mark L; Baird, Grayson L

    2008-11-01

    Internet-based sexuality research with hidden populations has become increasingly popular. Respondent anonymity may encourage participation and lower social desirability, but associated disinhibition may promote multiple submissions, especially when incentives are offered. The goal of this study was to identify the usefulness of different variables for detecting multiple submissions from repeat responders and to explore incentive effects. The data included 1,900 submissions from a three-session Internet intervention with a pretest and three post-test questionnaires. Participants were men who have sex with men and incentives were offered to rural participants for completing each questionnaire. The final number of submissions included 1,273 "unique", 132 first submissions by "repeat responders" and 495 additional submissions by the "repeat responders" (N = 1,900). Four categories of repeat responders were identified: "infrequent" (2-5 submissions), "persistent" (6-10 submissions), "very persistent" (11-30 submissions), and "hackers" (more than 30 submissions). Internet Provider (IP) addresses, user names, and passwords were the most useful for identifying "infrequent" repeat responders. "Hackers" often varied their IP address and identifying information to prevent easy identification, but investigating the data for small variations in IP, using reverse telephone look up, and patterns across usernames and passwords were helpful. Incentives appeared to play a role in stimulating multiple submissions, especially from the more sophisticated "hackers". Finally, the web is ever evolving and it will be necessary to have good programmers and staff who evolve as fast as "hackers".

  13. Getting Specific about Qualitative Research Generalizability

    Science.gov (United States)

    Chenail, Ronald J.

    2010-01-01

    The question of generalizability or the usefulness of qualitative research results beyond the confines of the primary site, sample, and study has been hotly debated by qualitative researchers for decades. When examining this question of generalization the first surprising finding is there appears to be no general consensus about the definition,…

  14. A bibliometric model for identifying emerging research topics

    DEFF Research Database (Denmark)

    Wang, Qi

    2018-01-01

    –1843, 2015), the most serious problems are the lack of an acknowledged definition of emergence and incomplete elaboration of the linkages between the definitions that are used and the indicators that are created. With these issues in mind, this study first adjusts the definition of an emerging technology...... that Rotolo et al. (2015) have proposed to accommodate the analysis. Next, a set of criteria for the identification of emerging topics is proposed according to the adjusted definition and attributes of emergence. Using two sets of parameter values, several emerging research topics are identified. Finally...

  15. Identifying Gender-Specific Developmental Trajectories of Nonviolent and Violent Delinquency from Adolescence to Young Adulthood

    Science.gov (United States)

    Zheng, Yao; Cleveland, H. Harrington

    2013-01-01

    Most research examining gender differences in developmental trajectories of antisocial behavior does not consider subtypes of antisocial behavior and is difficult to generalize due to small nonrepresentative samples. The current study investigated gender difference in developmental trajectories from adolescence to young adulthood while addressing those limitations. Analyses were limited to respondents ages 15 and 16 in wave 1 (16–17 in wave 2, and 21–22 in wave 3) of the National Longitudinal Study of Adolescent Health (n = 6244, 49.5% males). Self-report nonviolent and violent delinquencies were simultaneously entered into latent class analysis. Four latent classes were identified: low, desister, decliner, and chronic (male-only). In addition to finding a male-specific chronic class, gender differences included differences in levels of nonviolent and violent delinquency between synonymous classes of males and females, and differences in prevalence of classes across genders. Neighborhood disadvantage and family support predicted trajectories. PMID:23375843

  16. Research overview : design specifications for hybrid vehicles

    NARCIS (Netherlands)

    Hofman, T.; Druten, van R.M.

    2004-01-01

    In this paper a method is proposed for determination of the design specifications regarding the energy exchange systems for different chargesustaining hybrid vehicles of different vehicle classes. Hybrid drivetrains for vehicles combine multiple power sources in order to increase the driving

  17. Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

    Science.gov (United States)

    Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

    2016-09-07

    Testicular cancer is the most common cancer in men aged between 15 and 35 and more than 90% of testicular neoplasms are originated at germ cells. Recent research has shown the impact of microRNAs (miRNAs) in different types of cancer, including testicular germ cell tumor (TGCT). MicroRNAs are small non-coding RNAs which affect the development and progression of cancer cells by binding to mRNAs and regulating their expressions. The identification of functional miRNA-mRNA interactions in cancers, i.e. those that alter the expression of genes in cancer cells, can help delineate post-regulatory mechanisms and may lead to new treatments to control the progression of cancer. A number of sequence-based methods have been developed to predict miRNA-mRNA interactions based on the complementarity of sequences. While necessary, sequence complementarity is, however, not sufficient for presence of functional interactions. Alternative methods have thus been developed to refine the sequence-based interactions using concurrent expression profiles of miRNAs and mRNAs. This study aims to find functional cancer-specific miRNA-mRNA interactions in TGCT. To this end, the sequence-based predicted interactions are first refined using an ensemble learning method, based on two well-known methods of learning miRNA-mRNA interactions, namely, TaLasso and GenMiR++. Additional functional analyses were then used to identify a subset of interactions to be most likely functional and specific to TGCT. The final list of 13 miRNA-mRNA interactions can be potential targets for identifying TGCT-specific interactions and future laboratory experiments to develop new therapies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Top IS research on quality of transaction standards: a structured literature review to identify a research gap

    NARCIS (Netherlands)

    Folmer, E.J.A.; Berends, W.; Oude Luttighuis, P.; Hillegersberg, J. van

    2009-01-01

    This paper contains the results of a systematic literature review executed to determine the coverage of transaction standards in top information systems (IS) and management journals. Specifically, it aims to identify a research gap with respect to this topic. The top 25 journals are thoroughly

  19. Identifying future directions for subsurface hydrocarbon migration research

    Science.gov (United States)

    Leifer, I.; Clark, J. F.; Luyendyk, B.; Valentine, D.

    Subsurface hydrocarbon migration is important for understanding the input and impacts of natural hydrocarbon seepage on the environment. Great uncertainties remain in most aspects of hydrocarbon migration, including some basic mechanisms of this four-phase flow of tar, oil, water, and gas through the complex fracture-network geometry particularly since the phases span a wide range of properties. Academic, government, and industry representatives recently attended a workshop to identify the areas of greatest need for future research in shallow hydrocarbon migration.Novel approaches such as studying temporal and spatial seepage variations and analogous geofluid systems (e.g., geysers and trickle beds) allow deductions of subsurface processes and structures that remain largely unclear. Unique complexities exist in hydrocarbon migration due to its multiphase flow and complex geometry, including in-situ biological weathering. Furthermore, many aspects of the role of hydrocarbons (positive and negative) in the environment are poorly understood, including how they enter the food chain (respiration, consumption, etc.) and “percolate” to higher trophic levels. But understanding these ecological impacts requires knowledge of the emissions' temporal and spatial variability and trajectories.

  20. Identifying future research directions for biodiversity, ecosystem services and sustainability : perspectives from early-career researchers

    NARCIS (Netherlands)

    Hossain, S.; Pogue, S.J.; Trenchard, L.; Oudenhoven, van A.P.E.; Washbourne, C-L.; Muiruri, E.W.; Tomczyk, A.M.; García-Llorente, M.; Hale, R.; Hevia, V.; Adams, T.; Tavallali, L.; De, Bell S.; Pye, M.; Resende, F.

    2017-01-01

    We aimed to identify priority research questions in the field of biodiversity, ecosystem services and sustainability (BESS), based on a workshop held during the NRG BESS Conference for Early Career Researchers on BESS, and to compare these to existing horizon scanning exercises. This work highlights

  1. Research Priorities in Limb and Task-Specific Dystonias

    Science.gov (United States)

    Pirio Richardson, Sarah; Altenmüller, Eckart; Alter, Katharine; Alterman, Ron L.; Chen, Robert; Frucht, Steven; Furuya, Shinichi; Jankovic, Joseph; Jinnah, H. A.; Kimberley, Teresa J.; Lungu, Codrin; Perlmutter, Joel S.; Prudente, Cecília N.; Hallett, Mark

    2017-01-01

    Dystonia, which causes intermittent or sustained abnormal postures and movements, can present in a focal or a generalized manner. In the limbs, focal dystonia can occur in either the upper or lower limbs and may be task-specific causing abnormal motor performance for only a specific task, such as in writer’s cramp, runner’s dystonia, or musician’s dystonia. Focal limb dystonia can be non-task-specific and may, in some circumstances, be associated with parkinsonian disorders. The true prevalence of focal limb dystonia is not known and is likely currently underestimated, leaving a knowledge gap and an opportunity for future research. The pathophysiology of focal limb dystonia shares some commonalities with other dystonias with a loss of inhibition in the central nervous system and a loss of the normal regulation of plasticity, called homeostatic plasticity. Functional imaging studies revealed abnormalities in several anatomical networks that involve the cortex, basal ganglia, and cerebellum. Further studies should focus on distinguishing cause from effect in both physiology and imaging studies to permit focus on most relevant biological correlates of dystonia. There is no specific therapy for the treatment of limb dystonia given the variability in presentation, but off-label botulinum toxin therapy is often applied to focal limb and task-specific dystonia. Various rehabilitation techniques have been applied and rehabilitation interventions may improve outcomes, but small sample size and lack of direct comparisons between methods to evaluate comparative efficacy limit conclusions. Finally, non-invasive and invasive therapeutic modalities have been explored in small studies with design limitations that do not yet clearly provide direction for larger clinical trials that could support new clinical therapies. Given these gaps in our clinical, pathophysiologic, and therapeutic knowledge, we have identified priorities for future research including: the development of

  2. Research Priorities in Limb and Task-Specific Dystonias

    Directory of Open Access Journals (Sweden)

    Sarah Pirio Richardson

    2017-05-01

    Full Text Available Dystonia, which causes intermittent or sustained abnormal postures and movements, can present in a focal or a generalized manner. In the limbs, focal dystonia can occur in either the upper or lower limbs and may be task-specific causing abnormal motor performance for only a specific task, such as in writer’s cramp, runner’s dystonia, or musician’s dystonia. Focal limb dystonia can be non-task-specific and may, in some circumstances, be associated with parkinsonian disorders. The true prevalence of focal limb dystonia is not known and is likely currently underestimated, leaving a knowledge gap and an opportunity for future research. The pathophysiology of focal limb dystonia shares some commonalities with other dystonias with a loss of inhibition in the central nervous system and a loss of the normal regulation of plasticity, called homeostatic plasticity. Functional imaging studies revealed abnormalities in several anatomical networks that involve the cortex, basal ganglia, and cerebellum. Further studies should focus on distinguishing cause from effect in both physiology and imaging studies to permit focus on most relevant biological correlates of dystonia. There is no specific therapy for the treatment of limb dystonia given the variability in presentation, but off-label botulinum toxin therapy is often applied to focal limb and task-specific dystonia. Various rehabilitation techniques have been applied and rehabilitation interventions may improve outcomes, but small sample size and lack of direct comparisons between methods to evaluate comparative efficacy limit conclusions. Finally, non-invasive and invasive therapeutic modalities have been explored in small studies with design limitations that do not yet clearly provide direction for larger clinical trials that could support new clinical therapies. Given these gaps in our clinical, pathophysiologic, and therapeutic knowledge, we have identified priorities for future research including

  3. Priority setting partnership to identify the top 10 research priorities for the management of Parkinson's disease.

    Science.gov (United States)

    Deane, Katherine H O; Flaherty, Helen; Daley, David J; Pascoe, Roland; Penhale, Bridget; Clarke, Carl E; Sackley, Catherine; Storey, Stacey

    2014-12-14

    This priority setting partnership was commissioned by Parkinson's UK to encourage people with direct and personal experience of the condition to work together to identify and prioritise the top 10 evidential uncertainties that impact on everyday clinical practice for the management of Parkinson's disease (PD). The UK. Anyone with experience of PD including: people with Parkinson's (PwP), carers, family and friends, healthcare and social care professionals. Non-clinical researchers and employees of pharmaceutical or medical devices companies were excluded. 1000 participants (60% PwP) provided ideas on research uncertainties, 475 (72% PwP) initially prioritised them and 27 (37% PwP) stakeholders agreed a final top 10. Using a modified nominal group technique, participants were surveyed to identify what issues for the management of PD needed research. Unique research questions unanswered by current evidence were identified and participants were asked to identify their top 10 research priorities from this list. The top 26 uncertainties were presented to a consensus meeting with key stakeholders to agree the top 10 research priorities. 1000 participants provided 4100 responses, which contained 94 unique unanswered research questions that were initially prioritised by 475 participants. A consensus meeting with 27 stakeholders agreed the top 10 research priorities. The overarching research aspiration was an effective cure for PD. The top 10 research priorities for PD management included the need to address motor symptoms (balance and falls, and fine motor control), non-motor symptoms (sleep and urinary dysfunction), mental health issues (stress and anxiety, dementia and mild cognitive impairments), side effects of medications (dyskinesia) and the need to develop interventions specific to the phenotypes of PD and better monitoring methods. These research priorities identify crucial gaps in the existing evidence to address everyday practicalities in the management of the

  4. Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

    Science.gov (United States)

    Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

    2015-11-17

    A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

  5. SMM-system: A mining tool to identify specific markers in Salmonella enterica.

    Science.gov (United States)

    Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

    2011-03-01

    This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Identifying future research directions for biodiversity, ecosystem services and sustainability: perspectives from early-career researchers

    OpenAIRE

    Hossain, S.; Pogue, S.J.; Trenchard, L.; Oudenhoven, van, A.P.E.; Washbourne, C-L.; Muiruri, E.W.; Tomczyk, A.M.; García-Llorente, M.; Hale, R.; Hevia, V.; Adams, T.; Tavallali, L.; De, Bell S.; Pye, M.; Resende, F.

    2017-01-01

    We aimed to identify priority research questions in the field of biodiversity, ecosystem services and sustainability (BESS), based on a workshop held during the NRG BESS Conference for Early Career Researchers on BESS, and to compare these to existing horizon scanning exercises. This work highlights the need for improved data availability through collaboration and knowledge exchange, which, in turn, can support the integrated valuation and sustainable management of ecosystems in response to g...

  7. Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior

    Directory of Open Access Journals (Sweden)

    Julia Brasch

    2018-05-01

    Full Text Available Summary: Type II cadherins are cell-cell adhesion proteins critical for tissue patterning and neuronal targeting but whose molecular binding code remains poorly understood. Here, we delineate binding preferences for type II cadherin cell-adhesive regions, revealing extensive heterophilic interactions between specific pairs, in addition to homophilic interactions. Three distinct specificity groups emerge from our analysis with members that share highly similar heterophilic binding patterns and favor binding to one another. Structures of adhesive fragments from each specificity group confirm near-identical dimer topology conserved throughout the family, allowing interface residues whose conservation corresponds to specificity preferences to be identified. We show that targeted mutation of these residues converts binding preferences between specificity groups in biophysical and co-culture assays. Our results provide a detailed understanding of the type II cadherin interaction map and a basis for defining their role in tissue patterning and for the emerging importance of their heterophilic interactions in neural connectivity. : Type II cadherins are a family of vertebrate cell adhesion proteins expressed primarily in the CNS. Brasch et al. measure binding between adhesive fragments, revealing homophilic and extensive selective heterophilic binding with specificities that define groups of similar cadherins. Structures reveal common adhesive dimers, with residues governing cell-adhesive specificity. Keywords: cell adhesion, crystal structure, hemophilic specificity, heterophilic specificity, neural patterning, synaptic targeting, cadherin

  8. Saporin-conjugated tetramers identify efficacious anti-HIV CD8+ T-cell specificities

    DEFF Research Database (Denmark)

    Leitman, Ellen M.; Palmer, Christine D.; Buus, Søren

    2017-01-01

    Antigen-specific T-cells are highly variable, spanning potent antiviral efficacy and damaging auto-reactivity. In virus infections, identifying the most efficacious responses is critical to vaccine design. However, current methods depend on indirect measures or on ex vivo expanded CTL clones. We...

  9. Systems Engineering-Based Tool for Identifying Critical Research Systems

    Science.gov (United States)

    Abbott, Rodman P.; Stracener, Jerrell

    2016-01-01

    This study investigates the relationship between the designated research project system independent variables of Labor, Travel, Equipment, and Contract total annual costs and the dependent variables of both the associated matching research project total annual academic publication output and thesis/dissertation number output. The Mahalanobis…

  10. On the use of specific signal types in hearing research

    NARCIS (Netherlands)

    Kohlrausch, A.G.; Par, van de S.L.J.D.E.; Kurtz, T.; Parlitz, U.; Kaatze, U.

    2007-01-01

    In this contribution, we review a number of specific signal types that have been introduced in auditory research in the past 20 years. Through the introduction of digital computers into experimental and theoretical hearing research, the freedom to construct and use specific acoustic stimuli in

  11. Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.

    Directory of Open Access Journals (Sweden)

    Matthew R Mason

    Full Text Available Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

  12. Density and Specific Gravity Metrics in Biomass Research

    Science.gov (United States)

    Micheal C. Wiemann; G. Bruce Williamson

    2012-01-01

    Following the 2010 publication of Measuring Wood Specific Gravity… Correctly in the American Journal of Botany, readers contacted us to inquire about application of wood density and specific gravity to biomass research. Here we recommend methods for sample collection, volume measurement, and determination of wood density and specific gravity for...

  13. Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility.

    Directory of Open Access Journals (Sweden)

    Jesus Perez-Losada

    Full Text Available Genome-wide association studies (GWAS have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5-10%. There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001, but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility.

  14. Extension Systems in Tanzania: Identifying Gaps in Research

    African Journals Online (AJOL)

    in Tanzania on agricultural extension systems; review research globally on agricultural ... cal techniques, unique results and major recommendations. .... participation in decision-making, natural .... soil and water management technologies in.

  15. Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos.

    Directory of Open Access Journals (Sweden)

    Rong-Ping Zhang

    Full Text Available Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM and the pectoral muscle (PM of two genetically different duck breeds, Heiwu duck (H and Peking duck (P, at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P at the same developmental stage (embryonic 15 days. Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG were used to functionally annotate DEGs (differentially expression genes. The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05. In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05. In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only

  16. Monochromatic and identifiable photons used in photonuclear research

    International Nuclear Information System (INIS)

    Beil, Hans; Bergere, Roland.

    1980-07-01

    A general overview is given of the most common experimental procedures for the production and utilisation of monochromatic and (or) identifiable photon probes actually operational in 1979. Their basic characteristics, merits and drawbacks, together with their respective major domains of experimental physics to which they are usually applied, are also investigated. Methods for producing such monochromatic and (or) identifiable photon probes, with a continuously variable energy from a few MeV up till about 180 GeV, are treated in some detail. Some of the most promising future trends in the ulterior development of such electromagnetic probes are also mentioned

  17. Original Research Identifying patients at high risk for obstructive ...

    African Journals Online (AJOL)

    determine the factors associated with high risk for obstructive sleep apnoea and use it to identify patients at risk for the condition in ... mainstay of management is CPAP in addition to behavioral ..... the present study has some potential limitations which ... consequences of obstructive sleep apnea and short sleep duration.

  18. A novel data mining method to identify assay-specific signatures in functional genomic studies

    Directory of Open Access Journals (Sweden)

    Guidarelli Jack W

    2006-08-01

    Full Text Available Abstract Background: The highly dimensional data produced by functional genomic (FG studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays. Although dimensionality reduction methods such as principal component analysis (PCA have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of

  19. Citation algorithms for identifying research milestones driving biomedical innovation

    NARCIS (Netherlands)

    Comins, J.A.; Leydesdorff, L.

    Scientific activity plays a major role in innovation for biomedicine and healthcare. For instance, fundamental research on disease pathologies and mechanisms can generate potential targets for drug therapy. This co-evolution is punctuated by papers which provide new perspectives and open new

  20. Amusement Arcades Help Identify Teen Needs. Research Notes.

    Science.gov (United States)

    Jordan, Debra J.

    1995-01-01

    Reviews research on youth motivation for visiting amusement arcades and on the relationship among the school achievement, socioeconomic status, and self-esteem of fourth graders. Implications for camp involve providing adolescents with unstructured leisure time with little overt adult supervision and providing early intervention for low-achieving…

  1. Digital identifiers as permanent unique registers for researchers in the university context

    Directory of Open Access Journals (Sweden)

    Luisa F. Acosta-Ortega

    2016-09-01

    Full Text Available The increase in the use of Internet and the web allows a wide access to a greater warehouse of information sources in thousand of journals and publications, nets of almost unlimited number of people, computers and opportunities for learning and research without precedents. That makes the correct identification and recovery of scientific production of researchers very difficult. For that reason, during the last years different attemps of different organizations have been made to create a permanent unique register for authors, which permits to identify their articles wherever they are placed and without taking into account the specificity in the author’s name, publishing and  processing practices In data base,  and different bibliographic description styles as well. ORCID (Openn Researcher and Contribution ID is an identifier with the greatest posibilities of becoming universal to achieve visibility and positioning of Latin-American universities in the present international context.

  2. Industry-identified combustion research needs: Special study

    Energy Technology Data Exchange (ETDEWEB)

    Keller, J.G.; Soelberg, N.R.; Kessinger, G.F.

    1995-11-01

    This report discusses the development and demonstration of innovative combustion technologies that improve energy conservation and environmental practices in the US industrial sector. The report includes recommendations by industry on R&D needed to resolve current combustion-related problems. Both fundamental and applied R&D needs are presented. The report assesses combustion needs and suggests research ideas for seven major industries, which consume about 78% of all energy used by industry. Included are the glass, pulp and paper, refinery, steel, metal casting, chemicals, and aluminum industries. Information has been collected from manufacturers, industrial operators, trade organizations, and various funding organizations and has been supplemented with expertise at the Idaho National Engineering Laboratory to develop a list of suggested research and development needed for each of the seven industries.

  3. Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells.

    Science.gov (United States)

    Correa, Isabel; Ilieva, Kristina M; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F; Tutt, Andrew N J; Nestle, Frank O; Karagiannis, Panagiotis; Lacy, Katie E; Karagiannis, Sophia N

    2018-01-01

    Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

  4. Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

    Directory of Open Access Journals (Sweden)

    Isabel Correa

    2018-03-01

    Full Text Available Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1 specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

  5. Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

    Science.gov (United States)

    Correa, Isabel; Ilieva, Kristina M.; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F.; Tutt, Andrew N. J.; Nestle, Frank O.; Karagiannis, Panagiotis; Lacy, Katie E.; Karagiannis, Sophia N.

    2018-01-01

    Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires. PMID:29628923

  6. High-Throughput Screening to Identify Regulators of Meiosis-Specific Gene Expression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Kassir, Yona

    2017-01-01

    Meiosis and gamete formation are processes that are essential for sexual reproduction in all eukaryotic organisms. Multiple intracellular and extracellular signals feed into pathways that converge on transcription factors that induce the expression of meiosis-specific genes. Once triggered the meiosis-specific gene expression program proceeds in a cascade that drives progress through the events of meiosis and gamete formation. Meiosis-specific gene expression is tightly controlled by a balance of positive and negative regulatory factors that respond to a plethora of signaling pathways. The budding yeast Saccharomyces cerevisiae has proven to be an outstanding model for the dissection of gametogenesis owing to the sophisticated genetic manipulations that can be performed with the cells. It is possible to use a variety selection and screening methods to identify genes and their functions. High-throughput screening technology has been developed to allow an array of all viable yeast gene deletion mutants to be screened for phenotypes and for regulators of gene expression. This chapter describes a protocol that has been used to screen a library of homozygous diploid yeast deletion strains to identify regulators of the meiosis-specific IME1 gene.

  7. Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a.

    Science.gov (United States)

    Yelin-Bekerman, Laura; Elbaz, Idan; Diber, Alex; Dahary, Dvir; Gibbs-Bar, Liron; Alon, Shahar; Lerer-Goldshtein, Tali; Appelbaum, Lior

    2015-10-01

    Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron-specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron-specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a(-/-)) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.

  8. Personal identifiers in medical research networks: evaluation of the personal identifier generator in the Competence Network Paediatric Oncology and Haematology

    Directory of Open Access Journals (Sweden)

    Pommerening, Klaus

    2006-06-01

    Full Text Available The Society for Paediatric Oncology and Haematology (GPOH and the corresponding Competence Network Paediatric Oncology and Haematology conduct various clinical trials. The comprehensive analysis requires reliable identification of the recruited patients. Therefore, a personal identifier (PID generator is used to assign unambiguous, pseudonymous, non-reversible PIDs to participants in those trials. We tested the matching algorithm of the PID generator using a configuration specific to the GPOH. False data was used to verify the correct processing of PID requests (functionality tests, while test data was used to evaluate the matching outcome. We also assigned PIDs to more than 44,000 data records from the German Childhood Cancer Registry (GCCR and assessed the status of the associated patient list which contains the PIDs, partly encrypted data items and information on the PID generation process for each data record. All the functionality tests showed the expected results. Neither 14,915 test data records nor the GCCR data records yielded any homonyms. Six synonyms were found in the test data, due to erroneous birth dates, and 22 synonyms were found when the GCCR data was run against the actual patient list of 2579 records. In the resulting patient list of 45,693 entries, duplicate record submissions were found for about 7% of all listed patients, while more frequent submissions occurred in less than 1% of cases. The synonym error rate depends mainly on the quality of the input data and on the frequency of multiple submissions. Depending on the requirements on maximally tolerable synonym and homonym error rates, additional measures for securing input data quality might be necessary. The results demonstrate that the PID generator is an appropriate tool for reliably identifying trial participants in medical research networks.

  9. Novel HTS strategy identifies TRAIL-sensitizing compounds acting specifically through the caspase-8 apoptotic axis.

    Directory of Open Access Journals (Sweden)

    Darren Finlay

    Full Text Available Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL is potentially a very important therapeutic as it shows selectivity for inducing apoptosis in cancer cells whilst normal cells are refractory. TRAIL binding to its cognate receptors, Death Receptors-4 and -5, leads to recruitment of caspase-8 and classical activation of downstream effector caspases, leading to apoptosis. As with many drugs however, TRAIL's usefulness is limited by resistance, either innate or acquired. We describe here the development of a novel 384-well high-throughput screening (HTS strategy for identifying potential TRAIL-sensitizing agents that act solely in a caspase-8 dependent manner. By utilizing a TRAIL resistant cell line lacking caspase-8 (NB7 compared to the same cells reconstituted with the wild-type protein, or with a catalytically inactive point mutant of caspase-8, we are able to identify compounds that act specifically through the caspase-8 axis, rather than through general toxicity. In addition, false positive hits can easily be "weeded out" in this assay due to their activity in cells lacking caspase-8-inducible activity. Screening of the library of pharmacologically active compounds (LOPAC was performed as both proof-of-concept and to discover potential unknown TRAIL sensitizers whose mechanism is caspase-8 mediated. We identified known TRAIL sensitizers from the library and identified new compounds that appear to sensitize specifically through caspase-8. In sum, we demonstrate proof-of-concept and discovery of novel compounds with a screening strategy optimized for the detection of caspase-8 pathway-specific TRAIL sensitizers. This screen was performed in the 384-well format, but could easily be further miniaturized, allows easy identification of artifactual false positives, and is highly scalable to accommodate diverse libraries.

  10. Strategies to design clinical studies to identify predictive biomarkers in cancer research.

    Science.gov (United States)

    Perez-Gracia, Jose Luis; Sanmamed, Miguel F; Bosch, Ana; Patiño-Garcia, Ana; Schalper, Kurt A; Segura, Victor; Bellmunt, Joaquim; Tabernero, Josep; Sweeney, Christopher J; Choueiri, Toni K; Martín, Miguel; Fusco, Juan Pablo; Rodriguez-Ruiz, Maria Esperanza; Calvo, Alfonso; Prior, Celia; Paz-Ares, Luis; Pio, Ruben; Gonzalez-Billalabeitia, Enrique; Gonzalez Hernandez, Alvaro; Páez, David; Piulats, Jose María; Gurpide, Alfonso; Andueza, Mapi; de Velasco, Guillermo; Pazo, Roberto; Grande, Enrique; Nicolas, Pilar; Abad-Santos, Francisco; Garcia-Donas, Jesus; Castellano, Daniel; Pajares, María J; Suarez, Cristina; Colomer, Ramon; Montuenga, Luis M; Melero, Ignacio

    2017-02-01

    The discovery of reliable biomarkers to predict efficacy and toxicity of anticancer drugs remains one of the key challenges in cancer research. Despite its relevance, no efficient study designs to identify promising candidate biomarkers have been established. This has led to the proliferation of a myriad of exploratory studies using dissimilar strategies, most of which fail to identify any promising targets and are seldom validated. The lack of a proper methodology also determines that many anti-cancer drugs are developed below their potential, due to failure to identify predictive biomarkers. While some drugs will be systematically administered to many patients who will not benefit from them, leading to unnecessary toxicities and costs, others will never reach registration due to our inability to identify the specific patient population in which they are active. Despite these drawbacks, a limited number of outstanding predictive biomarkers have been successfully identified and validated, and have changed the standard practice of oncology. In this manuscript, a multidisciplinary panel reviews how those key biomarkers were identified and, based on those experiences, proposes a methodological framework-the DESIGN guidelines-to standardize the clinical design of biomarker identification studies and to develop future research in this pivotal field. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Identify alternative splicing events based on position-specific evolutionary conservation.

    Directory of Open Access Journals (Sweden)

    Liang Chen

    Full Text Available The evolution of eukaryotes is accompanied by the increased complexity of alternative splicing which greatly expands genome information. One of the greatest challenges in the post-genome era is a complete revelation of human transcriptome with consideration of alternative splicing. Here, we introduce a comparative genomics approach to systemically identify alternative splicing events based on the differential evolutionary conservation between exons and introns and the high-quality annotation of the ENCODE regions. Specifically, we focus on exons that are included in some transcripts but are completely spliced out for others and we call them conditional exons. First, we characterize distinguishing features among conditional exons, constitutive exons and introns. One of the most important features is the position-specific conservation score. There are dramatic differences in conservation scores between conditional exons and constitutive exons. More importantly, the differences are position-specific. For flanking intronic regions, the differences between conditional exons and constitutive exons are also position-specific. Using the Random Forests algorithm, we can classify conditional exons with high specificities (97% for the identification of conditional exons from intron regions and 95% for the classification of known exons and fair sensitivities (64% and 32% respectively. We applied the method to the human genome and identified 39,640 introns that actually contain conditional exons and classified 8,813 conditional exons from the current RefSeq exon list. Among those, 31,673 introns containing conditional exons and 5,294 conditional exons classified from known exons cannot be inferred from RefSeq, UCSC or Ensembl annotations. Some of these de novo predictions were experimentally verified.

  12. Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

    Directory of Open Access Journals (Sweden)

    Neil Arvin Bretaña

    Full Text Available Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific

  13. Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

    Science.gov (United States)

    Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

    2012-01-01

    Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

  14. Study of a methodology of identifying important research problems by the PIRT process

    International Nuclear Information System (INIS)

    Aoki, Takayuki; Takagi, Toshiyuki; Urayama, Ryoichi; Komura, Ichiro; Furukawa, Takashi; Yusa, Noritaka

    2013-01-01

    In this paper, we propose a new methodology of identifying important research problems to be solved to improve the performance of some specific scientific technologies by the phenomena identification and ranking table (PIRT) process, which has been used as a methodology for demonstrating the validity of the best estimate simulation codes in USNRC licensing of nuclear power plants. It keeps the fundamental concepts of the original PIRT process but makes it possible to identify important factors affecting the performance of the technologies from the viewpoint of the figure of merit and problems associated with them, which need to be solved to improve the performance. Also in this paper, we demonstrate the effectiveness of the developed method by showing a specific example of the application to physical events or phenomena in objects having fatigue or SCC crack(s) under ultrasonic testing and eddy current testing. (author)

  15. Study of a methodology of identifying important research problems by the PIRT process

    International Nuclear Information System (INIS)

    Aoki, Takayuki; Takagi, Toshiyuki; Urayama, Ryoichi; Komura, Ichiro; Furukawa, Takashi; Yusa, Noritaka

    2014-01-01

    In this paper, we propose a new methodology of identifying important research problems to be solved to improve the performance of some specific scientific technologies by the phenomena identification and ranking table (PIRT) process which has been used as a methodology for demonstrating the validity of the best estimate simulation codes in US Nuclear Regulatory Commission (USNRC) licensing of nuclear power plants. The new methodology makes it possible to identify important factors affecting the performance of the technologies from the viewpoint of the figure of merit and problems associated with them while it keeps the fundamental concepts of the original PIRT process. Also in this paper, we demonstrate the effectiveness of the new methodology by applying it to a task of extracting research problems for improving an inspection accuracy of ultrasonic testing or eddy current testing in the inspection of objects having cracks due to fatigue or stress corrosion cracking. (author)

  16. WMAXC: a weighted maximum clique method for identifying condition-specific sub-network.

    Directory of Open Access Journals (Sweden)

    Bayarbaatar Amgalan

    Full Text Available Sub-networks can expose complex patterns in an entire bio-molecular network by extracting interactions that depend on temporal or condition-specific contexts. When genes interact with each other during cellular processes, they may form differential co-expression patterns with other genes across different cell states. The identification of condition-specific sub-networks is of great importance in investigating how a living cell adapts to environmental changes. In this work, we propose the weighted MAXimum clique (WMAXC method to identify a condition-specific sub-network. WMAXC first proposes scoring functions that jointly measure condition-specific changes to both individual genes and gene-gene co-expressions. It then employs a weaker formula of a general maximum clique problem and relates the maximum scored clique of a weighted graph to the optimization of a quadratic objective function under sparsity constraints. We combine a continuous genetic algorithm and a projection procedure to obtain a single optimal sub-network that maximizes the objective function (scoring function over the standard simplex (sparsity constraints. We applied the WMAXC method to both simulated data and real data sets of ovarian and prostate cancer. Compared with previous methods, WMAXC selected a large fraction of cancer-related genes, which were enriched in cancer-related pathways. The results demonstrated that our method efficiently captured a subset of genes relevant under the investigated condition.

  17. Identifying indigenous peoples for health research in a global context: a review of perspectives and challenges.

    Science.gov (United States)

    Bartlett, Judith G; Madariaga-Vignudo, Lucia; O'Neil, John D; Kuhnlein, Harriet V

    2007-09-01

    Identifying Indigenous Peoples globally is complex and contested despite there being an estimated 370 million living in 70 countries. The specific context and use of locally relevant and clear definitions or characterizations of Indigenous Peoples is important for recognizing unique health risks Indigenous Peoples face, for understanding local Indigenous health aspirations and for reflecting on the need for culturally disaggregated data to plan meaningful research and health improvement programs. This paper explores perspectives on defining Indigenous Peoples and reflects on challenges in identifying Indigenous Peoples. Literature reviews and Internet searches were conducted, and some key experts were consulted. Pragmatic and political definitions by international institutions, including the United Nations, are presented as well as characterizations of Indigenous Peoples by governments and academic researchers. Assertions that Indigenous Peoples have about definitions of indigeneity are often related to maintenance of cultural integrity and sustainability of lifestyles. Described here are existing definitions and interests served by defining (or leaving undefined) such definitions, why there is no unified definition and implications of "too restrictive" a definition. Selected indigenous identities and dynamics are presented for North America, the Arctic, Australia and New Zealand, Latin America and the Caribbean, Asia and Africa. While health researchers need to understand the Indigenous Peoples with whom they work, ultimately, indigenous groups themselves best define how they wish to be viewed and identified for research purposes.

  18. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

    Science.gov (United States)

    Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

    2016-01-19

    Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

    Science.gov (United States)

    Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta’ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

    2016-01-01

    The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology. PMID:27435636

  20. An HTS-compatible 3D colony formation assay to identify tumor-specific chemotherapeutics.

    Science.gov (United States)

    Horman, Shane R; To, Jeremy; Orth, Anthony P

    2013-12-01

    There has been increasing interest in the development of cellular behavior models that take advantage of three-dimensional (3D) cell culture. To enable assessment of differential perturbagen impacts on cell growth in 2D and 3D, we have miniaturized and adapted for high-throughput screening (HTS) the soft agar colony formation assay, employing a laser-scanning cytometer to image and quantify multiple cell types simultaneously. The assay is HTS compatible, providing high-quality, image-based, replicable data for multiple, co-cultured cell types. As proof of concept, we subjected colorectal carcinoma colonies in 3D soft agar to a mini screen of 1528 natural product compounds. Hit compounds from the primary screen were rescreened in an HTS 3D co-culture matrix containing colon stromal cells and cancer cells. By combining tumor cells and normal, nontransformed colon epithelial cells in one primary screening assay, we were able to obtain differential IC50 data, thereby distinguishing tumor-specific compounds from general cytotoxic compounds. Moreover, we were able to identify compounds that antagonized tumor colony formation in 3D only, highlighting the importance of this assay in identifying agents that interfere with 3D tumor structural growth. This screening platform provides a fast, simple, and robust method for identification of tumor-specific agents in a biologically relevant microenvironment.

  1. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

    Science.gov (United States)

    Trinkle-Mulcahy, Laura; Boulon, Séverine; Lam, Yun Wah; Urcia, Roby; Boisvert, François-Michel; Vandermoere, Franck; Morrice, Nick A.; Swift, Sam; Rothbauer, Ulrich; Leonhardt, Heinrich; Lamond, Angus

    2008-01-01

    The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments. PMID:18936248

  2. Genome-wide association studies identify four ER negative-specific breast cancer risk loci

    DEFF Research Database (Denmark)

    Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara

    2013-01-01

    differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls......), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER...

  3. CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

    Science.gov (United States)

    Bais, Preeti; Namburi, Sandeep; Gatti, Daniel M; Zhang, Xinyu; Chuang, Jeffrey H

    2017-10-01

    We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data. The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors. jeff.chuang@jax.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  4. Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

    Directory of Open Access Journals (Sweden)

    Arehart Eric

    2009-03-01

    Full Text Available Abstract Background The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation. Results We modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR approach. MDR was originally developed to detect synergistic interactions between multiple SNPs that are predictive of disease susceptibility. We initially assembled data from the Broad Institute as a pilot test for the hypothesis that flanking region patterns associate with mutagenesis (n = 2194. We then confirmed and expanded our inquiry with human SNPs within coding regions and their flanking sequences collected from the National Center for Biotechnology Information (NCBI database (n = 29967 and a control set of sequences (coding region not associated with SNP sites randomly selected from the NCBI database (n = 29967. We discovered seven flanking region pattern associations in the Broad dataset which reached a minimum significance level of p ≤ 0.05. Significant models (p Conclusion The present study represents the first use of this computational methodology for modeling nonlinear patterns in molecular genetics. MDR was able to identify distinct nucleotide patterning around sites of mutations dependent upon the observed nucleotide change. We discovered one flanking region set that included five nucleotides clustered around a specific type of SNP site. Based on the strongly associated patterns identified in

  5. GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity.

    Directory of Open Access Journals (Sweden)

    Yi-Ju Chen

    Full Text Available S-glutathionylation, the covalent attachment of a glutathione (GSH to the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-glutathionylation remains unknown. Based on a total of 1783 experimentally identified S-glutathionylation sites from mouse macrophages, this work presents an informatics investigation on S-glutathionylation sites including structural factors such as the flanking amino acids composition and the accessible surface area (ASA. TwoSampleLogo presents that positively charged amino acids flanking the S-glutathionylated cysteine may influence the formation of S-glutathionylation in closed three-dimensional environment. A statistical method is further applied to iteratively detect the conserved substrate motifs with statistical significance. Support vector machine (SVM is then applied to generate predictive model considering the substrate motifs. According to five-fold cross-validation, the SVMs trained with substrate motifs could achieve an enhanced sensitivity, specificity, and accuracy, and provides a promising performance in an independent test set. The effectiveness of the proposed method is demonstrated by the correct identification of previously reported S-glutathionylation sites of mouse thioredoxin (TXN and human protein tyrosine phosphatase 1b (PTP1B. Finally, the constructed models are adopted to implement an effective web-based tool, named GSHSite (http://csb.cse.yzu.edu.tw/GSHSite/, for identifying uncharacterized GSH substrate sites on the protein sequences.

  6. Tobacco control recommendations identified by LGBT Atlantans in a community-based participatory research project.

    Science.gov (United States)

    Bryant, Lawrence; Damarin, Amanda K; Marshall, Zack

    2014-01-01

    Lesbian, gay, bisexual, and transgender (LGBT) people are increasingly aware that disproportionately high smoking rates severely impact the health of their communities. Motivated to make a change, a group of LGBT community members, policymakers, and researchers from Atlanta carried out a community-based participatory research (CBPR) project. This formative research study sought to identify recommendations for culturally relevant smoking prevention and cessation interventions that could improve the health of Atlanta's LGBT communities. Data presented here come from four focus groups with 36 participants and a community meeting with 30 participants. Among study participants, the most favored interventions were providing LGBT-specific cessation programs, raising awareness about LGBT smoking rates, and getting community venues to go smoke-free. Participants also suggested providing reduced-cost cessation products for low-income individuals, using LGBT "role models" to promote cessation, and ensuring that interventions reach all parts of the community. Findings reinforce insights from community-based research with other marginalized groups. Similarities include the importance of tailoring cessation programs for specific communities, the need to acknowledge differences within communities, and the significance of community spaces in shaping discussions of cessation. Further, this study highlights the need for heightened awareness. The Atlanta LGBT community is largely unaware that high smoking rates affect its health, and is unlikely to take collective action to address this problem until it is understood.

  7. Global Transcriptome Sequencing Identifies Chlamydospore Specific Markers in Candida albicans and Candida dubliniensis

    LENUS (Irish Health Repository)

    Palige, Katja

    2013-04-15

    Candida albicans and Candida dubliniensis are pathogenic fungi that are highly related but differ in virulence and in some phenotypic traits. During in vitro growth on certain nutrient-poor media, C. albicans and C. dubliniensis are the only yeast species which are able to produce chlamydospores, large thick-walled cells of unknown function. Interestingly, only C. dubliniensis forms pseudohyphae with abundant chlamydospores when grown on Staib medium, while C. albicans grows exclusively as a budding yeast. In order to further our understanding of chlamydospore development and assembly, we compared the global transcriptional profile of both species during growth in liquid Staib medium by RNA sequencing. We also included a C. albicans mutant in our study which lacks the morphogenetic transcriptional repressor Nrg1. This strain, which is characterized by its constitutive pseudohyphal growth, specifically produces masses of chlamydospores in Staib medium, similar to C. dubliniensis. This comparative approach identified a set of putatively chlamydospore-related genes. Two of the homologous C. albicans and C. dubliniensis genes (CSP1 and CSP2) which were most strongly upregulated during chlamydospore development were analysed in more detail. By use of the green fluorescent protein as a reporter, the encoded putative cell wall related proteins were found to exclusively localize to C. albicans and C. dubliniensis chlamydospores. Our findings uncover the first chlamydospore specific markers in Candida species and provide novel insights in the complex morphogenetic development of these important fungal pathogens.

  8. Machine-learning identifies substance-specific behavioral markers for opiate and stimulant dependence.

    Science.gov (United States)

    Ahn, Woo-Young; Vassileva, Jasmin

    2016-04-01

    Recent animal and human studies reveal distinct cognitive and neurobiological differences between opiate and stimulant addictions; however, our understanding of the common and specific effects of these two classes of drugs remains limited due to the high rates of polysubstance-dependence among drug users. The goal of the current study was to identify multivariate substance-specific markers classifying heroin dependence (HD) and amphetamine dependence (AD), by using machine-learning approaches. Participants included 39 amphetamine mono-dependent, 44 heroin mono-dependent, 58 polysubstance dependent, and 81 non-substance dependent individuals. The majority of substance dependent participants were in protracted abstinence. We used demographic, personality (trait impulsivity, trait psychopathy, aggression, sensation seeking), psychiatric (attention deficit hyperactivity disorder, conduct disorder, antisocial personality disorder, psychopathy, anxiety, depression), and neurocognitive impulsivity measures (Delay Discounting, Go/No-Go, Stop Signal, Immediate Memory, Balloon Analogue Risk, Cambridge Gambling, and Iowa Gambling tasks) as predictors in a machine-learning algorithm. The machine-learning approach revealed substance-specific multivariate profiles that classified HD and AD in new samples with high degree of accuracy. Out of 54 predictors, psychopathy was the only classifier common to both types of addiction. Important dissociations emerged between factors classifying HD and AD, which often showed opposite patterns among individuals with HD and AD. These results suggest that different mechanisms may underlie HD and AD, challenging the unitary account of drug addiction. This line of work may shed light on the development of standardized and cost-efficient clinical diagnostic tests and facilitate the development of individualized prevention and intervention programs for HD and AD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

    2017-09-05

    In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer.

    Science.gov (United States)

    Tang, Yew Chung; Ho, Szu-Chi; Tan, Elisabeth; Ng, Alvin Wei Tian; McPherson, John R; Goh, Germaine Yen Lin; Teh, Bin Tean; Bard, Frederic; Rozen, Steven G

    2018-03-22

    -SSL patterns of activity in a large proportion of PTEN-deficient breast cancer cell lines and are potential specific vulnerabilities in PTEN-deficient breast cancer. Furthermore, the NUAK1 PTEN-SSL vulnerability identified by RNA interference techniques can be recapitulated and exploited using the small molecule kinase inhibitor HTH-01-015. Thus, NUAK1 inhibition may be an effective strategy for precision treatment of PTEN-deficient breast tumors.

  11. Methods for Identifying Specific Language Impairment in Bilingual Populations in Germany

    Directory of Open Access Journals (Sweden)

    Cornelia Hamann

    2017-10-01

    Full Text Available This study investigates the performance of 22 monolingual and 54 bilingual children with and without specific language impairment (SLI, in a non-word repetition task (NWRT and a sentence repetition task (SRT. Both tasks were constructed according to the principles for LITMUS tools (Language Impairment Testing in Multilingual Settings developed within COST Action IS0804 and incorporated phonological or syntactic structures that are linguistically complex and have been shown to be difficult for children with SLI across languages. For phonology these are in particular (nonwords containing consonant clusters. In morphosyntax, complexity has been attributed to factors such as embedding and/or syntactic movement. Tasks focusing on such structures are expected to identify SLI in bilinguals across language combinations. This is notoriously difficult because structures that are problematic for typically developing bilinguals (BiTDs and monolingual children with SLI (MoSLI often overlap. We show that the NWRT and the SRT are reliable tools for identification of SLI in bilingual contexts. However, interpretation of the performance of bilingual children depends on background information as provided by parental questionnaires. To evaluate the accuracy of our tasks, we recruited children in ordinary kindergartens or schools and in speech language therapy centers and verified their status with a battery of standardized language tests, assessing bilingual children in both their languages. We consider a bilingual child language impaired if she shows impairments in two language domains in both her languages. For assessment, we used tests normed for monolinguals (with one exception and adjusted the norms for bilingualism and for language dominance. This procedure established the following groups: 10 typical monolinguals (MoTD, 12 MoSLI, 46 BiTD, and 8 bilingual children with SLI (BiSLI. Our results show that both tasks target relevant structures: monolingual

  12. Phospho-specific flow cytometry identifies aberrant signaling in indolent B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Blix Egil S

    2012-10-01

    Full Text Available Abstract Background Knowledge about signaling pathways in malignant cells may provide prognostic and diagnostic information in addition to identify potential molecular targets for therapy. B-cell receptor (BCR and co-receptor CD40 signaling is essential for normal B cells, and there is increasing evidence that signaling via BCR and CD40 plays an important role in the pathogenesis of B-cell lymphoma. The aim of this study was to investigate basal and induced signaling in lymphoma B cells and infiltrating T cells in single-cell suspensions of biopsies from small cell lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL and marginal zone lymphoma (MZL patients. Methods Samples from untreated SLL/CLL and MZL patients were examined for basal and activation induced signaling by phospho-specific flow cytometry. A panel of 9 stimulation conditions targeting B and T cells, including crosslinking of the B cell receptor (BCR, CD40 ligand and interleukins in combination with 12 matching phospho-protein readouts was used to study signaling. Results Malignant B cells from SLL/CLL patients had higher basal levels of phosphorylated (p-SFKs, p-PLCγ, p-ERK, p-p38, p-p65 (NF-κB, p-STAT5 and p-STAT6, compared to healthy donor B cells. In contrast, anti-BCR induced signaling was highly impaired in SLL/CLL and MZL B cells as determined by low p-SFK, p-SYK and p-PLCγ levels. Impaired anti-BCR-induced p-PLCγ was associated with reduced surface expression of IgM and CD79b. Similarly, CD40L-induced p-ERK and p-p38 were also significantly reduced in lymphoma B cells, whereas p-p65 (NF-κB was equal to that of normal B cells. In contrast, IL-2, IL-7 and IL-15 induced p-STAT5 in tumor-infiltrating T cells were not different from normal T cells. Conclusions BCR signaling and CD40L-induced p-p38 was suppressed in malignant B cells from SLL/CLL and MZL patients. Single-cell phospho-specific flow cytometry for detection of basal as well as activation

  13. Identifying context-specific competencies required by community Australian Football sports trainers.

    Science.gov (United States)

    Donaldson, Alex; Finch, Caroline F

    2012-08-01

    First-aid is a recommended injury prevention and risk management strategy in community sport; however, little is known about the sport-specific competencies required by first-aid providers. To achieve expert consensus on the competencies required by community Australian Football (community-AF) sports trainers. A three-round online Delphi process. Community-AF. 16 Australian sports first-aid and community-AF experts. Rating of competencies as either 'essential', 'expected', 'ideal' or 'not required'. Results After Round 3, 47 of the 77 (61%) competencies were endorsed as 'essential' or 'expected' for a sports trainer to effectively perform the activities required to the standards expected at a community-AF club by ≥75% of experts. These competencies covered: the role of the sports trainer; the responsibilities of the sports trainer; emergency management; injury and illness assessment and immediate management; taping; and injury prevention and risk management. Four competencies (5%) were endorsed as 'ideal' or 'not required' by ≥85% of experts and were excluded from further consideration. The 26 competencies where consensus was not reached were retained as second-tier, optional competencies. Sports trainers are important members of on-field first-aid teams, providing support to both injured players and other sports medicine professionals. The competencies identified in this study provide the basis of a proposed two-tiered community-AF-specific sports trainer education structure that can be implemented by the peak sports body. This includes six mandatory modules, relating to the 'required' competencies, and a further six optional modules covering competencies on which consensus was not reached.

  14. Theoretical and Numerical Modeling of Transport of Land Use-Specific Fecal Source Identifiers

    Science.gov (United States)

    Bombardelli, F. A.; Sirikanchana, K. J.; Bae, S.; Wuertz, S.

    2008-12-01

    Microbial contamination in coastal and estuarine waters is of particular concern to public health officials. In this work, we advocate that well-formulated and developed mathematical and numerical transport models can be combined with modern molecular techniques in order to predict continuous concentrations of microbial indicators under diverse scenarios of interest, and that they can help in source identification of fecal pollution. As a proof of concept, we present initially the theory, numerical implementation and validation of one- and two-dimensional numerical models aimed at computing the distribution of fecal source identifiers in water bodies (based on Bacteroidales marker DNA sequences) coming from different land uses such as wildlife, livestock, humans, dogs or cats. These models have been developed to allow for source identification of fecal contamination in large bodies of water. We test the model predictions using diverse velocity fields and boundary conditions. Then, we present some preliminary results of an application of a three-dimensional water quality model to address the source of fecal contamination in the San Pablo Bay (SPB), United States, which constitutes an important sub-embayment of the San Francisco Bay. The transport equations for Bacteroidales include the processes of advection, diffusion, and decay of Bacteroidales. We discuss the validation of the developed models through comparisons of numerical results with field campaigns developed in the SPB. We determine the extent and importance of the contamination in the bay for two decay rates obtained from field observations, corresponding to total host-specific Bacteroidales DNA and host-specific viable Bacteroidales cells, respectively. Finally, we infer transport conditions in the SPB based on the numerical results, characterizing the fate of outflows coming from the Napa, Petaluma and Sonoma rivers.

  15. SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity.

    Directory of Open Access Journals (Sweden)

    Tzong-Yi Lee

    Full Text Available S-nitrosylation, the covalent attachment of a nitric oxide to (NO the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1 and human hemoglobin subunit beta (HBB. Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (http://csb.cse.yzu.edu.tw/SNOSite/, for identifying S-nitrosylation sites on the uncharacterized protein sequences.

  16. Life support decision making in critical care: Identifying and appraising the qualitative research evidence.

    Science.gov (United States)

    Giacomini, Mita; Cook, Deborah; DeJean, Deirdre

    2009-04-01

    The objective of this study is to identify and appraise qualitative research evidence on the experience of making life-support decisions in critical care. In six databases and supplementary sources, we sought original research published from January 1990 through June 2008 reporting qualitative empirical studies of the experience of life-support decision making in critical care settings. Fifty-three journal articles and monographs were included. Of these, 25 reported prospective studies and 28 reported retrospective studies. We abstracted methodologic characteristics relevant to the basic critical appraisal of qualitative research (prospective data collection, ethics approval, purposive sampling, iterative data collection and analysis, and any method to corroborate findings). Qualitative research traditions represented include grounded theory (n = 15, 28%), ethnography or naturalistic methods (n = 15, 28%), phenomenology (n = 9, 17%), and other or unspecified approaches (n = 14, 26%). All 53 documents describe the research setting; 97% indicate purposive sampling of participants. Studies vary in their capture of multidisciplinary clinician and family perspectives. Thirty-one (58%) report research ethics board review. Only 49% report iterative data collection and analysis, and eight documents (15%) describe an analytically driven stopping point for data collection. Thirty-two documents (60%) indicated a method for corroborating findings. Qualitative evidence often appears outside of clinical journals, with most research from the United States. Prospective, observation-based studies follow life-support decision making directly. These involve a variety of participants and yield important insights into interactions, communication, and dynamics. Retrospective, interview-based studies lack this direct engagement, but focus on the recollections of fewer types of participants (particularly patients and physicians), and typically address specific issues (communication and

  17. Genome-wide association studies identify four ER negative–specific breast cancer risk loci

    Science.gov (United States)

    Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara; Michailidou, Kyriaki; Schmidt, Marjanka K; Brook, Mark N; orr, Nick; Rhie, Suhn Kyong; Riboli, Elio; Feigelson, Heather s; Le Marchand, Loic; Buring, Julie E; Eccles, Diana; Miron, Penelope; Fasching, Peter A; Brauch, Hiltrud; Chang-Claude, Jenny; Carpenter, Jane; Godwin, Andrew K; Nevanlinna, Heli; Giles, Graham G; Cox, Angela; Hopper, John L; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dicks, Ed; Howat, Will J; Schoof, Nils; Bojesen, Stig E; Lambrechts, Diether; Broeks, Annegien; Andrulis, Irene L; Guénel, Pascal; Burwinkel, Barbara; Sawyer, Elinor J; Hollestelle, Antoinette; Fletcher, Olivia; Winqvist, Robert; Brenner, Hermann; Mannermaa, Arto; Hamann, Ute; Meindl, Alfons; Lindblom, Annika; Zheng, Wei; Devillee, Peter; Goldberg, Mark S; Lubinski, Jan; Kristensen, Vessela; Swerdlow, Anthony; Anton-Culver, Hoda; Dörk, Thilo; Muir, Kenneth; Matsuo, Keitaro; Wu, Anna H; Radice, Paolo; Teo, Soo Hwang; Shu, Xiao-Ou; Blot, William; Kang, Daehee; Hartman, Mikael; Sangrajrang, Suleeporn; Shen, Chen-Yang; Southey, Melissa C; Park, Daniel J; Hammet, Fleur; Stone, Jennifer; Veer, Laura J Van’t; Rutgers, Emiel J; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Peto, Julian; Schrauder, Michael G; Ekici, Arif B; Beckmann, Matthias W; Silva, Isabel dos Santos; Johnson, Nichola; Warren, Helen; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Truong, Therese; Laurent-Puig, Pierre; Kerbrat, Pierre; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Milne, Roger L; Perez, Jose Ignacio Arias; Menéndez, Primitiva; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Lichtner, Peter; Lochmann, Magdalena; Justenhoven, Christina; Ko, Yon-Dschun; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Greco, Dario; Heikkinen, Tuomas; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Antonenkova, Natalia N; Margolin, Sara; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Balleine, Rosemary; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Neven, Patrick; Dieudonné, Anne-Sophie; Leunen, Karin; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Peterlongo, Paolo; Peissel, Bernard; Bernard, Loris; Olson, Janet E; Wang, Xianshu; Stevens, Kristen; Severi, Gianluca; Baglietto, Laura; Mclean, Catriona; Coetzee, Gerhard A; Feng, Ye; Henderson, Brian E; Schumacher, Fredrick; Bogdanova, Natalia V; Labrèche, France; Dumont, Martine; Yip, Cheng Har; Taib, Nur Aishah Mohd; Cheng, Ching-Yu; Shrubsole, Martha; Long, Jirong; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Kriege, Mieke; Hooning, Maartje J; Van den Ouweland, Ans M W; Van Deurzen, Carolien H M; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Balasubramanian, Sabapathy P; Cross, Simon S; Reed, Malcolm W R; Signorello, Lisa; Cai, Qiuyin; Shah, Mitul; Miao, Hui; Chan, Ching Wan; Chia, Kee Seng; Jakubowska, Anna; Jaworska, Katarzyna; Durda, Katarzyna; Hsiung, Chia-Ni; Wu, Pei-Ei; Yu, Jyh-Cherng; Ashworth, Alan; Jones, Michael; Tessier, Daniel C; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Vincent, Daniel; Bacot, Francois; Ambrosone, Christine B; Bandera, Elisa V; John, Esther M; Chen, Gary K; Hu, Jennifer J; Rodriguez-gil, Jorge L; Bernstein, Leslie; Press, Michael F; Ziegler, Regina G; Millikan, Robert M; Deming-Halverson, Sandra L; Nyante, Sarah; Ingles, Sue A; Waisfisz, Quinten; Tsimiklis, Helen; Makalic, Enes; Schmidt, Daniel; Bui, Minh; Gibson, Lorna; Müller-Myhsok, Bertram; Schmutzler, Rita K; Hein, Rebecca; Dahmen, Norbert; Beckmann, Lars; Aaltonen, Kirsimari; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Turnbull, Clare; Rahman, Nazneen; Meijers-Heijboer, Hanne; Uitterlinden, Andre G; Rivadeneira, Fernando; Olswold, Curtis; Slager, Susan; Pilarski, Robert; Ademuyiwa, Foluso; Konstantopoulou, Irene; Martin, Nicholas G; Montgomery, Grant W; Slamon, Dennis J; Rauh, Claudia; Lux, Michael P; Jud, Sebastian M; Bruning, Thomas; Weaver, Joellen; Sharma, Priyanka; Pathak, Harsh; Tapper, Will; Gerty, Sue; Durcan, Lorraine; Trichopoulos, Dimitrios; Tumino, Rosario; Peeters, Petra H; Kaaks, Rudolf; Campa, Daniele; Canzian, Federico; Weiderpass, Elisabete; Johansson, Mattias; Khaw, Kay-Tee; Travis, Ruth; Clavel-Chapelon, Françoise; Kolonel, Laurence N; Chen, Constance; Beck, Andy; Hankinson, Susan E; Berg, Christine D; Hoover, Robert N; Lissowska, Jolanta; Figueroa, Jonine D; Chasman, Daniel I; Gaudet, Mia M; Diver, W Ryan; Willett, Walter C; Hunter, David J; Simard, Jacques; Benitez, Javier; Dunning, Alison M; Sherman, Mark E; Chenevix-Trench, Georgia; Chanock, Stephen J; Hall, Per; Pharoah, Paul D P; Vachon, Celine; Easton, Douglas F; Haiman, Christopher A; Kraft, Peter

    2013-01-01

    Estrogen receptor (ER)-negative tumors represent 20–30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry1. The etiology2 and clinical behavior3 of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition4. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10−12 and LGR6, P = 1.4 × 10−8), 2p24.1 (P = 4.6 × 10−8) and 16q12.2 (FTO, P = 4.0 × 10−8), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers. PMID:23535733

  18. Genome-wide association studies identify four ER negative-specific breast cancer risk loci.

    Science.gov (United States)

    Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara; Michailidou, Kyriaki; Schmidt, Marjanka K; Brook, Mark N; Orr, Nick; Rhie, Suhn Kyong; Riboli, Elio; Feigelson, Heather S; Le Marchand, Loic; Buring, Julie E; Eccles, Diana; Miron, Penelope; Fasching, Peter A; Brauch, Hiltrud; Chang-Claude, Jenny; Carpenter, Jane; Godwin, Andrew K; Nevanlinna, Heli; Giles, Graham G; Cox, Angela; Hopper, John L; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dicks, Ed; Howat, Will J; Schoof, Nils; Bojesen, Stig E; Lambrechts, Diether; Broeks, Annegien; Andrulis, Irene L; Guénel, Pascal; Burwinkel, Barbara; Sawyer, Elinor J; Hollestelle, Antoinette; Fletcher, Olivia; Winqvist, Robert; Brenner, Hermann; Mannermaa, Arto; Hamann, Ute; Meindl, Alfons; Lindblom, Annika; Zheng, Wei; Devillee, Peter; Goldberg, Mark S; Lubinski, Jan; Kristensen, Vessela; Swerdlow, Anthony; Anton-Culver, Hoda; Dörk, Thilo; Muir, Kenneth; Matsuo, Keitaro; Wu, Anna H; Radice, Paolo; Teo, Soo Hwang; Shu, Xiao-Ou; Blot, William; Kang, Daehee; Hartman, Mikael; Sangrajrang, Suleeporn; Shen, Chen-Yang; Southey, Melissa C; Park, Daniel J; Hammet, Fleur; Stone, Jennifer; Veer, Laura J Van't; Rutgers, Emiel J; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Peto, Julian; Schrauder, Michael G; Ekici, Arif B; Beckmann, Matthias W; Dos Santos Silva, Isabel; Johnson, Nichola; Warren, Helen; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Truong, Therese; Laurent-Puig, Pierre; Kerbrat, Pierre; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Milne, Roger L; Perez, Jose Ignacio Arias; Menéndez, Primitiva; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Lichtner, Peter; Lochmann, Magdalena; Justenhoven, Christina; Ko, Yon-Dschun; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Greco, Dario; Heikkinen, Tuomas; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Antonenkova, Natalia N; Margolin, Sara; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Balleine, Rosemary; Tseng, Chiu-Chen; Berg, David Van Den; Stram, Daniel O; Neven, Patrick; Dieudonné, Anne-Sophie; Leunen, Karin; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Peterlongo, Paolo; Peissel, Bernard; Bernard, Loris; Olson, Janet E; Wang, Xianshu; Stevens, Kristen; Severi, Gianluca; Baglietto, Laura; McLean, Catriona; Coetzee, Gerhard A; Feng, Ye; Henderson, Brian E; Schumacher, Fredrick; Bogdanova, Natalia V; Labrèche, France; Dumont, Martine; Yip, Cheng Har; Taib, Nur Aishah Mohd; Cheng, Ching-Yu; Shrubsole, Martha; Long, Jirong; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Kriege, Mieke; Hooning, Maartje J; van den Ouweland, Ans M W; van Deurzen, Carolien H M; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Balasubramanian, Sabapathy P; Cross, Simon S; Reed, Malcolm W R; Signorello, Lisa; Cai, Qiuyin; Shah, Mitul; Miao, Hui; Chan, Ching Wan; Chia, Kee Seng; Jakubowska, Anna; Jaworska, Katarzyna; Durda, Katarzyna; Hsiung, Chia-Ni; Wu, Pei-Ei; Yu, Jyh-Cherng; Ashworth, Alan; Jones, Michael; Tessier, Daniel C; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Vincent, Daniel; Bacot, Francois; Ambrosone, Christine B; Bandera, Elisa V; John, Esther M; Chen, Gary K; Hu, Jennifer J; Rodriguez-Gil, Jorge L; Bernstein, Leslie; Press, Michael F; Ziegler, Regina G; Millikan, Robert M; Deming-Halverson, Sandra L; Nyante, Sarah; Ingles, Sue A; Waisfisz, Quinten; Tsimiklis, Helen; Makalic, Enes; Schmidt, Daniel; Bui, Minh; Gibson, Lorna; Müller-Myhsok, Bertram; Schmutzler, Rita K; Hein, Rebecca; Dahmen, Norbert; Beckmann, Lars; Aaltonen, Kirsimari; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Turnbull, Clare; Rahman, Nazneen; Meijers-Heijboer, Hanne; Uitterlinden, Andre G; Rivadeneira, Fernando; Olswold, Curtis; Slager, Susan; Pilarski, Robert; Ademuyiwa, Foluso; Konstantopoulou, Irene; Martin, Nicholas G; Montgomery, Grant W; Slamon, Dennis J; Rauh, Claudia; Lux, Michael P; Jud, Sebastian M; Bruning, Thomas; Weaver, Joellen; Sharma, Priyanka; Pathak, Harsh; Tapper, Will; Gerty, Sue; Durcan, Lorraine; Trichopoulos, Dimitrios; Tumino, Rosario; Peeters, Petra H; Kaaks, Rudolf; Campa, Daniele; Canzian, Federico; Weiderpass, Elisabete; Johansson, Mattias; Khaw, Kay-Tee; Travis, Ruth; Clavel-Chapelon, Françoise; Kolonel, Laurence N; Chen, Constance; Beck, Andy; Hankinson, Susan E; Berg, Christine D; Hoover, Robert N; Lissowska, Jolanta; Figueroa, Jonine D; Chasman, Daniel I; Gaudet, Mia M; Diver, W Ryan; Willett, Walter C; Hunter, David J; Simard, Jacques; Benitez, Javier; Dunning, Alison M; Sherman, Mark E; Chenevix-Trench, Georgia; Chanock, Stephen J; Hall, Per; Pharoah, Paul D P; Vachon, Celine; Easton, Douglas F; Haiman, Christopher A; Kraft, Peter

    2013-04-01

    Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.

  19. Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

    Science.gov (United States)

    San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

    2014-12-01

    Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

  20. The research on business rules classification and specification methods

    OpenAIRE

    Baltrušaitis, Egidijus

    2005-01-01

    The work is based on the research of business rules classification and specification methods. The basics of business rules approach are discussed. The most common business rules classification and modeling methods are analyzed. Business rules modeling techniques and tools for supporting them in the information systems are presented. Basing on the analysis results business rules classification method is proposed. Templates for every business rule type are presented. Business rules structuring ...

  1. A Framework for Rigorously Identifying Research Gaps in Qualitative Literature Reviews

    DEFF Research Database (Denmark)

    Müller-Bloch, Christoph; Kranz, Johann

    2015-01-01

    Identifying research gaps is a fundamental goal of literature reviewing. While it is widely acknowledged that literature reviews should identify research gaps, there are no methodological guidelines for how to identify research gaps in qualitative literature reviews ensuring rigor and replicability....... Our study addresses this gap and proposes a framework that should help scholars in this endeavor without stifling creativity. To develop the framework we thoroughly analyze the state-of-the-art procedure of identifying research gaps in 40 recent literature reviews using a grounded theory approach....... Based on the data, we subsequently derive a framework for identifying research gaps in qualitative literature reviews and demonstrate its application with an example. Our results provide a modus operandi for identifying research gaps, thus enabling scholars to conduct literature reviews more rigorously...

  2. 76 FR 44593 - Identifying the Center for Drug Evaluation and Research's Science and Research Needs...

    Science.gov (United States)

    2011-07-26

    ... research needs outlined in the report, CDER hopes to stimulate research and foster collaborations with... research needs, CDER hopes to stimulate research and foster collaborations with external partners and... issues across teams, divisions, or offices; and (3) emerging scientific challenges. A comprehensive set...

  3. Setting Priorities for Diabetic Retinopathy Clinical Research and Identifying Evidence Gaps.

    Science.gov (United States)

    Le, Jimmy T; Hutfless, Susan; Li, Tianjing; Bressler, Neil M; Heyward, James; Bittner, Ava K; Glassman, Adam; Dickersin, Kay

    2017-01-01

    Prioritizing comparative effectiveness research may contribute to obtaining answers that clinicians perceive they need and may minimize research that could be considered wasteful. Our objective was to identify evidence gaps and set priorities for new systematic reviews and randomized controlled trials for managing diabetic retinopathy (DR), including diabetic macular edema (DME). Cross-sectional study. Diabetic Retinopathy Clinical Research Network (DRCR.net) investigators. We provided recommendations from the American Academy of Ophthalmology's 2012 Preferred Practice Patterns for Diabetic Retinopathy as 91 answerable clinical research questions about intervention effectiveness to 410 DRCR.net investigators to rate each question's importance from 0 (not important) to 10 (very important) using a 2-round Delphi survey and to suggest additional questions. We considered questions as high priority if at least 75% of respondents to both rounds assigned an importance rating of 5 or more in round 2. We also extracted outcome measures relevant to DR and asked respondents to identify those that must be measured in all studies. We mapped Cochrane reviews published up to March 2016 to high-priority clinical research questions. Ranking of importance of each clinical question. Thirty-two individuals completed rounds 1 and 2 and suggested 15 questions. Among the final list of 106 clinical research questions, 22 questions met our definition of high priority: 9 of 22 concerned the effectiveness of anti-VEGF therapy, and 13 of 22 focused on how often patients should be followed up (re-examination) and treatment effectiveness in patients with specific characteristics (e.g., DME). Outcomes that 75% or more of respondents marked as "must be measured in all studies" included visual acuity and visual loss, death of participants, and intraocular pressure. Only 1 prioritized question was associated with conclusive evidence from a Cochrane systematic review. A limited response rate among

  4. Ethnographic research in immigrant-specific drug abuse recovery houses.

    Science.gov (United States)

    Pagano, Anna; Lee, Juliet P; García, Victor; Recarte, Carlos

    2018-01-01

    Access to study populations is a major concern for drug use and treatment researchers. Spaces related to drug use and treatment have varying levels of researcher accessibility based on several issues, including legality, public versus private settings, and insider/outsider status. Ethnographic research methods are indispensable for gaining and maintaining access to hidden or "hard-to-reach" populations. Here, we discuss our long-term ethnographic research on drug abuse recovery houses created by and for Latino migrants and immigrants in Northern California. We take our field work experiences as a case study to examine the problem of researcher access and how ethnographic strategies can be successfully applied to address it, focusing especially on issues of entrée, building rapport, and navigating field-specific challenges related to legality, public/private settings, and insider/outsider status. We conclude that continued funding support for ethnography is essential for promoting health disparities research focused on diverse populations in recovery from substance use disorders.

  5. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    NARCIS (Netherlands)

    van Leeuwen, E.M.; Karssen, L.C.; Deelen, J.; Isaacs, A.; Medina-Gomez, C.; Mbarek, H.; Kanterakis, A.; Trompet, S.; Postmus, I.; Verweij, N.; van Enckevort, D.; Huffman, J.E.; White, C.C.; Feitosa, M.F.; Bartz, T.M.; Manichaikul, A.; Joshi, P.K.; Peloso, G.M.; Deelen, P.; Dijk, F.; Willemsen, G.; de Geus, E.J.C.; Milaneschi, Y.; Penninx, B.W.J.H.; Francioli, L.C.; Menelaou, A.; Pulit, S.L.; Rivadeneira, F.; Hofman, A.; Oostra, B.A.; Franco, O.H.; Mateo Leach, I.; Beekman, M.; de Craen, A.J.; Uh, H.W.; Trochet, H.; Hocking, L.J.; Porteous, D.J.; Sattar, N.; Packard, C.J.; Buckley, B.M.; Brody, J.A.; Bis, J.C.; Rotter, J.I.; Mychaleckyj, J.C.; Campbell, H.; Duan, Q.; Lange, L.A.; Wilson, J.F.; Hayward, C.; Polasek, O.; Vitart, V.; Rudan, I.; Wright, A.F.; Rich, S.S.; Psaty, B.M.; Borecki, I.B.; Kearney, P.M.; Stott, D.J.; Cupples, L.A.; Jukema, J.W.; van der Harst, P.; Sijbrands, E.J.; Hottenga, J.J.; Uitterlinden, A.G.; Swertz, M.A.; van Ommen, G.J.B; Bakker, P.I.W.; Slagboom, P.E.; Boomsma, D.I.; Wijmenga, C.; van Duijn, C.M.

    2015-01-01

    Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created

  6. 75 FR 57768 - Access to Confidential Business Information by Eastern Research Group and Its Identified...

    Science.gov (United States)

    2010-09-22

    ... Business Information by Eastern Research Group and Its Identified Subcontractor AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: EPA has authorized its contractor, Eastern Research Group... the information may be claimed or determined to be Confidential Business Information (CBI). DATES...

  7. Using Latent Semantic Analysis to Identify Research Trends in OpenStreetMap

    Directory of Open Access Journals (Sweden)

    Sukhjit Singh Sehra

    2017-07-01

    Full Text Available OpenStreetMap (OSM, based on collaborative mapping, has become a subject of great interest to the academic community, resulting in a considerable body of literature produced by many researchers. In this paper, we use Latent Semantic Analysis (LSA to help identify the emerging research trends in OSM. An extensive corpus of 485 academic abstracts of papers published during the period 2007–2016 was used. Five core research areas and fifty research trends were identified in this study. In addition, potential future research directions have been provided to aid geospatial information scientists, technologists and researchers in undertaking future OSM research.

  8. Identifying Country-Specific Cultures of Physics Education: A differential item functioning approach

    Science.gov (United States)

    Mesic, Vanes

    2012-11-01

    In international large-scale assessments of educational outcomes, student achievement is often represented by unidimensional constructs. This approach allows for drawing general conclusions about country rankings with respect to the given achievement measure, but it typically does not provide specific diagnostic information which is necessary for systematic comparisons and improvements of educational systems. Useful information could be obtained by exploring the differences in national profiles of student achievement between low-achieving and high-achieving countries. In this study, we aimed to identify the relative weaknesses and strengths of eighth graders' physics achievement in Bosnia and Herzegovina in comparison to the achievement of their peers from Slovenia. For this purpose, we ran a secondary analysis of Trends in International Mathematics and Science Study (TIMSS) 2007 data. The student sample consisted of 4,220 students from Bosnia and Herzegovina and 4,043 students from Slovenia. After analysing the cognitive demands of TIMSS 2007 physics items, the correspondent differential item functioning (DIF)/differential group functioning contrasts were estimated. Approximately 40% of items exhibited large DIF contrasts, indicating significant differences between cultures of physics education in Bosnia and Herzegovina and Slovenia. The relative strength of students from Bosnia and Herzegovina showed to be mainly associated with the topic area 'Electricity and magnetism'. Classes of items which required the knowledge of experimental method, counterintuitive thinking, proportional reasoning and/or the use of complex knowledge structures proved to be differentially easier for students from Slovenia. In the light of the presented results, the common practice of ranking countries with respect to universally established cognitive categories seems to be potentially misleading.

  9. An Investigation to Validate the Grammar and Phonology Screening (GAPS) Test to Identify Children with Specific Language Impairment

    Science.gov (United States)

    van der Lely, Heather K. J.; Payne, Elisabeth; McClelland, Alastair

    2011-01-01

    Background The extraordinarily high incidence of grammatical language impairments in developmental disorders suggests that this uniquely human cognitive function is “fragile”. Yet our understanding of the neurobiology of grammatical impairments is limited. Furthermore, there is no “gold-standard” to identify grammatical impairments and routine screening is not undertaken. An accurate screening test to identify grammatical abilities would serve the research, health and education communities, further our understanding of developmental disorders, and identify children who need remediation, many of whom are currently un-diagnosed. A potential realistic screening tool that could be widely administered is the Grammar and Phonology Screening (GAPS) test – a 10 minute test that can be administered by professionals and non-professionals alike. Here we provide a further step in evaluating the validity and accuracy (sensitivity and specificity) of the GAPS test in identifying children who have Specific Language Impairment (SLI). Methods and Findings We tested three groups of children; two groups aged 3;6–6:6, a typically developing (n = 30) group, and a group diagnosed with SLI: (n = 11) (Young (Y)-SLI), and a further group aged 6;9–8;11 with SLI (Older (O)-SLI) (n = 10) who were above the test age norms. We employed a battery of language assessments including the GAPS test to assess the children's language abilities. For Y-SLI children, analyses revealed a sensitivity and specificity at the 5th and 10th percentile of 1.00 and 0.98, respectively, and for O-SLI children at the 10th and 15th percentile .83 and .90, respectively. Conclusions The findings reveal that the GAPS is highly accurate in identifying impaired vs. non-impaired children up to 6;8 years, and has moderate-to-high accuracy up to 9 years. The results indicate that GAPS is a realistic tool for the early identification of grammatical abilities and impairment in young children. A larger

  10. Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

    Science.gov (United States)

    Condie, Brian G; Urbanski, William M

    2014-01-01

    Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

  11. Identifying potentially eligible subjects for research: paper-based logs versus the hospital administrative database.

    Science.gov (United States)

    Magee, L A; Massey, K; von Dadelszen, P; Fazio, M; Payne, B; Liston, R

    2011-12-01

    The Canadian Perinatal Network (CPN) is a national database focused on threatened very pre-term birth. Women with one or more conditions most commonly associated with very pre-term birth are included if admitted to a participating tertiary perinatal unit at 22 weeks and 0 days to 28 weeks and 6 days. At BC Women's Hospital and Health Centre, we compared traditional paper-based ward logs and a search of the Canadian Institute for Health Information (CIHI) electronic database of inpatient discharges to identify patients. The study identified 244 women potentially eligible for inclusion in the CPN admitted between April and December 2007. Of the 155 eligible women entered into the CPN database, each method identified a similar number of unique records (142 and 147) not ascertained by the other: 10 (6.4%) by CIHI search and 5 (3.2%) by ward log review. However, CIHI search achieved these results after reviewing fewer records (206 vs. 223) in less time (0.67 vs. 13.6 hours for ward logs). Either method is appropriate for identification of potential research subjects using gestational age criteria. Although electronic methods are less time-consuming, they cannot be performed until after the patient is discharged and records and charts are reviewed. Each method's advantages and disadvantages will dictate use for a specific project.

  12. Interdisciplinary research framework for identifying research needs. Case: bioenergy-biodiversity interlinkages

    Energy Technology Data Exchange (ETDEWEB)

    Furman, E.; Peltola, T.; Varjopuro, R. (eds.)

    2009-05-15

    A loss of biological diversity continues in spite of the existing, and in some respects, rather elaborate and heavy attempts at management and protection. It has been argued that one of the reasons for the lack of success is the unmet and challenging knowledge needs. Meeting the needs requires integration of various sciences and expertise, since attempts to manage biodiversity gives rise also to many emerging, complex and political questions. Integration of the disciplines needs practices that are able to overcome practical, institutional and cultural obstacles. ALTER-Net, a European network for research on biological diversity under the 6th framework programme, has aimed to undertake further interdisciplinary research that will feed into the addressing of societal needs. This report describes how the integration of research progressed and succeeded during the five year life span of ALTER-Net. Initially the integration between disciplines was given as an overall goal, which did result in determining concrete practices of integration between the sciences, teams and partner organisations. The analysis shows that in spite of complications an interdisciplinary research approach can evolve in large research networks, but this can happen also through unanticipated channels. A large network allows room for several parallel processes of integration. The report depicts the development of and choices leading to the development of an interdisciplinary research framework for ALTER-Net, the IDR framework. The framework presents a method to enhance interdisciplinary syntheses of emerging policy-relevant issues and to further develop the identification of relevant topics as interdisciplinary research projects. The IDR framework was tested by focusing on the interlinkages between the bioenergy question and biodiversity. The report consists of a synthesis of pressing research needs pertaining to that topic. The report presents how the IDR framework was constructed using a method

  13. Specification Search for Identifying the Correct Mean Trajectory in Polynomial Latent Growth Models

    Science.gov (United States)

    Kim, Minjung; Kwok, Oi-Man; Yoon, Myeongsun; Willson, Victor; Lai, Mark H. C.

    2016-01-01

    This study investigated the optimal strategy for model specification search under the latent growth modeling (LGM) framework, specifically on searching for the correct polynomial mean or average growth model when there is no a priori hypothesized model in the absence of theory. In this simulation study, the effectiveness of different starting…

  14. Identifying research priorities for public health research to address health inequalities: use of Delphi-like survey methods.

    Science.gov (United States)

    Turner, S; Ollerhead, E; Cook, A

    2017-10-09

    In the funding of health research and public health research it is vital that research questions posed are important and that funded research meets a research need or a gap in evidence. Many methods are used in the identification of research priorities, however, these can be resource intensive, costly and logistically challenging. Identifying such research priorities can be particularly challenging for complex public health problems as there is a need to consult a number of experts across disciplines and with a range of expertise. This study investigated the use of Delphi-like survey methods in identifying important research priorities relating to health inequalities and framing tractable research questions for topic areas identified. The study was conducted in two phases, both using Delphi-like survey methods. Firstly, public health professionals with an interest in health inequalities were asked to identify research priorities. Secondly academic researchers were asked to frame tractable research questions relating to the priorities identified. These research priorities identified using Delphi-like survey methods were subsequently compared to those identified using different methods. A total of 52 public health professionals and 21 academics across the United Kingdom agreed to take part. The response rates were high, from public health professionals across three survey rounds (69%, 50% and 40%) and from academics across one round (52%), indicating that participants were receptive to the method and motivated to respond. The themes identified as encompassing the most important research priorities were mental health, healthy environment and health behaviours. Within these themes, the topic areas that emerged most strongly included community interventions for prevention of mental health problems and the food and alcohol environment. Some responses received from academic researchers were (as requested) in the form of tractable research questions, whereas others

  15. Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design.

    Science.gov (United States)

    Neshich, Izabella Agostinho Pena; Nishimura, Leticia; de Moraes, Fabio Rogerio; Salim, Jose Augusto; Villalta-Romero, Fabian; Borro, Luiz; Yano, Inacio Henrique; Mazoni, Ivan; Tasic, Ljubica; Jardine, Jose Gilberto; Neshich, Goran

    2015-01-01

    The term "agrochemicals" is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A "drug" on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally

  16. Your name is not good enough: introducing the ORCID researcher identifier at Imperial College London

    Directory of Open Access Journals (Sweden)

    Torsten Reimer

    2015-11-01

    Full Text Available The ORCID researcher identifier ensures that research outputs can always reliably be traced back to their authors. ORCID also makes it possible to automate the sharing of research information, thereby increasing data quality, reducing duplication of effort for academics and saving institutions money. In 2014, Imperial College London created ORCID identifiers (iDs for academic and research staff. This article discusses the implementation project in the context of the role of ORCID in the global scholarly communications system. It shows how ORCID can be used to automate reporting, help with research data publication and support open access (OA.

  17. A Research Agenda for Identifying and Developing Required Competencies in Software Engineering

    Directory of Open Access Journals (Sweden)

    Yvonne Sedelmaier

    2013-04-01

    Full Text Available 0 0 1 130 820 Hochschule Coburg 6 1 949 14.0 96 Normal 0 21 false false false DE JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normale Tabelle"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman";} Various issues make learning and teaching software engineering a challenge for both students and instructors. Since there are no standard curricula and no cookbook recipes for successful software engineering, it is fairly hard to figure out which specific topics and competencies should be learned or acquired by a particular group of students. Furthermore, it is not clear which particular didactic approaches might work well for a specific topic and a particular group of students. This contribution presents a research agenda that aims at identifying relevant competencies and environmental constraints as well as their effect on learning and teaching software engineering. To that end, an experimental approach will be taken. As a distinctive feature, this approach iteratively introduces additional or modified didactical methods into existing courses and carefully evaluates their appropriateness. Thus, it continuously improves these methods.

  18. A sex-specific metabolite identified in a marine invertebrate utilizing phosphorus-31 nuclear magnetic resonance.

    Directory of Open Access Journals (Sweden)

    Robert A Kleps

    Full Text Available Hormone level differences are generally accepted as the primary cause for sexual dimorphism in animal and human development. Levels of low molecular weight metabolites also differ between men and women in circulating amino acids, lipids and carbohydrates and within brain tissue. While investigating the metabolism of blue crab tissues using Phosphorus-31 Nuclear Magnetic Resonance, we discovered that only the male blue crab (Callinectes sapidus contained a phosphorus compound with a chemical shift well separated from the expected phosphate compounds. Spectra obtained from male gills were readily differentiated from female gill spectra. Analysis from six years of data from male and female crabs documented that the sex-specificity of this metabolite was normal for this species. Microscopic analysis of male and female gills found no differences in their gill anatomy or the presence of parasites or bacteria that might produce this phosphorus compound. Analysis of a rare gynandromorph blue crab (laterally, half male and half female proved that this sex-specificity was an intrinsic biochemical process and was not caused by any variations in the diet or habitat of male versus female crabs. The existence of a sex-specific metabolite is a previously unrecognized, but potentially significant biochemical phenomenon. An entire enzyme system has been synthesized and activated only in one sex. Unless blue crabs are a unique species, sex-specific metabolites are likely to be present in other animals. Would the presence or absence of a sex-specific metabolite affect an animal's development, anatomy and biochemistry?

  19. Lessons learned from England's Health Checks Programme: using qualitative research to identify and share best practice.

    Science.gov (United States)

    Ismail, Hanif; Kelly, Shona

    2015-10-20

    This study aimed to explore the challenges and barriers faced by staff involved in the delivery of the National Health Service (NHS) Health Check, a systematic cardiovascular disease (CVD) risk assessment and management program in primary care. Data have been derived from three qualitative evaluations that were conducted in 25 General Practices and involved in depth interviews with 58 staff involved all levels of the delivery of the Health Checks. Analysis of the data was undertaken using the framework approach and findings are reported within the context of research and practice considerations. Findings indicated that there is no 'one size fits all' blueprint for maximising uptake although success factors were identified: evolution of the programme over time in response to local needs to suit the particular characteristics of the patient population; individual staff characteristics such as being proactive, enthusiastic and having specific responsibility; a supportive team. Training was clearly identified as an area that needed addressing and practitioners would benefit from CVD specific baseline training and refresher courses to keep them up to date with recent developments in the area. However there were other external factors that impinged on an individual's ability to provide an effective service, some of these were outside the control of individuals and included cutbacks in referral services, insufficient space to run clinics or general awareness of the Health Checks amongst patients. The everyday experiences of practitioners who participated in this study suggest that overall, Health Check is perceived as a worthwhile exercise. But, organisational and structural barriers need to be addressed. We also recommend that clear referral pathways be in place so staff can refer patients to appropriate services (healthy eating sessions, smoking cessation, and exercise referrals). Local authorities need to support initiatives that enable data sharing and linkage so that

  20. Development and pilot test of a process to identify research needs from a systematic review.

    Science.gov (United States)

    Saldanha, Ian J; Wilson, Lisa M; Bennett, Wendy L; Nicholson, Wanda K; Robinson, Karen A

    2013-05-01

    To ensure appropriate allocation of research funds, we need methods for identifying high-priority research needs. We developed and pilot tested a process to identify needs for primary clinical research using a systematic review in gestational diabetes mellitus. We conducted eight steps: abstract research gaps from a systematic review using the Population, Intervention, Comparison, Outcomes, and Settings (PICOS) framework; solicit feedback from the review authors; translate gaps into researchable questions using the PICOS framework; solicit feedback from multidisciplinary stakeholders at our institution; establish consensus among multidisciplinary external stakeholders on the importance of the research questions using the Delphi method; prioritize outcomes; develop conceptual models to highlight research needs; and evaluate the process. We identified 19 research questions. During the Delphi method, external stakeholders established consensus for 16 of these 19 questions (15 with "high" and 1 with "medium" clinical benefit/importance). We pilot tested an eight-step process to identify clinically important research needs. Before wider application of this process, it should be tested using systematic reviews of other diseases. Further evaluation should include assessment of the usefulness of the research needs generated using this process for primary researchers and funders. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Using a research framework to identify knowledge gaps in research on food marketing to children in Australia.

    Science.gov (United States)

    Chapman, Kathy; Kelly, Bridget; King, Lesley

    2009-06-01

    Research in the field of food marketing to children requires a better understanding of the research gaps in order to inform policy development. The purpose of this paper was to propose a framework for classifying food marketing research, using Australian research on food marketing to children to demonstrate how this framework can be used to determine knowledge gaps. A literature review of research databases and 'grey' material was conducted to identify research from the previous 10 years. Studies were classified according to their research focus, and media type, as either: exposure, including content analyses; effects of exposure, including opinions, attitudes and actions resulting from food marketing exposure; regulations, including the type and level of regulation that applies to food marketing; or breaches of regulations, including instances where marketing regulations have been violated. The majority of Australian research on food marketing to children has focused on television advertising and exposure research. Research has consistently shown that the content of food marketing directed at children is predominately for unhealthy foods. There is a lack of research on the effects of food marketing, which would be valuable to inform policy. The development of a logical framework for food marketing research allows for the identification of research gaps and enables research priorities to be identified.

  2. Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory

    Science.gov (United States)

    Arbaugh, J. B.; Fornaciari, Charles J.; Hwang, Alvin

    2016-01-01

    Although the volume of business and management education (BME) research has expanded substantially, concerns remain about the field's legitimacy and its ability to attract new and dedicated scholars. An obstacle that may impede field development is lack of knowledge about influential works and authors to frame topical areas of inquiry and future…

  3. A New Tool for Identifying Research Standards and Evaluating Research Performance

    Science.gov (United States)

    Bacon, Donald R.; Paul, Pallab; Stewart, Kim A.; Mukhopadhyay, Kausiki

    2012-01-01

    Much has been written about the evaluation of faculty research productivity in promotion and tenure decisions, including many articles that seek to determine the rank of various marketing journals. Yet how faculty evaluators combine journal quality, quantity, and author contribution to form judgments of a scholar's performance is unclear. A…

  4. Defining the Undefinable: Operationalization of Methods to Identify Specific Learning Disabilities among Practicing School Psychologists

    Science.gov (United States)

    Cottrell, Joseph M.; Barrett, Courtenay A.

    2016-01-01

    Accurate and consistent identification of students with specific learning disabilities (SLDs) is crucial; however, state and district guidelines regarding identification methods lack operationalization and are inconsistent throughout the United States. In the current study, the authors surveyed 471 school psychologists about "school" SLD…

  5. Identifying Facial Emotions: Valence Specific Effects and an Exploration of the Effects of Viewer Gender

    Science.gov (United States)

    Jansari, Ashok; Rodway, Paul; Goncalves, Salvador

    2011-01-01

    The valence hypothesis suggests that the right hemisphere is specialised for negative emotions and the left hemisphere is specialised for positive emotions (Silberman & Weingartner, 1986). It is unclear to what extent valence-specific effects in facial emotion perception depend upon the gender of the perceiver. To explore this question 46…

  6. Training School Psychologists to Identify Specific Learning Disabilities: A Content Analysis of Syllabi

    Science.gov (United States)

    Barrett, Courtenay A.; Cottrell, Joseph M.; Newman, Daniel S.; Pierce, Benjamin G.; Anderson, Alisha

    2015-01-01

    Approximately 2.4 million children receive special education services for specific learning disabilities (SLDs), and school psychologists are key contributors to the SLD eligibility decision-making process. The Individuals with Disabilities Education Act (2004) enabled local education agencies to use response to intervention (RTI) instead of the…

  7. Using the Domain Specific Innovativeness Scale To Identify Innovative Internet Consumers.

    Science.gov (United States)

    Goldsmith, Ronald E.

    2001-01-01

    The Domain Specific Innovativeness Scale was included in a survey of student consumers to measure how innovative participants were with regard to buying online. Data analyses confirmed hypotheses that an innovative predisposition toward online buying would be associated positively with more hours of Internet use, greater Internet purchasing,…

  8. Identifying Learning Patterns of Children at Risk for Specific Reading Disability

    Science.gov (United States)

    Barbot, Baptiste; Krivulskaya, Suzanna; Hein, Sascha; Reich, Jodi; Thuma, Philip E.; Grigorenko, Elena L.

    2016-01-01

    Differences in learning patterns of vocabulary acquisition in children at risk (+SRD) and not at risk (-SRD) for Specific Reading Disability (SRD) were examined using a microdevelopmental paradigm applied to the multi-trial Foreign Language Learning Task (FLLT; Baddeley et al., 1995). The FLLT was administered to 905 children from rural…

  9. Using Discrete Trial Training to Identify Specific Learning Impairments in Boys with Fragile X Syndrome

    Science.gov (United States)

    Hall, Scott S.; Hustyi, Kristin M.; Hammond, Jennifer L.; Hirt, Melissa; Reiss, Allan L.

    2014-01-01

    We examined whether "discrete trial training" (DTT) could be used to identify learning impairments in mathematical reasoning in boys with fragile X syndrome (FXS). Boys with FXS, aged 10-23 years, and age and IQ-matched controls, were trained to match fractions to pie-charts and pie-charts to decimals either on a computer or with a…

  10. Culture, threat, and mental illness stigma: identifying culture-specific threat among Chinese-American groups.

    Science.gov (United States)

    Yang, Lawrence H; Purdie-Vaughns, Valerie; Kotabe, Hiroki; Link, Bruce G; Saw, Anne; Wong, Gloria; Phelan, Jo C

    2013-07-01

    We incorporate anthropological insights into a stigma framework to elucidate the role of culture in threat perception and stigma among Chinese groups. Prior work suggests that genetic contamination that jeopardizes the extension of one's family lineage may comprise a culture-specific threat among Chinese groups. In Study 1, a national survey conducted from 2002 to 2003 assessed cultural differences in mental illness stigma and perceptions of threat in 56 Chinese-Americans and 589 European-Americans. Study 2 sought to empirically test this culture-specific threat of genetic contamination to lineage via a memory paradigm. Conducted from June to August 2010, 48 Chinese-American and 37 European-American university students in New York City read vignettes containing content referring to lineage or non-lineage concerns. Half the participants in each ethnic group were assigned to a condition in which the illness was likely to be inherited (genetic condition) and the rest read that the illness was unlikely to be inherited (non-genetic condition). Findings from Study 1 and 2 were convergent. In Study 1, culture-specific threat to lineage predicted cultural variation in stigma independently and after accounting for other forms of threat. In Study 2, Chinese-Americans in the genetic condition were more likely to accurately recall and recognize lineage content than the Chinese-Americans in the non-genetic condition, but that memorial pattern was not found for non-lineage content. The identification of this culture-specific threat among Chinese groups has direct implications for culturally-tailored anti-stigma interventions. Further, this framework might be implemented across other conditions and cultural groups to reduce stigma across cultures. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention

    OpenAIRE

    Williams, Ben; Johnston, Iain

    2016-01-01

    Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modelling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondri...

  12. Comparative analyses identified species-specific functional roles in oral microbial genomes

    Science.gov (United States)

    Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

    2017-01-01

    ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

  13. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei

    OpenAIRE

    Zirlinger, M.; Kreiman, Gabriel; Anderson, D. J.

    2001-01-01

    Microarray technology represents a potentially powerful method for identifying cell type- and regionally restricted genes expressed in the brain. Here we have combined a microarray analysis of differential gene expression among five selected brain regions, including the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray, with in situ hybridization. On average, 0.3% of the 34,000 genes interrogated were highly enriched in each of the five regions...

  14. BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

    Science.gov (United States)

    Meyer, Michael J; Geske, Philip; Yu, Haiyuan

    2016-05-15

    Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Specific biases for identifying facial expression of emotion in children and adolescents with conversion disorders.

    Science.gov (United States)

    Kozlowska, Kasia; Brown, Kerri J; Palmer, Donna M; Williams, Lea M

    2013-04-01

    This study aimed to assess how children and adolescents with conversion disorders identify universal facial expressions of emotion and to determine whether identification of emotion in faces relates to subjective emotional distress. Fifty-seven participants (41 girls and 16 boys) aged 8.5 to 18 years with conversion disorders and 57 age- and sex-matched healthy controls completed a computerized task in which their accuracy and reaction times for identifying facial expressions were recorded. To isolate the effect of individual emotional expressions, participants' reaction times for each emotion (fear, anger, sadness, disgust, and happiness) were subtracted from their reaction times for the neutral control face. Participants also completed self-report measures of subjective emotional distress. Children/Adolescents with conversion disorders showed faster reaction times for identifying expressions of sadness (t(112) = -2.2, p = .03; 444 [609] versus 713 [695], p = .03) and slower reactions times for happy expressions (t(99.3) = 2.28, p ≤ .024; -33 [35] versus 174 [51], p = .024), compared with controls (F(33.75, 419.81) = 3.76, p .018). There were also no differences in identification accuracy for any emotion (p > .82). The observation of faster reaction times to sad faces in children and adolescents with conversion disorders suggests increased vigilance and motor readiness to emotional signals that are potential threats to self or to close others. These effects may occur before conscious processing.

  16. The sensitivity and specificity of four questions (HARK to identify intimate partner violence: a diagnostic accuracy study in general practice

    Directory of Open Access Journals (Sweden)

    Feder Gene

    2007-08-01

    Full Text Available Abstract Background Intimate partner violence (IPV including physical, sexual and emotional violence, causes short and long term ill-health. Brief questions that reliably identify women experiencing IPV who present in clinical settings are a pre-requisite for an appropriate response from health services to this substantial public health problem. We estimated the sensitivity and specificity of four questions (HARK developed from the Abuse Assessment screen, compared to a 30-item abuse questionnaire, the Composite Abuse Scale (CAS. Methods We administered the four HARK questions and the CAS to women approached by two researchers in general practice waiting rooms in Newham, east London. Inclusions: women aged more than 17 years waiting to see a doctor or nurse, who had been in an intimate relationship in the last year. Exclusions: women who were accompanied by children over four years of age or another adult, too unwell to complete the questionnaires, unable to understand English or unable to give informed consent. Results Two hundred and thirty two women were recruited. The response rate was 54%. The prevalence of current intimate partner violence, within the last 12 months, using the CAS cut off score of ≥3, was 23% (95% C.I. 17% to 28% with pre-test odds of 0.3 (95% C.I. 0.2 to 0.4. The receiver operator characteristic curve demonstrated that a HARK cut off score of ≥1 maximises the true positives whilst minimising the false positives. The sensitivity of the optimal HARK cut-off score of ≥1 was 81% (95% C.I. 69% to 90%, specificity 95% (95% C.I. 91% to 98%, positive predictive value 83% (95% C.I. 70% to 91%, negative predictive value 94% (95% C.I. 90% to 97%, likelihood ratio 16 (95% C.I. 8 to 31 and post-test odds 5. Conclusion The four HARK questions accurately identify women experiencing IPV in the past year and may help women disclose abuse in general practice. The HARK questions could be incorporated into the electronic medical record

  17. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Benfeard Williams

    2015-10-01

    Full Text Available The increased risk of developing Alzheimer's disease (AD is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD.

  18. A qualitative study examining methods of accessing and identifying research relevant to clinical practice among rehabilitation clinicians.

    Science.gov (United States)

    Patel, Drasti; Koehmstedt, Christine; Jones, Rebecca; Coffey, Nathan T; Cai, Xinsheng; Garfinkel, Steven; Shaewitz, Dahlia M; Weinstein, Ali A

    2017-01-01

    Research examining the utilization of evidence-based practice (EBP) specifically among rehabilitation clinicians is limited. The objective of this study was to examine how various rehabilitative clinicians including physical therapists, occupational therapists, rehabilitation counselors, and physiatrists are gaining access to literature and whether they are able to implement the available research into practice. A total of 21 total clinicians were interviewed via telephone. Using NVivo, a qualitative analysis of the responses was performed. There were similarities found with respect to the information-seeking behaviors and translation of research across the different clinician types. Lack of time was reported to be a barrier for both access to literature and implementation of research across all clinician types. The majority of clinicians who reported having difficulty with utilizing the published literature indicated that the literature was not applicable to their practice, the research was not specific enough to be put into practice, or the research found was too outdated to be relevant. In addition, having a supportive work environment aided in the search and utilization of research through providing resources central to assisting clinicians in gaining access to health information. Our study identified several barriers that affect EBP for rehabilitation clinicians. The findings suggest the need for researchers to ensure that their work is applicable and specific to clinical practice for implementation to occur.

  19. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

    Science.gov (United States)

    Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T; Texier, Yves; van Beersum, Sylvia E C; Horn, Nicola; Willer, Jason R; Mans, Dorus A; Dougherty, Gerard; Lamers, Ideke J C; Coene, Karlien L M; Arts, Heleen H; Betts, Matthew J; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J F; Marcelis, Carlo L; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A; Toedt, Grischa; van Dam, Teunis J P; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L; Blacque, Oliver E; Gibson, Toby J; Huynen, Martijn A; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E; Franco, Brunella; Giles, Rachel H; Ueffing, Marius; Russell, Robert B; Roepman, Ronald

    2016-05-13

    Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.

  20. Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

    Science.gov (United States)

    Johnston, Iain G; Williams, Ben P

    2016-02-24

    Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

    Science.gov (United States)

    Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

    2015-04-01

    To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Identifying and Prioritizing Information Needs and Research Priorities of Public Health Emergency Preparedness and Response Practitioners.

    Science.gov (United States)

    Siegfried, Alexa L; Carbone, Eric G; Meit, Michael B; Kennedy, Mallory J; Yusuf, Hussain; Kahn, Emily B

    2017-10-01

    This study describes findings from an assessment conducted to identify perceived knowledge gaps, information needs, and research priorities among state, territorial, and local public health preparedness directors and coordinators related to public health emergency preparedness and response (PHPR). The goal of the study was to gather information that would be useful for ensuring that future funding for research and evaluation targets areas most critical for advancing public health practice. We implemented a mixed-methods approach to identify and prioritize PHPR research questions. A web survey was sent to all state, city, and territorial health agencies funded through the Public Health Emergency Preparedness (PHEP) Cooperative Agreement program and a sample of local health departments (LHDs). Three focus groups of state and local practitioners and subject matter experts from the Centers for Disease Control and Prevention (CDC) were subsequently conducted, followed by 3 meetings of an expert panel of PHPR practitioners and CDC experts to prioritize and refine the research questions. We identified a final list of 44 research questions that were deemed by study participants as priority topics where future research can inform PHPR programs and practice. We identified differences in perceived research priorities between PHEP awardees and LHD survey respondents; the number of research questions rated as important was greater among LHDs than among PHEP awardees (75%, n=33, compared to 24%, n=15). The research questions identified provide insight into public health practitioners' perceived knowledge gaps and the types of information that would be most useful for informing and advancing PHPR practice. The study also points to a higher level of information need among LHDs than among PHEP awardees. These findings are important for CDC and the PHPR research community to ensure that future research studies are responsive to practitioners' needs and provide the information

  3. 78 FR 67139 - Access to Confidential Business Information by Eastern Research Group and Its Identified...

    Science.gov (United States)

    2013-11-08

    ... Business Information by Eastern Research Group and Its Identified Subcontractor, Energy Services, Inc..., Eastern Research Group (ERG) of Chantilly, VA, and subcontractor Energy Services, Inc., of Tallahassee, FL... Control Act (TSCA). Some of the information may be claimed or determined to be Confidential Business...

  4. Identifying specific prefrontal neurons that contribute to autism-associated abnormalities in physiology and social behavior

    DEFF Research Database (Denmark)

    Brumback, A C; Ellwood, I T; Kjaerby, C

    2017-01-01

    Functional imaging and gene expression studies both implicate the medial prefrontal cortex (mPFC), particularly deep-layer projection neurons, as a potential locus for autism pathology. Here, we explored how specific deep-layer prefrontal neurons contribute to abnormal physiology and behavior...... in mouse models of autism. First, we find that across three etiologically distinct models-in utero valproic acid (VPA) exposure, CNTNAP2 knockout and FMR1 knockout-layer 5 subcortically projecting (SC) neurons consistently exhibit reduced input resistance and action potential firing. To explore how altered...... SC neuron physiology might impact behavior, we took advantage of the fact that in deep layers of the mPFC, dopamine D2 receptors (D2Rs) are mainly expressed by SC neurons, and used D2-Cre mice to label D2R+ neurons for calcium imaging or optogenetics. We found that social exploration preferentially...

  5. Specific olfactory receptor populations projecting to identified glomeruli in the rat olfactory bulb.

    Science.gov (United States)

    Jastreboff, P J; Pedersen, P E; Greer, C A; Stewart, W B; Kauer, J S; Benson, T E; Shepherd, G M

    1984-08-01

    A critical gap exists in our knowledge of the topographical relationship between the olfactory epithelium and olfactory bulb. The present report describes the application to this problem of a method involving horseradish peroxidase conjugated to wheat germ agglutinin. This material was iontophoretically delivered to circumscribed glomeruli in the olfactory bulb and the characteristics and distribution of retrogradely labeled receptor cells were assessed. After discrete injections into small glomerular groups in the caudomedial bulb, topographically defined populations of receptor cells were labeled. Labeled receptor cell somata appeared at several levels within the epithelium. The receptor cell apical dendrites followed a tight helical course towards the surface of the epithelium. The data thus far demonstrate that functional units within the olfactory system may include not only glomeruli as previously suggested but, in addition, a corresponding matrix of receptor cells possessing functional and topographical specificity.

  6. In Vivo RNA Interference Screening Identifies a Leukemia-Specific Dependence on Integrin Beta 3 Signaling

    Science.gov (United States)

    Miller, Peter G.; Al-Shahrour, Fatima; Hartwell, Kimberly A.; Chu, Lisa P.; Järås, Marcus; Puram, Rishi V.; Puissant, Alexandre; Callahan, Kevin P.; Ashton, John; McConkey, Marie E.; Poveromo, Luke P.; Cowley, Glenn S.; Kharas, Michael G.; Labelle, Myriam; Shterental, Sebastian; Fujisaki, Joji; Silberstein, Lev; Alexe, Gabriela; Al-Hajj, Muhammad A.; Shelton, Christopher A.; Armstrong, Scott A.; Root, David E.; Scadden, David T.; Hynes, Richard O.; Mukherjee, Siddhartha; Stegmaier, Kimberly; Jordan, Craig T.; Ebert, Benjamin L.

    2013-01-01

    SUMMARY We used an in vivo short hairpin RNA (shRNA) screening approach to identify genes that are essential for MLL-AF9 acute myeloid leukemia (AML). We found that Integrin Beta 3 (Itgb3) is essential for murine leukemia cells in vivo, and for human leukemia cells in xenotransplantation studies. In leukemia cells, Itgb3 knockdown impaired homing, downregulated LSC transcriptional programs, and induced differentiation via the intracellular kinase, Syk. In contrast, loss of Itgb3 in normal HSPCs did not affect engraftment, reconstitution, or differentiation. Finally, we confirmed that Itgb3 is dispensable for normal hematopoiesis and required for leukemogenesis using an Itgb3 knockout mouse model. Our results establish the significance of the Itgb3 signaling pathway as a potential therapeutic target in AML. PMID:23770013

  7. The risk of re-identification versus the need to identify individuals in rare disease research.

    Science.gov (United States)

    Hansson, Mats G; Lochmüller, Hanns; Riess, Olaf; Schaefer, Franz; Orth, Michael; Rubinstein, Yaffa; Molster, Caron; Dawkins, Hugh; Taruscio, Domenica; Posada, Manuel; Woods, Simon

    2016-11-01

    There is a growing concern in the ethics literature and among policy makers that de-identification or coding of personal data and biospecimens is not sufficient for protecting research subjects from privacy invasions and possible breaches of confidentiality due to the possibility of unauthorized re-identification. At the same time, there is a need in medical science to be able to identify individual patients. In particular for rare disease research there is a special and well-documented need for research collaboration so that data and biosamples from multiple independent studies can be shared across borders. In this article, we identify the needs and arguments related to de-identification and re-identification of patients and research subjects and suggest how the different needs may be balanced within a framework of using unique encrypted identifiers.

  8. New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background

    Directory of Open Access Journals (Sweden)

    Marocchi Alessandro

    2008-05-01

    Full Text Available Abstract Background Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Results Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31% and from 69.1 to 86.2% (average 76.6% respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%. This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg

  9. New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background.

    Science.gov (United States)

    Penco, Silvana; Buscema, Massimo; Patrosso, Maria Cristina; Marocchi, Alessandro; Grossi, Enzo

    2008-05-30

    Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31%) and from 69.1 to 86.2% (average 76.6%) respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%). This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg158cys; hepatic lipase -480 C/T; endothelial

  10. A novel CpG island set identifies tissue-specific methylation at developmental gene loci.

    Directory of Open Access Journals (Sweden)

    Robert Illingworth

    2008-01-01

    Full Text Available CpG islands (CGIs are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%-8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues.

  11. A specific DNA probe which identifies Babesia bovis in whole blood.

    Science.gov (United States)

    Petchpoo, W; Tan-ariya, P; Boonsaeng, V; Brockelman, C R; Wilairat, P; Panyim, S

    1992-05-01

    A genomic library of Babesia bovis DNA from the Mexican strain M was constructed in plasmid pUN121 and cloned in Escherichia coli. Several recombinants which hybridized strongly to radioactively labeled B. bovis genomic DNA in an in situ screening were selected and further analyzed for those which specifically hybridized to B. bovis DNA. It was found that pMU-B1 had the highest sensitivity, detecting 25 pg of purified B. bovis DNA, and 300 parasites in 10 microliters of whole infected blood, or 0.00025% parasitemia. pMU-B1 contained a 6.0 kb B. bovis DNA insert which did not cross-hybridize to Babesia bigemina, Trypanosoma evansi, Plasmodium falciparum, Anaplasma marginale, Boophilus microplus and cow DNA. In the Southern blot analysis of genomic DNA, pMU-B1 could differentiate between two B. bovis geographic isolates, Mexican strain M and Thai isolate TS4. Thus, the pMU-B1 probe will be useful in the diagnosis of Babesia infection in cattle and ticks, and in the differentiation of B. bovis strains.

  12. CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes.

    Directory of Open Access Journals (Sweden)

    Timucin Avsar

    Full Text Available Multiple sclerosis (MS is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179. Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10-5 which is important in the immune cell migration, renin-angiotensin (p=6.88x10-5 system that induces Th17 dependent immunity, notch signaling (p=1.83x10-10 pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10-5. An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.

  13. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

    Directory of Open Access Journals (Sweden)

    Betty M Booker

    2016-03-01

    Full Text Available The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.

  14. An All-Recombinant Protein-Based Culture System Specifically Identifies Hematopoietic Stem Cell Maintenance Factors

    Directory of Open Access Journals (Sweden)

    Aki Ieyasu

    2017-03-01

    Full Text Available Hematopoietic stem cells (HSCs are considered one of the most promising therapeutic targets for the treatment of various blood disorders. However, due to difficulties in establishing stable maintenance and expansion of HSCs in vitro, their insufficient supply is a major constraint to transplantation studies. To solve these problems we have developed a fully defined, all-recombinant protein-based culture system. Through this system, we have identified hemopexin (HPX and interleukin-1α as responsible for HSC maintenance in vitro. Subsequent molecular analysis revealed that HPX reduces intracellular reactive oxygen species levels within cultured HSCs. Furthermore, bone marrow immunostaining and 3D immunohistochemistry revealed that HPX is expressed in non-myelinating Schwann cells, known HSC niche constituents. These results highlight the utility of this fully defined all-recombinant protein-based culture system for reproducible in vitro HSC culture and its potential to contribute to the identification of factors responsible for in vitro maintenance, expansion, and differentiation of stem cell populations.

  15. What specifications for a centre or network of excellence in clinical research?

    Science.gov (United States)

    Diebolt, Vincent; Lang, Marie; Thoby, Frédérique

    2016-02-01

    The Giens 2015 Workshop Round Table entitled "What specifications for a centre or network of excellence in clinical research?" took a viewpoint distinct from earlier work and studies on changes in clinical research activities in France. The purpose of the present work was to identify, starting from concrete examples, the main strengths and advantages of clinical research activity in France related, in part, to the background environment and also to the specific characteristics of the investigation centres considered to be among the most high-performance units in activity. The criteria retained were grouped into a set of specifications that could be used to establish a "label of excellence" upon which the different teams and clinical research centres could model themselves. It was thus considered that belonging to a centre or structured network with at least a national configuration, when this is possible for the medial topic in question, constitutes a real advantage. Four benchmarks were identified: the scientific and clinical expertise of the head investigator, as well as the qualification and operational capacity of the centre's team; definition and measurement of performance using clearly displayed indicators and evaluation procedures; the quality of the overall trial "process" and of each of its component steps; communication, because know-how and promotion go hand in hand, with the main objective of informing the professional and general public about the value of the research centre meeting the above-mentioned criteria, about its networks of competencies, and more generally, about the important assets of the background of clinical research in France. This sector of research is funded by the public authorities via calls for public grants, financial aids for structures supporting clinical research in the University Hospital Centres and other healthcare institutions allowing for a professionalization of the research occupations, and the national public health

  16. The kidney cancer research priority-setting partnership: Identifying the top 10 research priorities as defined by patients, caregivers, and expert clinicians.

    Science.gov (United States)

    Jones, Jennifer; Bhatt, Jaimin; Avery, Jonathan; Laupacis, Andreas; Cowan, Katherine; Basappa, Naveen; Basiuk, Joan; Canil, Christina; Al-Asaaed, Sohaib; Heng, Daniel; Wood, Lori; Stacey, Dawn; Kollmannsberger, Christian; Jewett, Michael A S

    2017-12-01

    It is critically important to define disease-specific research priorities to better allocate limited resources. There is growing recognition of the value of involving patients and caregivers, as well as expert clinicians in this process. To our knowledge, this has not been done this way for kidney cancer. Using the transparent and inclusive process established by the James Lind Alliance, the Kidney Cancer Research Network of Canada (KCRNC) sponsored a collaborative consensus-based priority-setting partnership (PSP) to identify research priorities in the management of kidney cancer. The final result was identification of 10 research priorities for kidney cancer, which are discussed in the context of current initiatives and gaps in knowledge. This process provided a systematic and effective way to collaboratively establish research priorities with patients, caregivers, and clinicians, and provides a valuable resource for researchers and funding agencies.

  17. Toward sustainable environmental quality: Identifying priority research questions for Latin America

    Science.gov (United States)

    Furley, Tatiana Heid; Brodeur, Julie; Silva de Assis, Helena C; Carriquiriborde, Pedro; Chagas, Katia R; Corrales, Jone; Denadai, Marina; Fuchs, Julio; Mascarenhas, Renata; Miglioranza, Karina SB; Miguez Caramés, Diana Margarita; Navas, José Maria; Nugegoda, Dayanthi; Planes, Estela; Rodriguez‐Jorquera, Ignacio Alejandro; Orozco‐Medina, Martha; Boxall, Alistair BA; Rudd, Murray A

    2018-01-01

    ABSTRACT The Global Horizon Scanning Project (GHSP) is an innovative initiative that aims to identify important global environmental quality research needs. Here we report 20 key research questions from Latin America (LA). Members of the Society of Environmental Toxicology and Chemistry (SETAC) LA and other scientists from LA were asked to submit research questions that would represent priority needs to address in the region. One hundred questions were received, then partitioned among categories, examined, and some rearranged during a workshop in Buenos Aires, Argentina. Twenty priority research questions were subsequently identified. These research questions included developing, improving, and harmonizing across LA countries methods for 1) identifying contaminants and degradation products in complex matrices (including biota); 2) advancing prediction of contaminant risks and effects in ecosystems, addressing lab‐to‐field extrapolation challenges, and understanding complexities of multiple stressors (including chemicals and climate change); and 3) improving management and regulatory tools toward achieving sustainable development. Whereas environmental contaminants frequently identified in these key questions were pesticides, pharmaceuticals, endocrine disruptors or modulators, plastics, and nanomaterials, commonly identified environmental challenges were related to agriculture, urban effluents, solid wastes, pulp and paper mills, and natural extraction activities. Several interesting research topics included assessing and preventing pollution impacts on conservation protected areas, integrating environment and health assessments, and developing strategies for identification, substitution, and design of less hazardous chemicals (e.g., green chemistry). Finally, a recurrent research need included developing an understanding of differential sensitivity of regional species and ecosystems to environmental contaminants and other stressors. Addressing these critical

  18. Identifying critical issues in recreation planning and management: improving the management-research partnership

    Science.gov (United States)

    John H. Schomaker; David W. Lime

    1988-01-01

    The "nominal group" process is a proven technique to systematically arrive at a consensus about critical information needs in recreation planning and management. Using this process, 41 managers who attended a 1983 conference on river management identified 114 specific information needs grouped under 11 general questions. Clearly, some concerns of...

  19. Identifying the barriers to conducting outcomes research in integrative health care clinic settings - a qualitative study

    Directory of Open Access Journals (Sweden)

    Findlay-Reece Barbara

    2010-01-01

    Full Text Available Abstract Background Integrative health care (IHC is an interdisciplinary blending of conventional medicine and complementary and alternative medicine (CAM with the purpose of enhancing patients' health. In 2006, we designed a study to assess outcomes that are relevant to people using such care. However, we faced major challenges in conducting this study and hypothesized that this might be due to the lack of a research climate in these clinics. To investigate these challenges, we initiated a further study in 2008, to explore the reasons why IHC clinics are not conducting outcomes research and to identify strategies for conducting successful in-house outcomes research programs. The results of the latter study are reported here. Methods A total of 25 qualitative interviews were conducted with key participants from 19 IHC clinics across Canada. Basic content analysis was used to identify key themes from the transcribed interviews. Results Barriers identified by participants fell into four categories: organizational culture, organizational resources, organizational environment and logistical challenges. Cultural challenges relate to the philosophy of IHC, organizational leadership and practitioner attitudes and beliefs. Participants also identified significant issues relating to their organization's lack of resources such as funding, compensation, infrastructure and partnerships/linkages. Environmental challenges such as the nature of a clinic's patient population and logistical issues such as the actual implementation of a research program and the applicability of research data also posed challenges to the conduct of research. Embedded research leadership, integration of personal and professional values about research, alignment of research activities and clinical workflow processes are some of the factors identified by participants that support IHC clinics' ability to conduct outcomes research. Conclusions Assessing and enhancing the broader

  20. Use of stream water pH and specific conductance measurements to identify ground water discharges of fly ash leachate

    International Nuclear Information System (INIS)

    Price, R.M.

    1992-01-01

    Low pH and high specific conductance are typical chemical characteristics of coal fly ash leachate. Measurements of these parameters in streams adjacent to a fly ash facility were used to identify areas of ground water discharge into the streams. In-situ specific conductance and pH were determined at approximately 50 surface water stations from on-site and off-site streams. The results of the in-situ determinations were used to select twelve surface water stations for more detailed chemical analyses. The chemical character of the stream water affected by ground water discharges was similar to the water quality of sedimentation ponds which received drainage from the fly ash embankment. The results indicated that in-situ measurements of indicator parameters such as pH and specific conductance can be used as a screening method for identifying surface water quality impacts at fly ash facilities

  1. Technical specifications for the Oak Ridge Research Reactor

    International Nuclear Information System (INIS)

    1982-03-01

    Technical specifications are presented concerning safety limits and limiting safety system settings; limiting conditions for operation; surveillance requirements; design features; and administrative controls

  2. A qualitative study examining methods of accessing and identifying research relevant to clinical practice among rehabilitation clinicians

    Directory of Open Access Journals (Sweden)

    Patel D

    2017-12-01

    Full Text Available Drasti Patel,1 Christine Koehmstedt,1 Rebecca Jones,1 Nathan T Coffey,1 Xinsheng Cai,2 Steven Garfinkel,2 Dahlia M Shaewitz,2 Ali A Weinstein1 1Center for Study of Chronic Illness and Disability, College of Health and Human Services, George Mason University, Fairfax, VA, 2American Institutes for Research, Washington, DC, USA Purpose: Research examining the utilization of evidence-based practice (EBP specifically among rehabilitation clinicians is limited. The objective of this study was to examine how various rehabilitative clinicians including physical therapists, occupational therapists, rehabilitation counselors, and physiatrists are gaining access to literature and whether they are able to implement the available research into practice.Methods: A total of 21 total clinicians were interviewed via telephone. Using NVivo, a qualitative analysis of the responses was performed.Results: There were similarities found with respect to the information-seeking behaviors and translation of research across the different clinician types. Lack of time was reported to be a barrier for both access to literature and implementation of research across all clinician types. The majority of clinicians who reported having difficulty with utilizing the published literature indicated that the literature was not applicable to their practice, the research was not specific enough to be put into practice, or the research found was too outdated to be relevant. In addition, having a supportive work environment aided in the search and utilization of research through providing resources central to assisting clinicians in gaining access to health information.Conclusion: Our study identified several barriers that affect EBP for rehabilitation clinicians. The findings suggest the need for researchers to ensure that their work is applicable and specific to clinical practice for implementation to occur. Keywords: health information, information behavior, knowledge utilization

  3. Persistent Identifiers for Field Expeditions: A Next Step for the US Oceanographic Research Fleet

    Science.gov (United States)

    Arko, Robert; Carbotte, Suzanne; Chandler, Cynthia; Smith, Shawn; Stocks, Karen

    2016-04-01

    Oceanographic research cruises are complex affairs, typically requiring an extensive effort to secure the funding, plan the experiment, and mobilize the field party. Yet cruises are not typically published online as first-class digital objects with persistent, citable identifiers linked to the scientific literature. The Rolling Deck to Repository (R2R; info@rvdata.us) program maintains a master catalog of oceanographic cruises for the United States research fleet, currently documenting over 6,000 expeditions on 37 active and retired vessels. In 2015, R2R started routinely publishing a Digital Object Identifier (DOI) for each completed cruise. Cruise DOIs, in turn, are linked to related persistent identifiers where available including the Open Researcher and Contributor ID (ORCID) for members of the science party, the International Geo Sample Number (IGSN) for physical specimens collected during the cruise, the Open Funder Registry (FundRef) codes that supported the experiment, and additional DOIs for datasets, journal articles, and other products resulting from the cruise. Publishing a persistent identifier for each field expedition will facilitate interoperability between the many different repositories that hold research products from cruises; will provide credit to the investigators who secured the funding and carried out the experiment; and will facilitate the gathering of fleet-wide altmetrics that demonstrate the broad impact of oceanographic research.

  4. Identifying research priorities for patient safety in mental health: an international expert Delphi study

    Science.gov (United States)

    Murray, Kevin; Thibaut, Bethan; Ramtale, Sonny Christian; Adam, Sheila; Darzi, Ara; Archer, Stephanie

    2018-01-01

    Objective Physical healthcare has dominated the patient safety field; research in mental healthcare is not as extensive but findings from physical healthcare cannot be applied to mental healthcare because it delivers specialised care that faces unique challenges. Therefore, a clearer focus and recognition of patient safety in mental health as a distinct research area is still needed. The study aim is to identify future research priorities in the field of patient safety in mental health. Design Semistructured interviews were conducted with the experts to ascertain their views on research priorities in patient safety in mental health. A three-round online Delphi study was used to ascertain consensus on 117 research priority statements. Setting and participants Academic and service user experts from the USA, UK, Switzerland, Netherlands, Ireland, Denmark, Finland, Germany, Sweden, Australia, New Zealand and Singapore were included. Main outcome measures Agreement in research priorities on a five-point scale. Results Seventy-nine statements achieved consensus (>70%). Three out of the top six research priorities were patient driven; experts agreed that understanding the patient perspective on safety planning, on self-harm and on medication was important. Conclusions This is the first international Delphi study to identify research priorities in safety in the mental field as determined by expert academic and service user perspectives. A reasonable consensus was obtained from international perspectives on future research priorities in patient safety in mental health; however, the patient perspective on their mental healthcare is a priority. The research agenda for patient safety in mental health identified here should be informed by patient safety science more broadly and used to further establish this area as a priority in its own right. The safety of mental health patients must have parity with that of physical health patients to achieve this. PMID:29502096

  5. Critical research needs for identifying future changes in Gulf coral reef ecosystems

    Science.gov (United States)

    Feary, David A.; Burt, John A.; Bauman, Andrew G.; Al Hazeem, Shaker; Abdel-Moati, Mohamed A.; Al-Khalifa, Khalifa A.; Anderson, Donald M.; Amos, Carl; Baker, Andrew; Bartholomew, Aaron; Bento, Rita; Cavalcante, Geórgenes H.; Chen, Chaolun Allen; Coles, Steve L.; Dab, Koosha; Fowler, Ashley M.; George, David; Grandcourt, Edwin; Hill, Ross; John, David M.; Jones, David A.; Keshavmurthy, Shashank; Mahmoud, Huda; Moradi Och Tapeh, Mahdi; Mostafavi, Pargol Ghavam; Naser, Humood; Pichon, Michel; Purkis, Sam; Riegl, Bernhard; Samimi-Namin, Kaveh; Sheppard, Charles; Vajed Samiei, Jahangir; Voolstra, Christian R.; Wiedenmann, Joerg

    2014-01-01

    Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/ Persian Gulf (thereafter ‘Gulf’) coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region. PMID:23643407

  6. Critical research needs for identifying future changes in Gulf coral reef ecosystems

    KAUST Repository

    Feary, David A.

    2013-07-01

    Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/Persian Gulf (thereafter \\'Gulf\\') coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region. © 2013 Elsevier Ltd.

  7. Critical research needs for identifying future changes in Gulf coral reef ecosystems

    KAUST Repository

    Feary, David A.; Burt, John A.; Bauman, Andrew G.; Al Hazeem, Shaker; Abdel-Moati, Mohamed A R; Al-Khalifa, Khalifa A.; Anderson, Donald M.; Amos, Carl L.; Baker, Andrew C.; Bartholomew, Aaron; Bento, Rita; Cavalcante, Geó rgenes H.; Chen, Chaolun Allen; Coles, Steve L.; Dab, Koosha; Fowler, Ashley M.; George, David Glen; Grandcourt, Edwin Mark; Hill, Ross; John, David Michael; Jones, David Alan; Keshavmurthy, Shashank; Mahmoud, Huda M A; Moradi Och Tapeh, Mahdi; Mostafavi, Pargol Ghavam; Naser, Humood A.; Pichon, Michel; Purkis, Sam J.; Riegl, Bernhard M.; Samimi-Namin, Kaveh; Sheppard, Charles R C; Vajed Samiei, Jahangir; Voolstra, Christian R.; Wiedenmann, Jö rg

    2013-01-01

    Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/Persian Gulf (thereafter 'Gulf') coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region. © 2013 Elsevier Ltd.

  8. Health Research and Millennium Development Goals: Identifying the Gap From Public Health Perspective.

    Science.gov (United States)

    El Lawindi, Mona I; Galal, Yasmine S; Khairy, Walaa A

    2015-08-23

    Assessing the research output within the universities could provide an effective means for tracking the Millennium Development Goals (MDGs) progress. This analytical database study was designed to assess the trend of research theses conducted by the Public Health Department (PHD), Faculty of Medicine, Cairo University during the period 1990 to 2014 as related to the: MDGS, Faculty and department research priority plans and to identify the discrepancies between researchers' priorities versus national and international research priorities. A manual search of the theses was done at the Postgraduate Library using a specially designed checklist to chart adherence of each thesis to: MDGs, Faculty and department research plans (RPs). The theses' profile showed that the highest research output was for addressing the MDGS followed by the PHD and Faculty RPs. Compliance to MDGs 5 and 6 was obvious, whereas; MDGs 2, 3, and 7 were not represented at all after year 2000. No significant difference was found between PH theses addressing the Faculty RPs and those which were not before and after 2010. A significantly lower percent of PH theses was fulfilling the PHD research priorities compared to those which were not after 2010. This study showed a definite decline in research output tackling the MDGS and PHD research priorities, with a non-significant increase in the production of theses addressing the Faculty RPs. The present study is a practical model for policy makers within the universities to develop and implement a reliable monitoring and evaluation system for assessment of research output.

  9. Research into specific risk assessment in project financing

    Directory of Open Access Journals (Sweden)

    Ivana Bestvina Bukvić

    2013-12-01

    Full Text Available An assessment of investment justification in terms of risk enables the decision maker (investor to select, among available alternatives, the one with the most favourable correlation between the expected profit and assumed risk. At the micro level, the uncertainty of business success is extremely high in production activities, which is an additional incentive for taking a comprehensive approach to the issue of investment decision-making and the development of risk assessment techniques applicable in this particular segment of industry. Given the complexity of the manufacturing process, the length of the production cycle, market conditions, and entity-specific risks (which are difficult to measure, projects in manufacturing industry require a detailed and comprehensive assessment of specific risk factors and their cost-effectiveness. Ne - vertheless, since specific risks can be diversified, investment proposal assessments in practice usually do not cover their quantification and analysis. However, the majority of business entities do not have enough active projects in various industries to be able to fully diversify their business and thus minimize the level of specific risks. The impact of specific factors becomes one of the most important elements for business success. This paper analyses how far risk assessment methods regarding specific risks are used in practice. Furthermore, it analyses the significance of specific risks for total investment risk. This study gives new insi - ghts into the significance of specific risks to the overall investment assessment and the need for permanent development of traditionally used investment assessment models.

  10. The use of citation indicators to identify and support high-quality research in Poland.

    Science.gov (United States)

    Pilc, Andrzej

    2008-01-01

    In large, mostly English-speaking countries, where the "critical mass" of scientists working in different subfields of science is achieved, the peer review system may be sufficient to assess the quality of scientific research. However, in smaller countries, outside the Anglo-American circle, it is important to introduce different systems to identify research of high quality. In Poland, a parametric system for assessing the quality of research has been introduced. It was largely based on the impact factor of scientific journals. While the use of this indicator to assess research quality is highly questionable, the implementation of the system in the Polish reality is even worse. Therefore it is important to change and improve the system currently used by the Ministry of Science and Higher Education to both evaluate and, more importantly, finance science in Poland. Here, a system based on three factors, i.e. the impact factor, the institutional h-index, and the institutional number of citations, is proposed. The scientific quality of institutions in Division VI: Medical Sciences of the Polish Academy of Sciences were evaluated and the results were compared with the existing system. Moreover, a method to identify high-quality researchers and institutions at the national level based on the quantity of highly cited papers is shown. Additionally, an attempt to identify the highest quality Polish research on an international level is proposed. This is based on the number of individual citations, the individual h-index, the number of publications, and the priority of the discovery.

  11. Identifying the conditions needed for integrated knowledge translation (IKT) in health care organizations: qualitative interviews with researchers and research users.

    Science.gov (United States)

    Gagliardi, Anna R; Dobrow, Mark J

    2016-07-12

    Collaboration among researchers and research users, or integrated knowledge translation (IKT), enhances the relevance and uptake of evidence into policy and practice. However, it is not widely practiced and, even when well-resourced, desired impacts may not be achieved. Given that large-scale investment is not the norm, further research is needed to identify how IKT can be optimized. Interviews were conducted with researchers and research users (clinicians, managers) in a health care delivery (HCDO) and health care monitoring (HCMO) organization that differed in size and infrastructure, and were IKT-naïve. Basic qualitative description was used. Participants were asked about IKT activities and challenges, and recommendations for optimizing IKT. Data were analysed inductively using constant comparative technique. Forty-three interviews were conducted (28 HCDO, 15 HCMO) with 13 researchers, 8 clinicians, and 22 managers. Little to no IKT took place. Participants articulated similar challenges and recommendations revealing that a considerable number of changes were needed at the organizational, professional and individual levels. Given the IKT-absent state of participating organizations, this research identified a core set of conditions which must be addressed to prepare an environment conducive to IKT. These conditions were compiled into a framework by which organizations can plan for, or evaluate their capacity for IKT. The IKT capacity framework is relevant for organizations in which there is no current IKT activity. Use of the IKT framework may result in more organizations that are ready to initiate and establish IKT, perhaps ultimately leading to more, and higher-quality collaboration for health system innovation. Further research is needed to confirm these findings in other organizations not yet resourced for, or undertaking IKT, and to explore the resource implications and mechanisms for establishing the conditions identified here as essential to preparing for

  12. General problems specific to hot nuclear materials research facilities

    International Nuclear Information System (INIS)

    Bart, G.

    1996-01-01

    During the sixties, governments have installed hot nuclear materials research facilities to characterize highly radioactive materials, to describe their in-pile behaviour, to develop and test new reactor core components, and to provide the industry with radioisotopes. Since then, the attitude towards the nuclear option has drastically changed and resources have become very tight. Within the changed political environment, the national research centres have defined new objectives. Given budgetary constraints, nuclear facilities have to co-operate internationally and to look for third party research assignments. The paper discusses the problems and needs within experimental nuclear research facilities as well as industrial requirements. Special emphasis is on cultural topics (definition of the scope of nuclear research facilities, the search for competitive advantages, and operational requirements), social aspects (overageing of personnel, recruitment, and training of new staff), safety related administrative and technical issues, and research needs for expertise and state of the art analytical infrastructure

  13. White paper on geothermal sustainability; Grundlagenpapier 'Geothermal sustainability - A review with identified research needs'

    Energy Technology Data Exchange (ETDEWEB)

    Rybach, L.; Megel, T.

    2006-12-15

    This comprehensive appendix contained in a comprehensive annual report 2006 for the Swiss Federal Office of Energy (SFOE) reviews research needs identified in connection with the topic of geothermal sustainability. It is noted that excessive production often pursued - mostly for economical reasons - can lead to the depletion of heat reservoirs. Sustainable production can be achieved with lower production rates and still provide similar total energy yields. The regeneration of geothermal resources following exploitation is discussed. The need for further research into geothermal production sustainability is noted. A doublet system realised in Riehen, Switzerland, is discussed, as is an Enhanced Geothermal System EGS using circulation in fractured rock layers. Research still needed is noted.

  14. Development and testing of a medline search filter for identifying patient and public involvement in health research.

    Science.gov (United States)

    Rogers, Morwenna; Bethel, Alison; Boddy, Kate

    2017-06-01

    Research involving the public as partners often proves difficult to locate due to the variations in terms used to describe public involvement, and inability of medical databases to index this concept effectively. To design a search filter to identify literature where patient and public involvement (PPI) was used in health research. A reference standard of 172 PPI papers was formed. The references were divided into a development set and a test set. Search terms were identified from common words, phrases and synonyms in the development set. These terms were combined as a search strategy for medline via OvidSP, which was then tested for sensitivity against the test set. The resultant search filter was then assessed for sensitivity, specificity and precision using a previously published systematic review. The search filter was found to be highly sensitive 98.5% in initial testing. When tested against results generated by a 'real-life' systematic review, the filter had a specificity of 81%. However, sensitivity dropped to 58%. Adjustments to the population group of terms increased the sensitivity to 73%. The PPI filter designed for medline via OvidSP could aid information specialists and researchers trying to find literature specific to PPI. © 2016 Health Libraries Group.

  15. Identifying and Investigating Difficult Concepts in Engineering Mechanics and Electric Circuits. Research Brief

    Science.gov (United States)

    Streveler, Ruth; Geist, Monica; Ammerman, Ravel; Sulzbach, Candace; Miller, Ronald; Olds, Barbara; Nelson, Mary

    2007-01-01

    This study extends ongoing work to identify difficult concepts in thermal and transport science and measure students' understanding of those concepts via a concept inventory. Two research questions provided the focal point: "What important concepts in electric circuits and engineering mechanics do students find difficult to learn?" and…

  16. Identifying Effective Methods of Instruction for Adult Emergent Readers through Community-Based Research

    Science.gov (United States)

    Blackmer, Rachel; Hayes-Harb, Rachel

    2016-01-01

    We present a community-based research project aimed at identifying effective methods and materials for teaching English literacy skills to adult English as a second language emergent readers. We conducted a quasi-experimental study whereby we evaluated the efficacy of two approaches, one based on current practices at the English Skills Learning…

  17. Identifying future research needs in landscape genetics: Where to from here?

    Science.gov (United States)

    Niko Balkenhol; Felix Gugerli; Sam A. Cushman; Lisette P. Waits; Aurelie Coulon; J. W. Arntzen; Rolf Holderegger; Helene H. Wagner

    2009-01-01

    Landscape genetics is an emerging interdisciplinary field that combines methods and concepts from population genetics, landscape ecology, and spatial statistics. The interest in landscape genetics is steadily increasing, and the field is evolving rapidly. We here outline four major challenges for future landscape genetic research that were identified during an...

  18. Safety of Research Reactors. Specific Safety Requirements (French Edition)

    International Nuclear Information System (INIS)

    2017-01-01

    This Safety Requirements publication establishes requirements for all main areas of safety for research reactors, with particular emphasis on requirements for design and operation. It explains the safety objectives and concepts that form the basis for safety and safety assessment for all stages in the lifetime of a research reactor. Technical and administrative requirements for the safety of new research reactors are established in accordance with these objectives and concepts, and they are to be applied to the extent practicable for existing research reactors. The safety requirements established in this publication for the management of safety and regulatory supervision apply to site evaluation, design, manufacturing, construction, commissioning, operation (including utilization and modification), and planning for decommissioning of research reactors (including critical assemblies and subcritical assemblies). The publication is intended for use by regulatory bodies and other organizations with responsibilities in these areas and in safety analysis, verification and review, and the provision of technical support.

  19. Transcriptome Analysis of Mycobacteria-Specific CD4+ T Cells Identified by Activation-Induced Expression of CD154.

    Science.gov (United States)

    Kunnath-Velayudhan, Shajo; Goldberg, Michael F; Saini, Neeraj K; Johndrow, Christopher T; Ng, Tony W; Johnson, Alison J; Xu, Jiayong; Chan, John; Jacobs, William R; Porcelli, Steven A

    2017-10-01

    Analysis of Ag-specific CD4 + T cells in mycobacterial infections at the transcriptome level is informative but technically challenging. Although several methods exist for identifying Ag-specific T cells, including intracellular cytokine staining, cell surface cytokine-capture assays, and staining with peptide:MHC class II multimers, all of these have significant technical constraints that limit their usefulness. Measurement of activation-induced expression of CD154 has been reported to detect live Ag-specific CD4 + T cells, but this approach remains underexplored and, to our knowledge, has not previously been applied in mycobacteria-infected animals. In this article, we show that CD154 expression identifies adoptively transferred or endogenous Ag-specific CD4 + T cells induced by Mycobacterium bovis bacillus Calmette-Guérin vaccination. We confirmed that Ag-specific cytokine production was positively correlated with CD154 expression by CD4 + T cells from bacillus Calmette-Guérin-vaccinated mice and show that high-quality microarrays can be performed from RNA isolated from CD154 + cells purified by cell sorting. Analysis of microarray data demonstrated that the transcriptome of CD4 + CD154 + cells was distinct from that of CD154 - cells and showed major enrichment of transcripts encoding multiple cytokines and pathways of cellular activation. One notable finding was the identification of a previously unrecognized subset of mycobacteria-specific CD4 + T cells that is characterized by the production of IL-3. Our results support the use of CD154 expression as a practical and reliable method to isolate live Ag-specific CD4 + T cells for transcriptomic analysis and potentially for a range of other studies in infected or previously immunized hosts. Copyright © 2017 by The American Association of Immunologists, Inc.

  20. Developing a matrix to identify and prioritise research recommendations in HIV Prevention

    Directory of Open Access Journals (Sweden)

    Coates Bob

    2011-05-01

    Full Text Available Abstract Background HIV prevention continues to be problematic in the UK, as it does globally. The UK Department of Health has a strategic direction with greater focus on prevention as part of its World Class Commissioning Programme. There is a need for targeted evidence-based prevention initiatives. This is an exploratory study to develop an evidence mapping tool in the form of a matrix: this will be used to identify important gaps in contemporary HIV prevention evidence relevant to the UK. It has the potential to aid prioritisation in future research. Methods Categories for prevention and risk groups were developed for HIV prevention in consultation with external experts. These were used as axes on a matrix tool to map evidence. Systematic searches for publications on HIV prevention were undertaken using electronic databases for primary and secondary research undertaken mainly in UK, USA, Canada, Australia and New Zealand, 2006-9. Each publication was screened for inclusion then coded. The risk groups and prevention areas in each paper were counted: several publications addressed multiple risk groups. The counts were exported to the matrix and clearly illustrate the concentrations and gaps of literature in HIV prevention. Results 716 systematic reviews, randomised control trials and other primary research met the inclusion criteria for HIV prevention. The matrix identified several under researched areas in HIV prevention. Conclusions This is the first categorisation system for HIV prevention and the matrix is a novel tool for evidence mapping. Some important yet under-researched areas have been identified in HIV prevention evidence: identifying the undiagnosed population; international adaptation; education; intervention combinations; transgender; sex-workers; heterosexuals and older age groups. Other research recommendations: develop the classification system further and investigate transferability of the matrix to other prevention areas

  1. Recent advances in cross-cultural measurement in psychiatric epidemiology: utilizing 'what matters most' to identify culture-specific aspects of stigma.

    Science.gov (United States)

    Yang, Lawrence Hsin; Thornicroft, Graham; Alvarado, Ruben; Vega, Eduardo; Link, Bruce George

    2014-04-01

    While stigma measurement across cultures has assumed growing importance in psychiatric epidemiology, it is unknown to what extent concepts arising from culture have been incorporated. We utilize a formulation of culture-as the everyday interactions that 'matter most' to individuals within a cultural group-to identify culturally-specific stigma dynamics relevant to measurement. A systematic literature review from January 1990 to September 2012 was conducted using PsycINFO, Medline and Google Scholar to identify articles studying: (i) mental health stigma-related concepts; (ii) ≥ 1 non-Western European cultural group. From 5292 abstracts, 196 empirical articles were located. The vast majority of studies (77%) utilized adaptations of existing Western-developed stigma measures to new cultural groups. Extremely few studies (2.0%) featured quantitative stigma measures derived within a non-Western European cultural group. A sizeable amount (16.8%) of studies employed qualitative methods to identify culture-specific stigma processes. The 'what matters most' perspective identified cultural ideals of the everyday activities that comprise 'personhood' of 'preserving lineage' among specific Asian groups, 'fighting hard to overcome problems and taking advantage of immigration opportunities' among specific Latino-American groups, and 'establishing trust among religious institutions due to institutional discrimination' among African-American groups. These essential cultural interactions shaped culture-specific stigma manifestations. Mixed method studies (3.6%) corroborated these qualitative results. Quantitatively-derived, culturally-specific stigma measures were lacking. Further, the vast majority of qualitative studies on stigma were conducted without using stigma-specific frameworks. We propose the 'what matters most' approach to address this key issue in future research.

  2. Ageing Management for Research Reactors. Specific Safety Guide

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-10-15

    This Safety Guide was developed under the IAEA programme for safety standards for research reactors, which covers all the important areas of research reactor safety. It supplements and elaborates upon the safety requirements for ageing management of research reactors that are established in paras 6.68-6.70 and 7.109 of the IAEA Safety Requirements publication, Safety of Research Reactors. The safety of a research reactor requires that provisions be made in its design to facilitate ageing management. Throughout the lifetime of a research reactor, including its decommissioning, ageing management of its structures, systems and components (SSCs) important to safety is required, to ensure continued adequacy of the safety level, reliable operation of the reactor, and compliance with the operational limits and conditions. Managing the safety aspects of research reactor ageing requires implementation of an effective programme for the monitoring, prediction, and timely detection and mitigation of degradation of SSCs important to safety, and for maintaining their integrity and functional capability throughout their service lives. Ageing management is defined as engineering, operation, and maintenance strategy and actions to control within acceptable limits the ageing degradation of SSCs. Ageing management includes activities such as repair, refurbishment and replacement of SSCs, which are similar to other activities carried out at a research reactor in maintenance and testing or when a modification project takes place. However, it is important to recognize that effective management of ageing requires the use of a methodology that will detect and evaluate ageing degradation as a consequence of the service conditions, and involves the application of countermeasures for prevention and mitigation of ageing degradation. The objective of this Safety Guide is to provide recommendations on managing ageing of SSCs important to safety at research reactors on the basis of international

  3. Ageing Management for Research Reactors. Specific Safety Guide

    International Nuclear Information System (INIS)

    2010-01-01

    This Safety Guide was developed under the IAEA programme for safety standards for research reactors, which covers all the important areas of research reactor safety. It supplements and elaborates upon the safety requirements for ageing management of research reactors that are established in paras 6.68-6.70 and 7.109 of the IAEA Safety Requirements publication, Safety of Research Reactors. The safety of a research reactor requires that provisions be made in its design to facilitate ageing management. Throughout the lifetime of a research reactor, including its decommissioning, ageing management of its structures, systems and components (SSCs) important to safety is required, to ensure continued adequacy of the safety level, reliable operation of the reactor, and compliance with the operational limits and conditions. Managing the safety aspects of research reactor ageing requires implementation of an effective programme for the monitoring, prediction, and timely detection and mitigation of degradation of SSCs important to safety, and for maintaining their integrity and functional capability throughout their service lives. Ageing management is defined as engineering, operation, and maintenance strategy and actions to control within acceptable limits the ageing degradation of SSCs. Ageing management includes activities such as repair, refurbishment and replacement of SSCs, which are similar to other activities carried out at a research reactor in maintenance and testing or when a modification project takes place. However, it is important to recognize that effective management of ageing requires the use of a methodology that will detect and evaluate ageing degradation as a consequence of the service conditions, and involves the application of countermeasures for prevention and mitigation of ageing degradation. The objective of this Safety Guide is to provide recommendations on managing ageing of SSCs important to safety at research reactors on the basis of international

  4. The potential for research-based information in public health: Identifying unrecognised information needs

    Directory of Open Access Journals (Sweden)

    Forsetlund Louise

    2001-01-01

    Full Text Available Abstract Objective To explore whether there is a potential for greater use of research-based information in public health practice in a local setting. Secondly, if research-based information is relevant, to explore the extent to which this generates questioning behaviour. Design Qualitative study using focus group discussions, observation and interviews. Setting Public health practices in Norway. Participants 52 public health practitioners. Results In general, the public health practitioners had a positive attitude towards research-based information, but believed that they had few cases requiring this type of information. They did say, however, that there might be a potential for greater use. During five focus groups and six observation days we identified 28 questions/cases where it would have been appropriate to seek out research evidence according to our definition. Three of the public health practitioners identified three of these 28 cases as questions for which research-based information could have been relevant. This gap is interpreted as representing unrecognised information needs. Conclusions There is an unrealised potential in public health practice for more frequent and extensive use of research-based information. The practitioners did not appear to reflect on the need for scientific information when faced with new cases and few questions of this type were generated.

  5. An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

    Science.gov (United States)

    Winter, Georg E; Rix, Uwe; Lissat, Andrej; Stukalov, Alexey; Müllner, Markus K; Bennett, Keiryn L; Colinge, Jacques; Nijman, Sebastian M; Kubicek, Stefan; Kovar, Heinrich; Kontny, Udo; Superti-Furga, Giulio

    2011-10-01

    Ewing's sarcoma is a pediatric cancer of the bone that is characterized by the expression of the chimeric transcription factor EWS-FLI1 that confers a highly malignant phenotype and results from the chromosomal translocation t(11;22)(q24;q12). Poor overall survival and pronounced long-term side effects associated with traditional chemotherapy necessitate the development of novel, targeted, therapeutic strategies. We therefore conducted a focused viability screen with 200 small molecule kinase inhibitors in 2 different Ewing's sarcoma cell lines. This resulted in the identification of several potential molecular intervention points. Most notably, tozasertib (VX-680, MK-0457) displayed unique nanomolar efficacy, which extended to other cell lines, but was specific for Ewing's sarcoma. Furthermore, tozasertib showed strong synergies with the chemotherapeutic drugs etoposide and doxorubicin, the current standard agents for Ewing's sarcoma. To identify the relevant targets underlying the specific vulnerability toward tozasertib, we determined its cellular target profile by chemical proteomics. We identified 20 known and unknown serine/threonine and tyrosine protein kinase targets. Additional target deconvolution and functional validation by RNAi showed simultaneous inhibition of Aurora kinases A and B to be responsible for the observed tozasertib sensitivity, thereby revealing a new mechanism for targeting Ewing's sarcoma. We further corroborated our cellular observations with xenograft mouse models. In summary, the multilayered chemical biology approach presented here identified a specific vulnerability of Ewing's sarcoma to concomitant inhibition of Aurora kinases A and B by tozasertib and danusertib, which has the potential to become a new therapeutic option.

  6. Toward sustainable environmental quality: Identifying priority research questions for Latin America.

    Science.gov (United States)

    Furley, Tatiana Heid; Brodeur, Julie; Silva de Assis, Helena C; Carriquiriborde, Pedro; Chagas, Katia R; Corrales, Jone; Denadai, Marina; Fuchs, Julio; Mascarenhas, Renata; Miglioranza, Karina Sb; Miguez Caramés, Diana Margarita; Navas, José Maria; Nugegoda, Dayanthi; Planes, Estela; Rodriguez-Jorquera, Ignacio Alejandro; Orozco-Medina, Martha; Boxall, Alistair Ba; Rudd, Murray A; Brooks, Bryan W

    2018-05-01

    The Global Horizon Scanning Project (GHSP) is an innovative initiative that aims to identify important global environmental quality research needs. Here we report 20 key research questions from Latin America (LA). Members of the Society of Environmental Toxicology and Chemistry (SETAC) LA and other scientists from LA were asked to submit research questions that would represent priority needs to address in the region. One hundred questions were received, then partitioned among categories, examined, and some rearranged during a workshop in Buenos Aires, Argentina. Twenty priority research questions were subsequently identified. These research questions included developing, improving, and harmonizing across LA countries methods for 1) identifying contaminants and degradation products in complex matrices (including biota); 2) advancing prediction of contaminant risks and effects in ecosystems, addressing lab-to-field extrapolation challenges, and understanding complexities of multiple stressors (including chemicals and climate change); and 3) improving management and regulatory tools toward achieving sustainable development. Whereas environmental contaminants frequently identified in these key questions were pesticides, pharmaceuticals, endocrine disruptors or modulators, plastics, and nanomaterials, commonly identified environmental challenges were related to agriculture, urban effluents, solid wastes, pulp and paper mills, and natural extraction activities. Several interesting research topics included assessing and preventing pollution impacts on conservation protected areas, integrating environment and health assessments, and developing strategies for identification, substitution, and design of less hazardous chemicals (e.g., green chemistry). Finally, a recurrent research need included developing an understanding of differential sensitivity of regional species and ecosystems to environmental contaminants and other stressors. Addressing these critical questions will

  7. Technical specifications for the Oak Ridge Research Reactor

    International Nuclear Information System (INIS)

    1986-05-01

    Information is presented concerning the Oak Ridge Research Reactor in the areas of: safety limits and limiting safety system settings; limiting conditions for operation; surveillance requirements; design features; administrative controls; and monitoring of effluents

  8. Identifying optimal postmarket surveillance strategies for medical and surgical devices: implications for policy, practice and research.

    Science.gov (United States)

    Gagliardi, Anna R; Umoquit, Muriah; Lehoux, Pascale; Ross, Sue; Ducey, Ariel; Urbach, David R

    2013-03-01

    Non-drug technologies offer many benefits, but have been associated with adverse events, prompting calls for improved postmarket surveillance. There is little empirical research to guide the development of such a system. The purpose of this study was to identify optimal postmarket surveillance strategies for medical and surgical devices. Qualitative methods were used for sampling, data collection and analysis. Stakeholders from Canada and the USA representing different roles and perspectives were first interviewed to identify examples and characteristics of different surveillance strategies. These stakeholders and others they recommended were then assembled at a 1-day nominal group meeting to discuss and prioritise the components of a postmarket device surveillance system, and research needed to achieve such a system. Consultations were held with 37 participants, and 47 participants attended the 1-day meeting. They recommended a multicomponent system including reporting by facilities, clinicians and patients, supported with some external surveillance for validation and real-time trials for high-risk devices. Many considerations were identified that constitute desirable characteristics of, and means by which to implement such a system. An overarching network was envisioned to broker linkages, establish a shared minimum dataset, and support communication and decision making. Numerous research questions were identified, which could be pursued in tandem with phased implementation of the system. These findings provide unique guidance for establishing a device safety network that is based on existing initiatives, and could be expanded and evaluated in a prospective, phased fashion as it was developed.

  9. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    Science.gov (United States)

    van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris; Isaacs, Aaron; Medina-Gomez, Carolina; Mbarek, Hamdi; Kanterakis, Alexandros; Trompet, Stella; Postmus, Iris; Verweij, Niek; van Enckevort, David J.; Huffman, Jennifer E.; White, Charles C.; Feitosa, Mary F.; Bartz, Traci M.; Manichaikul, Ani; Joshi, Peter K.; Peloso, Gina M.; Deelen, Patrick; van Dijk, Freerk; Willemsen, Gonneke; de Geus, Eco J.; Milaneschi, Yuri; Penninx, Brenda W.J.H.; Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Rivadeneira, Fernando; Hofman, Albert; Oostra, Ben A.; Franco, Oscar H.; Leach, Irene Mateo; Beekman, Marian; de Craen, Anton J.M.; Uh, Hae-Won; Trochet, Holly; Hocking, Lynne J.; Porteous, David J.; Sattar, Naveed; Packard, Chris J.; Buckley, Brendan M.; Brody, Jennifer A.; Bis, Joshua C.; Rotter, Jerome I.; Mychaleckyj, Josyf C.; Campbell, Harry; Duan, Qing; Lange, Leslie A.; Wilson, James F.; Hayward, Caroline; Polasek, Ozren; Vitart, Veronique; Rudan, Igor; Wright, Alan F.; Rich, Stephen S.; Psaty, Bruce M.; Borecki, Ingrid B.; Kearney, Patricia M.; Stott, David J.; Adrienne Cupples, L.; Neerincx, Pieter B.T.; Elbers, Clara C.; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P.; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H.; van den Berg, Leonard H.; Byelas, Heorhiy; den Dunnen, Johan T.; Dijkstra, Martijn; Amin, Najaf; Joeri van der Velde, K.; van Setten, Jessica; Kattenberg, Mathijs; van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Mei, Hailiang; Koval, Vyacheslav; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H.; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Sunyaev, Shamil R.; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; Suchiman, H. Eka D.; Wolffenbuttel, Bruce H.; Platteel, Mathieu; Pitts, Steven J.; Potluri, Shobha; Cox, David R.; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Jukema, J. Wouter; van der Harst, Pim; Sijbrands, Eric J.; Hottenga, Jouke-Jan; Uitterlinden, Andre G.; Swertz, Morris A.; van Ommen, Gert-Jan B.; de Bakker, Paul I.W.; Eline Slagboom, P.; Boomsma, Dorret I.; Wijmenga, Cisca; van Duijn, Cornelia M.

    2015-01-01

    Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10−4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR. PMID:25751400

  10. Coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae).

    Science.gov (United States)

    Yang, Xiaolong; Thannhauser, T W; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E; Gray, Stewart M

    2008-01-01

    Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F(2) progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F(2) genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission.

  11. Coupling Genetics and Proteomics To Identify Aphid Proteins Associated with Vector-Specific Transmission of Polerovirus (Luteoviridae)▿

    Science.gov (United States)

    Yang, Xiaolong; Thannhauser, T. W.; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E.; Gray, Stewart M.

    2008-01-01

    Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F2 progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F2 genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission. PMID:17959668

  12. Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study

    DEFF Research Database (Denmark)

    Druley, Todd E; Wang, Lihua; Lin, Shiow J

    2016-01-01

    from six pedigrees. OBFC1 (chromosome 10) is involved in telomere maintenance, and falls within a linkage peak recently reported from an analysis of telomere length in LLFS families. Two different algorithms for single gene associations identified three genes with an enrichment of variation......BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...

  13. Human Trafficking in Ethiopia: A Scoping Review to Identify Gaps in Service Delivery, Research, and Policy.

    Science.gov (United States)

    Beck, Dana C; Choi, Kristen R; Munro-Kramer, Michelle L; Lori, Jody R

    2017-12-01

    The purpose of this review is to integrate evidence on human trafficking in Ethiopia and identify gaps and recommendations for service delivery, research and training, and policy. A scoping literature review approach was used to systematically search nursing, medical, psychological, law, and international databases and synthesize information on a complex, understudied topic. The search yielded 826 articles, and 39 met the predetermined criteria for inclusion in the review. Trafficking in Ethiopia has occurred internally and externally in the form of adult and child labor and sex trafficking. There were also some reports of organ trafficking and other closely related human rights violations, such as child marriage, child soldiering, and exploitative intercountry adoption. Risk factors for trafficking included push factors (poverty, political instability, economic problems, and gender discrimination) and pull factors (demand for cheap labor). Trafficking was associated with poor health and economic outcomes for victims. Key recommendations for service delivery, research and training, and policy are identified, including establishing comprehensive services for survivor rehabilitation and reintegration, conducting quantitative health outcomes research, and reforming policy around migration and trafficking. Implementing the recommendations identified by this review will allow policy makers, researchers, and practitioners to take meaningful steps toward confronting human trafficking in Ethiopia.

  14. A Model for Data Citation in Astronomical Research Using Digital Object Identifiers (DOIs)

    Science.gov (United States)

    Novacescu, Jenny; Peek, Joshua E. G.; Weissman, Sarah; Fleming, Scott W.; Levay, Karen; Fraser, Elizabeth

    2018-05-01

    Standardizing and incentivizing the use of digital object identifiers (DOIs) to aggregate and identify both data analyzed and data generated by a research project will advance the field of astronomy to match best practices in other research fields like geoscience and medicine. An increase in the use of DOIs will prepare the discipline for changing expectations among funding agencies and publishers, who increasingly expect accurate and thorough data citation to accompany scientific outputs. The use of DOIs ensures a robust, sustainable, and interoperable approach to data citation in which due credit is given to the researchers and institutions who produce and maintain the primary data. We describe in this work the advantages of DOIs for data citation and best practices for integrating a DOI service in an astronomical archive. We report on a pilot project carried out in collaboration with AAS journals. During the course of the 1.5-year long pilot, over 75% of submitting authors opted to use the integrated DOI service to clearly identify data analyzed during their research project when prompted at the time of paper submission.

  15. Development of a framework to identify research gaps from systematic reviews.

    Science.gov (United States)

    Robinson, Karen A; Saldanha, Ian J; McKoy, Naomi A

    2011-12-01

    Our objective was to develop a framework to identify research gaps from systematic reviews. We reviewed the practices of (1) evidence-based practice centers (EPCs), and (2) other organizations that conduct evidence syntheses. We developed and pilot tested a framework for identifying research gaps. Four (33%) EPCs and three (8%) other organizations reported using an explicit framework to determine research gaps. Variations of the PICO (population, intervention, comparison, outcomes) framework were most common. We developed a framework incorporating both the characterization of the gap using PICOS elements (also including setting) and the identification of the reason(s) why the gap exists as (1) insufficient or imprecise information, (2) biased information, (3) inconsistency or unknown consistency, and (4) not the right information. We mapped each of these reasons to concepts from three common evidence-grading systems. Our framework determines from systematic reviews where the current evidence falls short and why or how the evidence falls short. This explicit identification of research gaps will allow systematic reviews to maximally inform the types of questions that need to be addressed and the types of studies needed to address the research gaps. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. FACEBOOK for CoP of Researchers: Identifying the Needs and Evaluating the Compatibility

    Directory of Open Access Journals (Sweden)

    Sami Miniaoui

    2011-11-01

    Full Text Available Communities of practice (CoPs are increasingly capturing the interest of many fields such as business companies, education and organizations. Many CoPs were developed for people who have common interest in healthcare, agriculture and environment, and teaching. However, there is lack of COPs dedicated for researchers. This research aims to explore the appropriateness of Facebook (FB as a platform for serving a CoP of researchers. To achieve this goal, first we identify the needs of CoPs for researchers within UAE context. Consequently, we adopted qualitative research approach to elicit the needs. We applied the grounded theory method to analyze the data. The results of the analysis showed seven main needs: collaboration, debating, awareness/ notification, reference management, cross search, customization, tracking, and user orientation. Secondly, we evaluated the compatibility of FB features to the identified needs. Although we found that FB covers most of CoPs needs, there are few needs which are not met successfully so this raised some technical and practical issues, which have been highlighted in the paper.

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

    Science.gov (United States)

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

    2016-02-01

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

  18. Functional requirements for the man-vehicle systems research facility. [identifying and correcting human errors during flight simulation

    Science.gov (United States)

    Clement, W. F.; Allen, R. W.; Heffley, R. K.; Jewell, W. F.; Jex, H. R.; Mcruer, D. T.; Schulman, T. M.; Stapleford, R. L.

    1980-01-01

    The NASA Ames Research Center proposed a man-vehicle systems research facility to support flight simulation studies which are needed for identifying and correcting the sources of human error associated with current and future air carrier operations. The organization of research facility is reviewed and functional requirements and related priorities for the facility are recommended based on a review of potentially critical operational scenarios. Requirements are included for the experimenter's simulation control and data acquisition functions, as well as for the visual field, motion, sound, computation, crew station, and intercommunications subsystems. The related issues of functional fidelity and level of simulation are addressed, and specific criteria for quantitative assessment of various aspects of fidelity are offered. Recommendations for facility integration, checkout, and staffing are included.

  19. Identifying Ethical Issues in Mental Health Research with Minors Adolescents: Results of a Delphi Study

    Directory of Open Access Journals (Sweden)

    Elisabeta Ioana Hiriscau

    2016-05-01

    Full Text Available Research with minors, especially for preventive purposes, e.g., suicide prevention, investigating risk or self-destructive behaviors such as deviance, drug abuse, or suicidal behavior, is ethically sensitive. We present a Delphi study exploring the ethical implications of the needs formulated by researchers in an international pre-conference who would benefit from ethics support and guidance in conducting Mental Health Research with minors. The resulting List of Ethical Issues (LEI was submitted to a 2-rounds Delphi process via the Internet, including 34 multidisciplinary experts. In the first round, the experts reviewed the LEI and completed a questionnaire. Results from this round were analyzed and grouped in nine categories comprising 40 items. In the second round, the experts had to agree/disagree with the needs expressed in the LEI leading to a final list of 25 ethical issues considered relevant for Mental Health Research with minors such as: confidentiality of the sensitive data, competence for consenting alone and risk of harm and stigma related to the methodology used in research. It was shown that studies like SEYLE (Saving and Empowering Young Lives in Europe trigger among researchers wishes to obtain specific recommendations helping to comply with standards for good practice in conducting research with minors.

  20. Identifying Ethical Issues in Mental Health Research with Minors Adolescents: Results of a Delphi Study.

    Science.gov (United States)

    Hiriscau, Elisabeta Ioana; Stingelin-Giles, Nicola; Wasserman, Danuta; Reiter-Theil, Stella

    2016-05-11

    Research with minors, especially for preventive purposes, e.g., suicide prevention, investigating risk or self-destructive behaviors such as deviance, drug abuse, or suicidal behavior, is ethically sensitive. We present a Delphi study exploring the ethical implications of the needs formulated by researchers in an international pre-conference who would benefit from ethics support and guidance in conducting Mental Health Research with minors. The resulting List of Ethical Issues (LEI) was submitted to a 2-rounds Delphi process via the Internet, including 34 multidisciplinary experts. In the first round, the experts reviewed the LEI and completed a questionnaire. Results from this round were analyzed and grouped in nine categories comprising 40 items. In the second round, the experts had to agree/disagree with the needs expressed in the LEI leading to a final list of 25 ethical issues considered relevant for Mental Health Research with minors such as: confidentiality of the sensitive data, competence for consenting alone and risk of harm and stigma related to the methodology used in research. It was shown that studies like SEYLE (Saving and Empowering Young Lives in Europe) trigger among researchers wishes to obtain specific recommendations helping to comply with standards for good practice in conducting research with minors.

  1. Identifying Ethical Issues in Mental Health Research with Minors Adolescents: Results of a Delphi Study

    Science.gov (United States)

    Hiriscau, Elisabeta Ioana; Stingelin-Giles, Nicola; Wasserman, Danuta; Reiter-Theil, Stella

    2016-01-01

    Research with minors, especially for preventive purposes, e.g., suicide prevention, investigating risk or self-destructive behaviors such as deviance, drug abuse, or suicidal behavior, is ethically sensitive. We present a Delphi study exploring the ethical implications of the needs formulated by researchers in an international pre-conference who would benefit from ethics support and guidance in conducting Mental Health Research with minors. The resulting List of Ethical Issues (LEI) was submitted to a 2-rounds Delphi process via the Internet, including 34 multidisciplinary experts. In the first round, the experts reviewed the LEI and completed a questionnaire. Results from this round were analyzed and grouped in nine categories comprising 40 items. In the second round, the experts had to agree/disagree with the needs expressed in the LEI leading to a final list of 25 ethical issues considered relevant for Mental Health Research with minors such as: confidentiality of the sensitive data, competence for consenting alone and risk of harm and stigma related to the methodology used in research. It was shown that studies like SEYLE (Saving and Empowering Young Lives in Europe) trigger among researchers wishes to obtain specific recommendations helping to comply with standards for good practice in conducting research with minors. PMID:27187425

  2. Specific features of occupational medicine in nuclear research and industry

    International Nuclear Information System (INIS)

    Giraud, J.M.; Quesne, B.

    2003-01-01

    Measures to prevent the exposure of personnel to ionising radiation were taken as soon as the first nuclear laboratories were set up. This branch of occupational preventive medicine has since kept pace with advances in research and in the industrial applications of nuclear energy. (authors)

  3. The next step for stress research in primates: To identify relationships between glucocorticoid secretion and fitness.

    Science.gov (United States)

    Beehner, Jacinta C; Bergman, Thore J

    2017-05-01

    Glucocorticoids are hormones that mediate the energetic demands that accompany environmental challenges. It is therefore not surprising that these metabolic hormones have come to dominate endocrine research on the health and fitness of wild populations. Yet, several problems have been identified in the vertebrate research that also apply to the non-human primate research. First, glucocorticoids should not be used as a proxy for fitness (unless a link has previously been established between glucocorticoids and fitness for a particular population). Second, stress research in behavioral ecology has been overly focused on "chronic stress" despite little evidence that chronic stress hampers fitness in wild animals. Third, research effort has been disproportionately focused on the causes of glucocorticoid variation rather than the fitness consequences. With these problems in mind, we have three objectives for this review. We describe the conceptual framework behind the "stress concept", emphasizing that high glucocorticoids do not necessarily indicate a stress response, and that a stress response does not necessarily indicate an animal is in poor health. Then, we conduct a comprehensive review of all studies on "stress" in wild primates, including any study that examined environmental factors, the stress response, and/or fitness (or proxies for fitness). Remarkably, not a single primate study establishes a connection between all three. Finally, we provide several recommendations for future research in the field of primate behavioral endocrinology, primarily the need to move beyond identifying the factors that cause glucocorticoid secretion to additionally focus on the relationship between glucocorticoids and fitness. We believe that this is an important next step for research on stress physiology in primates. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Survived so what? Identifying priorities for research with children and families post-paediatric intensive care unit.

    Science.gov (United States)

    Manning, Joseph C; Hemingway, Pippa; Redsell, Sarah A

    2018-03-01

    The involvement of patients and the public in the development, implementation and evaluation of health care services and research is recognized to have tangible benefits in relation to effectiveness and credibility. However, despite >96% of children and young people surviving critical illness or injury, there is a paucity of published reports demonstrating their contribution to informing the priorities for aftercare services and outcomes research. We aimed to identify the service and research priorities for Paediatric Intensive Care Unit survivors with children and young people, their families and other stakeholders. We conducted a face-to-face, multiple-stakeholder consultation event, held in the Midlands (UK), to provide opportunities for experiences, views and priorities to be elicited. Data were gathered using write/draw and tell and focus group approaches. An inductive content analytical approach was used to categorize and conceptualize feedback. A total of 26 individuals attended the consultation exercise, including children and young people who were critical care survivors; their siblings; parents and carers; health professionals; academics; commissioners; and service managers. Consultation findings indicated that future services, interventions and research must be holistic and family-centred. Children and young people advisors reported priorities that focused on longer-term outcomes, whereas adult advisors identified priorities that mapped against the pathways of care. Specific priorities included developing and testing interventions that address unmet communication and information needs. Furthermore, initiatives to optimize the lives and longer-term functional and psycho-social outcomes of Paediatric Intensive Care Unit survivors were identified. This consultation exercise provides further evidence of the value of meaningful patient and public involvement in identifying the priorities for research and services for Paediatric Intensive Care Unit survivors

  5. Progress in the Legitimacy of Business and Management Education Research: Rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory"

    Science.gov (United States)

    Bacon, Donald R.

    2016-01-01

    In this rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory," published in the "Journal of Management Education," Dec 2016 (see EJ1118407), Donald R. Bacon discusses the similarities between Arbaugh et al.'s (2016) findings and the scholarship…

  6. Economic Education within the BME Research Community: Rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory"

    Science.gov (United States)

    Asarta, Carlos J.

    2016-01-01

    Carlos Asarta comments here that Arbaugh, Fornaciari, and Hwang (2016) are to be commended for their work ("Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory" "Journal of Management Education," Dec 2016, see EJ1118407). Asarta says that they make several…

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

    Science.gov (United States)

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

    2010-08-23

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

  8. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.

    Directory of Open Access Journals (Sweden)

    Lihua J Zhu

    Full Text Available CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General

  9. Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen thi Man; Morris, G.E. (North East Wales Inst., Clwyd (United Kingdom))

    1993-06-01

    The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random [open quotes]libraries[close quotes] of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25--60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1--41, and the authors now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes. 38 refs., 2 figs., 4 tabs.

  10. Identifying knowledge gaps for gene drive research to control invasive animal species: The next CRISPR step

    Directory of Open Access Journals (Sweden)

    Dorian Moro

    2018-01-01

    Full Text Available Invasive animals have been linked to the extinctions of native wildlife, and to significant agricultural financial losses or impacts. Current approaches to control invasive species require ongoing resources and management over large geographic scales, and often result in the short-term suppression of populations. New and innovative approaches are warranted. Recently, the RNA guided gene drive system based on CRISPR/Cas9 is being proposed as a potential gene editing tool that could be used by wildlife managers as a non-lethal addition or alternative to help reduce pest animal populations. While regulatory control and social acceptance are crucial issues that must be addressed, there is an opportunity now to identify the knowledge and research gaps that exist for some important invasive species. Here we systematically determine the knowledge gaps for pest species for which gene drives could potentially be applied. We apply a conceptual ecological risk framework within the gene drive context within an Australian environment to identify key requirements for undertaking work on seven exemplar invasive species in Australia. This framework allows an evaluation of the potential research on an invasive species of interest and within a gene drive and risk context. We consider the currently available biological, genetic and ecological information for the house mouse, European red fox, feral cat, European rabbit, cane toad, black rat and European starling to evaluate knowledge gaps and identify candidate species for future research. We discuss these findings in the context of future thematic areas of research worth pursuing in preparation for a more formal assessment of the use of gene drives as a novel strategy for the control of these and other invasive species. Keywords: Invasive species, Gene drive, CRISPR, Pest management, Islands

  11. Using mixed methods to identify and answer clinically relevant research questions.

    Science.gov (United States)

    Shneerson, Catherine L; Gale, Nicola K

    2015-06-01

    The need for mixed methods research in answering health care questions is becoming increasingly recognized because of the complexity of factors that affect health outcomes. In this article, we argue for the value of using a qualitatively driven mixed method approach for identifying and answering clinically relevant research questions. This argument is illustrated by findings from a study on the self-management practices of cancer survivors and the exploration of one particular clinically relevant finding about higher uptake of self-management in cancer survivors who had received chemotherapy treatment compared with those who have not. A cross-sectional study generated findings that formed the basis for the qualitative study, by informing the purposive sampling strategy and generating new qualitative research questions. Using a quantitative research component to supplement a qualitative study can enhance the generalizability and clinical relevance of the findings and produce detailed, contextualized, and rich answers to research questions that would be unachievable through quantitative or qualitative methods alone. © The Author(s) 2015.

  12. Ethical issues in identifying and recruiting participants for familial genetic research.

    Science.gov (United States)

    Beskow, Laura M; Botkin, Jeffrey R; Daly, Mary; Juengst, Eric T; Lehmann, Lisa Soleymani; Merz, Jon F; Pentz, Rebecca; Press, Nancy A; Ross, Lainie Friedman; Sugarman, Jeremy; Susswein, Lisa R; Terry, Sharon F; Austin, Melissa A; Burke, Wylie

    2004-11-01

    Family-based research is essential to understanding the genetic and environmental etiology of human disease. The success of family-based research often depends on investigators' ability to identify, recruit, and achieve a high participation rate among eligible family members. However, recruitment of family members raises ethical concerns due to the tension between protecting participants' privacy and promoting research quality, and guidelines for these activities are not well established. The Cancer Genetics Network Bioethics Committee assembled a multidisciplinary group to explore the scientific and ethical issues that arise in the process of family-based recruitment. The group used a literature review as well as expert opinion to develop recommendations about appropriate approaches to identifying, contacting, and recruiting family members. We conclude that there is no single correct approach, but recommend a balanced approach that takes into account the nature of the particular study as well as its recruitment goals. Recruitment of family members should be viewed as part of the research protocol and should require appropriate informed consent of the already-enrolled participant. Investigators should inform prospective participants why they are being contacted, how information about them was obtained, and what will happen to that information if they decide not to participate. The recruitment process should also be sensitive to the fact that some individuals from families at increased genetic risk will have no prior knowledge of their risk status. These recommendations are put forward to promote further discussion about the advantages and disadvantages of various approaches to family-based recruitment. They suggest a framework for considering alternative recruitment strategies and their implications, as well as highlight areas in need of further empirical research. (c) 2004 Wiley-Liss, Inc.

  13. Inflammatory Mediators in Vascular Disease: Identifying Promising Targets for Intracranial Aneurysm Research

    Directory of Open Access Journals (Sweden)

    David M. Sawyer

    2015-01-01

    Full Text Available Inflammatory processes are implicated in many diseases of the vasculature and have been shown to play a key role in the formation of intracranial aneurysms (IAs. Although the specific mechanisms underlying these processes have been thoroughly investigated in related pathologies, such as atherosclerosis, there remains a paucity of information regarding the immunopathology of IA. Cells such as macrophages and lymphocytes and their effector molecules have been suggested to be players in IA, but their specific interactions and the role of other components of the inflammatory response have yet to be determined. Drawing parallels between the pathogenesis of IA and other vascular disorders could provide a roadmap for developing a mechanistic understanding of the immunopathology of IA and uncovering useful targets for therapeutic intervention. Future research should address the presence and function of leukocyte subsets, mechanisms of leukocyte recruitment and activation, and the role of damage-associated molecular patterns in IA.

  14. Identifying Domain-General and Domain-Specific Predictors of Low Mathematics Performance: A Classification and Regression Tree Analysis

    Directory of Open Access Journals (Sweden)

    David J. Purpura

    2017-12-01

    Full Text Available Many children struggle to successfully acquire early mathematics skills. Theoretical and empirical evidence has pointed to deficits in domain-specific skills (e.g., non-symbolic mathematics skills or domain-general skills (e.g., executive functioning and language as underlying low mathematical performance. In the current study, we assessed a sample of 113 three- to five-year old preschool children on a battery of domain-specific and domain-general factors in the fall and spring of their preschool year to identify Time 1 (fall factors associated with low performance in mathematics knowledge at Time 2 (spring. We used the exploratory approach of classification and regression tree analyses, a strategy that uses step-wise partitioning to create subgroups from a larger sample using multiple predictors, to identify the factors that were the strongest classifiers of low performance for younger and older preschool children. Results indicated that the most consistent classifier of low mathematics performance at Time 2 was children’s Time 1 mathematical language skills. Further, other distinct classifiers of low performance emerged for younger and older children. These findings suggest that risk classification for low mathematics performance may differ depending on children’s age.

  15. A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.

    Directory of Open Access Journals (Sweden)

    Warren D Anderson

    2017-07-01

    Full Text Available Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension. We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences. We obtained experimental data on the expression of 22 genes across five organs, over a time span that encompassed the development of autonomic nervous system dysfunction and hypertension. We pursued a unique approach for identification of continuous-time models that jointly described the dynamics and structure of multi-organ networks by estimating a sparse subset of ∼12,000 possible gene regulatory interactions. Our analyses revealed that an autonomic dysfunction-specific multi-organ sequence of gene expression activation patterns was associated with a distinct gene regulatory network. We analyzed the model structures for adaptation motifs, and identified disease-specific network motifs involving genes that exhibited aberrant temporal dynamics. Bioinformatic analyses identified disease-specific single nucleotide variants within or near transcription factor binding sites upstream of key genes implicated in maintaining physiological homeostasis. Our approach illustrates a novel framework for investigating the pathogenesis through model-based analysis of multi-organ system dynamics and network properties. Our results yielded novel candidate molecular targets driving the development of cardiovascular disease, metabolic syndrome, and immune dysfunction.

  16. THE SPECIFIC MARKET RESEARCH METHODOLOGY USED AT GENERAL MOTOR'S EUROPE ,

    Directory of Open Access Journals (Sweden)

    Zima Liliana Adela

    2011-12-01

    Full Text Available As difficult as segmenting consumer markets is, it is much simpler and easier than segmenting industrial markets. Often the same industrial products have multiple applications; likewise, several different products can be used in the same application. Customer differ greatly, and it is hard to discern which differences are important and which are trivial for developing a marketing strategy. Making the research at General Motor's Europe I realized that the most industrial marketers use segmentation as a way to explain results rather than as a way to plan. In fact, industrial segmentation can assist companies in several areas like: analysis of the market, selection of key markets and management and marketing. In this study I tried to make a better understanding of the total marketplace, including how and why customers buy and to develop strategies, plans and programs to profitability meet the needs of different market segments and to give the company a distinct competitive advantage. The Marketing Plan is based on an Information System which can be interpretaded in two different ways. In this case its singular form focusing on both formal and informal information system is appropriate. The investigation explains the environment of the European Business Team . The techniques used were: system maps, observations, interviews, questionnaires and company documents. The initial stage of exploring the situation starts usually with a dialog between the potential client - in this particular case the European Business Team – and the analyst. The vague impression is then given that not everything is running as it should be by the client. This was, however, not completely true in my case, as I had to go looking for problems. Preliminary investigations into product communication did show a feeling of unease between the departments. Having expressed the current situation of the European Business Team , I then chose three areas to study further. I had to

  17. Enhancing the Employability of Chinese International Students: Identifying Achievements and Gaps in the Research Field

    Directory of Open Access Journals (Sweden)

    Xuemeng Cao

    2017-10-01

    Full Text Available This article shows what achievements have been made by existing studies on graduate employability, and what gaps need to be filled in this field. It starts with a retrospective account of the changing concept of employability, followed by a presentation of the practices that have been used to support graduate employability enhancement in different countries. Moreover, this article gives a critical review of Chinese contexts of graduate labour market. Last but not least, limitations of existing studies are identified, which reflect an expectation for future research on graduate employability to meet the demand of an increasingly international dimension of higher education.

  18. Fluorescently labeled dengue viruses as probes to identify antigen-specific memory B cells by multiparametric flow cytometry.

    Science.gov (United States)

    Woda, Marcia; Mathew, Anuja

    2015-01-01

    Low frequencies of memory B cells in the peripheral blood make it challenging to measure the functional and phenotypic characteristics of this antigen experienced subset of B cells without in vitro culture. To date, reagents are lacking to measure ex vivo frequencies of dengue virus (DENV)-specific memory B cells. We wanted to explore the possibility of using fluorescently labeled DENV as probes to detect antigen-specific memory B cells in the peripheral blood of DENV immune individuals. Alexa Fluor dye-labeled DENV yielded viable virus that could be stored at -80°C for long periods of time. Using a careful gating strategy and methods to decrease non-specific binding, we were able to identify a small frequency of B cells from dengue immune individuals that bound labeled DENV. Sorted DENV(+) B cells from immune, but not naïve donors secreted antibodies that bound DENV after in vitro stimulation. Overall, Alexa Fluor dye-labeled DENVs are useful reagents to enable the detection and characterization of memory B cells in DENV immune individuals. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Research Methods Identifying Correlation Between Physical Environment of Schools and Educational Paradigms

    Directory of Open Access Journals (Sweden)

    Grėtė Brukštutė

    2016-04-01

    Full Text Available The article is analysing the research that was already carried out in order to determine correlation between a physical environment of schools and educational paradigms. While selecting materials for the analysis, the attention was focused on studies conducted in the USA and European countries. Based on these studies the methodological attitudes towards coherence of the education and spatial structures were tried to identify. Homogeneity and conformity of an educational character and a physical learning environment became especially important during changes of educational conceptions. The issue how educational paradigms affect the architecture of school buildings is not yet analysed in Lithuania, therefore the results of this research could actualize a theme on correlation between educational paradigms and the architecture of school buildings and form initial guidelines for the development of the modern physical learning environment.

  20. An Efficient Stepwise Statistical Test to Identify Multiple Linked Human Genetic Variants Associated with Specific Phenotypic Traits.

    Directory of Open Access Journals (Sweden)

    Iksoo Huh

    Full Text Available Recent advances in genotyping methodologies have allowed genome-wide association studies (GWAS to accurately identify genetic variants that associate with common or pathological complex traits. Although most GWAS have focused on associations with single genetic variants, joint identification of multiple genetic variants, and how they interact, is essential for understanding the genetic architecture of complex phenotypic traits. Here, we propose an efficient stepwise method based on the Cochran-Mantel-Haenszel test (for stratified categorical data to identify causal joint multiple genetic variants in GWAS. This method combines the CMH statistic with a stepwise procedure to detect multiple genetic variants associated with specific categorical traits, using a series of associated I × J contingency tables and a null hypothesis of no phenotype association. Through a new stratification scheme based on the sum of minor allele count criteria, we make the method more feasible for GWAS data having sample sizes of several thousands. We also examine the properties of the proposed stepwise method via simulation studies, and show that the stepwise CMH test performs better than other existing methods (e.g., logistic regression and detection of associations by Markov blanket for identifying multiple genetic variants. Finally, we apply the proposed approach to two genomic sequencing datasets to detect linked genetic variants associated with bipolar disorder and obesity, respectively.

  1. One Health approach to identify research needs in bovine and human babesioses: workshop report

    Directory of Open Access Journals (Sweden)

    McElwain Terry F

    2010-04-01

    Full Text Available Abstract Background Babesia are emerging health threats to humans and animals in the United States. A collaborative effort of multiple disciplines to attain optimal health for people, animals and our environment, otherwise known as the One Health concept, was taken during a research workshop held in April 2009 to identify gaps in scientific knowledge regarding babesioses. The impetus for this analysis was the increased risk for outbreaks of bovine babesiosis, also known as Texas cattle fever, associated with the re-infestation of the U.S. by cattle fever ticks. Results The involvement of wildlife in the ecology of cattle fever ticks jeopardizes the ability of state and federal agencies to keep the national herd free of Texas cattle fever. Similarly, there has been a progressive increase in the number of cases of human babesiosis over the past 25 years due to an increase in the white-tailed deer population. Human babesiosis due to cattle-associated Babesia divergens and Babesia divergens-like organisms have begun to appear in residents of the United States. Research needs for human and bovine babesioses were identified and are presented herein. Conclusions The translation of this research is expected to provide veterinary and public health systems with the tools to mitigate the impact of bovine and human babesioses. However, economic, political, and social commitments are urgently required, including increased national funding for animal and human Babesia research, to prevent the re-establishment of cattle fever ticks and the increasing problem of human babesiosis in the United States.

  2. Women-specific HIV/AIDS services: identifying and defining the components of holistic service delivery for women living with HIV/AIDS.

    Science.gov (United States)

    Carter, Allison J; Bourgeois, Sonya; O'Brien, Nadia; Abelsohn, Kira; Tharao, Wangari; Greene, Saara; Margolese, Shari; Kaida, Angela; Sanchez, Margarite; Palmer, Alexis K; Cescon, Angela; de Pokomandy, Alexandra; Loutfy, Mona R

    2013-01-11

    The increasing proportion of women living with HIV has evoked calls for tailored services that respond to women's specific needs. The objective of this investigation was to explore the concept of women-specific HIV/AIDS services to identify and define what key elements underlie this approach to care. A comprehensive review was conducted using online databases (CSA Social Service Abstracts, OvidSP, Proquest, Psycinfo, PubMed, CINAHL), augmented with a search for grey literature. In total, 84 articles were retrieved and 30 were included for a full review. Of these 30, 15 were specific to HIV/AIDS, 11 for mental health and addictions and four stemmed from other disciplines. The review demonstrated the absence of a consensual definition of women-specific HIV/AIDS services in the literature. We distilled this concept into its defining features and 12 additional dimensions (1) creating an atmosphere of safety, respect and acceptance; (2) facilitating communication and interaction among peers; (3) involving women in the planning, delivery and evaluation of services; (4) providing self-determination opportunities; (5) providing tailored programming for women; (6) facilitating meaningful access to care through the provision of social and supportive services; (7) facilitating access to women-specific and culturally sensitive information; (8) considering family as the unit of intervention; (9) providing multidisciplinary integration and coordination of a comprehensive array of services; (10) meeting women "where they are"; (11) providing gender-, culture- and HIV-sensitive training to health and social care providers; and (12) conducting gendered HIV/AIDS research. This review highlights that the concept of women-specific HIV/AIDS services is a complex and multidimensional one that has been shaped by diverse theoretical perspectives. Further research is needed to better understand this emerging concept and ultimately assess the effectiveness of women-specific services on HIV

  3. Women-specific HIV/AIDS services: identifying and defining the components of holistic service delivery for women living with HIV/AIDS

    Science.gov (United States)

    Carter, Allison J; Bourgeois, Sonya; O'Brien, Nadia; Abelsohn, Kira; Tharao, Wangari; Greene, Saara; Margolese, Shari; Kaida, Angela; Sanchez, Margarite; Palmer, Alexis K; Cescon, Angela; de Pokomandy, Alexandra; Loutfy, Mona R

    2013-01-01

    Introduction The increasing proportion of women living with HIV has evoked calls for tailored services that respond to women's specific needs. The objective of this investigation was to explore the concept of women-specific HIV/AIDS services to identify and define what key elements underlie this approach to care. Methods A comprehensive review was conducted using online databases (CSA Social Service Abstracts, OvidSP, Proquest, Psycinfo, PubMed, CINAHL), augmented with a search for grey literature. In total, 84 articles were retrieved and 30 were included for a full review. Of these 30, 15 were specific to HIV/AIDS, 11 for mental health and addictions and four stemmed from other disciplines. Results and discussion The review demonstrated the absence of a consensual definition of women-specific HIV/AIDS services in the literature. We distilled this concept into its defining features and 12 additional dimensions (1) creating an atmosphere of safety, respect and acceptance; (2) facilitating communication and interaction among peers; (3) involving women in the planning, delivery and evaluation of services; (4) providing self-determination opportunities; (5) providing tailored programming for women; (6) facilitating meaningful access to care through the provision of social and supportive services; (7) facilitating access to women-specific and culturally sensitive information; (8) considering family as the unit of intervention; (9) providing multidisciplinary integration and coordination of a comprehensive array of services; (10) meeting women “where they are”; (11) providing gender-, culture- and HIV-sensitive training to health and social care providers; and (12) conducting gendered HIV/AIDS research. Conclusions This review highlights that the concept of women-specific HIV/AIDS services is a complex and multidimensional one that has been shaped by diverse theoretical perspectives. Further research is needed to better understand this emerging concept and ultimately

  4. Using Market Research to Characterize College Students and Identify Potential Targets for Influencing Health Behaviors

    Science.gov (United States)

    Berg, Carla J.; Ling, Pamela M.; Guo, Hongfei; Windle, Michael; Thomas, Janet L.; Ahluwalia, Jasjit S.; An, Lawrence C.

    2013-01-01

    Marketing campaigns, such as those developed by the tobacco industry, are based on market research, which defines segments of a population by assessing psychographic characteristics (i.e., attitudes, interests). This study uses a similar approach to define market segments of college smokers, to examine differences in their health behaviors (smoking, drinking, binge drinking, exercise, diet), and to determine the validity of these segments. A total of 2,265 undergraduate students aged 18–25 years completed a 108-item online survey in fall 2008 assessing demographic, psychographic (i.e., attitudes, interests), and health-related variables. Among the 753 students reporting past 30-day smoking, cluster analysis was conducted using 21 psychographic questions and identified three market segments – Stoic Individualists, Responsible Traditionalists, and Thrill-Seeking Socializers. We found that segment membership was related to frequency of alcohol use, binge drinking, and limiting dietary fat. We then developed three messages targeting each segment and conducted message testing to validate the segments on a subset of 73 smokers representing each segment in spring 2009. As hypothesized, each segment indicated greater relevance and salience for their respective message. These findings indicate that identifying qualitatively different subgroups of young adults through market research may inform the development of engaging interventions and health campaigns targeting college students. PMID:25264429

  5. Alternative approaches for identifying acute systemic toxicity: Moving from research to regulatory testing.

    Science.gov (United States)

    Hamm, Jon; Sullivan, Kristie; Clippinger, Amy J; Strickland, Judy; Bell, Shannon; Bhhatarai, Barun; Blaauboer, Bas; Casey, Warren; Dorman, David; Forsby, Anna; Garcia-Reyero, Natàlia; Gehen, Sean; Graepel, Rabea; Hotchkiss, Jon; Lowit, Anna; Matheson, Joanna; Reaves, Elissa; Scarano, Louis; Sprankle, Catherine; Tunkel, Jay; Wilson, Dan; Xia, Menghang; Zhu, Hao; Allen, David

    2017-06-01

    Acute systemic toxicity testing provides the basis for hazard labeling and risk management of chemicals. A number of international efforts have been directed at identifying non-animal alternatives for in vivo acute systemic toxicity tests. A September 2015 workshop, Alternative Approaches for Identifying Acute Systemic Toxicity: Moving from Research to Regulatory Testing, reviewed the state-of-the-science of non-animal alternatives for this testing and explored ways to facilitate implementation of alternatives. Workshop attendees included representatives from international regulatory agencies, academia, nongovernmental organizations, and industry. Resources identified as necessary for meaningful progress in implementing alternatives included compiling and making available high-quality reference data, training on use and interpretation of in vitro and in silico approaches, and global harmonization of testing requirements. Attendees particularly noted the need to characterize variability in reference data to evaluate new approaches. They also noted the importance of understanding the mechanisms of acute toxicity, which could be facilitated by the development of adverse outcome pathways. Workshop breakout groups explored different approaches to reducing or replacing animal use for acute toxicity testing, with each group crafting a roadmap and strategy to accomplish near-term progress. The workshop steering committee has organized efforts to implement the recommendations of the workshop participants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Sharpe, Richard A. [European Centre for Environment and Human Health, University of Exeter Medical School, Truro TR1 3HD (United Kingdom); Cocq, Kate Le [Rothamsted Research, North Wyke, Okehampton EX20 2SB (United Kingdom); Nikolaou, Vasilis [University of Exeter Medical School, The Veysey Building, Salmon Pool Lane, Exeter EX2 4SG (United Kingdom); Osborne, Nicholas J. [European Centre for Environment and Human Health, University of Exeter Medical School, Truro TR1 3HD (United Kingdom); Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Sydney Medical School, The University of Sydney, NSW (Australia); Thornton, Christopher R., E-mail: c.r.thornton@exeter.ac.uk [Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD (United Kingdom)

    2016-01-15

    The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. - Highlights: • Monoclonal antibodies were used to track culturable allergenic moulds in homes. • Allergenic moulds were recovered from 82% of swabs from contaminated surfaces. • The mAbs were highly specific with 100% agreement to PCR of recovered fungi. • Improvements to energy

  7. Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies

    International Nuclear Information System (INIS)

    Sharpe, Richard A.; Cocq, Kate Le; Nikolaou, Vasilis; Osborne, Nicholas J.; Thornton, Christopher R.

    2016-01-01

    The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. - Highlights: • Monoclonal antibodies were used to track culturable allergenic moulds in homes. • Allergenic moulds were recovered from 82% of swabs from contaminated surfaces. • The mAbs were highly specific with 100% agreement to PCR of recovered fungi. • Improvements to energy

  8. Serum Metabolomics to Identify the Liver Disease-Specific Biomarkers for the Progression of Hepatitis to Hepatocellular Carcinoma

    Science.gov (United States)

    Gao, Rong; Cheng, Jianhua; Fan, Chunlei; Shi, Xiaofeng; Cao, Yuan; Sun, Bo; Ding, Huiguo; Hu, Chengjin; Dong, Fangting; Yan, Xianzhong

    2015-12-01

    Hepatocellular carcinoma (HCC) is a common malignancy that has region specific etiologies. Unfortunately, 85% of cases of HCC are diagnosed at an advanced stage. Reliable biomarkers for the early diagnosis of HCC are urgently required to reduced mortality and therapeutic expenditure. We established a non-targeted gas chromatography-time of flight-mass spectrometry (GC-TOFMS) metabolomics method in conjunction with Random Forests (RF) analysis based on 201 serum samples from healthy controls (NC), hepatitis B virus (HBV), liver cirrhosis (LC) and HCC patients to explore the metabolic characteristics in the progression of hepatocellular carcinogenesis. Ultimately, 15 metabolites were identified intimately associated with the process. Phenylalanine, malic acid and 5-methoxytryptamine for HBV vs. NC, palmitic acid for LC vs. HBV, and asparagine and β-glutamate for HCC vs. LC were screened as the liver disease-specific potential biomarkers with an excellent discriminant performance. All the metabolic perturbations in these liver diseases are associated with pathways for energy metabolism, macromolecular synthesis, and maintaining the redox balance to protect tumor cells from oxidative stress.

  9. Multiplexed screening of natural humoral immunity identifies antibodies at fine specificity for complex and dynamic viral targets.

    Science.gov (United States)

    McCutcheon, Krista M; Gray, Julia; Chen, Natalie Y; Liu, Keyi; Park, Minha; Ellsworth, Stote; Tripp, Ralph A; Tompkins, S Mark; Johnson, Scott K; Samet, Shelly; Pereira, Lenore; Kauvar, Lawrence M

    2014-01-01

    Viral entry targets with therapeutic neutralizing potential are subject to multiple escape mechanisms, including antigenic drift, immune dominance of functionally irrelevant epitopes, and subtle variations in host cell mechanisms. A surprising finding of recent years is that potent neutralizing antibodies to viral epitopes independent of strain exist, but are poorly represented across the diverse human population. Identifying these antibodies and understanding the biology mediating the specific immune response is thus difficult. An effective strategy for meeting this challenge is to incorporate multiplexed antigen screening into a high throughput survey of the memory B cell repertoire from immune individuals. We used this approach to discover suites of cross-clade antibodies directed to conformational epitopes in the stalk region of the influenza A hemagglutinin (HA) protein and to select high-affinity anti-peptide antibodies to the glycoprotein B (gB) of human cytomegalovirus. In each case, our screens revealed a restricted VH and VL germline usage, including published and previously unidentified gene families. The in vivo evolution of paratope specificity with optimal neutralizing activity was understandable after correlating biological activities with kinetic binding and epitope recognition. Iterative feedback between antigen probe design based on structure and function information with high throughput multiplexed screening demonstrated a generally applicable strategy for efficient identification of safe, native, finely tuned antibodies with the potential for high genetic barriers to viral escape.

  10. Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma

    DEFF Research Database (Denmark)

    Wittig-Blaich, Stephanie; Wittig, Rainer; Schmidt, Steffen

    2017-01-01

    Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technolo......Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few...... technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies. We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes......, a library of 108 isogenic melanoma cell lines was constructed and 8 genes were identified that significantly reduced viability in a discovery screen and in an independent validation screen. Here, we demonstrate the broad applicability of this recombination-based method and we proved its potential...

  11. Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia.

    Science.gov (United States)

    Badea, Liviu; Herlea, Vlad; Dima, Simona Olimpia; Dumitrascu, Traian; Popescu, Irinel

    2008-01-01

    The precise details of pancreatic ductal adenocarcinoma (PDAC) pathogenesis are still insufficiently known, requiring the use of high-throughput methods. However, PDAC is especially difficult to study using microarrays due to its strong desmoplastic reaction, which involves a hyperproliferating stroma that effectively "masks" the contribution of the minoritary neoplastic epithelial cells. Thus it is not clear which of the genes that have been found differentially expressed between normal and whole tumor tissues are due to the tumor epithelia and which simply reflect the differences in cellular composition. To address this problem, laser microdissection studies have been performed, but these have to deal with much smaller tissue sample quantities and therefore have significantly higher experimental noise. In this paper we combine our own large sample whole-tissue study with a previously published smaller sample microdissection study by Grützmann et al. to identify the genes that are specifically overexpressed in PDAC tumor epithelia. The overlap of this list of genes with other microarray studies of pancreatic cancer as well as with the published literature is impressive. Moreover, we find a number of genes whose over-expression appears to be inversely correlated with patient survival: keratin 7, laminin gamma 2, stratifin, platelet phosphofructokinase, annexin A2, MAP4K4 and OACT2 (MBOAT2), which are all specifically upregulated in the neoplastic epithelia, rather than the tumor stroma. We improve on other microarray studies of PDAC by putting together the higher statistical power due to a larger number of samples with information about cell-type specific expression and patient survival.

  12. An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.

    Directory of Open Access Journals (Sweden)

    Vijay C Antharam

    Full Text Available Clostridium difficile infection (CDI is characterized by dysbiosis of the intestinal microbiota and a profound derangement in the fecal metabolome. However, the contribution of specific gut microbes to fecal metabolites in C. difficile-associated gut microbiome remains poorly understood. Using gas-chromatography mass spectrometry (GC-MS and 16S rRNA deep sequencing, we analyzed the metabolome and microbiome of fecal samples obtained longitudinally from subjects with Clostridium difficile infection (n = 7 and healthy controls (n = 6. From 155 fecal metabolites, we identified two sterol metabolites at >95% match to cholesterol and coprostanol that significantly discriminated C. difficile-associated gut microbiome from healthy microbiota. By correlating the levels of cholesterol and coprostanol in fecal extracts with 2,395 bacterial operational taxonomic units (OTUs determined by 16S rRNA sequencing, we identified 63 OTUs associated with high levels of coprostanol and 2 OTUs correlated with low coprostanol levels. Using indicator species analysis (ISA, 31 of the 63 coprostanol-associated bacteria correlated with health, and two Veillonella species were associated with low coprostanol levels that correlated strongly with CDI. These 65 bacterial taxa could be clustered into 12 sub-communities, with each community containing a consortium of organisms that co-occurred with one another. Our studies identified 63 human gut microbes associated with cholesterol-reducing activities. Given the importance of gut bacteria in reducing and eliminating cholesterol from the GI tract, these results support the recent finding that gut microbiome may play an important role in host lipid metabolism.

  13. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.

    Directory of Open Access Journals (Sweden)

    Christopher G Bell

    2010-11-01

    Full Text Available Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D, focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip and absolute methylation values were estimated using a Bayesian algorithm (BATMAN. Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10(-4, permutation p = 1.0×10(-3. Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10(-7. Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM, encapsulates a Highly Conserved Non-Coding Element (HCNE that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.

  14. An extended data mining method for identifying differentially expressed assay-specific signatures in functional genomic studies

    Directory of Open Access Journals (Sweden)

    Rollins Derrick K

    2010-12-01

    Full Text Available Abstract Background Microarray data sets provide relative expression levels for thousands of genes for a small number, in comparison, of different experimental conditions called assays. Data mining techniques are used to extract specific information of genes as they relate to the assays. The multivariate statistical technique of principal component analysis (PCA has proven useful in providing effective data mining methods. This article extends the PCA approach of Rollins et al. to the development of ranking genes of microarray data sets that express most differently between two biologically different grouping of assays. This method is evaluated on real and simulated data and compared to a current approach on the basis of false discovery rate (FDR and statistical power (SP which is the ability to correctly identify important genes. Results This work developed and evaluated two new test statistics based on PCA and compared them to a popular method that is not PCA based. Both test statistics were found to be effective as evaluated in three case studies: (i exposing E. coli cells to two different ethanol levels; (ii application of myostatin to two groups of mice; and (iii a simulated data study derived from the properties of (ii. The proposed method (PM effectively identified critical genes in these studies based on comparison with the current method (CM. The simulation study supports higher identification accuracy for PM over CM for both proposed test statistics when the gene variance is constant and for one of the test statistics when the gene variance is non-constant. Conclusions PM compares quite favorably to CM in terms of lower FDR and much higher SP. Thus, PM can be quite effective in producing accurate signatures from large microarray data sets for differential expression between assays groups identified in a preliminary step of the PCA procedure and is, therefore, recommended for use in these applications.

  15. An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.

    Science.gov (United States)

    Antharam, Vijay C; McEwen, Daniel C; Garrett, Timothy J; Dossey, Aaron T; Li, Eric C; Kozlov, Andrew N; Mesbah, Zhubene; Wang, Gary P

    2016-01-01

    Clostridium difficile infection (CDI) is characterized by dysbiosis of the intestinal microbiota and a profound derangement in the fecal metabolome. However, the contribution of specific gut microbes to fecal metabolites in C. difficile-associated gut microbiome remains poorly understood. Using gas-chromatography mass spectrometry (GC-MS) and 16S rRNA deep sequencing, we analyzed the metabolome and microbiome of fecal samples obtained longitudinally from subjects with Clostridium difficile infection (n = 7) and healthy controls (n = 6). From 155 fecal metabolites, we identified two sterol metabolites at >95% match to cholesterol and coprostanol that significantly discriminated C. difficile-associated gut microbiome from healthy microbiota. By correlating the levels of cholesterol and coprostanol in fecal extracts with 2,395 bacterial operational taxonomic units (OTUs) determined by 16S rRNA sequencing, we identified 63 OTUs associated with high levels of coprostanol and 2 OTUs correlated with low coprostanol levels. Using indicator species analysis (ISA), 31 of the 63 coprostanol-associated bacteria correlated with health, and two Veillonella species were associated with low coprostanol levels that correlated strongly with CDI. These 65 bacterial taxa could be clustered into 12 sub-communities, with each community containing a consortium of organisms that co-occurred with one another. Our studies identified 63 human gut microbes associated with cholesterol-reducing activities. Given the importance of gut bacteria in reducing and eliminating cholesterol from the GI tract, these results support the recent finding that gut microbiome may play an important role in host lipid metabolism.

  16. Towards a community effort to identify ethical principles for research in hydrology

    Science.gov (United States)

    Montanari, Alberto

    2010-05-01

    The hydrological community in Europe is growing rapidly in both size and, more importantly, scientific relevance and integrity. The Hydrological Sciences (HS) Division of EGU actively is promoting the above development by identifying research targets, stimulating the involvement of young scientists and managing a scientific open access journal based on a public peer review process. The management of the Division itself and the organisation of the General Assembly are carried out transparently, with the aim to seek an improved involvement of top and young scientists, with a bottom up approach. I believe the HS community is animated by a strong enthusiasm which, however, is not adequately supported by economical funding. In my opinion this is a major problem which HS should consider and discuss. The relevance of the societal and environmental problems dealt with by hydrologists, in a professional way and with exceptional scientific skills, is without doubt and therefore the limited amount of funding is not justified in practice. In my opinion, in order to refine the structure of the HS community, and promote its visibility, we should formally identify HS ethical principles for research in environmental science. The principles should highlight the role of hydrology as well as the ethical and scientific solidity of the HS community. Establishing ethical principles is even more important in view of the transparent approach HS is adopting for reviewing and publishing contributions and in view of the increasing need to transparently prove how public funding for research is administered. Establishing ethical principles for hydrology is not a trivial task. Hydrology is characterised by a relevant uncertainty in data, models and parameters. Hydrology is also relying on a large variety of approaches, ranging from statistical to physically based. The purpose of this poster is to present a collection of ethical principles for scientific research presented by the literature and

  17. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    International Nuclear Information System (INIS)

    Samuelson, Emma; Karlsson, Sara; Partheen, Karolina; Nilsson, Staffan; Szpirer, Claude; Behboudi, Afrouz

    2012-01-01

    Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

  18. Identifying and categorizing cobenefits in state-supported Australian indigenous environmental management programs: international research implications

    Directory of Open Access Journals (Sweden)

    Marcus Barber

    2017-06-01

    Full Text Available Significant natural resource management investment is flowing to bioculturally diverse areas occupied by indigenous and other socioeconomically and politically marginalized groups. Such investment focuses on environmental benefit but may also generate ancillary economic, social, and other cobenefits. Increased investor interest in such cobenefits is driving the emerging research literature on cobenefit identification, categorization, and assessment. For local people undertaking community-based natural resource management, this emerging cobenefit discourse creates opportunities for more holistic program assessments that better reflect local perspectives, but it also contains risks of increased reporting burdens and institutional capture. Here, we synthesize and critically review the cobenefit literature arising from Australian indigenous cultural and natural resource management programs, a context in which there is a strong investor interest in cobenefits, particularly from government. We identify a wide suite of cobenefits in the existing literature and highlight previously unrecognized conceptual gaps and elisions in cobenefit categorization, including inconsistencies in category definition, the underanalysis of key categories, and a lack of systematic attention to beneficiaries as well as benefits. We propose a clarified and expanded conceptual framework to identify consistently the full suite of benefits, thereby enabling further assessment, valuation, and development of incentive mechanisms, standards, and guidelines. Our analysis has implications for community-based natural resource management assessment in a wide range of international contexts.

  19. Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons.

    Science.gov (United States)

    Juárez-Morales, José L; Martinez-De Luna, Reyna I; Zuber, Michael E; Roberts, Alan; Lewis, Katharine E

    2017-09-01

    A correctly functioning spinal cord is crucial for locomotion and communication between body and brain but there are fundamental gaps in our knowledge of how spinal neuronal circuitry is established and functions. To understand the genetic program that regulates specification and functions of this circuitry, we need to connect neuronal molecular phenotypes with physiological analyses. Studies using Xenopus laevis tadpoles have increased our understanding of spinal cord neuronal physiology and function, particularly in locomotor circuitry. However, the X. laevis tetraploid genome and long generation time make it difficult to investigate how neurons are specified. The opacity of X. laevis embryos also makes it hard to connect functional classes of neurons and the genes that they express. We demonstrate here that Tol2 transgenic constructs using zebrafish enhancers that drive expression in specific zebrafish spinal neurons label equivalent neurons in X. laevis and that the incorporation of a Gal4:UAS amplification cassette enables cells to be observed in live X. laevis tadpoles. This technique should enable the molecular phenotypes, morphologies and physiologies of distinct X. laevis spinal neurons to be examined together in vivo. We have used an islet1 enhancer to label Rohon-Beard sensory neurons and evx enhancers to identify V0v neurons, for the first time, in X. laevis spinal cord. Our work demonstrates the homology of spinal cord circuitry in zebrafish and X. laevis, suggesting that future work could combine their relative strengths to elucidate a more complete picture of how vertebrate spinal cord neurons are specified, and function to generate behavior. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1007-1020, 2017. © 2017 Wiley Periodicals, Inc.

  20. Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies.

    Science.gov (United States)

    Sharpe, Richard A; Cocq, Kate Le; Nikolaou, Vasilis; Osborne, Nicholas J; Thornton, Christopher R

    2016-01-01

    The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Gametogenesis in the Pacific oyster Crassostrea gigas: a microarrays-based analysis identifies sex and stage specific genes.

    Directory of Open Access Journals (Sweden)

    Nolwenn M Dheilly

    . CONCLUSIONS/SIGNIFICANCE: This study allowed us to identify potential markers of early sex differentiation in the oyster C. gigas, an alternative hermaphrodite mollusk. We also provided new highly valuable information on genes specifically expressed by mature spermatozoids and mature oocytes.

  2. Protocol for a thematic synthesis to identify key themes and messages from a palliative care research network.

    LENUS (Irish Health Repository)

    Nicholson, Emma

    2016-10-21

    Research networks that facilitate collaborative research are increasing both regionally and globally and such collaborations contribute greatly to knowledge transfer particularly in health research. The Palliative Care Research Network is an Irish-based network that seeks to create opportunities and engender a collaborative environment to encourage innovative research that is relevant for policy and practice. The current review outlines a methodology to identify cross-cutting messages to identify how dissemination outputs can be optimized to ensure that key messages from this research reaches all knowledge users.

  3. CXCR6, a newly defined biomarker of tissue-specific stem cell asymmetric self-renewal, identifies more aggressive human melanoma cancer stem cells.

    Directory of Open Access Journals (Sweden)

    Rouzbeh Taghizadeh

    2010-12-01

    Full Text Available A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that phenotypically identifiable and isolable subfractions of cells possess the tumor-forming ability. In the present paper, using two lineage-related human melanoma cell lines, primary melanoma line IGR39 and its metastatic derivative line IGR37, two main observations are reported. The first one is the first phenotypic evidence to support the origin of melanoma cancer stem cells (CSCs from mutated tissue-specific stem cells; and the second one is the identification of a more aggressive subpopulation of CSCs in melanoma that are CXCR6+.We defined CXCR6 as a new biomarker for tissue-specific stem cell asymmetric self-renewal. Thus, the relationship between melanoma formation and ABCG2 and CXCR6 expression was investigated. Consistent with their non-metastatic character, unsorted IGR39 cells formed significantly smaller tumors than unsorted IGR37 cells. In addition, ABCG2+ cells produced tumors that had a 2-fold greater mass than tumors produced by unsorted cells or ABCG2- cells. CXCR6+ cells produced more aggressive tumors. CXCR6 identifies a more discrete subpopulation of cultured human melanoma cells with a more aggressive MCSC phenotype than cells selected on the basis of the ABCG2+ phenotype alone.The association of a more aggressive tumor phenotype with asymmetric self-renewal phenotype reveals a previously unrecognized aspect of tumor cell physiology. Namely, the retention of some tissue-specific stem cell attributes, like the ability to asymmetrically self-renew, impacts the natural history of human tumor development. Knowledge of this new aspect of tumor development and progression may provide new targets for cancer prevention and treatment.

  4. Exploring patient experiences with prescription medicines to identify unmet patient needs: implications for research and practice.

    Science.gov (United States)

    Kucukarslan, Suzan N; Lewis, Nancy J W; Shimp, Leslie A; Gaither, Caroline A; Lane, Daniel C; Baumer, Andrea L

    2012-01-01

    Pharmacy services are offered to patients, and often, they decline participation. Research is needed to better understand patients' unmet needs when taking prescribed medications. To identify and characterize patients' unmet needs related to using prescribed medication for chronic conditions. Focus groups of patients using prescription medication for chronic conditions discussed their experiences with medications, starting from initial diagnosis to ongoing management. Sessions involved 40 patients from 1 Midwestern U.S. state. Major themes were identified using content analysis. Three major themes emerged. First, patients seek information to understand their health condition and treatment rationale. Patients form an illness perception (its consequence, controllability, cause, and duration) that dictates their actions. Second, patients desire to be involved in treatment decisions, and they often feel that decisions are made for them without their understanding of the risk-to-benefit trade-off. Third, patients monitor the impact of treatment decisions to determine if anticipated outcomes are achieved. The results were consistent with Dowell's therapeutic alliance model (TAM) and Leventhal's common sense model (CSM). The TAM can be used to model the consultative services between pharmacists and patients. The impact of the new services (or interventions) can be evaluated using the CSM. Patients expressed a strong desire to be involved in their treatment decisions. The effectiveness of medication therapy management services may be enhanced if pharmacists build on patients' desire to be involved in their treatment decisions and assist them to understand the role of medications and their risks and expected outcomes within the context of the patients' perceptions of illness and desired coping strategies. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Identified research directions for using manufacturing knowledge earlier in the product lifecycle.

    Science.gov (United States)

    Hedberg, Thomas D; Hartman, Nathan W; Rosche, Phil; Fischer, Kevin

    2017-01-01

    Design for Manufacturing (DFM), especially the use of manufacturing knowledge to support design decisions, has received attention in the academic domain. However, industry practice has not been studied enough to provide solutions that are mature for industry. The current state of the art for DFM is often rule-based functionality within Computer-Aided Design (CAD) systems that enforce specific design requirements. That rule-based functionality may or may not dynamically affect geometry definition. And, if rule-based functionality exists in the CAD system, it is typically a customization on a case-by-case basis. Manufacturing knowledge is a phrase with vast meanings, which may include knowledge on the effects of material properties decisions, machine and process capabilities, or understanding the unintended consequences of design decisions on manufacturing. One of the DFM questions to answer is how can manufacturing knowledge, depending on its definition, be used earlier in the product lifecycle to enable a more collaborative development environment? This paper will discuss the results of a workshop on manufacturing knowledge that highlights several research questions needing more study. This paper proposes recommendations for investigating the relationship of manufacturing knowledge with shape, behavior, and context characteristics of product to produce a better understanding of what knowledge is most important. In addition, the proposal includes recommendations for investigating the system-level barriers to reusing manufacturing knowledge and how model-based manufacturing may ease the burden of knowledge sharing. Lastly, the proposal addresses the direction of future research for holistic solutions of using manufacturing knowledge earlier in the product lifecycle.

  6. Trophic transfer of microplastics in aquatic ecosystems: Identifying critical research needs.

    Science.gov (United States)

    Au, Sarah Y; Lee, Cindy M; Weinstein, John E; van den Hurk, Peter; Klaine, Stephen J

    2017-05-01

    To evaluate the process of trophic transfer of microplastics, it is important to consider various abiotic and biotic factors involved in their ingestion, egestion, bioaccumulation, and biomagnification. Toward this end, a review of the literature on microplastics has been conducted to identify factors influencing their uptake and absorption; their residence times in organisms and bioaccumulation; the physical effects of their aggregation in gastrointestinal tracts; and their potential to act as vectors for the transfer of other contaminants. Limited field evidence from higher trophic level organisms in a variety of habitats suggests that trophic transfer of microplastics may be a common phenomenon and occurs concurrently with direct ingestion. Critical research needs include standardizing methods of field characterization of microplastics, quantifying uptake and depuration rates in organisms at different trophic levels, quantifying the influence that microplastics have on the uptake and/or depuration of environmental contaminants among different trophic levels, and investigating the potential for biomagnification of microplastic-associated chemicals. More integrated approaches involving computational modeling are required to fully assess trophic transfer of microplastics. Integr Environ Assess Manag 2017;13:505-509. © 2017 SETAC. © 2017 SETAC.

  7. Increasing organizational energy conservation behaviors: Comparing the theory of planned behavior and reasons theory for identifying specific motivational factors to target for change

    Science.gov (United States)

    Finlinson, Scott Michael

    Social scientists frequently assess factors thought to underlie behavior for the purpose of designing behavioral change interventions. Researchers commonly identify these factors by examining relationships between specific variables and the focal behaviors being investigated. Variables with the strongest relationships to the focal behavior are then assumed to be the most influential determinants of that behavior, and therefore often become the targets for change in a behavioral change intervention. In the current proposal, multiple methods are used to compare the effectiveness of two theoretical frameworks for identifying influential motivational factors. Assessing the relative influence of all factors and sets of factors for driving behavior should clarify which framework and methodology is the most promising for identifying effective change targets. Results indicated each methodology adequately predicted the three focal behaviors examined. However, the reasons theory approach was superior for predicting factor influence ratings compared to the TpB approach. While common method variance contamination had minimal impact on the results or conclusions derived from the present study's findings, there were substantial differences in conclusions depending on the questionnaire design used to collect the data. Examples of applied uses of the present study are discussed.

  8. Researchers and Institutions in the Periphery: Challenges in Measuring Research Capacity for Geographically Specific Programs in the U.S

    Energy Technology Data Exchange (ETDEWEB)

    Melkers, J.

    2016-07-01

    The U.S. research funding system supports two geographically targeted government programs designed to enhance the research capacity of less competitive states in seeking federal research funds. Program eligibility is based on a relatively narrow measures of overall jurisdiction research funding track record. Yet, in order to adequately measure and address improved capacity development in these areas, a more nuanced understanding of the research capacity in these settings is needed. While the metric of prior research funding metric may be useful in assigning jurisdictions program eligibility, they do not account for variations within or across these areas, nor for factors that may function differently in lower capacity regions. This paper addresses the particular institutional and social/human capital aspects of measuring and identifying research capacity in these regions. Institutional data are used to categorize institutions within and across eligible jurisdictions. Survey data are used to address capacity issues and factors relevant to capacity development at the researcher level. (Author)

  9. IgE to penicillins with different specificities can be identified by a multiepitope macromolecule: Bihaptenic penicillin structures and IgE specificities.

    Science.gov (United States)

    Ariza, A; Barrionuevo, E; Mayorga, C; Montañez, M I; Perez-Inestrosa, E; Ruiz-Sánchez, A; Rodríguez-Guéant, R M; Fernández, T D; Guéant, J L; Torres, M J; Blanca, M

    2014-04-01

    Quantitation of specific IgE by immunoassay is a recommended in vitro test for the diagnosis of immediate hypersensitivity reactions to betalactams (BLs), particularly when skin test results are negative. IgE antibodies that recognize the common nuclear structure of all BLs or the specific side chain structure can be mainly distinguished by immunoassays. The aim of this study was to develop an immunoassay system to detect IgE antibodies with different specificities. Cellulose discs conjugated with benzylpenicillin (BP), amoxicillin (AX) or both drugs, with poly-l-lysine (PLL) as carrier molecule, were used as solid phases in the radioallergosorbent test (RAST). Direct and inhibition radioimmunoassay studies were made to verify the structures recognized by serum IgE antibodies from penicillin-allergic patients. Our results indicated that the addition of both haptens did not decrease the capacity to capture IgE when serum specific to either BP or AX was used, at least in terms of sensitivity. In addition, the inclusion of two haptens improved significantly the levels of IgE detection in patients who recognized both BP and AX. Therefore, the use of a solid phase with a carrier molecule conjugated with two determinants (AX and BP) is helpful to recognize IgE antibodies against either of these determinants and is useful for screening sera with different specificities. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Graduate Education to Facilitate Interdisciplinary Research Collaboration: Identifying Individual Competencies and Developmental Activities

    Science.gov (United States)

    Holt, Valerie Ciocca

    2013-01-01

    Interdisciplinary research collaborations (IDRC) are considered essential for addressing the most complex global community problems concerning science, health, education, energy, the environment, and society. In spite of technological advances, supportive funding, and even researcher proclivity to collaborate, these complex interdisciplinary…

  11. Identifying Themes for Research-Based Development of Pedagogy and Guidance in Higher Education

    Science.gov (United States)

    Jääskelä, Päivikki; Nissilä, Pia

    2015-01-01

    The high value accorded to the research-based development of education in higher education communities means that researchers in the field have an important role in determining the foci of such efforts. However, it is important to ask whether higher education research is providing answers that satisfy practical educational needs. In this study,…

  12. Measuring the impact of methodological research: a framework and methods to identify evidence of impact.

    Science.gov (United States)

    Brueton, Valerie C; Vale, Claire L; Choodari-Oskooei, Babak; Jinks, Rachel; Tierney, Jayne F

    2014-11-27

    Providing evidence of impact highlights the benefits of medical research to society. Such evidence is increasingly requested by research funders and commonly relies on citation analysis. However, other indicators may be more informative. Although frameworks to demonstrate the impact of clinical research have been reported, no complementary framework exists for methodological research. Therefore, we assessed the impact of methodological research projects conducted or completed between 2009 and 2012 at the UK Medical Research Council Clinical Trials Unit Hub for Trials Methodology Research Hub, with a view to developing an appropriate framework. Various approaches to the collection of data on research impact were employed. Citation rates were obtained using Web of Science (http://www.webofknowledge.com/) and analyzed descriptively. Semistructured interviews were conducted to obtain information on the rates of different types of research output that indicated impact for each project. Results were then pooled across all projects. Finally, email queries pertaining to methodology projects were collected retrospectively and their content analyzed. Simple citation analysis established the citation rates per year since publication for 74 methodological publications; however, further detailed analysis revealed more about the potential influence of these citations. Interviews that spanned 20 individual research projects demonstrated a variety of types of impact not otherwise collated, for example, applications and further developments of the research; release of software and provision of guidance materials to facilitate uptake; formation of new collaborations and broad dissemination. Finally, 194 email queries relating to 6 methodological projects were received from 170 individuals across 23 countries. They provided further evidence that the methodologies were impacting on research and research practice, both nationally and internationally. We have used the information

  13. Identifying patients with myasthenia for epidemiological research by linkage of automated registers

    DEFF Research Database (Denmark)

    Pedersen, Emil Greve; Hallas, Jesper; Hansen, Klaus

    2011-01-01

    We validated a new method of identifying patients with incident myasthenia in automated Danish registers for the purpose of conducting epidemiological studies of the disorder.......We validated a new method of identifying patients with incident myasthenia in automated Danish registers for the purpose of conducting epidemiological studies of the disorder....

  14. Future e-government research : 13 research themes identified in the eGovRTD2020 project

    NARCIS (Netherlands)

    Wimmer, M.; Codagnone, C.; Janssen, M.F.W.H.A.

    2008-01-01

    E-government research has become a recognized research domain and many policies and strategies are formulated for e-government implementations. Most of these target the next few years and limited attention has been giving to the long term. The eGovRTD2020, a European Commission co-funded project,

  15. Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI.

    Science.gov (United States)

    Wang, Weijing; Jiang, Wenjie; Hou, Lin; Duan, Haiping; Wu, Yili; Xu, Chunsheng; Tan, Qihua; Li, Shuxia; Zhang, Dongfeng

    2017-11-13

    correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired.

  16. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

    KAUST Repository

    Abdel-Haleem, Alyaa M.; Hefzi, Hooman; Mineta, Katsuhiko; Gao, Xin; Gojobori, Takashi; Palsson, Bernhard O.; Lewis, Nathan E.; Jamshidi, Neema

    2018-01-01

    and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species

  17. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing

    OpenAIRE

    Moncini, S.; Bedeschi, M.F.; Castronovo, P.; Crippa, M.; Calvello, M.; Garghentino, R.R.; Scuvera, G.; Finelli, P.; Venturin, M.

    2013-01-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allow...

  18. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

    Science.gov (United States)

    Kim, Taehyung; Tyndel, Marc S; Huang, Haiming; Sidhu, Sachdev S; Bader, Gary D; Gfeller, David; Kim, Philip M

    2012-03-01

    Peptide recognition domains and transcription factors play crucial roles in cellular signaling. They bind linear stretches of amino acids or nucleotides, respectively, with high specificity. Experimental techniques that assess the binding specificity of these domains, such as microarrays or phage display, can retrieve thousands of distinct ligands, providing detailed insight into binding specificity. In particular, the advent of next-generation sequencing has recently increased the throughput of such methods by several orders of magnitude. These advances have helped reveal the presence of distinct binding specificity classes that co-exist within a set of ligands interacting with the same target. Here, we introduce a software system called MUSI that can rapidly analyze very large data sets of binding sequences to determine the relevant binding specificity patterns. Our pipeline provides two major advances. First, it can detect previously unrecognized multiple specificity patterns in any data set. Second, it offers integrated processing of very large data sets from next-generation sequencing machines. The results are visualized as multiple sequence logos describing the different binding preferences of the protein under investigation. We demonstrate the performance of MUSI by analyzing recent phage display data for human SH3 domains as well as microarray data for mouse transcription factors.

  19. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Je-Hyuk Lee

    2009-11-01

    Full Text Available Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.

  20. Identifying research advancements in supply chain risk management for Agri-food Industries: Literature review

    Science.gov (United States)

    Septiani, W.; Astuti, P.

    2017-12-01

    Agri-food supply chain has different characteristics related to the raw materials it uses. Food supply chain has a high risk of damage, thus drawing a lot of attention from researchers in supply chain management. This research aimed to investigate the development of supply chain risk management research on agri-food industries. These reviews were arranged in steps systematically, ranging from searching related to the review of SCRM paper, reviewing the general framework of SCRM and the framework of agri-food SCRM. Selection of literature review papers in the period 2005-2017, and obtained 45 papers. The results of the identification research were illustrated in a supply chain risk management framework model. This provided insight toward future research directions and needs.

  1. Mapping the author gender-distribution of disease-specific medical research

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, J.P.; Schneider, J.W.; Nielsen, M.W.

    2016-07-01

    This short paper responds to a recent call for attention to the “diversity challenge” in biomedical research, specifically with regard to gender diversity. The lack of diversity can be limiting for the progression of knowledge production, a viewpoint shared by both the European Commission, the League of European Research Universities and the National Institute of Health. (Author)

  2. A small interfering RNA screen of genes involved in DNA repair identifies tumor-specific radiosensitization by POLQ knockdown

    DEFF Research Database (Denmark)

    Higgins, Geoff S; Prevo, Remko; Lee, Yin-Fai

    2010-01-01

    The effectiveness of radiotherapy treatment could be significantly improved if tumor cells could be rendered more sensitive to ionizing radiation (IR) without altering the sensitivity of normal tissues. However, many of the key therapeutically exploitable mechanisms that determine intrinsic tumor...... radiosensitivity are largely unknown. We have conducted a small interfering RNA (siRNA) screen of 200 genes involved in DNA damage repair aimed at identifying genes whose knockdown increased tumor radiosensitivity. Parallel siRNA screens were conducted in irradiated and unirradiated tumor cells (SQ20B......) and irradiated normal tissue cells (MRC5). Using gammaH2AX foci at 24 hours after IR, we identified several genes, such as BRCA2, Lig IV, and XRCC5, whose knockdown is known to cause increased cell radiosensitivity, thereby validating the primary screening end point. In addition, we identified POLQ (DNA...

  3. Public Private Partnerships: Identifying Practical Issues for an Accounting Research Agenda

    OpenAIRE

    Nick Sciulli

    2014-01-01

    This article provides a structured framework for research into the accounting implications of Public Private Partnerships (PPPs). PPPs worldwide have taken on increasing significance as a tool that governments can use to develop infrastructure and for the delivery of services. Given the minimal coverage in the literature of the Victorian State Government experience to date regarding the efficacy of PPPs, this report establishes a number of parameters from which academics can conduct research ...

  4. Identifying Indicators of Progress in Thermal Spray Research Using Bibliometrics Analysis

    Science.gov (United States)

    Li, R.-T.; Khor, K. A.; Yu, L.-G.

    2016-12-01

    We investigated the research publications on thermal spray in the period of 1985-2015 using the data from Web of Science, Scopus and SciVal®. Bibliometrics analysis was employed to elucidate the country and institution distribution in various thermal spray research areas and to characterize the trends of topic change and technology progress. Results show that China, USA, Japan, Germany, India and France were the top countries in thermal spray research, and Xi'an Jiaotong University, Universite de Technologie Belfort-Montbeliard, Shanghai Institute of Ceramics, ETH Zurich, National Research Council of Canada, University of Limoges were among the top institutions that had high scholarly research output during 2005-2015. The terms of the titles, keywords and abstracts of the publications were analyzed by the Latent Dirichlet Allocation model and visually mapped using the VOSviewer software to reveal the progress of thermal spray technology. It is found that thermal barrier coating was consistently the main research area in thermal spray, and high-velocity oxy-fuel spray and cold spray developed rapidly in the last 10 years.

  5. Toward Greater Specificity in Identifying Associations among Interparental Aggression, Child Emotional Reactivity to Conflict, and Child Problems

    Science.gov (United States)

    Davies, Patrick T.; Cicchetti, Dante; Martin, Meredith J.

    2012-01-01

    This study examined specific forms of emotional reactivity to conflict and temperamental emotionality as explanatory mechanisms in pathways among interparental aggression and child psychological problems. Participants of the multimethod, longitudinal study included 201 two-year-old children and their mothers who had experienced elevated violence…

  6. Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone

    NARCIS (Netherlands)

    Bart, A.; Dankert, J.; van der Ende, A.

    2000-01-01

    Neisseria meningitidis may cause meningitis and septicemia. Since the early 1980s, an increased incidence of meningococcal disease has been caused by the lineage III clone in many countries in Europe and in New Zealand. We hypothesized that lineage III meningococci have specific DNA sequences,

  7. Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells

    DEFF Research Database (Denmark)

    Tarasova, Irina A; Tereshkova, Alesya V; Lobas, Anna A

    2018-01-01

    An acquisition of increased sensitivity of cancer cells to viruses is a common outcome of malignant progression that justifies the development of oncolytic viruses as anticancer therapeutics. Studying molecular changes that underlie the sensitivity to viruses would help to identify cases where on...

  8. Identifying long-term memory B-cells in vaccinated children despite waning antibody levels specific for Bordetella pertussis proteins.

    Science.gov (United States)

    Hendrikx, Lotte H; Oztürk, Kemal; de Rond, Lia G H; Veenhoven, Reinier H; Sanders, Elisabeth A M; Berbers, Guy A M; Buisman, Anne-Marie

    2011-02-04

    Whooping cough is a respiratory disease caused by Bordetella pertussis. Since the 1950s in developed countries pertussis vaccinations are included in the national immunization program. However, antibody levels rapidly wane after both whole cell and acellular pertussis vaccination. Therefore protection against pertussis may depend largely on long-term B- and T-cell immunities. We investigated long-term pertussis-specific memory B-cell responses in children who were primed at infant age with the Dutch wP-vaccine (ISRCTN65428640). Purified B-cells were characterized by FACS-analysis and after polyclonal stimulation memory B-cells were detected by ELISPOT-assays specific for pertussis toxin, filamentous haemagglutinin, pertactin and tetanus. In addition, plasma IgG levels directed to the same antigens were measured by a fluorescent bead-based multiplex immunoassay. Two and 3 years after wP priming as well as 2 and 5 years after the aP booster at the age of 4, low plasma IgG levels to the pertussis proteins were found. At the same time, however pertussis protein-specific memory B-cells could be detected and their number increased with age. The number of tetanus-specific memory B-cells was similar in all age groups, whereas IgG-tetanus levels were high 2 years after tetanus booster compared to pre- and 5 years post-booster levels. This study shows the presence of long-term pertussis protein-specific memory B-cells in children despite waning antibody levels after vaccination, which suggests that memory B-cells in addition to antibodies may contribute to protection against pertussis. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Research gaps identified during systematic reviews of clinical trials: glass-ionomer cements.

    Science.gov (United States)

    Mickenautsch, Steffen

    2012-06-29

    To report the results of an audit concerning research gaps in clinical trials that were accepted for appraisal in authored and published systematic reviews regarding the application of glass-ionomer cements (GIC) in dental practice Information concerning research gaps in trial precision was extracted, following a framework that included classification of the research gap reasons: 'imprecision of information (results)', 'biased information', 'inconsistency or unknown consistency' and 'not the right information', as well as research gap characterization using PICOS elements: population (P), intervention (I), comparison (C), outcomes (O) and setting (S). Internal trial validity assessment was based on the understanding that successful control for systematic error cannot be assured on the basis of inclusion of adequate methods alone, but also requires empirical evidence about whether such attempt was successful. A comprehensive and interconnected coverage of GIC-related clinical topics was established. The most common reasons found for gaps in trial precision were lack of sufficient trials and lack of sufficient large sample size. Only a few research gaps were ascribed to 'Lack of information' caused by focus on mainly surrogate trial outcomes. According to the chosen assessment criteria, a lack of adequate randomisation, allocation concealment and blinding/masking in trials covering all reviewed GIC topics was noted (selection- and detection/performance bias risk). Trial results appear to be less affected by loss-to-follow-up (attrition bias risk). This audit represents an adjunct of the systematic review articles it has covered. Its results do not change the systematic review's conclusions but highlight existing research gaps concerning the precision and internal validity of reviewed trials in detail. These gaps should be addressed in future GIC-related clinical research.

  10. Research gaps identified during systematic reviews of clinical trials: glass-ionomer cements

    Directory of Open Access Journals (Sweden)

    Mickenautsch Steffen

    2012-06-01

    Full Text Available Abstract Background To report the results of an audit concerning research gaps in clinical trials that were accepted for appraisal in authored and published systematic reviews regarding the application of glass-ionomer cements (GIC in dental practice Methods Information concerning research gaps in trial precision was extracted, following a framework that included classification of the research gap reasons: ‘imprecision of information (results’, ‘biased information’, ‘inconsistency or unknown consistency’ and ‘not the right information’, as well as research gap characterization using PICOS elements: population (P, intervention (I, comparison (C, outcomes (O and setting (S. Internal trial validity assessment was based on the understanding that successful control for systematic error cannot be assured on the basis of inclusion of adequate methods alone, but also requires empirical evidence about whether such attempt was successful. Results A comprehensive and interconnected coverage of GIC-related clinical topics was established. The most common reasons found for gaps in trial precision were lack of sufficient trials and lack of sufficient large sample size. Only a few research gaps were ascribed to ‘Lack of information’ caused by focus on mainly surrogate trial outcomes. According to the chosen assessment criteria, a lack of adequate randomisation, allocation concealment and blinding/masking in trials covering all reviewed GIC topics was noted (selection- and detection/performance bias risk. Trial results appear to be less affected by loss-to-follow-up (attrition bias risk. Conclusion This audit represents an adjunct of the systematic review articles it has covered. Its results do not change the systematic review’s conclusions but highlight existing research gaps concerning the precision and internal validity of reviewed trials in detail. These gaps should be addressed in future GIC-related clinical research.

  11. Identifying research fields within business and management: a journal cross-citation analysis

    NARCIS (Netherlands)

    Mingers, J.; Leydesdorff, L.

    2015-01-01

    A discipline such as business and management (B&M) is very broad and has many fields within it, ranging from fairly scientific ones such as management science or economics to softer ones such as information systems. There are at least three reasons why it is important to identify these sub-fields

  12. California Levee Risk, Now and in the Future:Identifying Research and Tool Development Needs

    Energy Technology Data Exchange (ETDEWEB)

    Newmark, R L; Hanemann, M; Farber, D

    2006-11-28

    The Center for Catastrophic Risk Management (CCRM) and the California Center for Environmental Law and Policy (CCELP) at UC Berkeley and the Lawrence Livermore National Laboratory (LLNL) joined together to cosponsor a workshop to define research requirements to mitigate the hazards facing the Sacramento-San Joaquin Delta Levee system. The Workshop was intended to provide a forum to (1) Report assessments of current vulnerabilities facing the levees, such as structural failure, seismic loading, flooding, terrorism; (2) Consider longer term challenges such as climate change, sea level rise; and (3) Define research requirements to fill gaps in knowledge and reduce uncertainties in hazard assessments.

  13. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing.

    Science.gov (United States)

    Moncini, S; Bedeschi, M F; Castronovo, P; Crippa, M; Calvello, M; Garghentino, R R; Scuvera, G; Finelli, P; Venturin, M

    2013-12-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allowed the identification of the ATRX c.109C>T (p.R37X) mutation in both the affected brothers. Sanger sequencing confirmed the presence of the mutation in the brothers and showed that the mother is a healthy carrier. Mutations in the ATRX gene cause the X-linked alpha thalassemia/mental retardation (ATR-X) syndrome (MIM #301040), a severe clinical condition usually associated with profound ID, facial dysmorphism and alpha thalassemia. However, the syndrome is clinically heterogeneous and some mutations, including the c.109C>T, are associated with a broad phenotypic spectrum, with patients displaying a less severe phenotype with only mild-moderate ID. In the case presented here, exome sequencing provided an effective strategy to achieve the molecular diagnosis of ATR-X syndrome, which otherwise would have been difficult to consider due to the mild non-specific phenotype and the absence of a family history with typical severe cases.

  14. Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

    Science.gov (United States)

    Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

    2017-07-01

    Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

  15. Using a Design-Based Research Study to Identify Principles for Training Instructors to Teach Online

    Science.gov (United States)

    Shattuck, Julie; Anderson, Terry

    2013-01-01

    Within the overall framework of design-based research, this paper reports on a study that focused on evaluating an online training course for online instructors. This intervention was designed as a possible solution to the problem facing some higher education institutions of how to provide quality, accessible training for mostly part-time…

  16. Maximizing Research and Development Resources: Identifying and Testing "Load-Bearing Conditions" for Educational Technology Innovations

    Science.gov (United States)

    Iriti, Jennifer; Bickel, William; Schunn, Christian; Stein, Mary Kay

    2016-01-01

    Education innovations often have a complicated set of assumptions about the contexts in which they are implemented, which may not be explicit. Education technology innovations in particular may have additional technical and cultural assumptions. As a result, education technology research and development efforts as well as scaling efforts can be…

  17. Rediscovering Paideia and the Meaning of a Scholarly Career: Rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory"

    Science.gov (United States)

    Antonacopoulou, Elena P.

    2016-01-01

    In "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory," authors J.B. Arbaugh, Charles J. Fornaciari, and Alvin Hwang ("Journal of Management Education," December 2016 vol. 40 no. 6 p654-691, see EJ1118407) used citation analysis to track the development of…

  18. Identifying research priorities in anaesthesia and perioperative care: final report of the joint National Institute of Academic Anaesthesia/James Lind Alliance Research Priority Setting Partnership

    OpenAIRE

    Boney, O.; Bell, M.; Bell, N.; Conquest, A.; Cumbers, M.; Drake, S.; Galsworthy, M.; Gath, J.; Grocott, M. P.; Harris, E.; Howell, S.; Ingold, A.; Nathanson, M. H.; Pinkney, T.; Metcalf, L.

    2015-01-01

    Objective To identify research priorities for Anaesthesia and Perioperative Medicine. Design Prospective surveys and consensus meetings guided by an independent adviser. Setting UK. Participants 45 stakeholder organisations (25 professional, 20 patient/carer) affiliated as James Lind Alliance partners. Outcomes First ?ideas-gathering? survey: Free text research ideas and suggestions. Second ?prioritisation? survey: Shortlist of ?summary? research questions (derived from the first survey) rank...

  19. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

    Directory of Open Access Journals (Sweden)

    Alyaa M Abdel-Haleem

    2018-01-01

    Full Text Available Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1, choline, and pantothenate (vitamin B5 metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  20. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

    KAUST Repository

    Abdel-Haleem, Alyaa M.

    2018-01-04

    Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  1. Identifying primary care patient safety research priorities in the UK: a James Lind Alliance Priority Setting Partnership.

    Science.gov (United States)

    Morris, Rebecca Lauren; Stocks, Susan Jill; Alam, Rahul; Taylor, Sian; Rolfe, Carly; Glover, Steven William; Whitcombe, Joanne; Campbell, Stephen M

    2018-02-28

    To identify the top 10 unanswered research questions for primary care patient safety research. A modified nominal group technique. UK. Anyone with experience of primary care including: patients, carers and healthcare professionals. 341 patients and 86 healthcare professionals submitted questions. A top 10, and top 30, future research questions for primary care patient safety. 443 research questions were submitted by 341 patients and 86 healthcare professionals, through a national survey. After checking for relevance and rephrasing, a total of 173 questions were collated into themes. The themes were largely focused on communication, team and system working, interfaces across primary and secondary care, medication, self-management support and technology. The questions were then prioritised through a national survey, the top 30 questions were taken forward to the final prioritisation workshop. The top 10 research questions focused on the most vulnerable in society, holistic whole-person care, safer communication and coordination between care providers, work intensity, continuity of care, suicide risk, complex care at home and confidentiality. This study was the first national prioritisation exercise to identify patient and healthcare professional priorities for primary care patient safety research. The research priorities identified a range of important gaps in the existing evidence to inform everyday practice to address primary care patient safety. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  2. Using Community-Based Participatory Research to Identify Environmental Justice Issues in an Inner-City Community and Inform Urban Planning.

    Science.gov (United States)

    Mansyur, Carol Leler; Jeng, Hueiwang Anna; Holloman, Erica; DeBrew, Linwood

    2016-01-01

    The Southeast CARE Coalition has been using community-based participatory research to examine environmental degradation in the Southeast Community, Newport News, Virginia. A survey was developed to collect assessment data. Up to 66% of respondents were concerned about environmental problems in their community. Those with health conditions were significantly more likely to identify specific environmental problems. The top 5 environmental concerns included coal dust, air quality, crime, water quality, and trash. The community-based participatory research process is building community capacity and participation, providing community input into strategic planning, and empowering community members to take control of environmental justice issues in their community.

  3. Identifying consumer preferences for specific beef flavor characteristics in relation to cattle production and postmortem processing parameters.

    Science.gov (United States)

    O'Quinn, T G; Woerner, D R; Engle, T E; Chapman, P L; Legako, J F; Brooks, J C; Belk, K E; Tatum, J D

    2016-02-01

    Sensory analysis of ground LL samples representing 12 beef product categories was conducted in 3 different regions of the U.S. to identify flavor preferences of beef consumers. Treatments characterized production-related flavor differences associated with USDA grade, cattle type, finishing diet, growth enhancement, and postmortem aging method. Consumers (N=307) rated cooked samples for 12 flavors and overall flavor desirability. Samples were analyzed to determine fatty acid content. Volatile compounds produced by cooking were extracted and quantified. Overall, consumers preferred beef that rated high for beefy/brothy, buttery/beef fat, and sweet flavors and disliked beef with fishy, livery, gamey, and sour flavors. Flavor attributes of samples higher in intramuscular fat with greater amounts of monounsaturated fatty acids and lesser proportions of saturated, odd-chain, omega-3, and trans fatty acids were preferred by consumers. Of the volatiles identified, diacetyl and acetoin were most closely correlated with desirable ratings for overall flavor and dimethyl sulfide was associated with an undesirable sour flavor. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts*

    Science.gov (United States)

    Anderson, Jonathan P.; Hane, James K.; Stoll, Thomas; Pain, Nicholas; Hastie, Marcus L.; Kaur, Parwinder; Hoogland, Christine; Gorman, Jeffrey J.; Singh, Karam B.

    2016-01-01

    Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806. PMID:26811357

  5. Methods of Identifying Limb Dominance in Adolescent Female Basketball Players: Implications for Clinical and Biomechanical Research.

    Science.gov (United States)

    Mulrey, Colleen R; Shultz, Sandra J; Ford, Kevin R; Nguyen, Anh-Dung; Taylor, Jeffrey B

    2018-03-29

    To identify relationships between self-reported limb preferences and performance measures for determining limb dominance in adolescent female basketball players. Cross-sectional cohort study. Forty adolescent female basketball players. Participants provided self-reported preferred kicking and jumping limbs, then completed 3 trials of a single-limb countermovement hop (HOPVER) and unilateral triple hop for distance (HOPHOR) on each limb. Each test was used to independently define limb dominance by the limb that produced the largest maximum vertical height and horizontal distance, respectively. Chi-square tests for independence identified a significant relationship between self-reported preferred kicking and jumping legs (χ = 7.41, P = 0.006). However, no significant relationships were found when comparing self-reported preference to measures of performance during the HOPHOR (χ = 0.33, P = 0.57) or HOPVER (χ = 0.06, P = 0.80). In addition, the 2 performance measures did not consistently produce the same definition of limb dominance among individuals (χ = 1.52, P = 0.22). Self-selection of the dominant limb is unrelated to performance. Furthermore, limb dominance, as defined by vertical jump height, is unrelated to limb dominance defined by horizontal jump distance. The results of this study call into question the validity of consistently defining limb dominance by self-reported measures in adolescent female basketball players.

  6. Interactive cervical motion kinematics: sensitivity, specificity and clinically significant values for identifying kinematic impairments in patients with chronic neck pain.

    Science.gov (United States)

    Sarig Bahat, Hilla; Chen, Xiaoqi; Reznik, David; Kodesh, Einat; Treleaven, Julia

    2015-04-01

    Chronic neck pain has been consistently shown to be associated with impaired kinematic control including reduced range, velocity and smoothness of cervical motion, that seem relevant to daily function as in quick neck motion in response to surrounding stimuli. The objectives of this study were: to compare interactive cervical kinematics in patients with neck pain and controls; to explore the new measures of cervical motion accuracy; and to find the sensitivity, specificity, and optimal cutoff values for defining impaired kinematics in those with neck pain. In this cross-section study, 33 patients with chronic neck pain and 22 asymptomatic controls were assessed for their cervical kinematic control using interactive virtual reality hardware and customized software utilizing a head mounted display with built-in head tracking. Outcome measures included peak and mean velocity, smoothness (represented by number of velocity peaks (NVP)), symmetry (represented by time to peak velocity percentage (TTPP)), and accuracy of cervical motion. Results demonstrated significant and strong effect-size differences in peak and mean velocities, NVP and TTPP in all directions excluding TTPP in left rotation, and good effect-size group differences in 5/8 accuracy measures. Regression results emphasized the high clinical value of neck motion velocity, with very high sensitivity and specificity (85%-100%), followed by motion smoothness, symmetry and accuracy. These finding suggest cervical kinematics should be evaluated clinically, and screened by the provided cut off values for identification of relevant impairments in those with neck pain. Such identification of presence or absence of kinematic impairments may direct treatment strategies and additional evaluation when needed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Jersie-Christensen, Rosa R; Lyon, David

    2016-01-01

    BACKGROUND: The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients...... with periodontitis and dental caries to healthy individuals. METHODS: Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically...... and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. CONCLUSIONS: Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease...

  8. Identifying diffusion patterns of research articles on Twitter: A case study of online engagement with open access articles.

    Science.gov (United States)

    Alperin, Juan Pablo; Gomez, Charles J; Haustein, Stefanie

    2018-03-01

    The growing presence of research shared on social media, coupled with the increase in freely available research, invites us to ask whether scientific articles shared on platforms like Twitter diffuse beyond the academic community. We explore a new method for answering this question by identifying 11 articles from two open access biology journals that were shared on Twitter at least 50 times and by analyzing the follower network of users who tweeted each article. We find that diffusion patterns of scientific articles can take very different forms, even when the number of times they are tweeted is similar. Our small case study suggests that most articles are shared within single-connected communities with limited diffusion to the public. The proposed approach and indicators can serve those interested in the public understanding of science, science communication, or research evaluation to identify when research diffuses beyond insular communities.

  9. Identifying key research objectives to make European forests greener for bats

    Directory of Open Access Journals (Sweden)

    Danilo Russo

    2016-07-01

    Full Text Available Bats are a biodiverse mammal order providing key ecosystem services such as pest suppression, pollination and seed dispersal. Bats are also very sensitive to human actions, and significant declines in many bat populations have been recorded consequently. Many bat species find crucial roosting and foraging opportunities in European forests. Such forests have historically been exploited by humans and are still influenced by harvesting. One of the consequences of this pressure is the loss of key habitat resources, often making forests inhospitable to bats. Despite the legal protection granted to bats across Europe, the impacts of forestry on bats are still often neglected. Because forest exploitation influences forest structure at several spatial scales, economically viable forestry could become more sustainable and even favour bats. We highlight that a positive future for bat conservation that simultaneously benefits forestry is foreseeable, although more applied research is needed to develop sound management. Key future research topics include the detection of factors influencing the carrying capacity of forests, and determining the impacts of forest management and the economic importance of bats in forests. Predictive tools to inform forest managers are much needed, together with greater synergies between forest managers and bat conservationists.

  10. The Use of Patient-Specific Induced Pluripotent Stem Cells (iPSCs to Identify Osteoclast Defects in Rare Genetic Bone Disorders

    Directory of Open Access Journals (Sweden)

    I-Ping Chen

    2014-12-01

    Full Text Available More than 500 rare genetic bone disorders have been described, but for many of them only limited treatment options are available. Challenges for studying these bone diseases come from a lack of suitable animal models and unavailability of skeletal tissues for studies. Effectors for skeletal abnormalities of bone disorders may be abnormal bone formation directed by osteoblasts or anomalous bone resorption by osteoclasts, or both. Patient-specific induced pluripotent stem cells (iPSCs can be generated from somatic cells of various tissue sources and in theory can be differentiated into any desired cell type. However, successful differentiation of hiPSCs into functional bone cells is still a challenge. Our group focuses on the use of human iPSCs (hiPSCs to identify osteoclast defects in craniometaphyseal dysplasia. In this review, we describe the impact of stem cell technology on research for better treatment of such disorders, the generation of hiPSCs from patients with rare genetic bone disorders and current protocols for differentiating hiPSCs into osteoclasts.

  11. Utilizing a logic model to identify clinical research problems: a lesson from philosophy of science

    Directory of Open Access Journals (Sweden)

    Collins CR

    2016-10-01

    Full Text Available Cynthia R Collins School of Nursing, College of Social Sciences, Loyola University, New Orleans, LA, USA Abstract: Communication and decision making in the health care workplace often involve finding solutions to ill-structured problems in uncertain, dynamic environments influenced by the competing interests of multiple stakeholders. In this environment, doctoral-prepared nurses who practice as administrators, policy makers, or advanced practice practitioners are often compelled to make important decisions based upon evaluating the merit of colleagues’ proposals against some desired organizational or population outcome. Of equal importance is the nurse leader’s own capacity to construct a compelling argument or proposal that will drive the organization forward to meet the evolving needs for quality health care. Where do we learn the skills necessary to foster this kind of critical thinking in our professional communications? The author suggests that one teaching–learning approach can be found through the thoughtful application of the work of British philosopher Steven Toulmin. Toulmin defined a model for both the analysis and derivation of logical arguments or proposals that can be readily learned and applied for use in health care systems. This model posits that a substantive argument or claim can be evaluated based on the assumptions it presumes (warrants and the strength of the evidence base (backing. Several of the social science professions have adapted Toulmin’s model to generate analysis and creative solutions to complex or emergent problems. The author proposes that an application of this model be included in the pedagogy of doctoral level Philosophy of Science or Nursing Theory courses. The Toulmin process often provides the doctoral student or novice researcher with their first real learning experience in defining the scope and inherent challenges of framing a clinical issue to be the focus of their scholarly translational

  12. Stroke and myocardial infarction: a comparative systematic evaluation of gender-specific analysis, funding and authorship patterns in cardiovascular research.

    Science.gov (United States)

    Oertelt-Prigione, Sabine; Wiedmann, Silke; Endres, Matthias; Nolte, Christian H; Regitz-Zagrosek, Vera; Heuschmann, Peter

    2011-01-01

    Major gender differences exist in cardiovascular diseases and lead to different outcomes in women and men. However, attention and incorporation of sex-/gender-specific research might vary among disciplines. We therefore conducted a systematic review comparing publication characteristics and trends between stroke and myocardial infarction (MI) with respect to sex- and gender-related aspects. A systematic literature search was performed in PubMed to identify gender-/sex-related articles published for stroke and MI between 1977 and 2008. A specifically designed text mining program was used, and all literature was rated by two independent investigators. Publications were classified according to type of research performed, publication year, funding, geographical location, and gender of first and last authors. 962 articles were retrieved and limited to 405 (42%) gender-relevant publications; 131 on stroke and 274 on MI. Type of performed research differed, especially in disease management, which received little attention (17%) in stroke, while representing the major focus in MI (40%). In both areas, clinical presentation received little attention (3 and 5%). Although publications progressively increased in both fields, an 8- to 10-year time gap emerged for stroke compared to MI. Last authors in both areas were predominantly men, but female last authorship is increasing more significantly over time in the field of stroke. Research on sex and gender differences in MI and stroke is largely underfunded, particularly by the EU. The data demonstrate how sex-/gender-specific research differs between specialties, most likely due to the diverse interest, funding opportunities and authorship distributions identified. Copyright © 2011 S. Karger AG, Basel.

  13. Systematic Expression Profiling Analysis Identifies Specific MicroRNA-Gene Interactions that May Differentiate between Active and Latent Tuberculosis Infection

    Directory of Open Access Journals (Sweden)

    Lawrence Shih-Hsin Wu

    2014-01-01

    Full Text Available Tuberculosis (TB is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic—the so-called latent TB infections (LTBI, with a 10% lifetime chance of progressing to active TB. To further understand the molecular pathogenesis of TB, several molecular studies have attempted to compare the expression profiles between healthy controls and active TB or LTBI patients. However, the results vary due to diverse genetic backgrounds and study designs and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. For the present study, we performed a systematic analysis of the gene and microRNA profiles of healthy individuals versus those affected with TB or LTBI. Combined with a series of in silico analysis utilizing publicly available microRNA knowledge bases and published literature data, we have uncovered several microRNA-gene interactions that specifically target both the blood and lungs. Some of these molecular interactions are novel and may serve as potential biomarkers of TB and LTBI, facilitating the development for a more sensitive, efficient, and cost-effective diagnostic assay for TB and LTBI for the Taiwanese population.

  14. Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection.

    Science.gov (United States)

    Wu, Lawrence Shih-Hsin; Lee, Shih-Wei; Huang, Kai-Yao; Lee, Tzong-Yi; Hsu, Paul Wei-Che; Weng, Julia Tzu-Ya

    2014-01-01

    Tuberculosis (TB) is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic--the so-called latent TB infections (LTBI), with a 10% lifetime chance of progressing to active TB. To further understand the molecular pathogenesis of TB, several molecular studies have attempted to compare the expression profiles between healthy controls and active TB or LTBI patients. However, the results vary due to diverse genetic backgrounds and study designs and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. For the present study, we performed a systematic analysis of the gene and microRNA profiles of healthy individuals versus those affected with TB or LTBI. Combined with a series of in silico analysis utilizing publicly available microRNA knowledge bases and published literature data, we have uncovered several microRNA-gene interactions that specifically target both the blood and lungs. Some of these molecular interactions are novel and may serve as potential biomarkers of TB and LTBI, facilitating the development for a more sensitive, efficient, and cost-effective diagnostic assay for TB and LTBI for the Taiwanese population.

  15. Cyclic peptide inhibitors of lysine-specific demethylase 1 with improved potency identified by alanine scanning mutagenesis.

    Science.gov (United States)

    Kumarasinghe, Isuru R; Woster, Patrick M

    2018-03-25

    Lysine-specific demethylase 1 (LSD1) is a chromatin-remodeling enzyme that plays an important role in cancer. Over-expression of LSD1 decreases methylation at histone 3 lysine 4, and aberrantly silences tumor suppressor genes. Inhibitors of LSD1 have been designed as chemical probes and potential antitumor agents. We recently reported the cyclic peptide 9, which potently and reversibly inhibits LSD1 (IC 50 2.1 μM; K i 385 nM). Systematic alanine mutagenesis of 9 revealed residues that are critical for LSD1 inhibition, and these mutated peptides were evaluated as LSD1 inhibitors. Alanine substitution at positions 2, 3, 4, 6 and 11-17 preserved inhibition, while substitution of alanine at positions 8 and 9 resulted in complete loss of activity. Cyclic mutant peptides 11 and 16 produced the greatest LSD1 inhibition, and 11, 16, 27 and 28 increased global H3K4me2 in K562 cells. In addition, 16, 27 and 28 promoted significant increases in H3K4me2 levels at the promoter sites of the genes IGFBP2 and FEZ1. Data from these LSD1 inhibitors will aid in the design of peptidomimetics with improved stability and pharmacokinetics. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  16. Identifying hazardous alcohol consumption during pregnancy: implementing a research-based model in real life.

    Science.gov (United States)

    Göransson, Mona; Magnusson, Asa; Heilig, Markus

    2006-01-01

    It has been repeatedly demonstrated that hazardous alcohol use during pregnancy is rarely detected in regular antenatal care, and that detection can be markedly improved using systematic screening. A major challenge is to translate research-based strategies into regular antenatal care. Here, we examined whether a screening strategy using the Alcohol Use Disorder Test (AUDIT) and time-line follow-back (TLFB) could be implemented under naturalistic conditions and within available resources; and whether it would improve detection to the extent previously shown in a research context. Regular midwives at a large antenatal care clinic were randomized to receive brief training and then implement AUDIT and TLFB ("intervention"); or to a waiting-list control group continuing to deliver regular care ("control"). In the intervention-condition, AUDIT was used to collect data about alcohol use during the year preceding pregnancy, and TLFB to assess actual consumption during the first trimester. Data were collected from new admissions over 6 months. Drop out was higher among patients of the intervention group than control midwives, 14% (23/162) versus 0% (0/153), and ppregnancy i.e. AUDIT score 6 or higher (17%, 23/139), and patients with ongoing consumption exceeding 70 g/week and/or binge consumption according to TLFB (17%, 24/139), to a significantly higher degree than regular antenatal screening (0/162). The AUDIT- and TLFB-positive populations overlapped partially, with 36/139 subjects screening positive with either of the instrument and 11/139 were positive for both. We confirm previous findings that alcohol use during pregnancy is more extensive in Sweden than has generally been realized. Systematic screening using AUDIT and TLFB detects hazardous use in a manner which regular antenatal care does not. This remains true under naturalistic conditions, following minimal training of regular antenatal care staff, and can be achieved with minimal resources. The proposed

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

    Science.gov (United States)

    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

  18. NASA Fixed Wing Project Propulsion Research and Technology Development Activities to Reduce Thrust Specific Energy Consumption

    Science.gov (United States)

    Hathaway, Michael D.; DelRasario, Ruben; Madavan, Nateri K.

    2013-01-01

    This paper presents an overview of the propulsion research and technology portfolio of NASA Fundamental Aeronautics Program Fixed Wing Project. The research is aimed at significantly reducing the thrust specific fuel/energy consumption of notional advanced fixed wing aircraft (by 60 % relative to a baseline Boeing 737-800 aircraft with CFM56-7B engines) in the 2030-2035 time frame. The research investments described herein are aimed at improving propulsive efficiency through higher bypass ratio fans, improving thermal efficiency through compact high overall pressure ratio gas generators, and exploring the potential benefits of boundary layer ingestion propulsion and hybrid gas-electric propulsion concepts.

  19. Characterization of the sterol 14α-demethylases of Fusarium graminearum identifies a novel genus-specific CYP51 function.

    Science.gov (United States)

    Fan, Jieru; Urban, Martin; Parker, Josie E; Brewer, Helen C; Kelly, Steven L; Hammond-Kosack, Kim E; Fraaije, Bart A; Liu, Xili; Cools, Hans J

    2013-05-01

    CYP51 encodes the cytochrome P450 sterol 14α-demethylase, an enzyme essential for sterol biosynthesis and the target of azole fungicides. In Fusarium species, including pathogens of humans and plants, three CYP51 paralogues have been identified with one unique to the genus. Currently, the functions of these three genes and the rationale for their conservation within the genus Fusarium are unknown. Three Fusarium graminearum CYP51s (FgCYP51s) were heterologously expressed in Saccharomyces cerevisiae. Single and double FgCYP51 deletion mutants were generated and the functions of the FgCYP51s were characterized in vitro and in planta. FgCYP51A and FgCYP51B can complement yeast CYP51 function, whereas FgCYP51C cannot. FgCYP51A deletion increases the sensitivity of F. graminearum to the tested azoles. In ΔFgCYP51B and ΔFgCYP51BC mutants, ascospore formation is blocked, and eburicol and two additional 14-methylated sterols accumulate. FgCYP51C deletion reduces virulence on host wheat ears. FgCYP51B encodes the enzyme primarily responsible for sterol 14α-demethylation, and plays an essential role in ascospore formation. FgCYP51A encodes an additional sterol 14α-demethylase, induced on ergosterol depletion and responsible for the intrinsic variation in azole sensitivity. FgCYP51C does not encode a sterol 14α-demethylase, but is required for full virulence on host wheat ears. This is the first example of the functional diversification of a fungal CYP51. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  20. Standardization of specifications and inspection procedures for LEU plate-type research reactor fuels

    International Nuclear Information System (INIS)

    1988-06-01

    With the transition to high density uranium LEU fuel, fabrication costs of research reactor fuel elements have a tendency to increase because of two reasons. First, the amount of the powder of the uranium compound required increases by more than a factor of five. Second, fabrication requirements are in many cases nearer the fabrication limits. Therefore, it is important that measures be undertaken to eliminate or reduce unnecessary requirements in the specification or inspection procedures of research reactor fuel elements utilizing LEU. An additional stimulus for standardizing specifications and inspection procedures at this time is provided by the fact that most LEU conversions will occur within a short time span, and that nearly all of them will require preparation of new specifications and inspection procedures. In this sense, the LEU conversions offer an opportunity for improving the rationality and efficiency of the fuel fabrication and inspection processes. This report focuses on the standardization of specifications and inspection processes of high uranium density LEU fuels for research reactors. However, in many cases the results can also be extended directly to other research reactor fuels. 15 refs, 1 fig., 3 tabs

  1. Are Language Learning Websites Special? Towards a Research Agenda for Discipline-Specific Usability

    Science.gov (United States)

    Shield, Lesley; Kukulska-Hulme, Agnes

    2006-01-01

    With the intention of defining an initial research agenda for discipline-specific factors in the usability of e-learning websites, this article focuses on the example of foreign language learning. First, general notions and concepts of usability are analyzed, and the term "pedagogical usability" is proposed as a means of focusing on the close…

  2. Tumor-Protective Mechanism Identified from Premature Aging Disease | Center for Cancer Research

    Science.gov (United States)

    Hutchinson-Gilford Progeria Syndrome (HGPS) is an extraordinarily rare genetic disorder caused by a mutation in the LMNA gene, which encodes architectural proteins of the human cell nucleus. The mutation causes the production of a mutant protein called progerin. Patients with HGPS display signs of premature aging, such as hair loss, slowed growth, weakening of bone and joint integrity, and cardiovascular disease. Most die in their mid-teens of heart disease or stroke. Intriguingly, these patients do not develop another aging-related disease, cancer, despite having dramatically elevated levels of DNA damage. Tom Misteli, Ph.D., of CCR’s Laboratory of Receptor Biology and Gene Expression, and his colleagues hypothesized that, rather than patients not living long enough to develop cancer, a resistance mechanism was operating in HGPS cells to prevent cancer formation. To begin testing this idea, the researchers transformed fibroblasts from HGPS patients or age-matched, healthy controls with telomerase, constitutively-activated HRAS, and SV40 large and small T antigens. Transformed HGPS cells displayed morphological changes and increased proliferation similar to transformed controls but formed fewer colonies in soft agar and fewer tumors when injected into mice. When the investigators examined global gene expression in the two populations of cells, they found that transformed HGPS cells failed to activate many of the genes that are induced in response to transformation in controls, including oncogenic and proliferation pathways. In addition the transformed HGPS cells were unable to undergo oncogenic de-differentiation. Importantly, the tumor resistance in HGPS cells was due to the presence of the progerin protein, which was both necessary and sufficient to protect cells from oncogenic transformation. Together these results suggested that HGPS cells resist cancer-inducing stimuli by not undergoing the genetic reprogramming necessary for tumor initiation. The scientists

  3. Learning in context: identifying gaps in research on the transfer of medical communication skills to the clinical workplace.

    NARCIS (Netherlands)

    Eertwegh, V. van den; Dulmen, S. van; Dalen, J. van; Scherpbier, A.J.J.A.; Vleuten, C.P.M. van der

    2013-01-01

    Objective: In order to reduce the inconsistencies of findings and the apparent low transfer of communication skills from training to medical practice, this narrative review identifies some main gaps in research on medical communication skills training and presents insights from theories on learning

  4. Learning in context: identifying gaps in research on the transfer of medical communication skills to the clinical workplace

    NARCIS (Netherlands)

    Eertwegh, V. van den; Dulmen, S. van; Dalen, J. Van; Scherpbier, A.J.J.A.; Vleuten, C.P.M. van der

    2013-01-01

    OBJECTIVE: In order to reduce the inconsistencies of findings and the apparent low transfer of communication skills from training to medical practice, this narrative review identifies some main gaps in research on medical communication skills training and presents insights from theories on learning

  5. Mechanisms of change in psychotherapy for depression : An empirical update and evaluation of research aimed at identifying psychological mediators

    NARCIS (Netherlands)

    Lemmens, L.H.J.M.; Müller, V.N.L.S.; Arntz, A.; Huibers, M.J.H.

    2016-01-01

    We present a systematic empirical update and critical evaluation of the current status of research aimed at identifying a variety of psychological mediators in various forms of psychotherapy for depression. We summarize study characteristics and results of 35 relevant studies, and discuss the extent

  6. South African exporter performance: new research into firm-specific and market characteristics

    Directory of Open Access Journals (Sweden)

    Christopher May

    2012-05-01

    Full Text Available The export marketing performance of any firm is influenced by a multitude of different factors. Given the multi-faceted nature of the export market, this research study investigated specific factors such as how firm-specific characteristics, product characteristics, market characteristics and export marketing strategies impact on the export marketing performance of South African manufacturing firms. Some of the findings of this research study indicated that firm size, investment commitment and careful planning, as firm-specific characteristics, had a significant influence on export marketing performance. The relationship between export experience and export marketing performance was insignificant. The degree of pricing adaptation and product adaptation had a significant effect on export marketing performance, while this was not the case with respect to the degree of promotion adaptation and distributor support.

  7. Mechanisms of change in psychotherapy for depression: An empirical update and evaluation of research aimed at identifying psychological mediators.

    Science.gov (United States)

    Lemmens, Lotte H J M; Müller, Viola N L S; Arntz, Arnoud; Huibers, Marcus J H

    2016-12-01

    We present a systematic empirical update and critical evaluation of the current status of research aimed at identifying a variety of psychological mediators in various forms of psychotherapy for depression. We summarize study characteristics and results of 35 relevant studies, and discuss the extent to which these studies meet several important requirements for mechanism research. Our review indicates that in spite of increased attention for the topic, advances in theoretical consensus about necessities for mechanism research, and sophistication of study designs, research in this field is still heterogeneous and unsatisfactory in methodological respect. Probably the biggest challenge in the field is demonstrating the causal relation between change in the mediator and change in depressive symptoms. The field would benefit from a further refinement of research methods to identify processes of therapeutic change. Recommendations for future research are discussed. However, even in the most optimal research designs, explaining psychotherapeutic change remains a challenge. Psychotherapy is a multi-dimensional phenomenon that might work through interplay of multiple mechanisms at several levels. As a result, it might be too complex to be explained in relatively simple causal models of psychological change. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Species-specific considerations in using the fish embryo test as an alternative to identify endocrine disruption.

    Science.gov (United States)

    Schiller, Viktoria; Zhang, Xiaowei; Hecker, Markus; Schäfers, Christoph; Fischer, Rainer; Fenske, Martina

    2014-10-01

    A number of regulations have been implemented that aim to control the release of potentially adverse endocrine disrupters into the aquatic environment based on evidence from laboratory studies. Currently, such studies rely on testing approaches with adult fish because reliable alternatives have not been validated so far. Fish embryo tests have been proposed as such an alternative, and here we compared two species (medaka and zebrafish) to determine their suitability for the assessment of substances with estrogenic and anti-androgenic activity. Changes in gene expression (in here the phrase gene expression is used synonymously to gene transcription, although it is acknowledged that gene expression is additionally regulated, e.g., by translation and protein stability) patterns between the two species were compared in short term embryo exposure tests (medaka: 7-day post fertilization [dpf]; zebrafish: 48 and 96h post fertilization [hpf]) by using relative quantitative real-time RT-PCR. The tested genes were related to the hypothalamic-gonadal-axis and early steroidogenesis. Test chemicals included 17α-ethinylestradiol and flutamide as estrogenic and anti-androgenic reference compounds, respectively, as well as five additional substances with endocrine activities, namely bisphenol A, genistein, prochloraz, linuron and propanil. Estrogenic responses were comparable in 7-dpf medaka and 48/96-hpf zebrafish embryos and included transcriptional upregulation of aromatase b, vitellogenin 1 as well as steroidogenic genes, suggesting that both species reliably detected exposure to estrogenic compounds. However, anti-androgenic responses differed between the two species, with each species providing specific information concerning the mechanism of anti-androgenic disruption in fish embryos. Although small but significant changes in the expression of selected genes was observed in 48-hpf zebrafish embryos, exposure prolonged to 96hpf was necessary to obtain a response indicative

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

    Science.gov (United States)

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

    2015-01-01

    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. 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. 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. 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. 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 with SLI do have the potential to reach or exceed educational targets that are set

  10. Identifying Obstacles and Research Gaps of Telemedicine Projects: Approach for a State-of-the-Art Analysis.

    Science.gov (United States)

    Harst, Lorenz; Timpel, Patrick; Otto, Lena; Wollschlaeger, Bastian; Richter, Peggy; Schlieter, Hannes

    2018-01-01

    This paper presents an approach for an evaluation of finished telemedicine projects using qualitative methods. Telemedicine applications are said to improve the performance of health care systems. While there are countless telemedicine projects, the vast majority never makes the threshold from testing to implementation and diffusion. Projects were collected from German project databases in the area of telemedicine following systematically developed criteria. In a testing phase, ten projects were subject to a qualitative content analysis to identify limitations, need for further research, and lessons learned. Using Mayring's method of inductive category development, six categories of possible future research were derived. Thus, the proposed method is an important contribution to diffusion and translation research regarding telemedicine, as it is applicable to a systematic research of databases.

  11. Identifying priorities in methodological research using ICD-9-CM and ICD-10 administrative data: report from an international consortium

    Directory of Open Access Journals (Sweden)

    Ma Jin

    2006-06-01

    Full Text Available Abstract Background Health administrative data are frequently used for health services and population health research. Comparative research using these data has been facilitated by the use of a standard system for coding diagnoses, the International Classification of Diseases (ICD. Research using the data must deal with data quality and validity limitations which arise because the data are not created for research purposes. This paper presents a list of high-priority methodological areas for researchers using health administrative data. Methods A group of researchers and users of health administrative data from Canada, the United States, Switzerland, Australia, China and the United Kingdom came together in June 2005 in Banff, Canada to discuss and identify high-priority methodological research areas. The generation of ideas for research focussed not only on matters relating to the use of administrative data in health services and population health research, but also on the challenges created in transitioning from ICD-9 to ICD-10. After the brain-storming session, voting took place to rank-order the suggested projects. Participants were asked to rate the importance of each project from 1 (low priority to 10 (high priority. Average ranks were computed to prioritise the projects. Results Thirteen potential areas of research were identified, some of which represented preparatory work rather than research per se. The three most highly ranked priorities were the documentation of data fields in each country's hospital administrative data (average score 8.4, the translation of patient safety indicators from ICD-9 to ICD-10 (average score 8.0, and the development and validation of algorithms to verify the logic and internal consistency of coding in hospital abstract data (average score 7.0. Conclusion The group discussions resulted in a list of expert views on critical international priorities for future methodological research relating to health

  12. Learning in context: identifying gaps in research on the transfer of medical communication skills to the clinical workplace.

    Science.gov (United States)

    van den Eertwegh, Valerie; van Dulmen, Sandra; van Dalen, Jan; Scherpbier, Albert J J A; van der Vleuten, Cees P M

    2013-02-01

    In order to reduce the inconsistencies of findings and the apparent low transfer of communication skills from training to medical practice, this narrative review identifies some main gaps in research on medical communication skills training and presents insights from theories on learning and transfer to broaden the view for future research. Relevant literature was identified using Pubmed, GoogleScholar, Cochrane database, and Web of Science; and analyzed using an iterative procedure. Research findings on the effectiveness of medical communication training still show inconsistencies and variability. Contemporary theories on learning based on a constructivist paradigm offer the following insights: acquisition of knowledge and skills should be viewed as an ongoing process of exchange between the learner and his environment, so called lifelong learning. This process can neither be atomized nor separated from the context in which it occurs. Four contemporary approaches are presented as examples. The following shift in focus for future research is proposed: beyond isolated single factor effectiveness studies toward constructivist, non-reductionistic studies integrating the context. Future research should investigate how constructivist approaches can be used in the medical context to increase effective learning and transition of communication skills. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. Application of FEPs analysis to identify research priorities relevant to the safety case for an Australian radioactive waste facility

    International Nuclear Information System (INIS)

    Payne, T.E.; McGlinn, P.J.

    2007-01-01

    The Australian Nuclear Science and Technology Organisation (ANSTO) has established a project to undertake research relevant to the safety case for the proposed Australian radioactive waste facility. This facility will comprise a store for intermediate level radioactive waste, and either a store or a near-surface repository for low-level waste. In order to identify the research priorities for this project, a structured analysis of the features, events and processes (FEPs) relevant to the performance of the facility was undertaken. This analysis was based on the list of 137 FEPs developed by the IAEA project on 'Safety Assessment Methodologies for Near Surface Disposal Facilities' (ISAM). A number of key research issues were identified, and some factors which differ in significance for the store, compared to the repository concept, were highlighted. For example, FEPs related to long-term groundwater transport of radionuclides are considered to be of less significance for a store than a repository. On the other hand, structural damage from severe weather, accident or human interference is more likely for a store. The FEPs analysis has enabled the scientific research skills required for the inter-disciplinary project team to be specified. The outcomes of the research will eventually be utilised in developing the design, and assessing the performance, of the future facility. It is anticipated that a more detailed application of the FEPs methodology will be undertaken to develop the safety case for the proposed radioactive waste management facility. (authors)

  14. Seismic Safety Margins Research Program (Phase I). Project VII. Systems analysis specification of computational approach

    International Nuclear Information System (INIS)

    Wall, I.B.; Kaul, M.K.; Post, R.I.; Tagart, S.W. Jr.; Vinson, T.J.

    1979-02-01

    An initial specification is presented of a computation approach for a probabilistic risk assessment model for use in the Seismic Safety Margin Research Program. This model encompasses the whole seismic calculational chain from seismic input through soil-structure interaction, transfer functions to the probability of component failure, integration of these failures into a system model and thereby estimate the probability of a release of radioactive material to the environment. It is intended that the primary use of this model will be in sensitivity studies to assess the potential conservatism of different modeling elements in the chain and to provide guidance on priorities for research in seismic design of nuclear power plants

  15. NHash: Randomized N-Gram Hashing for Distributed Generation of Validatable Unique Study Identifiers in Multicenter Research.

    Science.gov (United States)

    Zhang, Guo-Qiang; Tao, Shiqiang; Xing, Guangming; Mozes, Jeno; Zonjy, Bilal; Lhatoo, Samden D; Cui, Licong

    2015-11-10

    A unique study identifier serves as a key for linking research data about a study subject without revealing protected health information in the identifier. While sufficient for single-site and limited-scale studies, the use of common unique study identifiers has several drawbacks for large multicenter studies, where thousands of research participants may be recruited from multiple sites. An important property of study identifiers is error tolerance (or validatable), in that inadvertent editing mistakes during their transmission and use will most likely result in invalid study identifiers. This paper introduces a novel method called "Randomized N-gram Hashing (NHash)," for generating unique study identifiers in a distributed and validatable fashion, in multicenter research. NHash has a unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about a study participant for research purposes; (2) it can be generated automatically in a completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates a set of cryptographic hash functions based on N-grams, with a combination of additional encryption techniques such as a shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers. NHash consists of 2 phases. First, an intermediate string using randomized N-gram hashing is generated. This string consists of a collection of N-gram hashes f1, f2, ..., fk. The input for each function fi has 3 components: a random number r, an integer n, and input data m. The result, fi(r, n, m), is an n-gram of m with a starting position s, which is computed as (r mod |m|), where |m| represents the length of m. The output for Step 1 is the concatenation of the sequence f1(r1, n1, m1), f2(r2, n2, m2), ..., fk(rk, nk, mk). In the second phase, the intermediate string generated in Phase 1 is encrypted using techniques such as shift cipher. The result

  16. HEDIS Research Identifiable Files

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Healthcare Effectiveness Data and Information Set (HEDIS) is a tool used by more than 90 percent of Americas health plans to measure performance on important...

  17. Specificity in the licensing process of reduced enrichment in the Bulgarian research reactor

    International Nuclear Information System (INIS)

    Vitkova, Marietta; Gorinov, Ivan

    2005-01-01

    The presented paper considers some specific questions of the licensing process regarding the reconstruction of the Bulgarian IRT-2000 research reactor, which includes conversion to the low enriched fuel. This specificity has risen as a result of two facts. The design of the reactor reconstruction was made on the basis of the existing fresh 36% highly enriched fuel. But after finishing of the design process, this fresh highly enriched fuel was shipped back to Russia in the framework of the RERTR program. These facts have involved some changes in both - in the licensing and the design processes. Re-analysis of the neutronic and thermal-hydraulic calculations is required to be made on the base of the technical specifications of the new LEU fuel. To facilitate the licensing process the NRA has adopted regulatory acceptance criteria for approval of the reactor core design with LEU fuel. (author)

  18. Sparse feature selection identifies H2A.Z as a novel, pattern-specific biomarker for asymmetrically self-renewing distributed stem cells

    Directory of Open Access Journals (Sweden)

    Yang Hoon Huh

    2015-03-01

    Full Text Available There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow. Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify such useful and specific DSC biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells, with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ.

  19. Barriers to participation in mental health research: are there specific gender, ethnicity and age related barriers?

    Directory of Open Access Journals (Sweden)

    Howard Louise

    2010-12-01

    Full Text Available Abstract Background It is well established that the incidence, prevalence and presentation of mental disorders differ by gender, ethnicity and age, and there is evidence that there is also differential representation in mental health research by these characteristics. The aim of this paper is to a review the current literature on the nature of barriers to participation in mental health research, with particular reference to gender, age and ethnicity; b review the evidence on the effectiveness of strategies used to overcome these barriers. Method Studies published up to December 2008 were identified using MEDLINE, PsycINFO and EMBASE using relevant mesh headings and keywords. Results Forty-nine papers were identified. There was evidence of a wide range of barriers including transportation difficulties, distrust and suspicion of researchers, and the stigma attached to mental illness. Strategies to overcome these barriers included the use of bilingual staff, assistance with travel, avoiding the use of stigmatising language in marketing material and a focus on education about the disorder under investigation. There were very few evaluations of such strategies, but there was evidence that ethnically matching recruiters to potential participants did not improve recruitment rates. Educational strategies were helpful and increased recruitment. Conclusion Mental health researchers should consider including caregivers in recruitment procedures where possible, provide clear descriptions of study aims and describe the representativeness of their sample when reporting study results. Studies that systematically investigate strategies to overcome barriers to recruitment are needed.

  20. DISCONTOOLS: a database to identify research gaps on vaccines, pharmaceuticals and diagnostics for the control of infectious diseases of animals.

    Science.gov (United States)

    O'Brien, Declan; Scudamore, Jim; Charlier, Johannes; Delavergne, Morgane

    2017-01-03

    The public and private sector in the EU spend around €800 million per year on animal health and welfare related research. An objective process to identify critical gaps in knowledge and available control tools should aid the prioritisation of research in order to speed up the development of new or improved diagnostics, vaccines and pharmaceuticals and reduce the burden of animal diseases. Here, we describe the construction of a database based on expert consultation for 52 infectious diseases of animals. For each disease, an expert group produced a disease and product analysis document that formed the basis for gap analysis and prioritisation. The prioritisation model was based on a closed scoring system, employing identical weights for six evaluation criteria (disease knowledge; impact on animal health and welfare; impact on public health; impact on wider society; impact on trade; control tools). The diseases were classified into three groups: epizootic diseases, food-producing animal complexes or zoonotic diseases. The highly ranked diseases in the prioritisation model comprised mostly zoonotic and epizootic diseases with important gaps identified in vaccine development and pharmaceuticals, respectively. The most important outcome is the identification of key research needs by disease. The rankings and research needs by disease are provided on a public website ( www.discontools.eu ) which is currently being updated based on new expert consultations. As such, it can become a reference point for funders of research including the European Commission, member states, foundations, trusts along with private industry to prioritise research. This will deliver benefits in terms of animal health and welfare but also public health, societal benefits and a safe and secure food supply.

  1. An international eDelphi study identifying the research and education priorities in wound management and tissue repair.

    Science.gov (United States)

    Cowman, Seamus; Gethin, Georgina; Clarke, Eric; Moore, Zena; Craig, Gerardine; Jordan-O'Brien, Julie; McLain, Niamh; Strapp, Helen

    2012-02-01

    To incorporate an international and multidisciplinary consensus in the determination of the research and education priorities for wound healing and tissue repair. A compelling reason for the study is the lack of an agreed list of priorities for wound care research and education. Furthermore, there is a growth in the prevalence of chronic wounds, a growth in wound care products and marketing, and an increase in clinician attendance at conferences and education programmes. The study used a survey method. A four-round eDelphi technique was used to collect responses from an international population of health professionals across 24 countries. Responses were obtained from 360 professionals representing many health care settings. The top education priorities related to the standardisation of all foundation education programmes in wound care, the inclusion of wound care in all professional undergraduate and postgraduate education programmes, selecting dressings and the prevention of pressure ulcers. The top research priorities related to the dressing selection, pressure ulcer prevention and wound infection. conclusion: Professionals from different backgrounds and countries who are engaged in wound management share a common set of priorities for research and education. Most notably, the priorities identified relate to long-established clinical challenges in wound care and underpin the principles of good patient care practices. The priorities are closely allied to an ageing population and identify many challenges ahead for practitioners engaged in wound management services. The provision of wound care is a major investment of health service resources and remains a clinical challenge today. Research is essential to building evidence-based practice and fundamental to development of quality in standards of practice; education is central to achieving competence to deliver effective care. The determination of research and education priorities is therefore an absolute requirement

  2. An international eDelphi study identifying the research and education priorities in wound management and tissue repair.

    LENUS (Irish Health Repository)

    2012-02-01

    Aim. To incorporate an international and multidisciplinary consensus in the determination of the research and education priorities for wound healing and tissue repair. Background. A compelling reason for the study is the lack of an agreed list of priorities for wound care research and education. Furthermore, there is a growth in the prevalence of chronic wounds, a growth in wound care products and marketing, and an increase in clinician attendance at conferences and education programmes. Design. The study used a survey method. Methods. A four-round eDelphi technique was used to collect responses from an international population of health professionals across 24 countries. Results. Responses were obtained from 360 professionals representing many health care settings. The top education priorities related to the standardisation of all foundation education programmes in wound care, the inclusion of wound care in all professional undergraduate and postgraduate education programmes, selecting dressings and the prevention of pressure ulcers. The top research priorities related to the dressing selection, pressure ulcer prevention and wound infection. Conclusion. Professionals from different backgrounds and countries who are engaged in wound management share a common set of priorities for research and education. Most notably, the priorities identified relate to long-established clinical challenges in wound care and underpin the principles of good patient care practices. The priorities are closely allied to an ageing population and identify many challenges ahead for practitioners engaged in wound management services. Relevance to clinical practice. The provision of wound care is a major investment of health service resources and remains a clinical challenge today. Research is essential to building evidence-based practice and fundamental to development of quality in standards of practice; education is central to achieving competence to deliver effective care. The

  3. Geriatric-specific triage criteria are more sensitive than standard adult criteria in identifying need for trauma center care in injured older adults.

    Science.gov (United States)

    Ichwan, Brian; Darbha, Subrahmanyam; Shah, Manish N; Thompson, Laura; Evans, David C; Boulger, Creagh T; Caterino, Jeffrey M

    2015-01-01

    We evaluate the sensitivity of Ohio's 2009 emergency medical services (EMS) geriatric trauma triage criteria compared with the previous adult triage criteria in identifying need for trauma center care among older adults. We studied a retrospective cohort of injured patients aged 16 years or older in the 2006 to 2011 Ohio Trauma Registry. Patients aged 70 years or older were considered geriatric. We identified whether each patient met the geriatric and the adult triage criteria. The outcome measure was need for trauma center care, defined by surrogate markers: Injury Severity Score greater than 15, operating room in fewer than 48 hours, any ICU stay, and inhospital mortality. We calculated sensitivity and specificity of both triage criteria for both age groups. We included 101,577 patients; 33,379 (33%) were geriatric. Overall, 57% of patients met adult criteria and 68% met geriatric criteria. Using Injury Severity Score, for older adults geriatric criteria were more sensitive for need for trauma center care (93%; 95% confidence interval [CI] 92% to 93%) than adult criteria (61%; 95% CI 60% to 62%). Geriatric criteria decreased specificity in older adults from 61% (95% CI 61% to 62%) to 49% (95% CI 48% to 49%). Geriatric criteria in older adults (93% sensitivity, 49% specificity) performed similarly to the adult criteria in younger adults (sensitivity 87% and specificity 44%). Similar patterns were observed for other outcomes. Standard adult EMS triage guidelines provide poor sensitivity in older adults. Ohio's geriatric trauma triage guidelines significantly improve sensitivity in identifying Injury Severity Score and other surrogate markers of the need for trauma center care, with modest decreases in specificity for older adults. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

  4. Identifying appropriate reference data models for comparative effectiveness research (CER) studies based on data from clinical information systems.

    Science.gov (United States)

    Ogunyemi, Omolola I; Meeker, Daniella; Kim, Hyeon-Eui; Ashish, Naveen; Farzaneh, Seena; Boxwala, Aziz

    2013-08-01

    The need for a common format for electronic exchange of clinical data prompted federal endorsement of applicable standards. However, despite obvious similarities, a consensus standard has not yet been selected in the comparative effectiveness research (CER) community. Using qualitative metrics for data retrieval and information loss across a variety of CER topic areas, we compare several existing models from a representative sample of organizations associated with clinical research: the Observational Medical Outcomes Partnership (OMOP), Biomedical Research Integrated Domain Group, the Clinical Data Interchange Standards Consortium, and the US Food and Drug Administration. While the models examined captured a majority of the data elements that are useful for CER studies, data elements related to insurance benefit design and plans were most detailed in OMOP's CDM version 4.0. Standardized vocabularies that facilitate semantic interoperability were included in the OMOP and US Food and Drug Administration Mini-Sentinel data models, but are left to the discretion of the end-user in Biomedical Research Integrated Domain Group and Analysis Data Model, limiting reuse opportunities. Among the challenges we encountered was the need to model data specific to a local setting. This was handled by extending the standard data models. We found that the Common Data Model from the OMOP met the broadest complement of CER objectives. Minimal information loss occurred in mapping data from institution-specific data warehouses onto the data models from the standards we assessed. However, to support certain scenarios, we found a need to enhance existing data dictionaries with local, institution-specific information.

  5. Gender-specific research for emergency diagnosis and management of ischemic heart disease: proceedings from the 2014 Academic Emergency Medicine Consensus Conference Cardiovascular Research Workgroup.

    Science.gov (United States)

    Safdar, Basmah; Nagurney, John T; Anise, Ayodola; DeVon, Holli A; D'Onofrio, Gail; Hess, Erik P; Hollander, Judd E; Legato, Mariane J; McGregor, Alyson J; Scott, Jane; Tewelde, Semhar; Diercks, Deborah B

    2014-12-01

    Coronary artery disease (CAD) is the most common cause of death for both men and women. However, over the years, emergency physicians, cardiologists, and other health care practitioners have observed varying outcomes in men and women with symptomatic CAD. Women in general are 10 to 15 years older than men when they develop CAD, but suffer worse postinfarction outcomes compared to age-matched men. This article was developed by the cardiovascular workgroup at the 2014 Academic Emergency Medicine (AEM) consensus conference to identify sex- and gender-specific gaps in the key themes and research questions related to emergency cardiac ischemia care. The workgroup had diverse stakeholder representation from emergency medicine, cardiology, critical care, nursing, emergency medical services, patients, and major policy-makers in government, academia, and patient care. We implemented the nominal group technique to identify and prioritize themes and research questions using electronic mail, monthly conference calls, in-person meetings, and Web-based surveys between June 2013 and May 2014. Through three rounds of nomination and refinement, followed by an in-person meeting on May 13, 2014, we achieved consensus on five priority themes and 30 research questions. The overarching themes were as follows: 1) the full spectrum of sex-specific risk as well as presentation of cardiac ischemia may not be captured by our standard definition of CAD and needs to incorporate other forms of ischemic heart disease (IHD); 2) diagnosis is further challenged by sex/gender differences in presentation and variable sensitivity of cardiac biomarkers, imaging, and risk scores; 3) sex-specific pathophysiology of cardiac ischemia extends beyond conventional obstructive CAD to include other causes such as microvascular dysfunction, takotsubo, and coronary artery dissection, better recognized as IHD; 4) treatment and prognosis are influenced by sex-specific variations in biology, as well as patient

  6. Identifying factors which enhance capacity to engage in clinical education among podiatry practitioners: an action research project.

    Science.gov (United States)

    Abey, Sally; Lea, Susan; Callaghan, Lynne; Shaw, Steve; Cotton, Debbie

    2015-01-01

    Health profession students develop practical skills whilst integrating theory with practice in a real world environment as an important component of their training. Research in the area of practice placements has identified challenges and barriers to the delivery of effective placement learning. However, there has been little research in podiatry and the question of which factors impact upon clinical educators' capacity to engage with the role remains an under-researched area. This paper presents the second phase of an action research project designed to determine the factors that impact upon clinical educators' capacity to engage with the mentorship role. An online survey was developed and podiatry clinical educators recruited through National Health Service (NHS) Trusts. The survey included socio-demographic items, and questions relating to the factors identified as possible variables influencing clinical educator capacity; the latter was assessed using the 'Clinical Educator Capacity to Engage' scale (CECE). Descriptive statistics were used to explore demographic data whilst the relationship between the CECE and socio-demographic factors were examined using inferential statistics in relation to academic profile, career profile and organisation of the placement. The survey response rate was 42 % (n = 66). Multiple linear regression identified four independent variables which explain a significant proportion of the variability of the dependent variable, 'capacity to engage with clinical education', with an adjusted R2 of 0.428. The four variables were: protected mentorship time, clinical educator relationship with university, sign-off responsibility, and volunteer status. The identification of factors that impact upon clinical educators' capacity to engage in mentoring of students has relevance for strategic planning and policy-making with the emphasis upon capacity-building at an individual level, so that the key attitudes and characteristics that are linked

  7. Use of the Menopause-Specific Quality of Life (MENQOL) questionnaire in research and clinical practice: a comprehensive scoping review.

    Science.gov (United States)

    Sydora, Beate C; Fast, Hilary; Campbell, Sandy; Yuksel, Nese; Lewis, Jacqueline E; Ross, Sue

    2016-09-01

    The Menopause-Specific Quality of Life (MENQOL) questionnaire was developed as a validated research tool to measure condition-specific QOL in early postmenopausal women. We conducted a comprehensive scoping review to explore the extent of MENQOL's use in research and clinical practice to assess its value in providing effective, adequate, and comparable participant assessment information. Thirteen biomedical and clinical databases were systematically searched with "menqol" as a search term to find articles using MENQOL or its validated derivative MENQOL-Intervention as investigative or clinical tools from 1996 to November 2014 inclusive. Review articles, conference abstracts, proceedings, dissertations, and incomplete trials were excluded. Additional articles were collected from references within key articles. Three independent reviewers extracted data reflecting study design, intervention, sample characteristics, MENQOL questionnaire version, modifications and language, recall period, and analysis detail. Data analyses included categorization and descriptive statistics. The review included 220 eligible papers of various study designs, covering 39 countries worldwide and using MENQOL translated into more than 25 languages. A variety of modifications to the original questionnaire were identified, including omission or addition of items and alterations to the validated methodological analysis. No papers were found that described MENQOL's use in clinical practice. Our study found an extensive and steadily increasing use of MENQOL in clinical and epidemiological research over 18 years postpublication. Our results stress the importance of proper reporting and validation of translations and variations to ensure outcome comparison and transparency of MENQOL's use. The value of MENQOL in clinical practice remains unknown.

  8. Specifics of IFRS Adoption by Central and Eastern European Countries: Evidence from Research

    Directory of Open Access Journals (Sweden)

    Procházka David

    2017-03-01

    Full Text Available The paper reviews recent literature on the specifics of adoption of International Financial Reporting Standards (IFRS by the new EU members from the Central and Eastern Europe. Despite being members of the EU or OECD, the transition to a standard developed economy has not yet finished. The first part of the paper presents macroeconomic statistics and capital market data, which underline a unique economic structure of the region (relative unimportance of capital markets for raising capital, strong dependence on foreign direct investments combined with the lacks in institutional environment. Under such conditions, the economic consequences of IFRS adoption can be unpredictable and adverse. The second part of the paper analyses the reflection of specifics of the IFRS adoption in the CEE region in research studies covered by the Thomson Reuters’ Web of Science database. The analysis reveals (a cross-country disproportion in the research coverage of the area; (b relatively low coverage of the IFRS research focusing on these transition countries in top journals.

  9. Research supporting potential modification of the NASA specification for dry heat microbial reduction of spacecraft hardware

    Science.gov (United States)

    Spry, James A.; Beaudet, Robert; Schubert, Wayne

    Dry heat microbial reduction (DHMR) is the primary method currently used to reduce the microbial load of spacecraft and component parts to comply with planetary protection re-quirements. However, manufacturing processes often involve heating flight hardware to high temperatures for purposes other than planetary protection DHMR. At present, the specifica-tion in NASA document NPR8020.12, describing the process lethality on B. atrophaeus (ATCC 9372) bacterial spores, does not allow for additional planetary protection bioburden reduction credit for processing outside a narrow temperature, time and humidity window. Our results from a comprehensive multi-year laboratory research effort have generated en-hanced data sets on four aspects of the current specification: time and temperature effects in combination, the effect that humidity has on spore lethality, and the lethality for spores with exceptionally high thermal resistance (so called "hardies"). This paper describes potential modifications to the specification, based on the data set gener-ated in the referenced studies. The proposed modifications are intended to broaden the scope of the current specification while still maintaining confidence in a conservative interpretation of the lethality of the DHMR process on microorganisms.

  10. Safety in the Utilization and Modification of Research Reactors. Specific Safety Guide

    International Nuclear Information System (INIS)

    2012-01-01

    This Safety Guide is a revision of Safety Series No. 35-G2 on safety in the utilization and modification of research reactors. It provides recommendations on meeting the requirements for the categorization, safety assessment and approval of research reactor experiments and modification projects. Specific safety considerations in different phases of utilization and modification projects are covered, including the pre-implementation, implementation and post-implementation phases. Guidance is also provided on the operational safety of experiments, including in the handling, dismantling, post-irradiation examination and disposal of experimental devices. Examples of the application of the safety categorization process for experiments and modification projects and of the content of the safety analysis report for an experiment are also provided. Contents: 1. Introduction; 2. Management system for the utilization and modification of a research reactor; 3. Categorization, safety assessment and approval of an experiment or modification; 4. Safety considerations for the design of an experiment or modification; 5. Pre-implementation phase of a modification or utilization project; 6. Implementation phase of a modification or utilization project; 7. Post-implementation phase of a utilization or modification project; 8. Operational safety of experiments at a research reactor; 9. Safety considerations in the handling, dismantling, post-irradiation examination and disposal of experimental devices; 10. Safety aspects of out-of-reactor-core installations; Annex I: Example of a checklist for the categorization of an experiment or modification at a research reactor; Annex II: Example of the content of the safety analysis report for an experiment at a research reactor; Annex III: Examples of reasons for a modification at a research reactor.

  11. Safety in the Utilization and Modification of Research Reactors. Specific Safety Guide

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-07-15

    This Safety Guide is a revision of Safety Series No. 35-G2 on safety in the utilization and modification of research reactors. It provides recommendations on meeting the requirements for the categorization, safety assessment and approval of research reactor experiments and modification projects. Specific safety considerations in different phases of utilization and modification projects are covered, including the pre-implementation, implementation and post-implementation phases. Guidance is also provided on the operational safety of experiments, including in the handling, dismantling, post-irradiation examination and disposal of experimental devices. Examples of the application of the safety categorization process for experiments and modification projects and of the content of the safety analysis report for an experiment are also provided. Contents: 1. Introduction; 2. Management system for the utilization and modification of a research reactor; 3. Categorization, safety assessment and approval of an experiment or modification; 4. Safety considerations for the design of an experiment or modification; 5. Pre-implementation phase of a modification or utilization project; 6. Implementation phase of a modification or utilization project; 7. Post-implementation phase of a utilization or modification project; 8. Operational safety of experiments at a research reactor; 9. Safety considerations in the handling, dismantling, post-irradiation examination and disposal of experimental devices; 10. Safety aspects of out-of-reactor-core installations; Annex I: Example of a checklist for the categorization of an experiment or modification at a research reactor; Annex II: Example of the content of the safety analysis report for an experiment at a research reactor; Annex III: Examples of reasons for a modification at a research reactor.

  12. MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

    International Nuclear Information System (INIS)

    Alexander, A; DeBlois, F; Stroian, G; Al-Yahya, K; Heath, E; Seuntjens, J

    2007-01-01

    Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM R T, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform

  13. The ICF Core Sets for hearing loss--researcher perspective. Part I: Systematic review of outcome measures identified in audiological research.

    Science.gov (United States)

    Granberg, Sarah; Dahlström, Jennie; Möller, Claes; Kähäri, Kim; Danermark, Berth

    2014-02-01

    To review the literature in order to identify outcome measures used in research on adults with hearing loss (HL) as part of the ICF Core Sets development project, and to describe study and population characteristics of the reviewed studies. A systematic review methodology was applied using multiple databases. A comprehensive search was conducted and two search pools were created, pool I and pool II. The study population included adults (≥ 18 years of age) with HL and oral language as the primary mode of communication. 122 studies were included. Outcome measures were distinguished by 'instrument type', and 10 types were identified. In total, 246 (pool I) and 122 (pool II) different measures were identified, and only approximately 20% were extracted twice or more. Most measures were related to speech recognition. Fifty-one different questionnaires were identified. Many studies used small sample sizes, and the sex of participants was not revealed in several studies. The low prevalence of identified measures reflects a lack of consensus regarding the optimal outcome measures to use in audiology. Reflections and discussions are made in relation to small sample sizes and the lack of sex differentiation/descriptions within the included articles.

  14. Using c-Jun to identify fear extinction learning-specific patterns of neural activity that are affected by single prolonged stress.

    Science.gov (United States)

    Knox, Dayan; Stanfield, Briana R; Staib, Jennifer M; David, Nina P; DePietro, Thomas; Chamness, Marisa; Schneider, Elizabeth K; Keller, Samantha M; Lawless, Caroline

    2018-04-02

    Neural circuits via which stress leads to disruptions in fear extinction is often explored in animal stress models. Using the single prolonged stress (SPS) model of post traumatic stress disorder and the immediate early gene (IEG) c-Fos as a measure of neural activity, we previously identified patterns of neural activity through which SPS disrupts extinction retention. However, none of these stress effects were specific to fear or extinction learning and memory. C-Jun is another IEG that is sometimes regulated in a different manner to c-Fos and could be used to identify emotional learning/memory specific patterns of neural activity that are sensitive to SPS. Animals were either fear conditioned (CS-fear) or presented with CSs only (CS-only) then subjected to extinction training and testing. C-Jun was then assayed within neural substrates critical for extinction memory. Inhibited c-Jun levels in the hippocampus (Hipp) and enhanced functional connectivity between the ventromedial prefrontal cortex (vmPFC) and basolateral amygdala (BLA) during extinction training was disrupted by SPS in the CS-fear group only. As a result, these effects were specific to emotional learning/memory. SPS also disrupted inhibited Hipp c-Jun levels, enhanced BLA c-Jun levels, and altered functional connectivity among the vmPFC, BLA, and Hipp during extinction testing in SPS rats in the CS-fear and CS-only groups. As a result, these effects were not specific to emotional learning/memory. Our findings suggest that SPS disrupts neural activity specific to extinction memory, but may also disrupt the retention of fear extinction by mechanisms that do not involve emotional learning/memory. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Refining Current Scientific Priorities and Identifying New Scientific Gaps in HIV-Related Heart, Lung, Blood, and Sleep Research.

    Science.gov (United States)

    Twigg, Homer L; Crystal, Ronald; Currier, Judith; Ridker, Paul; Berliner, Nancy; Kiem, Hans-Peter; Rutherford, George; Zou, Shimian; Glynn, Simone; Wong, Renee; Peprah, Emmanuel; Engelgau, Michael; Creazzo, Tony; Colombini-Hatch, Sandra; Caler, Elisabet

    2017-09-01

    The National Heart, Lung, and Blood Institute (NHLBI) AIDS Program's goal is to provide direction and support for research and training programs in areas of HIV-related heart, lung, blood, and sleep (HLBS) diseases. To better define NHLBI current HIV-related scientific priorities and with the goal of identifying new scientific priorities and gaps in HIV-related HLBS research, a wide group of investigators gathered for a scientific NHLBI HIV Working Group on December 14-15, 2015, in Bethesda, MD. The core objectives of the Working Group included discussions on: (1) HIV-related HLBS comorbidities in the antiretroviral era; (2) HIV cure; (3) HIV prevention; and (4) mechanisms to implement new scientific discoveries in an efficient and timely manner so as to have the most impact on people living with HIV. The 2015 Working Group represented an opportunity for the NHLBI to obtain expert advice on HIV/AIDS scientific priorities and approaches over the next decade.

  16. Reporting intellectual capital in health care organizations: specifics, lessons learned, and future research perspectives.

    Science.gov (United States)

    Veltri, Stefania; Bronzetti, Giovanni; Sicoli, Graziella

    2011-01-01

    This article analyzes the concept of intellectual capital (IC) in the health sector sphere by studying the case of a major nonprofit research organization in this sector, which has for some time been publishing IC reports. In the last few years, health care organizations have been the object of great attention in the implementation and transfer of managerial models and tools; however, there is still a lack of attention paid to the strategic management of IC as a fundamental resource for supporting and enhancing performance improvement dynamics. The main aim of this article is to examine the IC reporting model used by the Center of Molecular Medicine (CMM), a Swedish health organization which is an outstanding benchmark in reporting its IC. We also consider the specifics of IC reporting for health organizations, the lessons learned by analyzing CMM's IC reporting, and future perspectives for research.

  17. LC-QTOF-MS identification of porcine-specific peptide in heat treated pork identifies candidate markers for meat species determination.

    Science.gov (United States)

    Sarah, S A; Faradalila, W N; Salwani, M S; Amin, I; Karsani, S A; Sazili, A Q

    2016-05-15

    The purpose of this study was to identify porcine-specific peptide markers from thermally processed meat that could differentiate pork from beef, chevon and chicken meat. In the initial stage, markers from tryptic digested protein of chilled, boiled and autoclaved pork were identified using LC-QTOF-MS. An MRM method was then established for verification. A thorough investigation of LC-QTOF-MS data showed that only seven porcine-specific peptides were consistently detected. Among these peptides, two were derived from lactate dehydrogenase, one from creatine kinase, and four from serum albumin protein. However, MRM could only detect four peptides (EVTEFAK, LVVITAGAR, FVIER and TVLGNFAAFVQK) that were consistently present in pork samples. In conclusion, meat species determination through a tandem mass spectrometry platform shows high potential in providing scientifically valid and reliable results even at peptide level. Besides, the specificity and selectivity offered by the proteomics approach also provide a robust platform for Halal authentication. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Ethics in Community-University-Artist Partnered Research: Tensions, Contradictions and Gaps Identified in an 'Arts for Social Change' Project.

    Science.gov (United States)

    Yassi, Annalee; Spiegel, Jennifer Beth; Lockhart, Karen; Fels, Lynn; Boydell, Katherine; Marcuse, Judith

    Academics from diverse disciplines are recognizing not only the procedural ethical issues involved in research, but also the complexity of everyday "micro" ethical issues that arise. While ethical guidelines are being developed for research in aboriginal populations and low-and-middle-income countries, multi-partnered research initiatives examining arts-based interventions to promote social change pose a unique set of ethical dilemmas not yet fully explored. Our research team, comprising health, education, and social scientists, critical theorists, artists and community-activists launched a five-year research partnership on arts-for-social change. Funded by the Social Science and Humanities Research Council in Canada and based in six universities, including over 40 community-based collaborators, and informed by five main field projects (circus with street youth, theatre by people with disabilities, dance for people with Parkinson's disease, participatory theatre with refugees and artsinfused dialogue), we set out to synthesize existing knowledge and lessons we learned. We summarized these learnings into 12 key points for reflection, grouped into three categories: community-university partnership concerns ( n  = 3), dilemmas related to the arts ( n  = 5), and team issues ( n  = 4). In addition to addressing previous concerns outlined in the literature (e.g., related to consent, anonymity, dangerous emotional terrain, etc.), we identified power dynamics (visible and hidden) hindering meaningful participation of community partners and university-based teams that need to be addressed within a reflective critical framework of ethical practice. We present how our team has been addressing these issues, as examples of how such concerns could be approached in community-university partnerships in arts for social change.

  19. A Development of Technical Specification of a Research Reactor with Plate Fuels Cooled by Upward Flow

    International Nuclear Information System (INIS)

    Park, Sujin; Kim, Jeongeun; Kim, Hyeonil

    2016-01-01

    The contents of the TS(Technical Specifications) are definitions, safety limits, limiting safety system settings, limiting conditions for operation, surveillance requirements, design features, and administrative controls. TS for Nuclear Power Plants (NPPs) have been developed since many years until now. On the other hands, there are no applicable modernized references of TS for research reactors with many differences from NPPs in purpose and characteristics. Fuel temperature and Departure from Nuclear Boiling Ratio (DNBR) are being used as references from the thermal-hydraulic analysis point of view for determining whether the design of research reactors satisfies acceptance criteria for the nuclear safety or not. Especially for research reactors using plate-type fuels, fuel temperature and critical heat flux, however, are very difficult to measure during the reactor operation. This paper described the outline of main contents of a TS for open-pool research reactor with plate-type fuels using core cooling through passive systems, where acceptance criteria for nuclear safety such as CHF and fuel temperature cannot be directly measured, different from circumstances in NPPs. Thus, three independent variables instead of non-measurable acceptance criteria: fuel temperature and CHF are considered as safety limits, i.e., power, flow, and flow temperature

  20. Discrimination and resilience and the needs of people who identify as Transgender: A narrative review of quantitative research studies.

    Science.gov (United States)

    McCann, Edward; Brown, Michael

    2017-12-01

    To examine discrimination and resilience experiences of people who identify as transgender and establish potential health service responses. People who identify as transgender face many challenges in society in terms of the knowledge, understanding and acceptance of a person's gender identity. A narrative review of quantitative empirical research. A comprehensive search of CINAHL, MEDLINE, PsycINFO and Sociological Abstracts electronic databases from 2006-2016 was conducted. The search yielded 1,478 papers and following the application of rigorous inclusion and exclusion criteria a total of 19 papers were included in the review. The findings reveal that there is a need to ensure that the needs of transgender people are represented, fully integrated and clearly linked to outcomes that improve their health and quality of life. Discrimination experiences can result in poorer health outcomes; however, many people have developed resilience and positive coping strategies. Nurses need to recognise and respond appropriately to the care and treatment needs of this population. Comprehensive nursing assessments and plans of care that encompass all aspects of the person should be in place supported by clear policy guidelines and evidence-based research. The education requirements of practitioners are outlined. © 2017 John Wiley & Sons Ltd.

  1. [Research advances in identifying nitrate pollution sources of water environment by using nitrogen and oxygen stable isotopes].

    Science.gov (United States)

    Mao, Wei; Liang, Zhi-wei; Li, Wei; Zhu, Yao; Yanng, Mu-yi; Jia, Chao-jie

    2013-04-01

    Water body' s nitrate pollution has become a common and severe environmental problem. In order to ensure human health and water environment benign evolution, it is of great importance to effectively identify the nitrate pollution sources of water body. Because of the discrepant composition of nitrogen and oxygen stable isotopes in different sources of nitrate in water body, nitrogen and oxygen stable isotopes can be used to identify the nitrate pollution sources of water environment. This paper introduced the fractionation factors of nitrogen and oxygen stable isotopes in the main processes of nitrogen cycling and the composition of these stable isotopes in main nitrate sources, compared the advantages and disadvantages of five pre-treatment methods for analyzing the nitrogen and oxygen isotopes in nitrate, and summarized the research advances in this aspect into three stages, i. e. , using nitrogen stable isotope alone, using nitrogen and oxygen stable isotopes simultaneously, and combining with mathematical models. The future research directions regarding the nitrate pollution sources identification of water environment were also discussed.

  2. Prognostic factors for specific lower extremity and spinal musculoskeletal injuries identified through medical screening and training load monitoring in professional football (soccer): a systematic review

    Science.gov (United States)

    Sergeant, Jamie C; Parkes, Matthew J; Callaghan, Michael J

    2017-01-01

    Background Medical screening and load monitoring procedures are commonly used in professional football to assess factors perceived to be associated with injury. Objectives To identify prognostic factors (PFs) and models for lower extremity and spinal musculoskeletal injuries in professional/elite football players from medical screening and training load monitoring processes. Methods The MEDLINE, AMED, EMBASE, CINAHL Plus, SPORTDiscus and PubMed electronic bibliographic databases were searched (from inception to January 2017). Prospective and retrospective cohort studies of lower extremity and spinal musculoskeletal injury incidence in professional/elite football players aged between 16 and 40 years were included. The Quality in Prognostic Studies appraisal tool and the modified Grading of Recommendations Assessment, Development and Evaluation synthesis approach was used to assess the quality of the evidence. Results Fourteen studies were included. 16 specific lower extremity injury outcomes were identified. No spinal injury outcomes were identified. Meta-analysis was not possible due to heterogeneity and study quality. All evidence related to PFs and specific lower extremity injury outcomes was of very low to low quality. On the few occasions where multiple studies could be used to compare PFs and outcomes, only two factors demonstrated consensus. A history of previous hamstring injuries (HSI) and increasing age may be prognostic for future HSI in male players. Conclusions The assumed ability of medical screening tests to predict specific musculoskeletal injuries is not supported by the current evidence. Screening procedures should currently be considered as benchmarks of function or performance only. The prognostic value of load monitoring modalities is unknown. PMID:29177074

  3. The Outwardly Rectifying Current of Layer 5 Neocortical Neurons that was Originally Identified as "Non-Specific Cationic" Is Essentially a Potassium Current.

    Directory of Open Access Journals (Sweden)

    Omer Revah

    Full Text Available In whole-cell patch clamp recordings from layer 5 neocortical neurons, blockade of voltage gated sodium and calcium channels leaves a cesium current that is outward rectifying. This current was originally identified as a "non-specific cationic current", and subsequently it was hypothesized that it is mediated by TRP channels. In order to test this hypothesis, we used fluorescence imaging of intracellular sodium and calcium indicators, and found no evidence to suggest that it is associated with influx of either of these ions to the cell body or dendrites. Moreover, the current is still prominent in neurons from TRPC1-/- and TRPC5-/- mice. The effects on the current of various blocking agents, and especially its sensitivity to intracellular tetraethylammonium, suggest that it is not a non-specific cationic current, but rather that it is generated by cesium-permeable delayed rectifier potassium channels.

  4. Organization, execution and evaluation of the 2014 Academic Emergency Medicine consensus conference on Gender-Specific Research in Emergency Care - an executive summary.

    Science.gov (United States)

    Safdar, Basmah; Greenberg, Marna R

    2014-12-01

    With the goal of reducing inequalities in patient care, the 2014 Academic Emergency Medicine (AEM) consensus conference, "Gender-Specific Research in Emergency Care: Investigate, Understand, and Translate How Gender Affects Patient Outcomes," convened a diverse group of researchers, clinicians, health care providers, patients, and representatives of federal agencies and policy-makers in Dallas, Texas, in May 2014. The executive and steering committees identified seven clinical domains as key to gender-specific emergency care: cardiovascular, neurological, trauma/injury, substance abuse, pain, mental health, and diagnostic imaging. The main aims of the conference were to: 1) summarize and consolidate current data related to sex- and gender-specific research for acute care and identify critical gender-related gaps in knowledge to inform an EM research agenda; 2) create a consensus-driven research agenda that advances sex- and gender-specific research in the prevention, diagnosis, and management of acute diseases and identify strategies to investigate them; and 3) build a multinational interdisciplinary consortium to disseminate and study the sex and gender medicine of acute conditions. Over a 2-year period, this collaborative network of stakeholders identified key areas where sex- and gender-specific research is most likely to improve clinical care and ultimately patient outcomes. The iterative consensus process culminated in a daylong conference on May 13, 2014, with a total of 133 registrants, with the majority being between ages 31 and 50 years (57%), females (71%), and whites (79%). Content experts led the consensus-building workshops at the conference and used the nominal group technique to consolidate consensus recommendations for priority research. In addition, panel sessions addressed funding mechanisms for gender-specific research as well as gender-specific regulatory challenges to product development and approval. This special issue of AEM reports the

  5. Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci

    DEFF Research Database (Denmark)

    Jones, Gregory T; Tromp, Gerard; Kuivaniemi, Helena

    2017-01-01

    studies (GWAS). Through a meta-analysis of 6 GWAS datasets and a validation study totalling 10,204 cases and 107,766 controls we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches we observed no new...... associations between the lead AAA SNPs and coronary artery disease, blood pressure, lipids or diabetes. Network analyses identified ERG, IL6R and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9. The 4 new risk loci for AAA appear to be specific for AAA compared with other...

  6. Discussion about the use of the volume-specific surface area (VSSA) as criteria to identify nanomaterials according to the EU definition

    International Nuclear Information System (INIS)

    Lecloux, André J.

    2015-01-01

    In the EU regulation, a material containing particles is considered as nano if, for 50 % or more of the particles in the number size distribution, one or more external dimensions is in the size range 1–100 nm. Due to the difficulty to measure in a reliable way the number particle size distribution, it is suggested to use the volume-specific surface area (VSSA) >60 m 2 /cm 3 as simple screening criterion to identify nanomaterials. This threshold corresponds to monodispersed spherical particles with a size of 100 nm. In this paper, a theoretical study is carried out to identify the effect of the particle shape, polydispersity, agglomeration and aggregation on the VSSA threshold. It appears that the VSSA approach is overprotective because a lot of samples are identified as nanomaterials even if less than 50 % of the particles have a size lower than 100 nm, this 50 % in number criterion being the main identification criterion in the EU definition. Even if the VSSA is leading to many false positive results, it can be used to identify non-nanomaterials as soon as its value is lower than the threshold at the condition to take into account the shape of the particles and their external surface area. This conclusion is true for monomodal distributions of particles but is subject to some restrictions for bimodal distributions

  7. Discussion about the use of the volume-specific surface area (VSSA) as criteria to identify nanomaterials according to the EU definition

    Energy Technology Data Exchange (ETDEWEB)

    Lecloux, André J., E-mail: alecloux@nanocyl.com, E-mail: envicat@skynet.be [ENVICAT Consulting (Belgium)

    2015-11-15

    In the EU regulation, a material containing particles is considered as nano if, for 50 % or more of the particles in the number size distribution, one or more external dimensions is in the size range 1–100 nm. Due to the difficulty to measure in a reliable way the number particle size distribution, it is suggested to use the volume-specific surface area (VSSA) >60 m{sup 2}/cm{sup 3} as simple screening criterion to identify nanomaterials. This threshold corresponds to monodispersed spherical particles with a size of 100 nm. In this paper, a theoretical study is carried out to identify the effect of the particle shape, polydispersity, agglomeration and aggregation on the VSSA threshold. It appears that the VSSA approach is overprotective because a lot of samples are identified as nanomaterials even if less than 50 % of the particles have a size lower than 100 nm, this 50 % in number criterion being the main identification criterion in the EU definition. Even if the VSSA is leading to many false positive results, it can be used to identify non-nanomaterials as soon as its value is lower than the threshold at the condition to take into account the shape of the particles and their external surface area. This conclusion is true for monomodal distributions of particles but is subject to some restrictions for bimodal distributions.

  8. Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained.

    Directory of Open Access Journals (Sweden)

    Ying Wu

    2013-03-01

    Full Text Available Genome-wide association studies (GWAS have identified ~100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG, high-density lipoprotein cholesterol (HDL-C, and low-density lipoprotein cholesterol (LDL-C, respectively, in individuals of African American (n = 6,832, East Asian (n = 9,449, and European (n = 10,829 ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1 × 10(-4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies.

  9. An international survey to identify the intrinsic and extrinsic factors of research studies most likely to change orthopaedic practice.

    Science.gov (United States)

    Thornley, P; de Sa, D; Evaniew, N; Farrokhyar, F; Bhandari, M; Ghert, M

    2016-04-01

    Evidence -based medicine (EBM) is designed to inform clinical decision-making within all medical specialties, including orthopaedic surgery. We recently published a pilot survey of the Canadian Orthopaedic Association (COA) membership and demonstrated that the adoption of EBM principles is variable among Canadian orthopaedic surgeons. The objective of this study was to conduct a broader international survey of orthopaedic surgeons to identify characteristics of research studies perceived as being most influential in informing clinical decision-making. A 29-question electronic survey was distributed to the readership of an established orthopaedic journal with international readership. The survey aimed to analyse the influence of both extrinsic (journal quality, investigator profiles, etc.) and intrinsic characteristics (study design, sample size, etc.) of research studies in relation to their influence on practice patterns. A total of 353 surgeons completed the survey. Surgeons achieved consensus on the 'importance' of three key designs on their practices: randomised controlled trials (94%), meta-analyses (75%) and systematic reviews (66%). The vast majority of respondents support the use of current evidence over historical clinical training; however subjective factors such as journal reputation (72%) and investigator profile (68%) continue to influence clinical decision-making strongly. Although intrinsic factors such as study design and sample size have some influence on clinical decision-making, surgeon respondents are equally influenced by extrinsic factors such as investigator reputation and perceived journal quality.Cite this article: Dr M. Ghert. An international survey to identify the intrinsic and extrinsic factors of research studies most likely to change orthopaedic practice. Bone Joint Res 2016;5:130-136. DOI: 10.1302/2046-3758.54.2000578. © 2016 Ghert et al.

  10. An Action Research Inquiry into the Relationship Among Aerobic Activities, Memory, and Stress with Students Identified as Gifted

    Science.gov (United States)

    Ford, Denise Marie

    Students identified as gifted come from varying socio-economic strata and nationalities with a range of talents and temperaments comprising a diverse community. They may experience stress for a variety of reasons. Although a certain amount of stress can enhance the learning process, too much stress can impede learning, especially memory. Strategies have been offered for relieving stress, yet the benefits of physical activities as stress reducers for the gifted have frequently been overlooked. The purpose of this study was to investigate the relationship among aerobic activity, stress, and memory ability in students in an elementary school gifted program. An exceptional aspect of this research was that the students were an integral part of their own study. As co-researchers they had a vested interest in what they were doing, enhancing the significance of the experience and heightening learning. This action research project conducted in a mid-western school district with fourth and fifth grade students examined the impact of aerobic movement on physical indicators of stress and memory. The study lasted twelve weeks with data collected on physical indicators of stress, memory test scores, parent observations, interviews with students, a parent focus group session, observational data, student comments, and investigator/teacher journal. By infusing regular exercise into curricula, stress levels in students identified as gifted were examined. Students' scores on declarative memory tasks conducted with and without an accompanying aerobic activity were documented. Students learned of the delicate relationship between stress and memory as they studied the physiology of the brain. Twenty-four hour retention rates of declarative memory items were higher when a 20-minute aerobic activity intervention preceded the memory activity. Perceived stress levels were lowered for 14 of the 16 co-researchers. Students indicated a positive attitude toward physical activity and its

  11. Gender- and sex-specific sports-related injury research in emergency medicine: a consensus on future research direction and focused application.

    Science.gov (United States)

    Raukar, Neha P; Zonfrillo, Mark R; Kane, Kathleen; Davenport, Moira; Espinoza, Tamara R; Weiland, Jessica; Franco, Vanessa; Vaca, Federico E

    2014-12-01

    Title IX, the commercialization of sports, the social change in sports participation, and the response to the obesity epidemic have contributed to the rapid proliferation of participation in both competitive organized sports and nontraditional athletic events. As a consequence, emergency physicians are regularly involved in the acute diagnosis, management, disposition, and counseling of a broad range of sports-related pathology. Three important and highly publicized mechanisms of injury in sports relevant to emergency medicine (EM) include concussion, heat illness, and sudden cardiac death. In conjunction with the 2014 Academic Emergency Medicine consensus conference "Gender-specific Research in Emergency Care: Investigate, Understand, and Translate How Gender Affects Patient Outcomes," a consensus group consisting of experts in EM, emergency neurology, sports medicine, and public health convened to deliberate and develop research questions that could ultimately advance the field of sports medicine and allow for meaningful application in the emergency department (ED) clinical setting. Sex differences in injury risk, diagnosis, ED treatment, and counseling are identified in each of these themes. This article presents the consensus-based priority research agenda. © 2014 by the Society for Academic Emergency Medicine.

  12. General Aspects and First Progress Report on a Frame of a Research on Specific Professional Knowledge of Chemistry Teachers Associated with the Notion of Chemical Nomenclature

    Directory of Open Access Journals (Sweden)

    Gerardo Andrés Perafán Echeverri

    2014-04-01

    Full Text Available Within the framework of research about professional teacher’s knowledge, our business is to identify and to characterize with case study method, a kind of specific professional teacher´s knowledge of Chemistry professorate, associated to the chemical nomenclature notion. This kind of research guides the sight to the teaching contents, but it postulates the teacher as an essential actor of that knowledge, rather than ignore of the other actors (didactic community, researchers, specialists, students, etc. our research realizes the specific construction that the teacher makes, beyond the «spontaneous epistemologies» category, between others, which seems to deny an academic and discipline character of the built knowledge by the teachers. First, we show a brief reference to the research program on professional teacher´s knowledge which frames in the development of research line about Specific Professional Teacher´s Knowledge associated with Particular Categories, which belongs to the research group «Por las Aulas Colombianas- INVAUCOL». After that, we show a short justification about the choice of the particular category: chemical nomenclature, as a studied object, besides the historical importance that it has to the professional teaching consolidation, recognizing the teacher´s specific contributions to discipline body construction of school knowledge. Finally, weset in consideration some general methodological criteria defined in this research, and we show too, some preliminary reflections derived from field work in thepresent state of the project.

  13. Specific schedule conditions for the formation of personnel of A or B category working in nuclear facilities. Option research center

    CERN Document Server

    Int. At. Energy Agency, Wien

    2002-01-01

    This document describes the specific dispositions relative to the Research Center, for the formation to the conventional and radiation risks prevention of personnel of A or B category working in nuclear facilities. The application domain, the applicable documents, the liability, the specificity of the Research Center and of the retraining, the Passerelle formation, are presented. (A.L.B.)

  14. Identifying research priorities in anaesthesia and perioperative care: final report of the joint National Institute of Academic Anaesthesia/James Lind Alliance Research Priority Setting Partnership.

    Science.gov (United States)

    Boney, Oliver; Bell, Madeline; Bell, Natalie; Conquest, Ann; Cumbers, Marion; Drake, Sharon; Galsworthy, Mike; Gath, Jacqui; Grocott, Michael P W; Harris, Emma; Howell, Simon; Ingold, Anthony; Nathanson, Michael H; Pinkney, Thomas; Metcalf, Leanne

    2015-12-16

    To identify research priorities for Anaesthesia and Perioperative Medicine. Prospective surveys and consensus meetings guided by an independent adviser. UK. 45 stakeholder organisations (25 professional, 20 patient/carer) affiliated as James Lind Alliance partners. First 'ideas-gathering' survey: Free text research ideas and suggestions. Second 'prioritisation' survey: Shortlist of 'summary' research questions (derived from the first survey) ranked by respondents in order of priority. Final 'top ten': Agreed by consensus at a final prioritisation workshop. First survey: 1420 suggestions received from 623 respondents (49% patients/public) were refined into a shortlist of 92 'summary' questions. Second survey: 1718 respondents each nominated up to 10 questions as research priorities. Top ten: The 25 highest-ranked questions advanced to the final workshop, where 23 stakeholders (13 professional, 10 patient/carer) agreed the 10 most important questions: ▸ What can we do to stop patients developing chronic pain after surgery? ▸ How can patient care around the time of emergency surgery be improved? ▸ What long-term harm may result from anaesthesia, particularly following repeated anaesthetics?▸ What outcomes should we use to measure the 'success' of anaesthesia and perioperative care? ▸ How can we improve recovery from surgery for elderly patients? ▸ For which patients does regional anaesthesia give better outcomes than general anaesthesia? ▸ What are the effects of anaesthesia on the developing brain? ▸ Do enhanced recovery programmes improve short and long-term outcomes? ▸ How can preoperative exercise or fitness training, including physiotherapy, improve outcomes after surgery? ▸ How can we improve communication between the teams looking after patients throughout their surgical journey? Almost 2000 stakeholders contributed their views regarding anaesthetic and perioperative research priorities. This is the largest example of patient and public

  15. Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Pradhan, Seema; Kant, Chandra; Verma, Subodh; Bhatia, Sabhyata

    2017-01-01

    The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

  16. A screen for kinase inhibitors identifies antimicrobial imidazopyridine aminofurazans as specific inhibitors of the Listeria monocytogenes PASTA kinase PrkA.

    Science.gov (United States)

    Schaenzer, Adam J; Wlodarchak, Nathan; Drewry, David H; Zuercher, William J; Rose, Warren E; Striker, Rob; Sauer, John-Demian

    2017-10-13

    Bacterial signaling systems such as protein kinases and quorum sensing have become increasingly attractive targets for the development of novel antimicrobial agents in a time of rising antibiotic resistance. The family of bacterial P enicillin-binding-protein A nd S erine/ T hreonine kinase- A ssociated (PASTA) kinases is of particular interest due to the role of these kinases in regulating resistance to β-lactam antibiotics. As such, small-molecule kinase inhibitors that target PASTA kinases may prove beneficial as treatments adjunctive to β-lactam therapy. Despite this interest, only limited progress has been made in identifying functional inhibitors of the PASTA kinases that have both activity against the intact microbe and high kinase specificity. Here, we report the results of a small-molecule screen that identified GSK690693, an imidazopyridine aminofurazan-type kinase inhibitor that increases the sensitivity of the intracellular pathogen Listeria monocytogenes to various β-lactams by inhibiting the PASTA kinase PrkA. GSK690693 potently inhibited PrkA kinase activity biochemically and exhibited significant selectivity for PrkA relative to the Staphylococcus aureus PASTA kinase Stk1. Furthermore, other imidazopyridine aminofurazans could effectively inhibit PrkA and potentiate β-lactam antibiotic activity to varying degrees. The presence of the 2-methyl-3-butyn-2-ol (alkynol) moiety was important for both biochemical and antimicrobial activity. Finally, mutagenesis studies demonstrated residues in the back pocket of the active site are important for GSK690693 selectivity. These data suggest that targeted screens can successfully identify PASTA kinase inhibitors with both biochemical and antimicrobial specificity. Moreover, the imidazopyridine aminofurazans represent a family of PASTA kinase inhibitors that have the potential to be optimized for selective PASTA kinase inhibition.

  17. A system architecture for sharing de-identified, research-ready brain scans and health information across clinical imaging centers.

    Science.gov (United States)

    Chervenak, Ann L; van Erp, Theo G M; Kesselman, Carl; D'Arcy, Mike; Sobell, Janet; Keator, David; Dahm, Lisa; Murry, Jim; Law, Meng; Hasso, Anton; Ames, Joseph; Macciardi, Fabio; Potkin, Steven G

    2012-01-01

    Progress in our understanding of brain disorders increasingly relies on the costly collection of large standardized brain magnetic resonance imaging (MRI) data sets. Moreover, the clinical interpretation of brain scans benefits from compare and contrast analyses of scans from patients with similar, and sometimes rare, demographic, diagnostic, and treatment status. A solution to both needs is to acquire standardized, research-ready clinical brain scans and to build the information technology infrastructure to share such scans, along with other pertinent information, across hospitals. This paper describes the design, deployment, and operation of a federated imaging system that captures and shares standardized, de-identified clinical brain images in a federation across multiple institutions. In addition to describing innovative aspects of the system architecture and our initial testing of the deployed infrastructure, we also describe the Standardized Imaging Protocol (SIP) developed for the project and our interactions with the Institutional Review Board (IRB) regarding handling patient data in the federated environment.

  18. Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

    Directory of Open Access Journals (Sweden)

    Jiang Wei

    2008-08-01

    Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

  19. Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

    Science.gov (United States)

    Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

    2008-08-10

    With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

  20. Enzyme-labeled Antigen Method: Development and Application of the Novel Approach for Identifying Plasma Cells Locally Producing Disease-specific Antibodies in Inflammatory Lesions

    International Nuclear Information System (INIS)

    Mizutani, Yasuyoshi; Shiogama, Kazuya; Onouchi, Takanori; Sakurai, Kouhei; Inada, Ken-ichi; Tsutsumi, Yutaka

    2016-01-01

    In chronic inflammatory lesions of autoimmune and infectious diseases, plasma cells are frequently observed. Antigens recognized by antibodies produced by the plasma cells mostly remain unclear. A new technique identifying these corresponding antigens may give us a breakthrough for understanding the disease from a pathophysiological viewpoint, simply because the immunocytes are seen within the lesion. We have developed an enzyme-labeled antigen method for microscopic identification of the antigen recognized by specific antibodies locally produced in plasma cells in inflammatory lesions. Firstly, target biotinylated antigens were constructed by the wheat germ cell-free protein synthesis system or through chemical biotinylation. Next, proteins reactive to antibodies in tissue extracts were screened and antibody titers were evaluated by the AlphaScreen method. Finally, with the enzyme-labeled antigen method using the biotinylated antigens as probes, plasma cells producing specific antibodies were microscopically localized in fixed frozen sections. Our novel approach visualized tissue plasma cells that produced 1) autoantibodies in rheumatoid arthritis, 2) antibodies against major antigens of Porphyromonas gingivalis in periodontitis or radicular cyst, and 3) antibodies against a carbohydrate antigen, Strep A, of Streptococcus pyogenes in recurrent tonsillitis. Evaluation of local specific antibody responses expectedly contributes to clarifying previously unknown processes in inflammatory disorders

  1. Breeding of maize types with specific traits at the Maize Research Institute, Zemun Polje

    Directory of Open Access Journals (Sweden)

    Pajić Zorica

    2007-01-01

    Full Text Available Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a certain trait, the following specific procedures in evaluation of the trait are necessary: the estimation of a popping volume and flake quality in popping maize; the determination of sugars and harvest maturity in sweet maize; the determination of oil in selected samples of high-oil maize types, and so forth. Breeding programmes for speciality maize, except high-amylose maize, have been implemented at the Maize Research Institute, Zemun Polje, Belgrade, for the last 45 years. A great number of high-yielding sweet maize hybrids, popping maize, high-oil and high-lysine, flint and white-seeded maize hybrids were developed during this 45-year period. Auspicious selection and breeding for these traits is facilitated by the abundant genetic variability and technical and technological possibilities necessary for successful selection.

  2. Examining emergency department communication through a staff-based participatory research method: identifying barriers and solutions to meaningful change.

    Science.gov (United States)

    Cameron, Kenzie A; Engel, Kirsten G; McCarthy, Danielle M; Buckley, Barbara A; Mercer Kollar, Laura Min; Donlan, Sarah M; Pang, Peter S; Makoul, Gregory; Tanabe, Paula; Gisondi, Michael A; Adams, James G

    2010-12-01

    We test an initiative with the staff-based participatory research (SBPR) method to elicit communication barriers and engage staff in identifying strategies to improve communication within our emergency department (ED). ED staff at an urban hospital with 85,000 ED visits per year participated in a 3.5-hour multidisciplinary workshop. The workshop was offered 6 times and involved: (1) large group discussion to review the importance of communication within the ED and discuss findings from a recent survey of patient perceptions of ED-team communication; (2) small group discussions eliciting staff perceptions of communication barriers and best practices/strategies to address these challenges; and (3) large group discussions sharing and refining emergent themes and suggested strategies. Three coders analyzed summaries from group discussions by using latent content and constant comparative analysis to identify focal themes. A total of 127 staff members, including attending physicians, residents, nurses, ED assistants, and secretaries, participated in the workshop (overall participation rate 59.6%; range 46.7% to 73.3% by staff type). Coders identified a framework of 4 themes describing barriers and proposed interventions: (1) greeting and initial interaction, (2) setting realistic expectations, (3) team communication and respect, and (4) information provision and delivery. The majority of participants (81.4%) reported that their participation would cause them to make changes in their clinical practice. Involving staff in discussing barriers and facilitators to communication within the ED can result in a meaningful process of empowerment, as well as the identification of feasible strategies and solutions at both the individual and system levels. Copyright © 2010 American College of Emergency Physicians. Published by Mosby, Inc. All rights reserved.

  3. The research of Proactive Coping Behavior of Patients with Chronic Non-Specific Lung Disease

    Directory of Open Access Journals (Sweden)

    Marija A. Yaroslavskaya

    2011-01-01

    Full Text Available The purpose of the research was to study the patterns of using proactive coping and adherences to it's different types in patients with chronic non-specifi c lung diseases. Participants of the study (N=180 were 30 to 60 years old. The Proactive Coping Inventory was used to assess the patients' psychological status. According to the results of the study patients with chronic non-specifi c lung diseases use dif-ferent types of proactive coping behavior while solving problematic and stressful situations. The research revealed that patients with bronchial asthma don't have the skills of independent decision making, definition of objectives, considering of options in solving conflicts or other inconvenient situations sufficiently developed. Patients with chronic obstructive pulmonary disease are less satisfied with the emotional support that they receive from their relatives and closest people, it's harder for them to reveal their feelings and emotions than for those who suffer from bronchial asthma and healthy ones. The results of the study may be useful in developing educational systems of proactive coping behavior skills for patients with chronic non-specific lung diseases for their health and well-being support.

  4. Plants used for making recreational tea in Europe: a review based on specific research sites.

    Science.gov (United States)

    Sõukand, Renata; Quave, Cassandra L; Pieroni, Andrea; Pardo-de-Santayana, Manuel; Tardío, Javier; Kalle, Raivo; Łuczaj, Łukasz; Svanberg, Ingvar; Kolosova, Valeria; Aceituno-Mata, Laura; Menendez-Baceta, Gorka; Kołodziejska-Degórska, Iwona; Pirożnikow, Ewa; Petkevičius, Rolandas; Hajdari, Avni; Mustafa, Behxhet

    2013-08-13

    This paper is a review of local plants used in water infusions as aromatic and refreshing hot beverages (recreational tea) consumed in food-related settings in Europe, and not for specific medicinal purposes. The reviewed 29 areas are located across Europe, covering the post-Soviet countries, eastern and Mediterranean Europe. Altogether, 142 taxa belonging to 99 genera and 40 families were reported. The most important families for making herbal tea in all research areas were Lamiaceae and Asteraceae, while Rosaceae was popular only in eastern and central Europe. With regards to botanical genera, the dominant taxa included Mentha, Tilia, Thymus, Origanum, Rubus and Matricaria. The clear favorite was Origanum vulgare L., mentioned in 61% of the regions. Regionally, other important taxa included Rubus idaeus L. in eastern Europe, Chamaemelum nobile (L.) All. in southern Europe and Rosa canina L. in central Europe. Future research on the pharmacological, nutritional and chemical properties of the plants most frequently used in the tea-making process is essential to ensure their safety and appropriateness for daily consumption. Moreover, regional studies dedicated to the study of local plants used for making recreational tea are important to improve our understanding of their selection criteria, cultural importance and perceived properties in Europe and abroad.

  5. Systemic approaches identify a garlic-derived chemical, Z-ajoene, as a glioblastoma multiforme cancer stem cell-specific targeting agent.

    Science.gov (United States)

    Jung, Yuchae; Park, Heejoo; Zhao, Hui-Yuan; Jeon, Raok; Ryu, Jae-Ha; Kim, Woo-Young

    2014-07-01

    Glioblastoma multiforme (GBM) is one of the most common brain malignancies and has a very poor prognosis. Recent evidence suggests that the presence of cancer stem cells (CSC) in GBM and the rare CSC subpopulation that is resistant to chemotherapy may be responsible for the treatment failure and unfavorable prognosis of GBM. A garlic-derived compound, Z-ajoene, has shown a range of biological activities, including anti-proliferative effects on several cancers. Here, we demonstrated for the first time that Z-ajoene specifically inhibits the growth of the GBM CSC population. CSC sphere-forming inhibition was achieved at a concentration that did not exhibit a cytotoxic effect in regular cell culture conditions. The specificity of this inhibitory effect on the CSC population was confirmed by detecting CSC cell surface marker CD133 expression and biochemical marker ALDH activity. In addition, stem cell-related mRNA profiling and real-time PCR revealed the differential expression of CSC-specific genes, including Notch, Wnt, and Hedgehog, upon treatment with Z-ajoene. A proteomic approach, i.e., reverse-phase protein array (RPPA) and Western blot analysis, showed decreased SMAD4, p-AKT, 14.3.3 and FOXO3A expression. The protein interaction map (http://string-db.org/) of the identified molecules suggested that the AKT, ERK/p38 and TGFβ signaling pathways are key mediators of Z-ajoene's action, which affects the transcriptional network that includes FOXO3A. These biological and bioinformatic analyses collectively demonstrate that Z-ajoene is a potential candidate for the treatment of GBM by specifically targeting GBM CSCs. We also show how this systemic approach strengthens the identification of new therapeutic agents that target CSCs.

  6. Identifying Patient-Specific Epstein-Barr Nuclear Antigen-1 Genetic Variation and Potential Autoreactive Targets Relevant to Multiple Sclerosis Pathogenesis.

    Directory of Open Access Journals (Sweden)

    Monika Tschochner

    Full Text Available Epstein-Barr virus (EBV infection represents a major environmental risk factor for multiple sclerosis (MS, with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome.Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan and candidates were evaluated for cross recognition with human brain proteins.EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cut-off. In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577, and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogenesis.This study demonstrates the feasibility of obtaining autologous EBNA-1 sequences directly from buffy coat samples, and confirms divergence of these sequences from standard laboratory strains. This approach has identified a number of

  7. From viral genome to specific peptide epitopes: methods for identifying porcine T cell epitopes based on in silico predictions, in vitro identification and ex vivo verification

    DEFF Research Database (Denmark)

    Pedersen, Lasse Eggers; Rasmussen, Michael; Harndah, Mikkel

    2013-01-01

    to predict likely candidates for peptide-SLA binding. These results were combined with binding predictions generated by the algorithm, NetMHCpan (http://www.cbs.dtu.dk/services/NetMHCpan/) in order to select peptide candidates for in vitro analysis. The correlation between high affinity and high stability.......000 peptides. T cell epitopes were identified using peptide-SLA complexes assembled into fluorescent tetramers to stain swine influenza specific CTLs derived from immunized animals and MHC-defined pigs vaccinated against foot-and-mouth disease virus. These results demonstrate the broad applicability of methods...... originally developed for analysis of human leukocyte antigen (HLA) presentation of peptides. The methods presented provide a timely and cost-effective approach to CTL epitope discovery that can be applied to diseases of swine and of other mammalian species of interest....

  8. The Interferon-signature of Sjögren’s Syndrome: How Unique Biomarkers Can Identify Underlying Inflammatory and Immunopathological Mechanisms of Specific Diseases

    Directory of Open Access Journals (Sweden)

    Cuong eNguyen

    2013-07-01

    Full Text Available Innate immune responses direct the nature and specificity of downstream adaptive responses in autoimmune diseases. One of the strongest markers of innate immunity is the up-regulated expression of interferon (IFN and IFN-responsive/stimulated genes (IRGs/ISGs. While multiple IRGs are induced during the innate phase of host responses, transcriptome data suggest unique IRG-signatures for different diseases. Sjögren’s syndrome (SjS is characterized by chronic immune attacks against exocrine glands leading to exocrine dysfunction, plus strong up-regulated expressions of IFN IRG transcripts. Genome-wide transcriptome analyses indicate that differentially-expressed IRGs are restricted during disease development and therefore define underlying etiopathological mechanisms. Here we review the innate immune-associated IFN-signature of SjS and show how differential gene expressions of IRG/ISG sets interact molecularly and biologically to identify critical details of SjS etiopathogenesis.

  9. Mission Specific Platforms: Past achievements and future developments in European led ocean research drilling.

    Science.gov (United States)

    Cotterill, Carol; McInroy, David; Stevenson, Alan

    2013-04-01

    Mission Specific Platform (MSP) expeditions are operated by the European Consortium for Ocean Research Drilling (ECORD). Each MSP expedition is unique within the Integrated Ocean Drilling Program (IODP). In order to complement the abilities of the JOIDES Resolution and the Chikyu, the ECORD Science Operator (ESO) must source vessels and technology suitable for each MSP proposal on a case-by-case basis. The result is that ESO can meet scientific requirements in a flexible manner, whilst maintaining the measurements required for the IODP legacy programme. The process of tendering within EU journals for vessels and technology means that the planning process for each MSP Expedition starts many years in advance of the operational phase. Involvement of proposal proponents from this early stage often leads to the recognition for technological research and development to best meet the scientific aims and objectives. One example of this is the planning for the Atlantis Massif proposal, with collaborative development between the British Geological Survey (BGS) and MARUM, University of Bremen, on suitable instruments for seabed drills, with the European Petrophysics Consortium (EPC) driving the development of suitable wireline logging tools that can be used in association with such seabed systems. Other technological developments being undertaken within the European IODP community include in-situ pressure sampling for gas hydrate expeditions, deep biosphere and fluid sampling equipment and CORK technology. This multi-national collaborative approach is also employed by ESO in the operational phase. IODP Expedition 302 ACEX saw vessel and ice management support from Russia and Sweden to facilitate the first drilling undertaken in Arctic sea ice. A review of MSP expeditions past, present and future reveal the significant impact of European led operations and scientific research within the current IODP programme, and also looking forward to the start of the new International

  10. Flash visual evoked potentials are not specific enough to identify parieto-occipital lobe involvement in term neonates after significant hypoglycaemia.

    Science.gov (United States)

    Hu, Liyuan; Gu, Qiufang; Zhu, Zhen; Yang, Chenhao; Chen, Chao; Cao, Yun; Zhou, Wenhao

    2014-08-01

    Hypoglycaemia is a significant problem in high-risk neonates and predominant parieto-occipital lobe involvement has been observed after severe hypoglycaemic insult. We explored the use of flash visual evoked potentials (FVEP) in detecting parieto-occipital lobe involvement after significant hypoglycaemia. Full-term neonates (n = 15) who underwent FVEP from January 2008 to May 2013 were compared with infants (n = 11) without hypoglycaemia or parietal-occipital lobe injury. Significant hypoglycaemia was defined as being symptomatic or needing steroids, glucagon or a glucose infusion rate of ≥12 mg/kg/min. The hypoglycaemia group exhibited delayed latency of the first positive waveform on FVEP. The initial detected time for hypoglycaemia was later in the eight subjects with seizures (median 51-h-old) than those without (median 22-h-old) (P = 0.003). Magnetic resonance imaging showed that 80% of the hypoglycaemia group exhibited occipital-lobe injuries, and they were more likely to exhibit abnormal FVEP morphology (P = 0.007) than the controls. FVEP exhibited 100% sensitivity, but only 25% specificity, for detecting injuries to the parieto-occipital lobes. Flash visual evoked potential (FVEP) was sensitive, but not sufficiently specific, in identifying parieto-occipital lobe injuries among term neonates exposed to significant hypoglycaemia. Larger studies exploring the potential role of FVEP in neonatal hypoglycaemia are required. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  11. A trans-ethnic genome-wide association study identifies gender-specific loci influencing pediatric aBMD and BMC at the distal radius.

    Science.gov (United States)

    Chesi, Alessandra; Mitchell, Jonathan A; Kalkwarf, Heidi J; Bradfield, Jonathan P; Lappe, Joan M; McCormack, Shana E; Gilsanz, Vicente; Oberfield, Sharon E; Hakonarson, Hakon; Shepherd, John A; Kelly, Andrea; Zemel, Babette S; Grant, Struan F A

    2015-09-01

    Childhood fractures are common, with the forearm being the most common site. Genome-wide association studies (GWAS) have identified more than 60 loci associated with bone mineral density (BMD) in adults but less is known about genetic influences specific to bone in childhood. To identify novel genetic factors that influence pediatric bone strength at a common site for childhood fractures, we performed a sex-stratified trans-ethnic genome-wide association study of areal BMD (aBMD) and bone mineral content (BMC) Z-scores measured by dual energy X-ray absorptiometry at the one-third distal radius, in a cohort of 1399 children without clinical abnormalities in bone health. We tested signals with P BMC-Z). Signals at the CPED1-WNT16-FAM3C locus have been previously associated with BMD at other skeletal sites in adults and children. Our result at the distal radius underscores the importance of this locus at multiple skeletal sites. The 9p21.3 locus is within a gene desert, with the nearest gene flanking each side being MIR31HG and MTAP, neither of which has been implicated in BMD or BMC previously. These findings suggest that genetic determinants of childhood bone accretion at the radius, a skeletal site that is primarily cortical bone, exist and also differ by sex. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

    Science.gov (United States)

    Wei, Guifang; Pan, Li; Du, Huimin; Chen, Junyi; Zhao, Liping

    2004-10-01

    Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

  13. Genome-Wide Association Study Identifies Two Novel Loci with Sex-Specific Effects for Type 2 Diabetes Mellitus and Glycemic Traits in a Korean Population

    Directory of Open Access Journals (Sweden)

    Min Jin Go

    2014-10-01

    Full Text Available BackgroundUntil recently, genome-wide association study (GWAS-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population.MethodsWe performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842. The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500. A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively.ResultsA combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356 loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of β-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study.ConclusionOur study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population.

  14. Clinical education and training: Using the nominal group technique in research with radiographers to identify factors affecting quality and capacity

    International Nuclear Information System (INIS)

    Williams, P.L.; White, N.; Klem, R.; Wilson, S.E.; Bartholomew, P.

    2006-01-01

    There are a number of group-based research techniques available to determine the views or perceptions of individuals in relation to specific topics. This paper reports on one method, the nominal group technique (NGT) which was used to collect the views of important stakeholders on the factors affecting the quality of, and capacity to provide clinical education and training in diagnostic imaging and radiotherapy and oncology departments in the UK. Inclusion criteria were devised to recruit learners, educators, practitioners and service managers to the nominal groups. Eight regional groups comprising a total of 92 individuals were enrolled; the numbers in each group varied between 9 and 13. A total of 131 items (factors) were generated across the groups (mean = 16.4). Each group was then asked to select the top three factors from their original list. Consensus on the important factors amongst groups found that all eight groups agreed on one item: staff attitude, motivation and commitment to learners. The 131 items were organised into themes using content analysis. Five main categories and a number of subcategories emerged. The study concluded that the NGT provided data which were congruent with the issues faced by practitioners and learners in their daily work; this was of vital importance if the findings are to be regarded with credibility. Further advantages and limitations of the method are discussed, however it is argued that the NGT is a useful technique to gather relevant opinion; to select priorities and to reach consensus on a wide range of issues

  15. Integrated Healthcare Delivery: A Qualitative Research Approach to Identifying and Harmonizing Perspectives of Integrated Neglected Tropical Disease Programs.

    Directory of Open Access Journals (Sweden)

    Arianna Rubin Means

    2016-10-01

    Full Text Available While some evidence supports the beneficial effects of integrating neglected tropical disease (NTD programs to optimize coverage and reduce costs, there is minimal information regarding when or how to effectively operationalize program integration. The lack of systematic analyses of integration experiences and of integration processes may act as an impediment to achieving more effective NTD programming. We aimed to learn about the experiences of NTD stakeholders and their perceptions of integration.We evaluated differences in the definitions, roles, perceived effectiveness, and implementation experiences of integrated NTD programs among a variety of NTD stakeholder groups, including multilateral organizations, funding partners, implementation partners, national Ministry of Health (MOH teams, district MOH teams, volunteer rural health workers, and community members participating in NTD campaigns. Semi-structured key informant interviews were conducted. Coding of themes involved a mix of applying in-vivo open coding and a priori thematic coding from a start list.In total, 41 interviews were conducted. Salient themes varied by stakeholder, however dominant themes on integration included: significant variations in definitions, differential effectiveness of specific integrated NTD activities, community member perceptions of NTD programs, the influence of funders, perceived facilitators, perceived barriers, and the effects of integration on health system strength. In general, stakeholder groups provided unique perspectives, rather than contrarian points of view, on the same topics. The stakeholders identified more advantages to integration than disadvantages, however there are a number of both unique facilitators and challenges to integration from the perspective of each stakeholder group.Qualitative data suggest several structural, process, and technical opportunities that could be addressed to promote more effective and efficient integrated NTD

  16. Urinary Metabolomics Identifies a Molecular Correlate of Interstitial Cystitis/Bladder Pain Syndrome in a Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP Research Network Cohort

    Directory of Open Access Journals (Sweden)

    Kaveri S. Parker

    2016-05-01

    Full Text Available Interstitial cystitis/bladder pain syndrome (IC/BPS is a poorly understood syndrome affecting up to 6.5% of adult women in the U.S. The lack of broadly accepted objective laboratory markers for this condition hampers efforts to diagnose and treat this condition. To identify biochemical markers for IC/BPS, we applied mass spectrometry-based global metabolite profiling to urine specimens from a cohort of female IC/BPS subjects from the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP Research Network. These analyses identified multiple metabolites capable of discriminating IC/BPS and control subjects. Of these candidate markers, etiocholan-3α-ol-17-one sulfate (Etio-S, a sulfoconjugated 5-β reduced isomer of testosterone, distinguished female IC/BPS and control subjects with a sensitivity and specificity >90%. Among IC/BPS subjects, urinary Etio-S levels are correlated with elevated symptom scores (symptoms, pelvic pain, and number of painful body sites and could resolve high- from low-symptom IC/BPS subgroups. Etio-S-associated biochemical changes persisted through 3–6 months of longitudinal follow up. These results raise the possibility that an underlying biochemical abnormality contributes to symptoms in patients with severe IC/BPS.

  17. Identifying obstacles and ranking common biological control research priorities for Europe to manage most economically important pests in arable, vegetable and perennial crops.

    Science.gov (United States)

    Lamichhane, Jay Ram; Bischoff-Schaefer, Monika; Bluemel, Sylvia; Dachbrodt-Saaydeh, Silke; Dreux, Laure; Jansen, Jean-Pierre; Kiss, Jozsef; Köhl, Jürgen; Kudsk, Per; Malausa, Thibaut; Messéan, Antoine; Nicot, Philippe C; Ricci, Pierre; Thibierge, Jérôme; Villeneuve, François

    2017-01-01

    EU agriculture is currently in transition from conventional crop protection to integrated pest management (IPM). Because biocontrol is a key component of IPM, many European countries recently have intensified their national efforts on biocontrol research and innovation (R&I), although such initiatives are often fragmented. The operational outputs of national efforts would benefit from closer collaboration among stakeholders via transnationally coordinated approaches, as most economically important pests are similar across Europe. This paper proposes a common European framework on biocontrol R&I. It identifies generic R&I bottlenecks and needs as well as priorities for three crop types (arable, vegetable and perennial crops). The existing gap between the market offers of biocontrol solutions and the demand of growers, the lengthy and expensive registration process for biocontrol solutions and their varying effectiveness due to variable climatic conditions and site-specific factors across Europe are key obstacles hindering the development and adoption of biocontrol solutions in Europe. Considering arable, vegetable and perennial crops, a dozen common target pests are identified for each type of crop and ranked by order of importance at European level. Such a ranked list indicates numerous topics on which future joint transnational efforts would be justified. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. Discussion about the use of the volume specific surface area (VSSA) as a criterion to identify nanomaterials according to the EU definition. Part two: experimental approach.

    Science.gov (United States)

    Lecloux, André J; Atluri, Rambabu; Kolen'ko, Yury V; Deepak, Francis Leonard

    2017-10-12

    The first part of this study was dedicated to the modelling of the influence of particle shape, porosity and particle size distribution on the volume specific surface area (VSSA) values in order to check the applicability of this concept to the identification of nanomaterials according to the European Commission Recommendation. In this second part, experimental VSSA values are obtained for various samples from nitrogen adsorption isotherms and these values were used as a screening tool to identify and classify nanomaterials. These identification results are compared to the identification based on the 50% of particles with a size below 100 nm criterion applied to the experimental particle size distributions obtained by analysis of electron microscopy images on the same materials. It is concluded that the experimental VSSA values are able to identify nanomaterials, without false negative identification, if they have a mono-modal particle size, if the adsorption data cover the relative pressure range from 0.001 to 0.65 and if a simple, qualitative image of the particles by transmission or scanning electron microscopy is available to define their shape. The experimental conditions to obtain reliable adsorption data as well as the way to analyze the adsorption isotherms are described and discussed in some detail in order to help the reader in using the experimental VSSA criterion. To obtain the experimental VSSA values, the BET surface area can be used for non-porous particles, but for porous, nanostructured or coated nanoparticles, only the external surface of the particles, obtained by a modified t-plot approach, should be considered to determine the experimental VSSA and to avoid false positive identification of nanomaterials, only the external surface area being related to the particle size. Finally, the availability of experimental VSSA values together with particle size distributions obtained by electron microscopy gave the opportunity to check the

  19. An in vivo cis-regulatory screen at the type 2 diabetes associated TCF7L2 locus identifies multiple tissue-specific enhancers.

    Directory of Open Access Journals (Sweden)

    Daniel Savic

    Full Text Available Genome-wide association studies (GWAS have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D, implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition.

  20. Identifying the Research Process to Analyse the Adoption of the International Baccalaureate's Diploma Programme in England

    Science.gov (United States)

    Outhwaite, Deborah

    2018-01-01

    This article analyses the flow-line around the methodology used inside an educational research process that was originally established to examine the expansion of the International Baccalaureate's Diploma Programme (IBDP) in England. This article analyses the research question, then assesses the research focus, aims and objectives. The article…

  1. Efficient Culture Adaptation of Hepatitis C Virus Recombinants with Genotype-Specific Core-NS2 by Using Previously Identified Mutations

    DEFF Research Database (Denmark)

    Scheel, Troels Kasper Høyer; Gottwein, Judith M; Carlsen, Thomas H R

    2011-01-01

    Hepatitis C virus (HCV) is an important cause of chronic liver disease, and interferon-based therapy cures only 40 to 80% of patients, depending on HCV genotype. Research was accelerated by genotype 2a (strain JFH1) infectious cell culture systems. We previously developed viable JFH1-based...... (HC-TN and DH6), 1b (DH1 and DH5), and 3a (DBN) isolates, using previously identified adaptive mutations. Introduction of mutations from isolates of the same subtype either led to immediate efficient virus production or accelerated culture adaptation. The DH6 and DH5 recombinants without introduced...... mutations did not adapt to culture. Universal adaptive effects of mutations in NS3 (Q1247L, I1312V, K1398Q, R1408W, and Q1496L) and NS5A (V2418L) were investigated for JFH1-based genotype 1 to 5 core-NS2 recombinants; several mutations conferred adaptation to H77C (1a), J4 (1b), S52 (3a), and SA13 (5a...

  2. A novel type of peptidoglycan-binding domain highly specific for amidated D-Asp cross-bridge, identified in Lactobacillus casei bacteriophage endolysins.

    Science.gov (United States)

    Regulski, Krzysztof; Courtin, Pascal; Kulakauskas, Saulius; Chapot-Chartier, Marie-Pierre

    2013-07-12

    Peptidoglycan hydrolases (PGHs) are responsible for bacterial cell lysis. Most PGHs have a modular structure comprising a catalytic domain and a cell wall-binding domain (CWBD). PGHs of bacteriophage origin, called endolysins, are involved in bacterial lysis at the end of the infection cycle. We have characterized two endolysins, Lc-Lys and Lc-Lys-2, identified in prophages present in the genome of Lactobacillus casei BL23. These two enzymes have different catalytic domains but similar putative C-terminal CWBDs. By analyzing purified peptidoglycan (PG) degradation products, we showed that Lc-Lys is an N-acetylmuramoyl-L-alanine amidase, whereas Lc-Lys-2 is a γ-D-glutamyl-L-lysyl endopeptidase. Remarkably, both lysins were able to lyse only Gram-positive bacterial strains that possess PG with D-Ala(4)→D-Asx-L-Lys(3) in their cross-bridge, such as Lactococcus casei, Lactococcus lactis, and Enterococcus faecium. By testing a panel of L. lactis cell wall mutants, we observed that Lc-Lys and Lc-Lys-2 were not able to lyse mutants with a modified PG cross-bridge, constituting D-Ala(4)→L-Ala-(L-Ala/L-Ser)-L-Lys(3); moreover, they do not lyse the L. lactis mutant containing only the nonamidated D-Asp cross-bridge, i.e. D-Ala(4)→D-Asp-L-Lys(3). In contrast, Lc-Lys could lyse the ampicillin-resistant E. faecium mutant with 3→3 L-Lys(3)-D-Asn-L-Lys(3) bridges replacing the wild-type 4→3 D-Ala(4)-D-Asn-L-Lys(3) bridges. We showed that the C-terminal CWBD of Lc-Lys binds PG containing mainly D-Asn but not PG with only the nonamidated D-Asp-containing cross-bridge, indicating that the CWBD confers to Lc-Lys its narrow specificity. In conclusion, the CWBD characterized in this study is a novel type of PG-binding domain targeting specifically the D-Asn interpeptide bridge of PG.

  3. High IL-17E and low IL-17C dermal expression identifies a fibrosis-specific motif common to morphea and systemic sclerosis.

    Directory of Open Access Journals (Sweden)

    Paola Adele Lonati

    identifies a fibrosis-specific motif. The specific IL-17C/IL-17E cytokine combination may thus play a role in the development of fibrosis.

  4. Integrated corridor management : phase I, concept development and foundational research. Task 3.4, identify integrated corridor management institutional strategies and administration

    Science.gov (United States)

    2006-04-12

    Task 3 involves overall foundational research to further the understanding of various aspects of Integrated Corridor Management (ICM) and to identify integration issues needed to evaluate the feasibility of the ICM initiative. The focus of Task 3.4 a...

  5. Mixed Methods Research Prevalence Studies: Field-Specific Studies on the State of the Art of Mixed Methods Research

    OpenAIRE

    Molina-Azorín, José F.; Fetters, Michael D.

    2016-01-01

    The Journal of Mixed Methods Research (JMMR) has always welcomed two main kinds of manuscripts: original empirical articles and methodological/theoretical articles (Creswell & Tashakkori, 2007; Fetters & Freshwater, 2015a; Mertens, 2011). Both types of articles must clearly state methodological aims, review mixed methods literature relative to the methodological aim, and advance the field of mixed methods—empirical articles must address integration (Fetters & Freshwater, 2015b). In this edito...

  6. Allele-Specific Alternative mRNA processing (ASARP) | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    A software pipeline for prediction of allele-specific alternative RNA processing events using single RNA-seq data. The current version focuses on prediction of alternative splicing and alternative polyadenylation modulated by genetic variants.

  7. Research

    African Journals Online (AJOL)

    GCSA) urged ... Students' ability to learn is to a great extent affected by their perception of the specific ... discussions were held with the class leaders to identify possible themes/ topics to describe ... Unpublished Doctoral Thesis. Bloemfontein:.

  8. Using Multi-Group Confirmatory Factor Analysis to Evaluate Cross-Cultural Research: Identifying and Understanding Non-Invariance

    Science.gov (United States)

    Brown, Gavin T. L.; Harris, Lois R.; O'Quin, Chrissie; Lane, Kenneth E.

    2017-01-01

    Multi-group confirmatory factor analysis (MGCFA) allows researchers to determine whether a research inventory elicits similar response patterns across samples. If statistical equivalence in responding is found, then scale score comparisons become possible and samples can be said to be from the same population. This paper illustrates the use of…

  9. TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine.

    Science.gov (United States)

    Li, Guang-Qing; Liu, Zi; Shen, Hong-Bin; Yu, Dong-Jun

    2016-10-01

    As one of the most ubiquitous post-transcriptional modifications of RNA, N 6 -methyladenosine ( [Formula: see text]) plays an essential role in many vital biological processes. The identification of [Formula: see text] sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target [Formula: see text] sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide/dinucleotide propensities (PSNP/PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences. The extracted features are further optimized to obtain a much more compact and discriminative feature subset by applying an incremental feature selection (IFS) procedure. Based on the optimized feature subset, we trained TargetM6A on the training dataset with a support vector machine (SVM) as the prediction engine. We compared the proposed TargetM6A method with existing methods for predicting [Formula: see text] sites by performing stringent jackknife tests and independent validation tests on benchmark datasets. The experimental results show that the proposed TargetM6A method outperformed the existing methods for predicting [Formula: see text] sites and remarkably improved the prediction performances, with MCC = 0.526 and AUC = 0.818. We also provided a user-friendly web server for TargetM6A, which is publicly accessible for academic use at http://csbio.njust.edu.cn/bioinf/TargetM6A.

  10. Specifics of Cyberbullying of Teachers in Czech Schools--A National Research

    Science.gov (United States)

    Kopecký, Kamil; Szotkowski, René

    2017-01-01

    This paper focuses on the results of the national research of cyberbullying of Czech teachers, which was realized in year 2016 in the entire Czech Republic. The research focused on the prevalence of cyberbullying of teachers, the impact of cyberbullying on teachers, strategies of coping with cyberbullying and methods of solving the incidents. The…

  11. Site-Specific Research Conducted in Support of the Salton Sea Solar Pond Project - FY 1982 Report

    Science.gov (United States)

    French, R. L.; Marsh, H. E.; Roschke, E. J.; Wu, Y. C.

    1984-01-01

    The design and operation of a salt-gradient solar pond power plant at the Salton Sea presents problems not encountered at small research ponds that were built in the United States. The specific characteristics of the Salton Sea site and the desire to construct the pond using the local clay as a sealant represent major deviations from previous solar pond experience. The site-specific research in support of the plant design is described. The research activity included validation of the spectrophotometric light transmission measurement technique, a search for options for clarifying the turbid and colored water of the Salton Sea, development of water clarification specifications in terms common to industry practice, quantification of gas production from microbiological reactions in the ground, a determination of the combined effects of temperature and salinity on the permeation of the local clays, and a preliminary evaluation of material corrosion.

  12. Action Research of a Color-Coded, Onset-Rime Decoding Intervention: Examining the Effects with First Grade Students Identified as at Risk

    Science.gov (United States)

    Wall, Candace A.; Rafferty, Lisa A.; Camizzi, Mariya A.; Max, Caroline A.; Van Blargan, David M.

    2016-01-01

    Many students who struggle to obtain the alphabetic principle are at risk for being identified as having a reading disability and would benefit from additional explicit phonics instruction as a remedial measure. In this action research case study, the research team conducted two experiments to investigate the effects of a color-coded, onset-rime,…

  13. Using Participatory and Service Design to Identify Emerging Needs and Perceptions of Library Services among Science and Engineering Researchers Based at a Satellite Campus

    Science.gov (United States)

    Johnson, Andrew; Kuglitsch, Rebecca; Bresnahan, Megan

    2015-01-01

    This study used participatory and service design methods to identify emerging research needs and existing perceptions of library services among science and engineering faculty, post-graduate, and graduate student researchers based at a satellite campus at the University of Colorado Boulder. These methods, and the results of the study, allowed us…

  14. Here, KAPTUR This! Identifying and Selecting the Infrastructure Required to Support the Curation and Preservation of Visual Arts Research Data

    Directory of Open Access Journals (Sweden)

    Leigh Garrett

    2013-11-01

    Full Text Available Research data is increasingly perceived as a valuable resource and, with appropriate curation and preservation, it has much to offer learning, teaching, research, knowledge transfer and consultancy activities in the visual arts. However, very little is known about the curation and preservation of this data: none of the specialist arts institutions have research data management policies or infrastructure and anecdotal evidence suggests that practice is ad hoc, left to individual researchers and teams with little support or guidance. In addition, the curation and preservation of such diverse and complex digital resources as found in the visual arts is, in itself, challenging. Led by the Visual Arts Data Service, a research centre of the University for the Creative Arts, in collaboration with the Glasgow School of Art; Goldsmiths College, University of London; and University of the Arts London, and funded by JISC, the KAPTUR project (2011-2013 seeks to address the lack of awareness and explore the potential of research data management systems in the arts by discovering the nature of research data in the visual arts, investigating the current state of research data management, developing a model of best practice applicable to both specialist arts institutions and arts departments in multidisciplinary institutions, and by applying, testing and piloting the model with the four institutional partners. Utilising the findings of the KAPTUR user requirement and technical review, this paper will outline the method and selection of an appropriate research data management system for the visual arts and the issues the team encountered along the way.

  15. Action research to promote medical students' motivation in an English for Specific Purposes class.

    Science.gov (United States)

    Dehnad, Afsaneh; Nasser, Hayedeh

    2014-01-01

    Action research is an attempt to seek immediate solutions to the problems experienced in educational settings. In this type of research, teachers are the researchers who intend to make instant reforms to develop, and improve their teaching styles and reflect on pedagogical practices. The purpose of this study was to conduct an action research to tackle the problem of students' low motivation in English classes at the medical school of Iran University of Medical Sciences in fall 2010. Participants of this study were 98 third-semester ESP students of medicine. To reform the situation and promote students' motivation to participate in classes more actively and eagerly, the researchers changed the syllabus by applying Kemmis and McTaggart's (1988) cyclical model of action research, and adopting task-based teaching. Data was collected by means of interviews with both teachers and students to determine the changes to be made in the syllabus, classroom observations to monitor students' behavioral changes, and a questionnaire to assess students' attitudes towards the changes. This research study had a number of valuable outcomes the most important of which was a change in classroom behavior of the students.

  16. Action research to promote medical students' motivation in an English for Specific Purposes class.

    Directory of Open Access Journals (Sweden)

    Afsaneh Dehnad

    2014-06-01

    Full Text Available Action research is an attempt to seek immediate solutions to the problems experienced in educational settings. In this type of research, teachers are the researchers who intend to make instant reforms to develop, and improve their teaching styles and reflect on pedagogical practices. The purpose of this study was to conduct an action research to tackle the problem of students' low motivation in English classes at the medical school of Iran University of Medical Sciences in fall 2010. Participants of this study were 98 third-semester ESP students of medicine. To reform the situation and promote students' motivation to participate in classes more actively and eagerly, the researchers changed the syllabus by applying Kemmis and McTaggart's (1988 cyclical model of action research, and adopting task-based teaching. Data was collected by means of interviews with both teachers and students to determine the changes to be made in the syllabus, classroom observations to monitor students' behavioral changes, and a questionnaire to assess students' attitudes towards the changes. This research study had a number of valuable outcomes the most important of which was a change in classroom behavior of the students.

  17. Research

    African Journals Online (AJOL)

    abp

    2016-04-29

    Apr 29, 2016 ... specific causes of maternal deaths and identify specific contributing factors. This study therefore aimed to ... third delay were mainly contributed by lack of blood transfusion. (5%, n=18), lack of skills (2%, n=8), .... observed in Rift Valley Provincial General Hospital, where slightly over a half had died within 24 ...

  18. Explaining Variance and Identifying Predictors of Children's Communication via a Multilevel Model of Single-Case Design Research: Brief Report

    Science.gov (United States)

    Ottley, Jennifer Riggie; Ferron, John M.; Hanline, Mary Frances

    2016-01-01

    The purpose of this study was to explain the variability in data collected from a single-case design study and to identify predictors of communicative outcomes for children with developmental delays or disabilities (n = 4). Using SAS® University Edition, we fit multilevel models with time nested within children. Children's level of baseline…

  19. Research Resource: A Dual Proteomic Approach Identifies Regulated Islet Proteins During β-Cell Mass Expansion In Vivo

    DEFF Research Database (Denmark)

    Horn, Signe; Kirkegaard, Jeannette S.; Hoelper, Soraya

    2016-01-01

    to be up regulated as a response to pregnancy. These included several proteins, not previously associated with pregnancy-induced islet expansion, such as CLIC1, STMN1, MCM6, PPIB, NEDD4, and HLTF. Confirming the validity of our approach, we also identified proteins encoded by genes known to be associated...

  20. A nationwide survey concerning practices in pessary use for pelvic organ prolapse in The Netherlands : identifying needs for further research

    NARCIS (Netherlands)

    Velzel, Joost; Roovers, Jan Paul; van der Vaart, C. H.; Broekman, Bart; Vollebregt, Astrid; Hakvoort, Robert

    2015-01-01

    Introduction and hypothesis: To identify practice variation in management of patients with a vaginal pessary for pelvic organ prolapse (POP). Methods: A nationwide survey was sent to all Dutch gynecologists with a special interest in urogynecology. Results: The response rate was 59 %. Of the

  1. A nationwide survey concerning practices in pessary use for pelvic organ prolapse in The Netherlands: identifying needs for further research

    NARCIS (Netherlands)

    J. Velzel (Joost); J.P. Roovers (Jan Paul); C.H. Van der Vaart; B.M.W. Broekman (Bart); A. Vollebregt (Astrid); R. Hakvoort (Robert)

    2015-01-01

    textabstractIntroduction and hypothesis: To identify practice variation in management of patients with a vaginal pessary for pelvic organ prolapse (POP). Methods: A nationwide survey was sent to all Dutch gynecologists with a special interest in urogynecology. Results: The response rate was 59 %. Of

  2. A nationwide survey concerning practices in pessary use for pelvic organ prolapse in The Netherlands: identifying needs for further research

    NARCIS (Netherlands)

    Velzel, Joost; Roovers, Jan Paul; van der Vaart, C. H.; Broekman, Bart; Vollebregt, Astrid; Hakvoort, Robert

    2015-01-01

    To identify practice variation in management of patients with a vaginal pessary for pelvic organ prolapse (POP). A nationwide survey was sent to all Dutch gynecologists with a special interest in urogynecology. The response rate was 59 %. Of the respondents, 13 % had a written protocol for pessary

  3. 78 FR 20672 - Literature Review Approach “Identifying Research Needs for Assessing Safe Use of High Intakes of...

    Science.gov (United States)

    2013-04-05

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Literature Review Approach... Needs for Assessing Safe Use of High Intakes of Folic Acid,'' for review of the pertinent literature... folate and folic acid, screening of the literature was undertaken to identify the potential adverse...

  4. The Research Potential of Educational Theory: On the Specific Characteristics of the Issues of Education

    Science.gov (United States)

    Les, Tomasz

    2017-01-01

    In this article, I present the argument that educational theory has specific character, which distinguishes it from most scientific disciplines. It requires the application of not only strictly scientific methods, which essentially consist of descriptions and explanations, but also normative ones, which indicate how it is related to philosophy and…

  5. Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research

    NARCIS (Netherlands)

    Tetteh, Paul W.; Kretzschmar, Kai; Begthel, Harry; Van Den Born, Maaike; Korving, Jeroen; Morsink, Folkert; Farin, Henner; Van Es, Johan H.; Offerhaus, G. Johan A; Clevers, Hans

    2016-01-01

    Current mouse models for colorectal cancer often differ significantly from human colon cancer, being largely restricted to the small intestine. Here, we aim to develop a colon-specific inducible mouse model that can faithfully recapitulate human colon cancer initiation and progression. Carbonic

  6. Genome-wide association study of glioma subtypes identifies specific differences in genetic susceptibility to glioblastoma and non-glioblastoma tumors

    DEFF Research Database (Denmark)

    Melin, Beatrice S; Barnholtz-Sloan, Jill S; Wrensch, Margaret R

    2017-01-01

    Genome-wide association studies (GWAS) have transformed our understanding of glioma susceptibility, but individual studies have had limited power to identify risk loci. We performed a meta-analysis of existing GWAS and two new GWAS, which totaled 12,496 cases and 18,190 controls. We identified fi...

  7. Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci

    NARCIS (Netherlands)

    Jones, G.T.; Tromp, G.; Kuivaniemi, H.; Gretarsdottir, S.; Baas, A.F.; Giusti, B.; Strauss, E.; Hof, F.N. van 't; Webb, T.R.; Erdman, R.; Ritchie, M.D.; Elmore, J.R.; Verma, A.; Pendergrass, S.; Kullo, I.J.; Ye, Z.; Peissig, P.L.; Gottesman, O.; Verma, S.S.; Malinowski, J.; Rasmussen-Torvik, L.J.; Borthwick, K.M.; Smelser, D.T.; Crosslin, D.R.; Andrade, M. de; Ryer, E.J.; McCarty, C.A.; Bottinger, E.P.; Pacheco, J.A.; Crawford, D.C.; Carrell, D.S.; Gerhard, G.S.; Franklin, D.P.; Carey, D.J.; Phillips, V.L.; Williams, M.J.; Wei, W.; Blair, R.; Hill, A.A.; Vasudevan, T.M.; Lewis, D.R.; Thomson, I.A.; Krysa, J.; Hill, G.B.; Roake, J.; Merriman, T.R.; Oszkinis, G.; Galora, S.; Saracini, C.; Abbate, R.; Pulli, R.; Pratesi, C.; Saratzis, A.; Verissimo, A.R.; Bumpstead, S.; Badger, S.A.; Clough, R.E.; Cockerill, G.; Hafez, H.; Scott, D.J.; Futers, T.S.; Romaine, S.P.; Bridge, K.; Griffin, K.J.; Bailey, M.A.; Smith, A.; Thompson, M.M.; Bockxmeer, F.M. van; Matthiasson, S.E.; Thorleifsson, G.; Thorsteinsdottir, U.; Blankensteijn, J.D.; Teijink, J.A.; Wijmenga, C.; Graaf, J. de; Kiemeney, L.A.L.M.; Lindholt, J.S.; Hughes, A.; Bradley, D.T.; Stirrups, K.; Golledge, J.; Norman, P.E.; Powell, J.T.; Humphries, S.E.; Hamby, S.E.; Goodall, A.H.; Nelson, C.P.; Sakalihasan, N.; Courtois, A.; Ferrell, R.E.; Eriksson, P.; Folkersen, L.; Franco-Cereceda, A.; Eicher, J.D.; Johnson, A.D.; Betsholtz, C.; Ruusalepp, A.; Franzen, O.; Schadt, E.E.; Bjorkegren, J.L.; et al.,

    2017-01-01

    RATIONALE: Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA. OBJECTIVE: To identify additional AAA risk loci using data from all available

  8. Information Management at a Health Services Research Organization in Toronto, Ontario, Canada: Moving from Identifiable Data to Coded Data

    Directory of Open Access Journals (Sweden)

    Lisa Thurairasu

    2017-04-01

    The processing practices used at the organization comply with Canadian privacy laws such as the Personal Health Information Protection Act (PHIPA as well as organizational policies and Research Ethics Board approvals. The approaches used to conceal individual identities yet allow linkage to various data sources can be modelled by other health agencies, ministries, and non-health related organizations that work with sensitive data but face challenges in maintaining both privacy and research quality. Our organization strives to make processing as efficient as possible and create maximum linkability to the various data sources in house while upholding privacy and confidentiality.

  9. A School-University Research Partnership to Identify Disengaged Students: A Descriptive Case Analysis of School Climate

    Science.gov (United States)

    Biag, Manuelito D.; Sanchez, Monika A.

    2016-01-01

    Background/Context: Much of the literature on school-university research partnerships has focused on collaborations that address curriculum, instruction, and leadership. Less scholarly attention has been paid to how practitioners and academics work together to improve school climate. Purpose: We seek to deepen understanding of how educators and…

  10. Research Relating to the Learning of Children Identified as Having Experienced Malnutrition and/or Heavy Metal Poisoning. Final Report.

    Science.gov (United States)

    Snowdon, Charles T.

    Described was research on the behavioral and learning effects of lead poisoning or malnutrition in rats. It is explained that approximately 200 rats (either weanling, adult, pregnant, or nursing) were injected with various amounts of lead. It was found that symtomatic levels of lead in weanling or adult rats produced no obvious behavioral or…

  11. Epilepsy research methods update: Understanding the causes of epileptic seizures and identifying new treatments using non-mammalian model organisms.

    Science.gov (United States)

    Cunliffe, Vincent T; Baines, Richard A; Giachello, Carlo N G; Lin, Wei-Hsiang; Morgan, Alan; Reuber, Markus; Russell, Claire; Walker, Matthew C; Williams, Robin S B

    2015-01-01

    This narrative review is intended to introduce clinicians treating epilepsy and researchers familiar with mammalian models of epilepsy to experimentally tractable, non-mammalian research models used in epilepsy research, ranging from unicellular eukaryotes to more complex multicellular organisms. The review focuses on four model organisms: the social amoeba Dictyostelium discoideum, the roundworm Caenorhabditis elegans, the fruit fly Drosophila melanogaster and the zebrafish Danio rerio. We consider recent discoveries made with each model organism and discuss the importance of these advances for the understanding and treatment of epilepsy in humans. The relative ease with which mutations in genes of interest can be produced and studied quickly and cheaply in these organisms, together with their anatomical and physiological simplicity in comparison to mammalian species, are major advantages when researchers are trying to unravel complex disease mechanisms. The short generation times of most of these model organisms also mean that they lend themselves particularly conveniently to the investigation of drug effects or epileptogenic processes across the lifecourse. Copyright © 2014 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  12. ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

    Science.gov (United States)

    2013-01-01

    Background and motivation The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials. Results We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata. Conclusion The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption. PMID

  13. Breeding of maize types with specific traits at the Maize Research Institute, Zemun Polje

    OpenAIRE

    Pajić Zorica

    2007-01-01

    Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a...

  14. Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research.

    Science.gov (United States)

    Tetteh, Paul W; Kretzschmar, Kai; Begthel, Harry; van den Born, Maaike; Korving, Jeroen; Morsink, Folkert; Farin, Henner; van Es, Johan H; Offerhaus, G Johan A; Clevers, Hans

    2016-10-18

    Current mouse models for colorectal cancer often differ significantly from human colon cancer, being largely restricted to the small intestine. Here, we aim to develop a colon-specific inducible mouse model that can faithfully recapitulate human colon cancer initiation and progression. Carbonic anhydrase I (Car1) is a gene expressed uniquely in colonic epithelial cells. We generated a colon-specific inducible Car1 CreER knock-in (KI) mouse with broad Cre activity in epithelial cells of the proximal colon and cecum. Deletion of the tumor suppressor gene Apc using the Car1 CreER KI caused tumor formation in the cecum but did not yield adenomas in the proximal colon. Mutation of both Apc and Kras yielded microadenomas in both the cecum and the proximal colon, which progressed to macroadenomas with significant morbidity. Aggressive carcinomas with some invasion into lymph nodes developed upon combined induction of oncogenic mutations of Apc, Kras, p53, and Smad4 Importantly, no adenomas were observed in the small intestine. Additionally, we observed tumors from differentiated Car1-expressing cells with Apc/Kras mutations, suggesting that a top-down model of intestinal tumorigenesis can occur with multiple mutations. Our results establish the Car1 CreER KI as a valuable mouse model to study colon-specific tumorigenesis and metastasis as well as cancer-cell-of-origin questions.

  15. Training cardiovascular outcomes researchers: A survey of mentees and mentors to identify critical training gaps and needs.

    Science.gov (United States)

    Khazanie, Prateeti; Al-Khatib, Sana M; Wang, Tracy Y; Crowley, Matthew J; Kressin, Nancy R; Krumholz, Harlan M; Kiefe, Catarina I; Wells, Barbara L; O'Brien, Sean M; Peterson, Eric D; Sanders, Gillian D

    2018-02-01

    Many young investigators are interested in cardiovascular (CV) outcomes research; however, the current training experience of early investigators across the United States is uncertain. From April to November 2014, we surveyed mentees and mentors of early-stage CV outcomes investigators across the United States. We contacted successful grantees of government agencies, members of professional organizations, and trainees in CV outcomes training programs. A total of 185 (of 662) mentees and 76 (of 541) mentors completed the survey. Mentees were equally split by sex; most had completed training >3 years before completing the survey and were clinicians. Mentors were more likely women, mostly ≥20 years posttraining, and at an associate/full professor rank. Mentors reported devoting more time currently to clinical work than when they were early in their career and mentoring 2-4 people simultaneously. More than 80% of mentees started training to become academicians and completed training with the same goal. More than 70% of mentees desired at least 50% research time in future jobs. More than 80% of mentors believed that future investigators would need more than 50% time dedicated to research. Most mentees (80%) were satisfied with their relationship with their mentor and reported having had opportunities to develop independently. Mentors more frequently than mentees reported that funding cutbacks had negatively affected mentees' ability to succeed (84% vs 58%). Across funding mechanisms, mentees were more optimistic than mentors about securing funding. Both mentees and mentors reported greatest preparedness for job/career satisfaction (79% for both) and publications (84% vs 92%) and least preparedness for future financial stability (48% vs 46%) and work-life balance (47% vs 42%). Survey findings may stimulate future discourse and research on how best to attract, train, and retain young investigators in CV outcomes research. Insights may help improve existing training

  16. Detectable end of radiation prostate specific antigen assists in identifying men with unfavorable intermediate-risk prostate cancer at high risk of distant recurrence and cancer-specific mortality.

    Science.gov (United States)

    Hayman, Jonathan; Phillips, Ryan; Chen, Di; Perin, Jamie; Narang, Amol K; Trieu, Janson; Radwan, Noura; Greco, Stephen; Deville, Curtiland; McNutt, Todd; Song, Daniel Y; DeWeese, Theodore L; Tran, Phuoc T

    2018-06-01

    Undetectable End of Radiation PSA (EOR-PSA) has been shown to predict improved survival in prostate cancer (PCa). While validating the unfavorable intermediate-risk (UIR) and favorable intermediate-risk (FIR) stratifications among Johns Hopkins PCa patients treated with radiotherapy, we examined whether EOR-PSA could further risk stratify UIR men for survival. A total of 302 IR patients were identified in the Johns Hopkins PCa database (178 UIR, 124 FIR). Kaplan-Meier curves and multivariable analysis was performed via Cox regression for biochemical recurrence free survival (bRFS), distant metastasis free survival (DMFS), and overall survival (OS), while a competing risks model was used for PCa specific survival (PCSS). Among the 235 patients with known EOR-PSA values, we then stratified by EOR-PSA and performed the aforementioned analysis. The median follow-up time was 11.5 years (138 months). UIR was predictive of worse DMFS and PCSS (P = 0.008 and P = 0.023) on multivariable analysis (MVA). Increased radiation dose was significant for improved DMFS (P = 0.016) on MVA. EOR-PSA was excluded from the models because it did not trend towards significance as a continuous or binary variable due to interaction with UIR, and we were unable to converge a multivariable model with a variable to control for this interaction. However, when stratifying by detectable versus undetectable EOR-PSA, UIR had worse DMFS and PCSS among detectable EOR-PSA patients, but not undetectable patients. UIR was significant on MVA among detectable EOR-PSA patients for DMFS (P = 0.021) and PCSS (P = 0.033), while RT dose also predicted PCSS (P = 0.013). EOR-PSA can assist in predicting DMFS and PCSS among UIR patients, suggesting a clinically meaningful time point for considering intensification of treatment in clinical trials of intermediate-risk men. © 2018 Wiley Periodicals, Inc.

  17. Gender specific analysis of occupational diseases of the low back caused by carrying, lifting or extreme trunk flexion—use of a prevention index to identify occupations with high prevention needs

    Science.gov (United States)

    Thiede, Markus; Liebers, Falk; Seidler, Andreas; Gravemeyer, Stefan; Latza, Ute

    2014-01-01

    Background Gender specific analysis of the occupational disease of the lumbar spine caused by carrying, lifting, or extreme trunk flexion in Germany (OD No.2108) with the aim to identify areas of focus for prevention and research with a prevention index (PI). Methods Data from the German Statutory Accident Insurance stratified by gender are shown. Results From 2002 until 2009 there were 2,877 confirmed cases of an OD No. 2108 (40.1% male and 59.1% female). The PI indicated the highest prevention need for female nursing/midwifery associate professionals and male building frame and related trades workers. Patient transfer and working in extremely bent posture were the most frequent exposures. Conclusions The identified occupations with high need for prevention among men come from nearly all major occupational groups whereas women cluster in occupational groups from the health and care sectors. Am. J. Ind. Med. 57:233–244, 2014. © 2013 The Authors. American Journal of Industrial Medicine Published by Wiley Periodicals, Inc. PMID:24243091

  18. Substantiation of the TVR-M reactor parameter selection and specific features of the research program

    International Nuclear Information System (INIS)

    Abov, Yu.G.; Kiselev, G.V.; Shvedov, O.V.

    1986-01-01

    Comparative analysis of characteristics of the T-VR-M(ITEP, USSR), GRHF(France) and PIK(LNPI USSR) high-flux heavy water cooled and moderated research reactors is given. The TVR-M reactor design concepts are mainly based on a 35-year experience in operating of the first Soviet heavy water research TVR reactor. As a result of the reactor reconstruction its thermal power will increase up to 25 MW neutron flux in experimental channels will increase 10 fold and reach 5.6x10 14 neutron/cm 2 xc. The TVR-M reactor has the quality value the ratio of maximum thermal neutron flux value the reflector to reactor power in practically the same as for the GRHF reactor (2.24x10 13 (neutron/cm 2 xc)/MW) which allows one to place it among the best research reactors in the world. Maximum fuel burnup of the order of 50% and minimum fuel loading are forseen for the TVR-M reactor which provides for operation cost minimum as compared to the GRHF and PIK reactors. The TVR-M reactor practically does not yield to the PIK and GRMF reactors in experimental channel quantity and exceeds the in the number of vertical channels. The TVR-M reactor experimental capabilities allow one to reduce measuring time and provide for conducting the experiments at a qualitatively new level. At the same time capabilities of radioactive nuclide production in qualitative and quantitative senses are increased

  19. IDENTIFYING CONCERNS OF POSTGRADUATES IN COMMUNITY MEDICINE USING A QUALITATIVE RESEARCH METHOD- VISUALISATION IN PARTICIPATORY PROGRAMMES (VIPP

    Directory of Open Access Journals (Sweden)

    Vinay Babu Koganti

    2017-06-01

    Full Text Available BACKGROUND Postgraduation in Community Medicine finds few takers and those who do take it up as a career option have many concerns regarding the course. To understand the issues involved, a qualitative method called VIPP was used, which is a people centered approach to identify issues from the perspectives of those involved. This study is set to identify the problems faced by postgraduate students in Community Medicine regarding their course of study. MATERIALS AND METHODS This study was conducted during a regional postgraduate CME of the NTR University of Health Sciences, Andhra Pradesh. Postgraduates and junior faculty from 5 medical colleges in the region were involved in the exercise after taking their informed consent. Visualisation in Participatory Programmes (VIPP, a qualitative method was used as a means of obtaining information followed by a discussion with visual display of all the mentioned items. RESULTS The themes that emerged are problems faced due to the student’s felt inadequacies, faculty shortcomings, issues regarding the department/college management and lacunae in the course structure and implementation. CONCLUSION In VIPP, sensitive issues are visually displayed for all to see and contemplate. Many of the student’s issues were actually brought on by poor curriculum planning and implementation. This was also undermining students’ self-esteem and causing anxiety about future career prospects.

  20. When in London, It's a Burger and Neapolitan Ice Cream for You: Rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory"

    Science.gov (United States)

    Kenworthy, Amy L.; Hrivnak, George A.

    2016-01-01

    In this rejoinder, Kenworthy and Hrivnak, recognized as thought leaders in the tertiary education domain, report their greatest concern with Arbaugh et al.'s (2016) work is its inherently narrow and restrictive nature. In their rejoinder they report, first, the search terms use to identify the BME top 100 are confined to business education.…

  1. Competitive Enzyme-Linked Immunosorbent Assay Based on a Rhoptry-Associated Protein 1 Epitope Specifically Identifies Babesia bovis-Infected Cattle

    Science.gov (United States)

    Goff, Will L.; McElwain, Terry F.; Suarez, Carlos E.; Johnson, Wendell C.; Brown, Wendy C.; Norimine, Junzo; Knowles, Donald P.

    2003-01-01

    The competitive enzyme-linked immunosorbent assay (cELISA) format has proven to be an accurate, reliable, easily standardized, and high-throughput method for detecting hemoparasite infections. In the present study, a species-specific, broadly conserved, and tandemly repeated B-cell epitope within the C terminus of the rhoptry-associated protein 1 of the hemoparasite Babesia bovis was cloned and expressed as a histidine-tagged thioredoxin fusion peptide and used as antigen in a cELISA. The assay was optimized with defined negative and positive bovine sera, where positive sera inhibited the binding of the epitope-specific monoclonal antibody BABB75A4. The cELISA accurately differentiated animals with B. bovis-specific antibodies from uninfected animals and from animals with antibodies against other tick-borne hemoparasites (98.7% specificity). In addition, B. bovis-specific sera from Australia, Argentina, Bolivia, Puerto Rico, and Morocco inhibited the binding of BABB75A4, confirming conservation of the epitope. The assay first detected experimentally infected animals between 13 and 17 days postinfection, and with sera from naturally infected carrier cattle, was comparable to indirect immunofluorescence (98.3% concordance). The assay appears to have the characteristics necessary for an epidemiologic and disease surveillance tool. PMID:12522037

  2. Research

    African Journals Online (AJOL)

    abp

    2017-01-24

    Jan 24, 2017 ... and the specific rotavirus VP4 (P-types) and VP7 (G-types) determined. Results: The .... Centre for Virus Research (CVR) of the Kenya Medical Research. Institute (KEMRI) ... rotavirus dsRNA was run on 10% polyacrylamide resolving gels using a large format .... What is known about this topic. •. Rotavirus is ...

  3. Applying Machine Learning to Workers' Compensation Data to Identify Industry-Specific Ergonomic and Safety Prevention Priorities: Ohio, 2001 to 2011.

    Science.gov (United States)

    Meyers, Alysha R; Al-Tarawneh, Ibraheem S; Wurzelbacher, Steven J; Bushnell, P Timothy; Lampl, Michael P; Bell, Jennifer L; Bertke, Stephen J; Robins, David C; Tseng, Chih-Yu; Wei, Chia; Raudabaugh, Jill A; Schnorr, Teresa M

    2018-01-01

    This study leveraged a state workers' compensation claims database and machine learning techniques to target prevention efforts by injury causation and industry. Injury causation auto-coding methods were developed to code more than 1.2 million Ohio Bureau of Workers' Compensation claims for this study. Industry groups were ranked for soft-tissue musculoskeletal claims that may have been preventable with biomechanical ergonomic (ERGO) or slip/trip/fall (STF) interventions. On the basis of the average of claim count and rate ranks for more than 200 industry groups, Skilled Nursing Facilities (ERGO) and General Freight Trucking (STF) were the highest risk for lost-time claims (>7 days). This study created a third, major causation-specific U.S. occupational injury surveillance system. These findings are being used to focus prevention resources on specific occupational injury types in specific industry groups, especially in Ohio. Other state bureaus or insurers may use similar methods.

  4. Community-Engaged Research to Identify House Parent Perspectives on Support and Risk within the House and Ball Scene

    Science.gov (United States)

    Kubicek, Katrina; Beyer, William H.; McNeeley, Miles; Weiss, George; Omni, Legendary Father Taz Ultra; Kipke, Michele D.

    2012-01-01

    This paper describes a community-engaged study with the Los Angeles House and Ball scene, in which the perspectives of the leaders of these communities are captured to better understand how the House and Ball communities may protect and/or increase its members’ risks for HIV infection. Data were collected through in-depth interviews with House parents (N=26). This study identified key features of both support (e.g., family and support; acceptance; validation and recognition) and risk (e.g., members’ struggle to maintain status in the Ballroom scene; sex work; substance use; danger of becoming too involved in the Ball community; perception and stigma of Ballroom scene within the larger gay community) within these communities. Findings are discussed in relation to framing how to leverage the supportive aspects of the House and Ball communities to design relevant HIV prevention interventions. PMID:22206442

  5. Towards Python-based Domain-specific Languages for Self-reconfigurable Modular Robotics Research

    DEFF Research Database (Denmark)

    Moghadam, Mikael; Johan Christensen, David; Brandt, David

    2013-01-01

    This paper explores the role of operating system and high-level languages in the development of software and domain-specific languages (DSLs) for self-reconfigurable robotics. We review some of the current trends in self-reconfigurable robotics and describe the development of a software system...... for ATRON II which utilizes Linux and Python to significantly improve software abstraction and portability while providing some basic features which could prove useful when using Python, either stand-alone or via a DSL, on a self-reconfigurable robot system. These features include transparent socket...... communication, module identification, easy software transfer and reliable module-to-module communication. The end result is a software platform for modular robots that where appropriate builds on existing work in operating systems, virtual machines, middleware and high-level languages....

  6. Research of coincidence method for calculation model of the specific detector

    Energy Technology Data Exchange (ETDEWEB)

    Guangchun, Hu; Suping, Liu; Jian, Gong [China Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

    2003-07-01

    The physical size of specific detector is known normally, but production business is classified for some sizes that is concerned with the property of detector, such as the well diameter, well depth of detector and dead region. The surface source of even distribution and the sampling method of source particle isotropy sport have been established with the method of Monte Carlo, and gamma ray respond spectral with the {sup 152}Eu surface source been calculated. The experiment have been performed under the same conditions. Calculation and experiment results are compared with relative efficiency coincidence method and spectral similar degree coincidence method. According to comparison as a result, detector model is revised repeatedly to determine the calculation model of detector and to calculate efficiency of detector and spectra. (authors)

  7. Novel Monoclonal Antibodies Recognizing Human Prostate-Specific Membrane Antigen (PSMA) as Research and Theranostic Tools.

    Science.gov (United States)

    Nováková, Zora; Foss, Catherine A; Copeland, Benjamin T; Morath, Volker; Baranová, Petra; Havlínová, Barbora; Skerra, Arne; Pomper, Martin G; Barinka, Cyril

    2017-05-01

    Prostate-specific membrane antigen (PSMA) is a validated target for the imaging and therapy of prostate cancer. Here, we report the detailed characterization of four novel murine monoclonal antibodies (mAbs) recognizing human PSMA as well as PSMA orthologs from different species. Performance of purified mAbs was assayed using a comprehensive panel of in vitro experimental setups including Western blotting, immunofluorescence, immunohistochemistry, ELISA, flow cytometry, and surface-plasmon resonance. Furthermore, a mouse xenograft model of prostate cancer was used to compare the suitability of the mAbs for in vivo applications. All mAbs demonstrate high specificity for PSMA as documented by the lack of cross-reactivity to unrelated human proteins. The 3F11 and 1A11 mAbs bind linear epitopes spanning residues 226-243 and 271-288 of human PSMA, respectively. 3F11 is also suitable for the detection of PSMA orthologs from mouse, pig, dog, and rat in experimental setups where the denatured form of PSMA is used. 5D3 and 5B1 mAbs recognize distinct surface-exposed conformational epitopes and are useful for targeting PSMA in its native conformation. Most importantly, using a mouse xenograft model of prostate cancer we show that both the intact 5D3 and its Fab fragment are suitable for in vivo imaging. With apparent affinities of 0.14 and 1.2 nM as determined by ELISA and flow cytometry, respectively, 5D3 has approximately 10-fold higher affinity for PSMA than the clinically validated mAb J591 and, therefore, is a prime candidate for the development of next-generation theranostics to target PSMA. Prostate 77:749-764, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  8. Seeing and Being Seen as a Management Learning and Education Scholar: Rejoinder to "Identifying Research Topic Development in Business and Management Education Research Using Legitimation Code Theory"

    Science.gov (United States)

    Bridgman, Todd; Bell, Emma

    2016-01-01

    In this rejoinder to Arbaugh et al. (2016), the authors write that they want to reflect critically on two assumptions Arbaugh et al. make about what constitutes successful academic fields. They suggest: (1) such fields have taken-for-granted knowledge that forms the foundation that future research can build on; and (2) they have a high degree of…

  9. Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease

    DEFF Research Database (Denmark)

    Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J

    2017-01-01

    Most genome-wide association studies have been of European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we used a...

  10. Dlx1 and Rgs5 in the ductus arteriosus: vessel-specific genes identified by transcriptional profiling of laser-capture microdissected endothelial and smooth muscle cells

    NARCIS (Netherlands)

    Bokenkamp, R.; Brempt, R. van; Munsteren, J.C. van; Wijngaert, I. van den; Hoogt, R. de; Finos, L.; Goeman, J.J.; Groot, A.C de; Poelmann, R.E.; Blom, N.A.; DeRuiter, M.C.

    2014-01-01

    Closure of the ductus arteriosus (DA) is a crucial step in the transition from fetal to postnatal life. Patent DA is one of the most common cardiovascular anomalies in children with significant clinical consequences especially in premature infants. We aimed to identify genes that specify the DA in

  11. Lost and misplaced items and assistive devices in nursing homes: Identifying problems and technological opportunities through participatory design research.

    Science.gov (United States)

    Oude Weernink, C E; Sweegers, L; Relou, L; van der Zijpp, T J; van Hoof, J

    2018-02-06

    Modern healthcare, including nursing home care, goes together with the use of technologies to support treatment, the provision of care and daily activities. The challenges concerning the implementation of such technologies are numerous. One of these emerging technologies are location technologies (RTLS or Real-Time Location Systems). that can be utilized in the nursing home for monitoring the use and location of assets. This paper describes a participatory design study of RTLS based on context mapping, conducted in two nursing home organizations. Rather than investigating the technological possibilities, this study investigates the needs and wishes from the perspective of the care professional. The study identified semantic themes that relate to the practicalities of lost and misplaced items in the nursing home, as well as latent themes that cover the wishes regarding technology in the nursing homes. The organizational culture and building typology may play a role in losing items. The participants in this study indicated that RTLS can provide a solution to some of the challenges that they encounter in the workplace. However, the implementation of new technologies should be done with care and should be integrated into existing ICT systems in order to minimize additional training and posing a burden on the workload.

  12. Etiology of Organ-Specific Autoimmunity: Basic Research and Clinical Implications in IBD

    Directory of Open Access Journals (Sweden)

    George S Eisenbarth

    1996-01-01

    Full Text Available Autoimmunity develops in the setting of genetic susceptibility and can be monogenic (eg, autoimmune polyendocrine syndrome type I with Addison’s disease, mucocutaneous candidiasis and hypoparathyroidism, which is autosomal recessive with the causative gene on the tip of chromosome 21 or polygenic (usually with important alleles within the major histocompatibility complex [eg, type I diabetes]. In addition to genetic susceptibility, many autoimmune disorders can be classified into etiological categories (oncogenic, drug-induced, diet-induced, infectious or idiopathic. For most autoimmune disorders there are multiple target autoantigens and, for type I diabetes, a combinatorial approach (eg, expression of at least two autoantibodies of insulin, glutamic acid decarboxylase and/or ICA512/IA-2 is the best predictor of diabetes risk. Finally, antigen-specific therapies hold promise for the prevention and therapy of autoimmunity, eg, parenteral or oral therapy with insulin delays or prevents type I diabetes in animal models, and a small pilot trial of parenteral insulin in humans suggests that such therapy may similarly prevent diabetes in humans.

  13. HTTR hydrogen production system. Structure and main specifications of mock-up test facility (Contract research)

    International Nuclear Information System (INIS)

    Kato, Michio; Aita, Hideki; Inagaki, Yoshiyuki; Hayashi, Koji; Ohashi, Hirofumi; Sato, Hiroyuki; Iwatsuki, Jin; Takada, Shoji; Inaba, Yoshitomo

    2007-03-01

    The mock-up test facility was fabricated to investigate performance of the steam generator for mitigation of the temperature fluctuation of helium gas and transient behavior of the hydrogen production system for HTTR and to obtain experimental data for verification of a dynamic analysis code. The test facility has an approximate hydrogen production capacity of 120Nm 3 /h and the steam reforming process of methane; CH 4 +H 2 O=3H 2 +CO, was used for hydrogen production of the test facility. An electric heater was used as a heat source instead of the reactor in order to heat helium gas up to 880degC (4MPa) at the chemical reactor inlet which is the same temperature as the HTTR hydrogen production system. Fabrication of the test facility was completed in February in 2002, and seven cycle operations were carried out from March in 2002 to December in 2004. This report describes the structure and main specifications of the test facility. (author)

  14. Study designs for identifying risk compensation behavior among users of biomedical HIV prevention technologies: balancing methodological rigor and research ethics.

    Science.gov (United States)

    Underhill, Kristen

    2013-10-01

    The growing evidence base for biomedical HIV prevention interventions - such as oral pre-exposure prophylaxis, microbicides, male circumcision, treatment as prevention, and eventually prevention vaccines - has given rise to concerns about the ways in which users of these biomedical products may adjust their HIV risk behaviors based on the perception that they are prevented from infection. Known as risk compensation, this behavioral adjustment draws on the theory of "risk homeostasis," which has previously been applied to phenomena as diverse as Lyme disease vaccination, insurance mandates, and automobile safety. Little rigorous evidence exists to answer risk compensation concerns in the biomedical HIV prevention literature, in part because the field has not systematically evaluated the study designs available for testing these behaviors. The goals of this Commentary are to explain the origins of risk compensation behavior in risk homeostasis theory, to reframe risk compensation as a testable response to the perception of reduced risk, and to assess the methodological rigor and ethical justification of study designs aiming to isolate risk compensation responses. Although the most rigorous methodological designs for assessing risk compensation behavior may be unavailable due to ethical flaws, several strategies can help investigators identify potential risk compensation behavior during Phase II, Phase III, and Phase IV testing of new technologies. Where concerns arise regarding risk compensation behavior, empirical evidence about the incidence, types, and extent of these behavioral changes can illuminate opportunities to better support the users of new HIV prevention strategies. This Commentary concludes by suggesting a new way to conceptualize risk compensation behavior in the HIV prevention context. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Validity of the Male Depression Risk Scale in a representative Canadian sample: sensitivity and specificity in identifying men with recent suicide attempt.

    Science.gov (United States)

    Rice, Simon M; Ogrodniczuk, John S; Kealy, David; Seidler, Zac E; Dhillon, Haryana M; Oliffe, John L

    2017-12-22

    Clinical practice and literature has supported the existence of a phenotypic sub-type of depression in men. While a number of self-report rating scales have been developed in order to empirically test the male depression construct, psychometric validation of these scales is limited. To confirm the psychometric properties of the multidimensional Male Depression Risk Scale (MDRS-22) and to develop clinical cut-off scores for the MDRS-22. Data were obtained from an online sample of 1000 Canadian men (median age (M) = 49.63, standard deviation (SD) = 14.60). Confirmatory factor analysis (CFA) was used to replicate the established six-factor model of the MDRS-22. Psychometric values of the MDRS subscales were comparable to the widely used Patient Health Questionnaire-9. CFA model fit indices indicated adequate model fit for the six-factor MDRS-22 model. ROC curve analysis indicated the MDRS-22 was effective for identifying those with a recent (previous four-weeks) suicide attempt (area under curve (AUC) values = 0.837). The MDRS-22 cut-off identified proportionally more (84.62%) cases of recent suicide attempt relative to the PHQ-9 moderate range (53.85%). The MDRS-22 is the first male-sensitive depression scale to be psychometrically validated using CFA techniques in independent and cross-nation samples. Additional studies should identify differential item functioning and evaluate cross-cultural effects.

  16. Tackling the Reproducibility Problem in Systems Research with Declarative Experiment Specifications

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, Ivo [Univ. of California, Santa Cruz, CA (United States); Maltzahn, Carlos [Univ. of California, Santa Cruz, CA (United States); Lofstead, Jay [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Moody, Adam [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Arpaci-Dusseau, Remzi [Univ. of Wisconsin, Madison, WI (United States); Arpaci-Dusseau, Andrea [Univ. of Wisconsin, Madison, WI (United States)

    2015-05-04

    Validating experimental results in the field of computer systems is a challenging task, mainly due to the many changes in software and hardware that computational environments go through. Determining if an experiment is reproducible entails two separate tasks: re-executing the experiment and validating the results. Existing reproducibility efforts have focused on the former, envisioning techniques and infrastructures that make it easier to re-execute an experiment. In this work we focus on the latter by analyzing the validation workflow that an experiment re-executioner goes through. We notice that validating results is done on the basis of experiment design and high-level goals, rather than exact quantitative metrics. Based on this insight, we introduce a declarative format for specifying the high-level components of an experiment as well as describing generic, testable conditions that serve as the basis for validation. We present a use case in the area of storage systems to illustrate the usefulness of this approach. We also discuss limitations and potential benefits of using this approach in other areas of experimental systems research.

  17. Alternatives to project-specific consent for access to personal information for health research: Insights from a public dialogue

    Directory of Open Access Journals (Sweden)

    Abelson Julia

    2008-11-01

    Full Text Available Abstract Background The role of consent for research use of health information is contentious. Most discussion has focused on when project-specific consent may be waived but, recently, a broader range of consent options has been entertained, including broad opt-in for multiple studies with restrictions and notification with opt-out. We sought to elicit public values in this matter and to work toward an agreement about a common approach to consent for use of personal information for health research through deliberative public dialogues. Methods We conducted seven day-long public dialogues, involving 98 participants across Canada. Immediately before and after each dialogue, participants completed a fixed-response questionnaire rating individuals' support for 3 approaches to consent in the abstract and their consent choices for 5 health research scenarios using personal information. They also rated how confident different safeguards made them feel that their information was being used responsibly. Results Broad opt-in consent for use of personal information garnered the greatest support in the abstract. When presented with specific research scenarios, no one approach to consent predominated. When profit was introduced into the scenarios, consent choices shifted toward greater control over use. Despite lively and constructive dialogues, and considerable shifting in opinion at the individual level, at the end of the day, there was no substantive aggregate movement in opinion. Personal controls were among the most commonly cited approaches to improving people's confidence in the responsible use of their information for research. Conclusion Because no one approach to consent satisfied even a simple majority of dialogue participants and the importance placed on personal controls, a mechanism should be developed for documenting consent choice for different types of research, including ways for individuals to check who has accessed their medical record

  18. Alternatives to project-specific consent for access to personal information for health research: insights from a public dialogue.

    Science.gov (United States)

    Willison, Donald J; Swinton, Marilyn; Schwartz, Lisa; Abelson, Julia; Charles, Cathy; Northrup, David; Cheng, Ji; Thabane, Lehana

    2008-11-19

    The role of consent for research use of health information is contentious. Most discussion has focused on when project-specific consent may be waived but, recently, a broader range of consent options has been entertained, including broad opt-in for multiple studies with restrictions and notification with opt-out. We sought to elicit public values in this matter and to work toward an agreement about a common approach to consent for use of personal information for health research through deliberative public dialogues. We conducted seven day-long public dialogues, involving 98 participants across Canada. Immediately before and after each dialogue, participants completed a fixed-response questionnaire rating individuals' support for 3 approaches to consent in the abstract and their consent choices for 5 health research scenarios using personal information. They also rated how confident different safeguards made them feel that their information was being used responsibly. Broad opt-in consent for use of personal information garnered the greatest support in the abstract. When presented with specific research scenarios, no one approach to consent predominated. When profit was introduced into the scenarios, consent choices shifted toward greater control over use. Despite lively and constructive dialogues, and considerable shifting in opinion at the individual level, at the end of the day, there was no substantive aggregate movement in opinion. Personal controls were among the most commonly cited approaches to improving people's confidence in the responsible use of their information for research. Because no one approach to consent satisfied even a simple majority of dialogue participants and the importance placed on personal controls, a mechanism should be developed for documenting consent choice for different types of research, including ways for individuals to check who has accessed their medical record for purposes other than clinical care. This could be done, for

  19. Meeting Expanding Needs to Collect Food Intake Specificity: The Nutrition Data System for Research (NDS-R)

    Science.gov (United States)

    VanHeel, Nancy; Pettit, Janet; Rice, Barbara; Smith, Scott M.

    2003-01-01

    Food and nutrient databases are populated with data obtained from a variety of sources including USDA Reference Tables, scientific journals, food manufacturers and foreign food tables. The food and nutrient database maintained by the Nutrition Coordinating Center (NCC) at the University of Minnesota is continually updated with current nutrient data and continues to be expanded with additional nutrient fields to meet diverse research endeavors. Data are strictly evaluated for reliability and relevance before incorporation into the database; however, the values are obtained from various sources and food samples rather than from direct chemical analysis of specific foods. Precise nutrient values for specific foods are essential to the nutrition program at the National Aeronautics and Space Administration (NASA). Specific foods to be included in the menus of astronauts are chemically analyzed at the Johnson Space Center for selected nutrients. A request from NASA for a method to enter the chemically analyzed nutrient values for these space flight food items into the Nutrition Data System for Research (NDS-R) software resulted in modification of the database and interview system for use by NASA, with further modification to extend the method for related uses by more typical research studies.

  20. Early sex differences are not autism-specific: A Baby Siblings Research Consortium (BSRC) study.

    Science.gov (United States)

    Messinger, Daniel S; Young, Gregory S; Webb, Sara Jane; Ozonoff, Sally; Bryson, Susan E; Carter, Alice; Carver, Leslie; Charman, Tony; Chawarska, Katarzyna; Curtin, Suzanne; Dobkins, Karen; Hertz-Picciotto, Irva; Hutman, Ted; Iverson, Jana M; Landa, Rebecca; Nelson, Charles A; Stone, Wendy L; Tager-Flusberg, Helen; Zwaigenbaum, Lonnie

    2015-01-01

    high-risk children with ASD, but also in high-risk children without ASD and in low-risk children. Sex differences in young children with ASD do not appear to be ASD-specific but instead reflect typically occurring sex differences seen in children without ASD. Results did not support a female protective effect hypothesis.

  1. Results of a Research Study to Identify Historical RDTE (Research, Development, Test and Evaluation) Obligations and Expenditures on Major Army Materiel and Non-Materiel Systems,

    Science.gov (United States)

    1983-10-01

    CHAPARRAL ROLAND HAWK NIKE HERCULES PATRIOT HELLFIRE ELECTRONICS PEWS MILES IRETS ARTBASS TACFIRE i RADAR CHRONOGRAPH, M90 BCS GLLD FIREFINDER AN/TMQ...6ll02Hr 5200 RESEARCH IN SFT OF EOUIP FOR THE IND SOLDIER L1.. 61,102RH37n R E RCH IN SC:IEN PROBl.. 16 1) WITH ,IL APPL 11-161 ,6 02AH6000 RESEAF.,-., IN...MAXILLOFACIAL INJURY 62777 SYSTEMS HEALTH HAZARD PREVENT TECH 62781 ENERGY TECH APPL . FOR MILITARY FACIL 63102 MATERIALS + STRUCTURE ADVANCED DEV 63104

  2. Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI

    DEFF Research Database (Denmark)

    Wang, Weijing; Jiang, Wenjie; Hou, Lin

    2017-01-01

    BACKGROUND: The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis......) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database...

  3. Safety Assessment for Research Reactors and Preparation of the Safety Analysis Report. Specific Safety Guide

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-11-15

    . The standards are also applied by regulatory bodies and operators around the world to enhance safety in nuclear power generation and in nuclear applications in medicine, industry, agriculture and research. Safety is not an end in itself but a prerequisite for the purpose of the protection of people in all States and of the environment - now and in the future. The risks associated with ionizing radiation must be assessed and controlled without unduly limiting the contribution of nuclear energy to equitable and sustainable development. Governments, regulatory bodies and operators everywhere must ensure that nuclear material and radiation sources are used beneficially, safely and ethically. The IAEA safety standards are designed to facilitate this, and I encourage all Member States to make use of them.

  4. Safety Assessment for Research Reactors and Preparation of the Safety Analysis Report. Specific Safety Guide

    International Nuclear Information System (INIS)

    2011-01-01

    . The standards are also applied by regulatory bodies and operators around the world to enhance safety in nuclear power generation and in nuclear applications in medicine, industry, agriculture and research. Safety is not an end in itself but a prerequisite for the purpose of the protection of people in all States and of the environment - now and in the future. The risks associated with ionizing radiation must be assessed and controlled without unduly limiting the contribution of nuclear energy to equitable and sustainable development. Governments, regulatory bodies and operators everywhere must ensure that nuclear material and radiation sources are used beneficially, safely and ethically. The IAEA safety standards are designed to facilitate this, and I encourage all Member States to make use of them.

  5. Introduction to four reviews addressing critical topics identified by the 2015 Nurse Practitioner Research Agenda Roundtable: Priorities for policy, workforce, education, and practice.

    Science.gov (United States)

    Buchholz, Susan W; Klein, Tracy; Cooke, Cindy; Cook, Michelle L; Knestrick, Joyce; Dickins, Kirsten

    2018-05-04

    In 2015, an invitational think tank was convened by the Fellows of the American Association of Nurse Practitioners to update the 2010 Nurse Practitioner (NP) Research Agenda Roundtable. This effort was undertaken to provide guidance for future health care research. The purpose of this article is to introduce the process used for conducting four reviews that address critical topics related to specific research priorities emanating from the 2015 NP Research Agenda Roundtable. The four reviews are published in this issue of Journal of the American Association of Nurse Practitioners (JAANP) to address the state of current research relevant to NP policy, workforce, education, and practice. This introductory article provides an overview of the systematic process used to evaluate the four topical area. The type of review selected, the search strategy, critical appraisal, data extraction, and data synthesis will be further described in the four review articles. Four reviews that examine literature regarding specific aims important to NPs will address strengths as well as gaps in the literature. The knowledge offered by the four reviews has the potential to inform future research, which will benefit NPs and other health care stakeholders.

  6. Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

    Science.gov (United States)

    Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

    2000-01-01

    A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

  7. Anti-citrullinated heat shock protein 90 antibodies identified in bronchoalveolar lavage fluid are a marker of lung-specific immune responses.

    Science.gov (United States)

    Harlow, Lisa; Gochuico, Bernadette R; Rosas, Ivan O; Doyle, Tracy J; Osorio, Juan C; Travers, Timothy S; Camacho, Carlos C; Oddis, Chester V; Ascherman, Dana P

    2014-11-01

    Previous work has demonstrated a correlation between serum anti-citrullinated HSP90 antibodies and rheumatoid arthritis-associated interstitial lung disease (RA-ILD). To further investigate this potential pathogenic relationship, we used ELISA-based techniques to assess anti-citrullinated HSP90 antibody profiles in bronchoalveolar lavage fluid (BALF) of patients with different stages of RA-ILD. 9/21 RA-derived BALF specimens demonstrated IgG and/or IgA antibodies targeting citrullinated HSP90 proteins/peptides, highlighting disease specific responses (with a predilection for RA-ILD) that did not occur in IPF patients (0/5) or healthy control subjects (0/5). Comparison of antibody profiles between BALF and matching serum specimens revealed various recognition patterns favoring predominant production of anti-citrullinated HSP90 antibodies within the lung microenvironment-further supporting the connection between this antibody specificity and parenchymal lung disease. Equally important, qualitative as well as quantitative differences in anti-citrullinated HSP90 profiles between BALF and serum indicate that the lung plays a direct role in shaping the immune repertoire of RA/RA-ILD. Published by Elsevier Inc.

  8. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

    Science.gov (United States)

    Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

    2009-01-01

    Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

  9. Genomic, Epigenomic, and Transcriptomic Profiling towards Identifying Omics Features and Specific Biomarkers That Distinguish Uterine Leiomyosarcoma and Leiomyoma at Molecular Levels

    Directory of Open Access Journals (Sweden)

    Tomoko Miyata

    2015-01-01

    Full Text Available Uterine leiomyosarcoma (LMS is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM, a benign tumor of myometrial origin, is the most common among women of childbearing age. Because of their similar symptoms, it is difficult to preoperatively distinguish the two conditions only by ultrasound and pelvic MRI. While histopathological diagnosis is currently the main approach used to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Therefore, development of molecular diagnosis as an alternative or confirmatory means will help to diagnose LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM and revealed that copy number, gene expression, and DNA methylation profiles successfully distinguished these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle-related genes, hypomethylation spreading through large genomic regions, and frequent hypermethylation at the polycomb group target genes and protocadherin genes. We also identified candidate expression and DNA methylation markers, which will facilitate establishing postoperative molecular diagnostic tests based on conventional quantitative assays. Our results demonstrate the feasibility of establishing such tests and the possibility of developing preoperative and noninvasive methods.

  10. On area-specific underground research laboratory for geological disposal of high-level radioactive waste in China

    Directory of Open Access Journals (Sweden)

    Ju Wang

    2014-04-01

    Full Text Available Underground research laboratories (URLs, including “generic URLs” and “site-specific URLs”, are underground facilities in which characterisation, testing, technology development, and/or demonstration activities are carried out in support of the development of geological repositories for high-level radioactive waste (HLW disposal. In addition to the generic URL and site-specific URL, a concept of “area-specific URL”, or the third type of URL, is proposed in this paper. It is referred to as the facility that is built at a site within an area that is considered as a potential area for HLW repository or built at a place near the future repository site, and may be regarded as a precursor to the development of a repository at the site. It acts as a “generic URL”, but also acts as a “site-specific URL” to some extent. Considering the current situation in China, the most suitable option is to build an “area-specific URL” in Beishan area, the first priority region for China's high-level waste repository. With this strategy, the goal to build China's URL by 2020 may be achieved, but the time left is limited.

  11. Lung cancer risk and cancer-specific mortality in subjects undergoing routine imaging test when stratified with and without identified lung nodule on imaging study

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Saez, Noemi [Miguel Hernandez University, Public Health, History of Science and Ginecology Department, Alicante (Spain); Hernandez-Aguado, Ildefonso; Pastor Valero, Maria; Parker, Lucy Anne; Lumbreras, Blanca [Miguel Hernandez University, Public Health, History of Science and Ginecology Department, Alicante (Spain); CIBER en Epidemiologia y Salud Publica, Madrid (Spain); Vilar, Jose; Domingo, Maria Luisa [Peset Hospital, Radiodiagnostic Department, Valencia (Spain); Gonzalez-Alvarez, Isabel; Lorente, Maria Fermina [San Juan Hospital, Radiodiagnostic Department, San Juan de Alicante (Spain)

    2015-12-15

    To assess the risk of lung cancer and specific mortality rate in patients with and without solitary pulmonary nodules (SPN) on chest radiograph and CT. This prospective study included 16,078 patients ≥35 years old (893 of them had an SPN detected with either chest radiograph or CT) and 15,185 without SPN. Patients were followed up for 18 months or until being diagnosed with lung cancer. Risk and mortality lung cancer were calculated in both groups with Poisson regression. In patients with SPN, incidence of lung cancer was 8.3 % (95 % CI 6.0-11.2) on radiograph and 12.4 % (95 % CI 9.3-15.9) on CT. A chronic obstructive pulmonary disease in patients with radiographs (odds ratio 2.62; 95 % CI 1.03, 6.67) and smoking habit (odds ratio 20.63; 95 % CI 3.84, 110.77) in patients with CT were associated with a higher probability of lung cancer. Large nodule size and spiculated edge were associated with lung cancer on both CT and radiograph. Lung cancer-specific mortality was lower in patients with SPN than in those without SPN (1.73/1000 person-years, 95 % CI 1.08-2.88 vs. 2.15/1000 person-years, 95 % CI 1.25-3.96). The risk of lung cancer for patients with SPN is higher in clinical populations than in screening studies. Moreover, patients with SPN showed lower mortality than those without SPN. (orig.)

  12. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    Directory of Open Access Journals (Sweden)

    O'Gara Fergal

    2010-11-01

    Full Text Available Abstract Background Catabolite repression control (CRC is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas

  13. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    Science.gov (United States)

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  14. Lung cancer risk and cancer-specific mortality in subjects undergoing routine imaging test when stratified with and without identified lung nodule on imaging study

    International Nuclear Information System (INIS)

    Gomez-Saez, Noemi; Hernandez-Aguado, Ildefonso; Pastor Valero, Maria; Parker, Lucy Anne; Lumbreras, Blanca; Vilar, Jose; Domingo, Maria Luisa; Gonzalez-Alvarez, Isabel; Lorente, Maria Fermina

    2015-01-01

    To assess the risk of lung cancer and specific mortality rate in patients with and without solitary pulmonary nodules (SPN) on chest radiograph and CT. This prospective study included 16,078 patients ≥35 years old (893 of them had an SPN detected with either chest radiograph or CT) and 15,185 without SPN. Patients were followed up for 18 months or until being diagnosed with lung cancer. Risk and mortality lung cancer were calculated in both groups with Poisson regression. In patients with SPN, incidence of lung cancer was 8.3 % (95 % CI 6.0-11.2) on radiograph and 12.4 % (95 % CI 9.3-15.9) on CT. A chronic obstructive pulmonary disease in patients with radiographs (odds ratio 2.62; 95 % CI 1.03, 6.67) and smoking habit (odds ratio 20.63; 95 % CI 3.84, 110.77) in patients with CT were associated with a higher probability of lung cancer. Large nodule size and spiculated edge were associated with lung cancer on both CT and radiograph. Lung cancer-specific mortality was lower in patients with SPN than in those without SPN (1.73/1000 person-years, 95 % CI 1.08-2.88 vs. 2.15/1000 person-years, 95 % CI 1.25-3.96). The risk of lung cancer for patients with SPN is higher in clinical populations than in screening studies. Moreover, patients with SPN showed lower mortality than those without SPN. (orig.)

  15. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  16. Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

    Science.gov (United States)

    Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

    2015-01-01

    Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.

  17. World Workshop on Oral Medicine VI: Utilization of Oral Medicine-specific software for support of clinical care, research, and education: current status and strategy for broader implementation.

    Science.gov (United States)

    Brailo, Vlaho; Firriolo, Francis John; Tanaka, Takako Imai; Varoni, Elena; Sykes, Rosemary; McCullough, Michael; Hua, Hong; Sklavounou, Alexandra; Jensen, Siri Beier; Lockhart, Peter B; Mattsson, Ulf; Jontell, Mats

    2015-08-01

    To assess the current scope and status of Oral Medicine-specific software (OMSS) utilized to support clinical care, research, and education in Oral Medicine and to propose a strategy for broader implementation of OMSS within the global Oral Medicine community. An invitation letter explaining the objectives was sent to the global Oral Medicine community. Respondents were interviewed to obtain information about different aspects of OMSS functionality. Ten OMSS tools were identified. Four were being used for clinical care, one was being used for research, two were being used for education, and three were multipurpose. Clinical software was being utilized as databases developed to integrate of different type of clinical information. Research software was designed to facilitate multicenter research. Educational software represented interactive, case-orientated technology designed for clinical training in Oral Medicine. Easy access to patient data was the most commonly reported advantage. Difficulty of use and poor integration with other software was the most commonly reported disadvantage. The OMSS presented in this paper demonstrate how information technology (IT) can have an impact on the quality of patient care, research, and education in the field of Oral Medicine. A strategy for broader implementation of OMSS is proposed. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Reactions to Participating in Intimate Partner Violence and Minority Stress Research: A Mixed Methodological Study of Self-Identified Lesbian and Gay Emerging Adults.

    Science.gov (United States)

    Edwards, Katie M; Sylaska, Kateryna M

    2016-01-01

    The purpose of this study was to examine lesbian and gay (LG) young adults' reactions to participating in intimate partner violence (IPV) and minority stress research using a mixed methodological design. Participants were 277 U.S. college students currently involved in same-sex relationships and self-identified cisgender LG who completed an online questionnaire that included closed- and open-ended questions. Results suggested that IPV research was well tolerated by the vast majority of participants; close to one in 10 participants reported being upset by the study questions, yet 75% of upset individuals reported some level of personal benefit. Reasons for upset as identified in the open-ended responses included thinking about personal experiences with IPV, as the perpetrator or friend of a victim, as well as thinking about the uncertainty of their future with their current partner. The correlates of emotional reactions and personal benefits to research participation were also examined, and these varied among gay men and lesbian women. Implications of these findings underscore the importance of accurate reflection of risk and benefits in informed consent documents as well as systematic evaluation of sexual minority participants' reactions to research participation in an effort to conduct ethically sound sexual science research.

  19. Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs

    Directory of Open Access Journals (Sweden)

    Chan Zhou

    2017-08-01

    Full Text Available N6-methyladenosine (m6A is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m6A modifications to circular (circ RNAs. We developed a computational pipeline (AutoCirc that, together with depletion of ribosomal RNA and m6A immunoprecipitation, defined thousands of m6A circRNAs with cell-type-specific expression. The presence of m6A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m6A sites in mRNAs, and by reduced m6A levels upon depletion of METTL3, the m6A writer. Despite sharing m6A readers and writers, m6A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m6A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m6A modifications and uncover regulation of circRNAs through m6A modification.

  20. Structure-function relationship of a plant NCS1 member - Homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis

    KAUST Repository

    Witz, Sandra

    2014-03-12

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. 2014 Witz et al.

  1. The use of sterol distributions combined with compound specific isotope analyses as a tool to identify the origin of fecal contamination in rivers.

    Science.gov (United States)

    Biache, Coralie; Philp, R Paul

    2013-03-01

    The sterol distributions of 9 sediment samples from the Illinois River Basin (OK and AR, USA) were examined in order to identify the source of fecal contamination. The samples were extracted with organic solvent using sonication and the fractions containing the sterols were isolated and analyzed by gas chromatography-mass spectrometry. The sterol distributions of the Illinois River samples were dominated by phytosterols. They were compared to those of different animal feces and manures using a principal component analysis and correspondence appeared between the sediments and one group of chicken feces samples. Gas chromatography-isotope ratio mass spectrometry analyses were also performed to determine the δ(13)C values for the phytosterols and to get an indication of their origin based on the C(3)/C(4) plant signatures. The δ(13)C values obtained ranged from -30.6 ‰ to -17.4 ‰ (VPDB) corresponding to a mixed signature between C(3) and C(4) plants, indicating a C(4) plant contribution to the C(3) plant natural background. These observations indicate that a proportion of the phytosterols originated from chicken feces. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

    Directory of Open Access Journals (Sweden)

    Jacqueline Zoe-Munn Chan

    2014-10-01

    Full Text Available Two bacteriophages, RPP1 and RLP1, infecting members of the marine Roseobacter clade were isolated from seawater. Their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding DNA sequences, respectively. Around 30% of these are homologous to genes found in Enterobacter phage N4. Comparative genomics of these two new Roseobacter phages and twenty-three other sequenced N4-like phages (three infecting members of the Roseobacter lineage and twenty infecting other Gammaproteobacteria revealed that N4-like phages share a core genome of 14 genes responsible for control of gene expression, replication and virion proteins. Phylogenetic analysis of these genes placed the five N4-like roseophages (RN4 into a distinct subclade. Analysis of the RN4 phage genomes revealed they share a further 19 genes of which nine are found exclusively in RN4 phages and four appear to have been acquired from their bacterial hosts. Proteomic analysis of the RPP1 and RLP1 virions identified a second structural module present in the RN4 phages similar to that found in the Pseudomonas N4-like phage LIT1. Searches of various metagenomic databases, included the GOS database, using CDS sequences from RPP1 suggests these phages are widely distributed in marine environments in particular in the open ocean environment.

  3. The scientific legacy of Little Hans and Little Albert: future directions for research on specific phobias in youth.

    Science.gov (United States)

    Ollendick, Thomas H; Muris, Peter

    2015-01-01

    We review issues associated with the phenomenology, etiology, assessment, and treatment of specific phobias in children and adolescents and provide suggestions for future research and clinical practice. In doing so, we highlight the early case studies of Little Hans and Little Albert and the advances that have been made following the publication of these seminal cases. In recent years, we have witnessed a deeper understanding of the etiology of specific phobias and developed a rich array of evidence-based assessments and treatments with which to address specific phobias in youth. Although much has been accomplished in this area of inquiry, we also note that much remains to be done before we can advance more fully our understanding, assessment, and treatment of specific phobias in youth. It will be important for future work to build more firmly on these developments and to better determine the moderators and mediators of change with our evidence-based treatments and to more vigorously pursue their dissemination in real-word settings.

  4. Reciprocal Genetics: Identifying QTL for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups.

    Science.gov (United States)

    Giraud, Héloïse; Bauland, Cyril; Falque, Matthieu; Madur, Delphine; Combes, Valérie; Jamin, Philippe; Monteil, Cécile; Laborde, Jacques; Palaffre, Carine; Gaillard, Antoine; Blanchard, Philippe; Charcosset, Alain; Moreau, Laurence

    2017-11-01

    Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize ( Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using "testers" to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent-flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers. Copyright © 2017 by the Genetics Society of America.

  5. Post-genome wide association studies and functional analyses identify association of MPP7 gene variants with site-specific bone mineral density.

    Science.gov (United States)

    Xiao, Su-Mei; Kung, Annie Wai Chee; Gao, Yi; Lau, Kam-Shing; Ma, Alvin; Zhang, Zhen-Lin; Liu, Jian-Min; Xia, Wiebo; He, Jin-Wei; Zhao, Lin; Nie, Min; Fu, Wei-Zhen; Zhang, Min-Jia; Sun, Jing; Kwan, Johnny S H; Tso, Gloria Hoi Wan; Dai, Zhi-Jie; Cheung, Ching-Lung; Bow, Cora H; Leung, Anskar Yu Hung; Tan, Kathryn Choon Beng; Sham, Pak Chung

    2012-04-01

    Our previous genome-wide association study (GWAS) in a Hong Kong Southern Chinese population with extreme bone mineral density (BMD) scores revealed suggestive association with MPP7, which ranked second after JAG1 as a candidate gene for BMD. To follow-up this suggestive signal, we replicated the top single-nucleotide polymorphism rs4317882 of MPP7 in three additional independent Asian-descent samples (n= 2684). The association of rs4317882 reached the genome-wide significance in the meta-analysis of all available subjects (P(meta)= 4.58 × 10(-8), n= 4204). Site heterogeneity was observed, with a larger effect on spine than hip BMD. Further functional studies in a zebrafish model revealed that vertebral bone mass was lower in an mpp7 knock-down model compared with the wide-type (P= 9.64 × 10(-4), n= 21). In addition, MPP7 was found to have constitutive expression in human bone-derived cells during osteogenesis. Immunostaining of murine MC3T3-E1 cells revealed that the Mpp7 protein is localized in the plasma membrane and intracytoplasmic compartment of osteoblasts. In an assessment of the function of identified variants, an electrophoretic mobility shift assay demonstrated the binding of transcriptional factor GATA2 to the risk allele 'A' but not the 'G' allele of rs4317882. An mRNA expression study in human peripheral blood mononuclear cells confirmed that the low BMD-related allele 'A' of rs4317882 was associated with lower MPP7 expression (P= 9.07 × 10(-3), n= 135). Our data suggest a genetic and functional association of MPP7 with BMD variation.

  6. Propensity score estimation to address calendar time-specific channeling in comparative effectiveness research of second generation antipsychotics.

    Directory of Open Access Journals (Sweden)

    Stacie B Dusetzina

    Full Text Available Channeling occurs when a medication and its potential comparators are selectively prescribed based on differences in underlying patient characteristics. Drug safety advisories can provide new information regarding the relative safety or effectiveness of a drug product which might increase selective prescribing. In particular, when reported adverse effects vary among drugs within a therapeutic class, clinicians may channel patients toward or away from a drug based on the patient's underlying risk for an adverse outcome. If channeling is not identified and appropriately managed it might lead to confounding in observational comparative effectiveness studies.To demonstrate channeling among new users of second generation antipsychotics following a Food and Drug Administration safety advisory and to evaluate the impact of channeling on cardiovascular risk estimates over time.Florida Medicaid data from 2001-2006.Retrospective cohort of adults initiating second generation antipsychotics. We used propensity scores to match olanzapine initiators with other second generation antipsychotic initiators. To evaluate channeling away from olanzapine following an FDA safety advisory, we estimated calendar time-specific propensity scores. We compare the performance of these calendar time-specific propensity scores with conventionally-estimated propensity scores on estimates of cardiovascular risk.Increased channeling away from olanzapine was evident for some, but not all, cardiovascular risk factors and corresponded with the timing of the FDA advisory. Covariate balance was optimized within period and across all periods when using the calendar time-specific propensity score. Hazard ratio estimates for cardiovascular outcomes did not differ across models (Conventional PS: 0.97, 95%CI: 0.81-3.18 versus calendar time-specific PS: 0.93, 95%CI: 0.77-3.04.Changes in channeling over time was evident for several covariates but had limited impact on cardiovascular risk

  7. Synthesis and evaluation of lightweight concrete research relevant to the AASHTO LRFD bridge design specifications : potential revisions for definition and mechanical properties.

    Science.gov (United States)

    2012-11-01

    Much of the fundamental basis for the current lightweight concrete provisions in the AASHTO LRFD Bridge : Design Specifications is based on research of lightweight concrete (LWC) from the 1960s. The LWC that was : part of this research used tradition...

  8. Physical activity and exercise training in multiple sclerosis: a review and content analysis of qualitative research identifying perceived determinants and consequences.

    Science.gov (United States)

    Learmonth, Yvonne C; Motl, Robert W

    2016-01-01

    This systematic review was conducted to provide rich and deep evidence of the perceived determinants and consequences of physical activity and exercise based on qualitative research in multiple sclerosis (MS). Electronic databases and article reference lists were searched to identify qualitative studies of physical activity and exercise in MS. Studies were included if they were written in English and examined consequences/determinants of physical activity in persons with MS. Content analysis of perceived determinants and consequences of physical activity and exercise was undertaken using an inductive analysis guided by the Physical Activity for people with Disabilities framework and Social Cognitive Theory, respectively. Nineteen articles were reviewed. The most commonly identified perceived barriers of physical activity and exercise were related to the environmental (i.e. minimal or no disabled facilities, and minimal or conflicting advice from healthcare professionals) and related to personal barriers (i.e. fatigue, and fear and apprehension). The most commonly identified perceived facilitators of physical activity were related to the environment (i.e. the type of exercise modality and peer support) and related to personal facilitators (i.e. appropriate exercise and feelings of accomplishment). The most commonly identified perceived beneficial consequences of physical activity and exercise were maintaining physical functions, increased social participation and feelings of self-management and control. The most commonly identified perceived adverse consequences were increased fatigue and feelings of frustration and lost control. Results will inform future research on the perceived determinants and consequences of physical activity and exercise in those with MS and can be adopted for developing professional education and interventions for physical activity and exercise in MS. Physical activity and exercise behaviour in people with multiple sclerosis (MS) is subject

  9. Dense genotyping of immune-related loci identifies variants associated with clearance of HPV among HIV-positive women in the HIV epidemiology research study (HERS.

    Directory of Open Access Journals (Sweden)

    Staci L Sudenga

    Full Text Available Persistent high-risk human papillomavirus (HR-HPV is a necessary and causal factor of cervical cancer. Most women naturally clear HPV infections; however, the biological mechanisms related to HPV pathogenesis have not been clearly elucidated. Host genetic factors that specifically regulate immune response could play an important role. All HIV-positive women in the HIV Epidemiology Research Study (HERS with a HR-HPV infection and at least one follow-up biannual visit were included in the study. Cervicovaginal lavage samples were tested for HPV using type-specific HPV hybridization assays. Type-specific HPV clearance was defined as two consecutive HPV-negative tests after a positive test. DNA from participants was genotyped for 196,524 variants within 186 known immune related loci using the custom ImmunoChip microarray. To assess the influence of each single-nucleotide polymorphism (SNP with HR-HPV clearance, the Cox proportional hazards model with the Wei-Lin-Weissfeld approach was used, adjusting for CD4+ count, low risk HPV (LR-HPV co-infection, and relevant confounders. Three analytical models were performed: race-specific (African Americans (n = 258, European Americans (n = 87, Hispanics (n = 55, race-adjusted combined analysis, and meta-analysis of pooled independent race-specific analyses. Women were followed for a median time of 1,617 days. Overall, three SNPs (rs1112085, rs11102637, and rs12030900 in the MAGI-3 gene and one SNP (rs8031627 in the SMAD3 gene were associated with HR-HPV clearance (p<10(-6. A variant (rs1633038 in HLA-G were also significantly associated in African American. Results from this study support associations of immune-related genes, having potential biological mechanism, with differential cervical HR-HPV infection outcomes.

  10. Haematoxylin and eosin staining identifies medium to large bacterial aggregates with a reliable specificity: A comparative analysis of follicular bacterial aggregates in axillary biopsies using peptide nucleic acid-fluorescence in situ hybridization and haematoxylin and eosin staining

    DEFF Research Database (Denmark)

    Ring, Hans Christian; Riis, Peter Theut; Bay, Lene

    2017-01-01

    between bacterial aggregates identified by haematoxylin and eosin (HE) staining vs bacterial aggregates in corresponding PNA-FISH samples. Axillary biopsies were obtained in 24 healthy controls. HE-stained and PNA-FISH samples were investigated using traditional light microscopy and CLSM, respectively....... The data demonstrate that HE staining identifies large bacterial aggregates (>10 μm) with a sensitivity of 0.43 and specificity of 1. The methods, however, are not equivalent as demonstrated by a McNemar's test (P=.04). Where bacterial aggregates >10 μm in diameter, HE staining may offer a rapid...... and practical low-cost tool to evaluate bacterial aggregates....

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

    Science.gov (United States)

    Knight, Rod; Small, Will; Pakula, Basia; Thomson, Kimberly; Shoveller, Jean

    2014-07-03

    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 promis