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Sample records for identifying key research

  1. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

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

  2. Nanofluids research: key issues.

    PubMed

    Wang, Liqiu; Fan, Jing

    2010-05-22

    Nanofluids are a new class of fluids engineered by dispersing nanometer-size structures (particles, fibers, tubes, droplets) in base fluids. The very essence of nanofluids research and development is to enhance fluid macroscopic and megascale properties such as thermal conductivity through manipulating microscopic physics (structures, properties and activities). Therefore, the success of nanofluid technology depends very much on how well we can address issues like effective means of microscale manipulation, interplays among physics at different scales and optimization of microscale physics for the optimal megascale properties. In this work, we take heat-conduction nanofluids as examples to review methodologies available to effectively tackle these key but difficult problems and identify the future research needs as well. The reviewed techniques include nanofluids synthesis through liquid-phase chemical reactions in continuous-flow microfluidic microreactors, scaling-up by the volume averaging and constructal design with the constructal theory. The identified areas of future research contain microfluidic nanofluids, thermal waves and constructal nanofluids.

  3. Nanofluids Research: Key Issues

    PubMed Central

    2010-01-01

    Nanofluids are a new class of fluids engineered by dispersing nanometer-size structures (particles, fibers, tubes, droplets) in base fluids. The very essence of nanofluids research and development is to enhance fluid macroscopic and megascale properties such as thermal conductivity through manipulating microscopic physics (structures, properties and activities). Therefore, the success of nanofluid technology depends very much on how well we can address issues like effective means of microscale manipulation, interplays among physics at different scales and optimization of microscale physics for the optimal megascale properties. In this work, we take heat-conduction nanofluids as examples to review methodologies available to effectively tackle these key but difficult problems and identify the future research needs as well. The reviewed techniques include nanofluids synthesis through liquid-phase chemical reactions in continuous-flow microfluidic microreactors, scaling-up by the volume averaging and constructal design with the constructal theory. The identified areas of future research contain microfluidic nanofluids, thermal waves and constructal nanofluids. PMID:20676214

  4. IDENTIFYING KEY CONTRIBUTIONS TO INFORMATION SCIENCE,

    DTIC Science & Technology

    Several alternative approaches were examined to determine how one might identify some of the key (written) contributions to ’ information science ’. The...references. The unclear selective patterns in current bibliographies in the information science field also present problems. It is suggested that in...identifying key contributions we are far from common agreement on the conceptual, methodological or practical contributions to the information science field

  5. Why Patient Matching Is a Challenge: Research on Master Patient Index (MPI) Data Discrepancies in Key Identifying Fields

    PubMed Central

    Just, Beth Haenke; Marc, David; Munns, Megan; Sandefer, Ryan

    2016-01-01

    Patient identification matching problems are a major contributor to data integrity issues within electronic health records. These issues impede the improvement of healthcare quality through health information exchange and care coordination, and contribute to deaths resulting from medical errors. Despite best practices in the area of patient access and medical record management to avoid duplicating patient records, duplicate records continue to be a significant problem in healthcare. This study examined the underlying causes of duplicate records using a multisite data set of 398,939 patient records with confirmed duplicates and analyzed multiple reasons for data discrepancies between those record matches. The field that had the greatest proportion of mismatches (nondefault values) was the middle name, accounting for 58.30 percent of mismatches. The Social Security number was the second most frequent mismatch, occurring in 53.54 percent of the duplicate pairs. The majority of the mismatches in the name fields were the result of misspellings (53.14 percent in first name and 33.62 percent in last name) or swapped last name/first name, first name/middle name, or last name/middle name pairs. The use of more sophisticated technologies is critical to improving patient matching. However, no amount of advanced technology or increased data capture will completely eliminate human errors. Thus, the establishment of policies and procedures (such as standard naming conventions or search routines) for front-end and back-end staff to follow is foundational for the overall data integrity process. Training staff on standard policies and procedures will result in fewer duplicates created on the front end and more accurate duplicate record matching and merging on the back end. Furthermore, monitoring, analyzing trends, and identifying errors that occur are proactive ways to identify data integrity issues. PMID:27134610

  6. Why Patient Matching Is a Challenge: Research on Master Patient Index (MPI) Data Discrepancies in Key Identifying Fields.

    PubMed

    Just, Beth Haenke; Marc, David; Munns, Megan; Sandefer, Ryan

    2016-01-01

    Patient identification matching problems are a major contributor to data integrity issues within electronic health records. These issues impede the improvement of healthcare quality through health information exchange and care coordination, and contribute to deaths resulting from medical errors. Despite best practices in the area of patient access and medical record management to avoid duplicating patient records, duplicate records continue to be a significant problem in healthcare. This study examined the underlying causes of duplicate records using a multisite data set of 398,939 patient records with confirmed duplicates and analyzed multiple reasons for data discrepancies between those record matches. The field that had the greatest proportion of mismatches (nondefault values) was the middle name, accounting for 58.30 percent of mismatches. The Social Security number was the second most frequent mismatch, occurring in 53.54 percent of the duplicate pairs. The majority of the mismatches in the name fields were the result of misspellings (53.14 percent in first name and 33.62 percent in last name) or swapped last name/first name, first name/middle name, or last name/middle name pairs. The use of more sophisticated technologies is critical to improving patient matching. However, no amount of advanced technology or increased data capture will completely eliminate human errors. Thus, the establishment of policies and procedures (such as standard naming conventions or search routines) for front-end and back-end staff to follow is foundational for the overall data integrity process. Training staff on standard policies and procedures will result in fewer duplicates created on the front end and more accurate duplicate record matching and merging on the back end. Furthermore, monitoring, analyzing trends, and identifying errors that occur are proactive ways to identify data integrity issues.

  7. Student Success Factors: Identifying Key Predictors

    ERIC Educational Resources Information Center

    Sulaiman, Ainin; Mohezar, Suhana

    2006-01-01

    The authors' main aim in this study was to identify key predictors of Master of Business Administration (MBA) students' academic performance. The authors measured performance by the students' cumulative grade point average achieved, using data from the Students Information Systems and Application database. The authors found that a student's…

  8. Key questions for conducting role delineation research.

    PubMed

    Taub, Alyson; Gilmore, Gary D; Olsen, Larry K; Connell, Dave

    2011-06-01

    Role delineation research for the verification of professional competencies is essential in many professions to promote quality assurance and support capacity building and workforce development. In this article, guidance is provided about key aspects of role delineation research. The information contained in this article focuses on 13 key questions within three selected research phases when attempting to identify and verify the roles that are inherent within any given profession. The major sections in the paper include planning the research, collecting and analyzing the data, interpreting findings, and considering the future. Recommendations and examples related to each of the important questions are provided to assist others undertaking role delineation research.

  9. Identifying the key concerns of Irish persons with intellectual disability.

    PubMed

    García Iriarte, Edurne; O'Brien, Patricia; McConkey, Roy; Wolfe, Marie; O'Doherty, Siobhain

    2014-11-01

    Internationally, people with intellectual disability are socially marginalized, and their rights under the United Nations Convention for the Rights of Persons with Disabilities (CRPD) are often ignored. This paper aims to define the key concerns of adults with an intellectual disability in relation to their participation in society using an inclusive research strategy for both data gathering and data analysis. A national study involving 23 focus groups and 168 persons was conducted on the island of Ireland with people with intellectual disability as co-facilitators. A thematic content analysis was undertaken of the verbatim transcripts initially by university co-researchers, and 19 themes were identified. Co-researchers with intellectual disability joined in identifying the eight core themes. These were as follows: living options, employment, relationships, citizenship, leisure time, money management, self-advocacy, and communication. The concerns are discussed within the framework of the CRPD, and implications for transforming service policy are drawn. Why we did the research In many countries, people with intellectual disability have difficulties doing things other people without disabilities do, for example to study, to get a job or to live independently. They also find that their rights are not respected under the Convention on the Rights of Persons with Disabilities (the Convention). We did this study to Learn what are the main issues for adults with intellectual disability in Ireland. Do research with people with intellectual disability. How we did the research People with intellectual disability and their supporters worked with university researchers to plan and do the research. We met with people in groups and 168 people told us about things important to them. What we found out We found that there were very important things that people talked about in the groups. We chose the most important: living options, employment, relationships, rights, leisure, money

  10. Public key infrastructure for DOE security research

    SciTech Connect

    Aiken, R.; Foster, I.; Johnston, W.E.

    1997-06-01

    This document summarizes the Department of Energy`s Second Joint Energy Research/Defence Programs Security Research Workshop. The workshop, built on the results of the first Joint Workshop which reviewed security requirements represented in a range of mission-critical ER and DP applications, discussed commonalties and differences in ER/DP requirements and approaches, and identified an integrated common set of security research priorities. One significant conclusion of the first workshop was that progress in a broad spectrum of DOE-relevant security problems and applications could best be addressed through public-key cryptography based systems, and therefore depended upon the existence of a robust, broadly deployed public-key infrastructure. Hence, public-key infrastructure ({open_quotes}PKI{close_quotes}) was adopted as a primary focus for the second workshop. The Second Joint Workshop covered a range of DOE security research and deployment efforts, as well as summaries of the state of the art in various areas relating to public-key technologies. Key findings were that a broad range of DOE applications can benefit from security architectures and technologies built on a robust, flexible, widely deployed public-key infrastructure; that there exists a collection of specific requirements for missing or undeveloped PKI functionality, together with a preliminary assessment of how these requirements can be met; that, while commercial developments can be expected to provide many relevant security technologies, there are important capabilities that commercial developments will not address, due to the unique scale, performance, diversity, distributed nature, and sensitivity of DOE applications; that DOE should encourage and support research activities intended to increase understanding of security technology requirements, and to develop critical components not forthcoming from other sources in a timely manner.

  11. Research Advances: Less Expensive and More Convenient Gaucher's Disease Treatment; Structural Loop Regions: Key to Multidrug-Resistance Transporters?; New Method Identifies Proteins in Old Artwork

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

    The X-ray structure of EmrD, a multidrug transporter protein from Escherichia coli, common bacteria known to cause several food-borne illnesses was determined by scientists at The Scripps Research Institute. The hydrophobic residues in the EmrD internal cavity are likely to contribute to the general mechanism transporting various compounds through…

  12. Research Advances: Less Expensive and More Convenient Gaucher's Disease Treatment; Structural Loop Regions: Key to Multidrug-Resistance Transporters?; New Method Identifies Proteins in Old Artwork

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

    The X-ray structure of EmrD, a multidrug transporter protein from Escherichia coli, common bacteria known to cause several food-borne illnesses was determined by scientists at The Scripps Research Institute. The hydrophobic residues in the EmrD internal cavity are likely to contribute to the general mechanism transporting various compounds through…

  13. Methods for identifying translational researchers.

    PubMed

    Feeney, Mary K; Johnson, Timothy; Welch, Eric W

    2014-03-01

    There is currently no generally accepted method for identifying the community of translational researchers when evaluating Clinical and Translational Science Centers. We use data from the multiyear evaluation of the University of Illinois at Chicago Center for Clinical and Translational Science (CCTS) to investigate the complexities of reliably identifying translational researchers. We use three methods to identify translational researchers: (1) participating in CCTS services and programs; (2) self-identifying as a translational researcher; and (3) engaging in activities that are characteristic of translational science. We find little overlap of these differently defined research groups. We conclude with a discussion of how the findings suggest challenges for evaluating translational science programs and the need for better definition, communication, and demonstration of translational science for scientists and evaluators.

  14. Identifying the key performance improvement domains for home health agencies

    PubMed Central

    Koru, Güneş; Alhuwail, Dari; Rosati, Robert J.

    2015-01-01

    Objective: The objective of this study was to support home health agencies (HHAs) in the United States (US) in their individualized quality assessment and performance improvement (QAPI) initiatives by identifying their key performance improvement domains (KPIDs). Methods: Qualitative research was conducted by following the Framework method. Rich contextual data were obtained through focus group meetings participated by domain experts. The analysis results were further refined in an online forum and validated at a final meeting. Results: Four focus groups involving a total of 20 participants resulted in useful discussions during which various perspectives were expressed by the expert participants. A well-defined set of 17 KPIDs emerged under four categories, namely, economical value, sociocultural sensitivity, interpersonal relationships, and clinical capabilities. Conclusions: The feedback we received from the focus groups indicates that performance improvement in HHAs is a lot more complicated than simply assessing whether certain clinical tasks are performed. The KPIDs identified in this study can help HHAs in their focused and individualized QAPI initiatives. Therefore, the results should be immediately relevant, interesting, and useful to the home care industry and policy makers in the US. PMID:27092266

  15. Identifying key hospital service quality factors in online health communities.

    PubMed

    Jung, Yuchul; Hur, Cinyoung; Jung, Dain; Kim, Minki

    2015-04-07

    The volume of health-related user-created content, especially hospital-related questions and answers in online health communities, has rapidly increased. Patients and caregivers participate in online community activities to share their experiences, exchange information, and ask about recommended or discredited hospitals. However, there is little research on how to identify hospital service quality automatically from the online communities. In the past, in-depth analysis of hospitals has used random sampling surveys. However, such surveys are becoming impractical owing to the rapidly increasing volume of online data and the diverse analysis requirements of related stakeholders. As a solution for utilizing large-scale health-related information, we propose a novel approach to identify hospital service quality factors and overtime trends automatically from online health communities, especially hospital-related questions and answers. We defined social media-based key quality factors for hospitals. In addition, we developed text mining techniques to detect such factors that frequently occur in online health communities. After detecting these factors that represent qualitative aspects of hospitals, we applied a sentiment analysis to recognize the types of recommendations in messages posted within online health communities. Korea's two biggest online portals were used to test the effectiveness of detection of social media-based key quality factors for hospitals. To evaluate the proposed text mining techniques, we performed manual evaluations on the extraction and classification results, such as hospital name, service quality factors, and recommendation types using a random sample of messages (ie, 5.44% (9450/173,748) of the total messages). Service quality factor detection and hospital name extraction achieved average F1 scores of 91% and 78%, respectively. In terms of recommendation classification, performance (ie, precision) is 78% on average. Extraction and

  16. Identifying Key Hospital Service Quality Factors in Online Health Communities

    PubMed Central

    Jung, Yuchul; Hur, Cinyoung; Jung, Dain

    2015-01-01

    Background The volume of health-related user-created content, especially hospital-related questions and answers in online health communities, has rapidly increased. Patients and caregivers participate in online community activities to share their experiences, exchange information, and ask about recommended or discredited hospitals. However, there is little research on how to identify hospital service quality automatically from the online communities. In the past, in-depth analysis of hospitals has used random sampling surveys. However, such surveys are becoming impractical owing to the rapidly increasing volume of online data and the diverse analysis requirements of related stakeholders. Objective As a solution for utilizing large-scale health-related information, we propose a novel approach to identify hospital service quality factors and overtime trends automatically from online health communities, especially hospital-related questions and answers. Methods We defined social media–based key quality factors for hospitals. In addition, we developed text mining techniques to detect such factors that frequently occur in online health communities. After detecting these factors that represent qualitative aspects of hospitals, we applied a sentiment analysis to recognize the types of recommendations in messages posted within online health communities. Korea’s two biggest online portals were used to test the effectiveness of detection of social media–based key quality factors for hospitals. Results To evaluate the proposed text mining techniques, we performed manual evaluations on the extraction and classification results, such as hospital name, service quality factors, and recommendation types using a random sample of messages (ie, 5.44% (9450/173,748) of the total messages). Service quality factor detection and hospital name extraction achieved average F1 scores of 91% and 78%, respectively. In terms of recommendation classification, performance (ie, precision) is

  17. Identifying and tracking key odorants from cattle feedlots

    USDA-ARS?s Scientific Manuscript database

    Odors from cattle feedlots negatively affect air quality in local communities. The purpose of this study was to identifying key odorants using both analytical (odor activity values, OAV) and gas chromatrography GC-O (olfactometry) techniques, compare odor threshold databases, and track the movement ...

  18. Identifying Key Odors Offsite From Animal Feeding Operation

    USDA-ARS?s Scientific Manuscript database

    Odors from animal feeding operations are some of the most significant emissions at the local level. Current methods used to measure agricultural odor are bias and inadequate. The purpose of this study was to evaluate the ability of 2 different techniques to identify key odorants. The first techni...

  19. Supporting Educational Success for Aboriginal Students: Identifying Key Influences

    ERIC Educational Resources Information Center

    Whitley, Jessica

    2014-01-01

    The academic difficulties experienced by many Aboriginal (First Nations, Métis, Inuit) students in Canada have been well-documented. Indicators such as school persistence and post-secondary enrollment are typically far lower for Aboriginal students as a group compared to non-Aboriginal students. Identifying facilitators of success is key to…

  20. Food irradiation: Key research needs

    SciTech Connect

    Morehouse, K.M. )

    1993-01-01

    Treatment of foods with ionizing radiation reduces microbial infection and insect infestations, inhibits sprouting, and delays maturation, thereby extending the shelf life of foods. The treatment of different types of foods with ionizing radiation for specific purposes is accepted in several countries, although it is prohibited in others. The US Food and Drug Administration has established regulations to allow the treatment of several different foods with ionizing radiation and has received petitions for the approval of radiation treatment of additional foods. When carried out according to established good manufacturing practices, food irradiation yields safe, wholesome foods. The irradiated product may be often chemically or microbiologically [open quotes]safer[close quotes] than the nonirradiated product. This paper presents several areas of scientific research in which more information would facilitate the expansion of this technology and points out major areas of concern. The question of the public acceptance of foods that have been treated with ionizing radiation is discussed only briefly in order to make the presentation complete.

  1. Distant Odors: Identifying Key Odors Associated With Cattle Feedlots Downwind

    USDA-ARS?s Scientific Manuscript database

    The National Research Council identified odors as the most significant animal emission at the local level and has highlighted the need for the development of standardized protocols for sampling and analysis of odors. To date, however, little progress has been made on identifying sampling and analys...

  2. Identifying and tracking key odorants from cattle feedlots

    NASA Astrophysics Data System (ADS)

    Trabue, Steven; Scoggin, Kenwood; McConnell, Laura; Maghirang, Ronaldo; Razote, Edna; Hatfield, Jerry

    2011-08-01

    Odors from cattle feedlots can negatively affect air quality in local communities. Our objectives were the following: 1) identify key odor-causing compounds using odor activity values (OAVs) and gas chromatography-olfactometry (GC-O) techniques; 2) compare odor threshold values from published databases; and 3) track the movement of odors from a cattle feedlot to receptor community. Odorous compounds emitted from a cattle feedlot were sampled on-site, 250 m downwind and 3.2 km downwind using both sorbent tubes and denuders. Sorbent tubes were analyzed by both GC-MS and GC-MS-O and key odorants determined using both OAV and GC-Surface Nasal Impact Frequency (SNIF) analysis, while denuders were analyzed by ion chromatography. Odorant concentrations had a diurnal pattern with peak concentrations during early morning and late evening periods. Volatile fatty acids (VFAs) were the most abundant of the major odorants. Odorants with concentrations above their odor threshold values at the feedlot included amines, VFAs, phenol compounds, and indole compounds. Key odorants at the feedlot were VFAs and phenol compounds, but their relative importance diminished with downwind distance. Indole compounds, while not the key odorants at the feedlot, increased in relative importance downwind of the feedlot. In general, the odorous compounds identified by GC-SNIF and OAV as having fecal/manure nature were similar. GC-SNIF was the more sensitive analytical technique; it identified several compounds that may have contributed to the unpleasantness of the cattle feedlot odor, but its throughput was extremely low thereby limiting its usefulness. There is a need to improve field sampling devices and odor threshold databases to enhance understanding and confidence in evaluating odors.

  3. Multiple differential expression networks identify key genes in rectal cancer.

    PubMed

    Li, Ri-Heng; Zhang, Ai-Min; Li, Shuang; Li, Tian-Yang; Wang, Lian-Jing; Zhang, Hao-Ran; Li, Ping; Jia, Xiong-Jie; Zhang, Tao; Peng, Xin-Yu; Liu, Min-Di; Wang, Xu; Lang, Yan; Xue, Wei-Lan; Liu, Jing; Wang, Yan-Yan

    2016-01-01

    Rectal cancer is an important contributor to cancer mortality. The objective of this paper is to identify key genes across three phenotypes (fungating, polypoid and polypoid & small-ulcer) of rectal cancer based on multiple differential expression networks (DENs). Differential interactions and non-differential interactions were evaluated according to Spearman correlation coefficient (SCC) algorithm, and were selected to construct DENs. Topological analysis was performed for exploring hub genes in largest components of DENs. Key genes were denoted as intersections between nodes of DENs and rectal cancer associated genes from Genecards. Finally, we utilized hub genes to classify phenotypes of rectal cancer on the basis of support vector machines (SVM) methodology. We obtained 19 hub genes and total 12 common key genes of three largest components of DENs, and EGFR was the common element. The SVM results revealed that hub genes could classify phenotypes, and validated feasibility of DEN methods. We have successfully identified significant genes (such as EGFR and UBC) across fungating, polypoid and polypoid & small-ulcer phenotype of rectal cancer. They might be potential biomarkers for classification, detection and therapy of this cancer.

  4. Key Actions of Successful Summer Research Mentors

    ERIC Educational Resources Information Center

    Raman, D. Raj; Geisinger, Brandi N.; Kemis, Mari R.; de la Mora, Arlene

    2016-01-01

    Summer research opportunities for undergraduates, such as those supported by the National Science Foundation's Research Experience for Undergraduates (REU) program, can be critical experiences that help persuade students to pursue research through graduate studies. Studies analyzing the key actions of successful mentors are scarce. The goal of…

  5. Key Actions of Successful Summer Research Mentors

    ERIC Educational Resources Information Center

    Raman, D. Raj; Geisinger, Brandi N.; Kemis, Mari R.; de la Mora, Arlene

    2016-01-01

    Summer research opportunities for undergraduates, such as those supported by the National Science Foundation's Research Experience for Undergraduates (REU) program, can be critical experiences that help persuade students to pursue research through graduate studies. Studies analyzing the key actions of successful mentors are scarce. The goal of…

  6. Key Issue: Identifying Professional Contexts to Support Highly Effective Teachers

    ERIC Educational Resources Information Center

    Hirsch, Eric

    2008-01-01

    Policymakers, practitioners, and researchers have long understood that teacher quality is the most important variable for the success of students. The context in which educators work is critical to their success and satisfaction; however, identifying and addressing the conditions that teachers want and need is difficult. Assessing context is not…

  7. Identifying key nursing and team behaviours to achieve high reliability.

    PubMed

    Miller, Kristi; Riley, William; Davis, Stanley

    2009-03-01

    The aim of the present study was to measure markers of key nursing behaviours in interdisciplinary teams during critical events to assess the extent of high reliability. Technical and team competence are necessary to achieve high reliability to ensure safe patient care. Technical competence is generally assured because of professional training, licensure and practice standards. During critical events, team competence is difficult to observe, measure and evaluate in interdisciplinary teams. During critical events, in situ simulation was the method used to observe interdisciplinary interaction of nursing behaviours regarding communication. Seventeen trials were conducted and videotaped for evaluation at four hospital sites. Key nursing behavioural markers for interdisciplinary interaction were described: situational awareness, use of situation, background, assessment, recommendation-response (SBAR-R), closed-loop communication and shared mental model. Skills necessary for nurses to contribute to highly reliable, interdisciplinary teams are not consistently observed during critical events and constitute breaches in defensive barriers for ensuring patient safety. Nurses have a key role in assuring effective team performance through the transfer of critical information. Nurses need to recognize and identify important clinical and environmental cues, and act in order to ensure that the team progresses along the optimal course for patient safety.

  8. Keys to Survival: Highlights in Resilience Research.

    ERIC Educational Resources Information Center

    Burger, Joseph V.

    1994-01-01

    Presents key themes from expanding literature on resilience, drawing from both psychological research and narratives of survivors. Focuses on Kauai study, landmark 30-year longitudinal study on resilience in 698 infants. Also examines survivors of child abuse, distinguishes between unhealthy and healthy resilience, discusses issues of separation…

  9. Identifying key nodes in multilayer networks based on tensor decomposition

    NASA Astrophysics Data System (ADS)

    Wang, Dingjie; Wang, Haitao; Zou, Xiufen

    2017-06-01

    The identification of essential agents in multilayer networks characterized by different types of interactions is a crucial and challenging topic, one that is essential for understanding the topological structure and dynamic processes of multilayer networks. In this paper, we use the fourth-order tensor to represent multilayer networks and propose a novel method to identify essential nodes based on CANDECOMP/PARAFAC (CP) tensor decomposition, referred to as the EDCPTD centrality. This method is based on the perspective of multilayer networked structures, which integrate the information of edges among nodes and links between different layers to quantify the importance of nodes in multilayer networks. Three real-world multilayer biological networks are used to evaluate the performance of the EDCPTD centrality. The bar chart and ROC curves of these multilayer networks indicate that the proposed approach is a good alternative index to identify real important nodes. Meanwhile, by comparing the behavior of both the proposed method and the aggregated single-layer methods, we demonstrate that neglecting the multiple relationships between nodes may lead to incorrect identification of the most versatile nodes. Furthermore, the Gene Ontology functional annotation demonstrates that the identified top nodes based on the proposed approach play a significant role in many vital biological processes. Finally, we have implemented many centrality methods of multilayer networks (including our method and the published methods) and created a visual software based on the MATLAB GUI, called ENMNFinder, which can be used by other researchers.

  10. Identifying Context Variables in Research.

    ERIC Educational Resources Information Center

    Piazza, Carolyn L.

    1987-01-01

    Identifies context variables in written composition from theoretical perspectives in cognitive psychology, sociology, and anthropology. Considers how multiple views of context from across the disciplines can build toward a broader definition of writing. (JD)

  11. Identifying Context Variables in Research.

    ERIC Educational Resources Information Center

    Piazza, Carolyn L.

    1987-01-01

    Identifies context variables in written composition from theoretical perspectives in cognitive psychology, sociology, and anthropology. Considers how multiple views of context from across the disciplines can build toward a broader definition of writing. (JD)

  12. Key Clinical Features to Identify Girls with "CDKL5" Mutations

    ERIC Educational Resources Information Center

    Bahi-Buisson, Nadia; Nectoux, Juliette; Rosas-Vargas, Haydee; Milh, Mathieu; Boddaert, Nathalie; Girard, Benoit; Cances, Claude; Ville, Dorothee; Afenjar, Alexandra; Rio, Marlene; Heron, Delphine; Morel, Marie Ange N'Guyen; Arzimanoglou, Alexis; Philippe, Christophe; Jonveaux, Philippe; Chelly, Jamel; Bienvenu, Thierry

    2008-01-01

    Mutations in the human X-linked cyclin-dependent kinase-like 5 ("CDKL5") gene have been shown to cause infantile spasms as well as Rett syndrome (RTT)-like phenotype. To date, less than 25 different mutations have been reported. So far, there are still little data on the key clinical diagnosis criteria and on the natural history of…

  13. Identifying the Key Concerns of Irish Persons with Intellectual Disability

    ERIC Educational Resources Information Center

    García Iriarte, Edurne; O'Brien, Patricia; McConkey, Roy; Wolfe, Marie; O'Doherty, Siobhain

    2014-01-01

    Background: Internationally, people with intellectual disability are socially marginalized, and their rights under the United Nations Convention for the Rights of Persons with Disabilities (CRPD) are often ignored. Aims: This paper aims to define the key concerns of adults with an intellectual disability in relation to their participation in…

  14. Key Clinical Features to Identify Girls with "CDKL5" Mutations

    ERIC Educational Resources Information Center

    Bahi-Buisson, Nadia; Nectoux, Juliette; Rosas-Vargas, Haydee; Milh, Mathieu; Boddaert, Nathalie; Girard, Benoit; Cances, Claude; Ville, Dorothee; Afenjar, Alexandra; Rio, Marlene; Heron, Delphine; Morel, Marie Ange N'Guyen; Arzimanoglou, Alexis; Philippe, Christophe; Jonveaux, Philippe; Chelly, Jamel; Bienvenu, Thierry

    2008-01-01

    Mutations in the human X-linked cyclin-dependent kinase-like 5 ("CDKL5") gene have been shown to cause infantile spasms as well as Rett syndrome (RTT)-like phenotype. To date, less than 25 different mutations have been reported. So far, there are still little data on the key clinical diagnosis criteria and on the natural history of…

  15. Identifying the Key Concerns of Irish Persons with Intellectual Disability

    ERIC Educational Resources Information Center

    García Iriarte, Edurne; O'Brien, Patricia; McConkey, Roy; Wolfe, Marie; O'Doherty, Siobhain

    2014-01-01

    Background: Internationally, people with intellectual disability are socially marginalized, and their rights under the United Nations Convention for the Rights of Persons with Disabilities (CRPD) are often ignored. Aims: This paper aims to define the key concerns of adults with an intellectual disability in relation to their participation in…

  16. Identify the key amino acid of BAFF binding with TACI.

    PubMed

    Wang, Renxi; Wang, Ru; Ma, Ning; Guo, Yueling; Xiao, He; Chen, Guojiang; Han, Gencheng; Hou, Chunmei; Shen, Beifen; Feng, Jiannan; Li, Yan

    2013-01-01

    B-cell activating factor (BAFF) has been used as a therapeutic target. To develop BAFF-specific small molecular inhibitors, it is necessary to know the key amino acid in the BAFF binding with its receptor. The key binding amino acid of BAFF interacting with its receptor TACI (trans-membrane activator and calcium modulator and cyclophilin ligand interactor) was analyzed based on the computer-guided molecular modeling method. According to theoretical prediction, a series of key amino acid mutants of BAFF, including M204 (Lys(204) to Ala), M208 (Met(208) to Ala), M209 (Gly(209) to Ala), M210 (His(210) to Ala), M234 (Gln(234) to Ala), M236 (Met(236) to Ala), and M237 (Pro(237) to Ala) were designed and evaluated with biological experiments. The results show that M208, M209, M236, and M237 of BAFF were the key amino acids and in accord with the theoretical results. The results highlight clues for the further development of BAFF-specific small molecular inhibitors.

  17. Identifying the Key Weaknesses in Network Security at Colleges.

    ERIC Educational Resources Information Center

    Olsen, Florence

    2000-01-01

    A new study identifies and ranks the 10 security gaps responsible for most outsider attacks on college computer networks. The list is intended to help campus system administrators establish priorities as they work to increase security. One network security expert urges that institutions utilize multiple security layers. (DB)

  18. Scholars Identify 5 Keys to Urban School Success

    ERIC Educational Resources Information Center

    Viadero, Debra

    2010-01-01

    Offering a counter-narrative to the school improvement prescriptions that dominate national education debates, a new book based on 15 years of data on public elementary schools in Chicago identifies five tried-and-true ingredients that work, in combination with one another, to spur success in urban schools. The authors liken their "essential…

  19. Scholars Identify 5 Keys to Urban School Success

    ERIC Educational Resources Information Center

    Viadero, Debra

    2010-01-01

    Offering a counter-narrative to the school improvement prescriptions that dominate national education debates, a new book based on 15 years of data on public elementary schools in Chicago identifies five tried-and-true ingredients that work, in combination with one another, to spur success in urban schools. The authors liken their "essential…

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

    NASA Astrophysics Data System (ADS)

    Ferguson, J. E.

    2016-12-01

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

  1. Identifying key conservation threats to Alpine birds through expert knowledge.

    PubMed

    Chamberlain, Dan E; Pedrini, Paolo; Brambilla, Mattia; Rolando, Antonio; Girardello, Marco

    2016-01-01

    Alpine biodiversity is subject to a range of increasing threats, but the scarcity of data for many taxa means that it is difficult to assess the level and likely future impact of a given threat. Expert opinion can be a useful tool to address knowledge gaps in the absence of adequate data. Experts with experience in Alpine ecology were approached to rank threat levels for 69 Alpine bird species over the next 50 years for the whole European Alps in relation to ten categories: land abandonment, climate change, renewable energy, fire, forestry practices, grazing practices, hunting, leisure, mining and urbanization. There was a high degree of concordance in ranking of perceived threats among experts for most threat categories. The major overall perceived threats to Alpine birds identified through expert knowledge were land abandonment, urbanization, leisure and forestry, although other perceived threats were ranked highly for particular species groups (renewable energy and hunting for raptors, hunting for gamebirds). For groups of species defined according to their breeding habitat, open habitat species and treeline species were perceived as the most threatened. A spatial risk assessment tool based on summed scores for the whole community showed threat levels were highest for bird communities of the northern and western Alps. Development of the approaches given in this paper, including addressing biases in the selection of experts and adopting a more detailed ranking procedure, could prove useful in the future in identifying future threats, and in carrying out risk assessments based on levels of threat to the whole bird community.

  2. Identifying key conservation threats to Alpine birds through expert knowledge

    PubMed Central

    Pedrini, Paolo; Brambilla, Mattia; Rolando, Antonio; Girardello, Marco

    2016-01-01

    Alpine biodiversity is subject to a range of increasing threats, but the scarcity of data for many taxa means that it is difficult to assess the level and likely future impact of a given threat. Expert opinion can be a useful tool to address knowledge gaps in the absence of adequate data. Experts with experience in Alpine ecology were approached to rank threat levels for 69 Alpine bird species over the next 50 years for the whole European Alps in relation to ten categories: land abandonment, climate change, renewable energy, fire, forestry practices, grazing practices, hunting, leisure, mining and urbanization. There was a high degree of concordance in ranking of perceived threats among experts for most threat categories. The major overall perceived threats to Alpine birds identified through expert knowledge were land abandonment, urbanization, leisure and forestry, although other perceived threats were ranked highly for particular species groups (renewable energy and hunting for raptors, hunting for gamebirds). For groups of species defined according to their breeding habitat, open habitat species and treeline species were perceived as the most threatened. A spatial risk assessment tool based on summed scores for the whole community showed threat levels were highest for bird communities of the northern and western Alps. Development of the approaches given in this paper, including addressing biases in the selection of experts and adopting a more detailed ranking procedure, could prove useful in the future in identifying future threats, and in carrying out risk assessments based on levels of threat to the whole bird community. PMID:26966659

  3. Starting Vortex Identified as Key to Unsteady Ejector Performance

    NASA Technical Reports Server (NTRS)

    Paxson, Daniel E.

    2004-01-01

    Unsteady ejectors are currently under investigation for use in some pulse-detonation-engine-based propulsion systems. Experimental measurements made in the past, and recently at the NASA Glenn Research Center, have demonstrated that thrust augmentation can be enhanced considerably when the driver is unsteady. In ejector systems, thrust augmentation is defined as = T(sup Total)/T(sup j), where T(sup Total) is the total thrust of the combined ejector and driving jet and T(sup j) is the thrust due to the driving jet alone. There are three images in this figure, one for each of the named thrust sources. The images are color contours of measured instantaneous vorticity. Each image is an ensemble average of at least 150 phase-locked measurements. The flow is from right to left, and the shape and location of each driver is shown on the far right of each image. The emitted vortex is a clearly defined "doughnut" of highly vortical (spinning) flow. In these planar images, the vortex appears as two distorted circles, one above, and one below the axis of symmetry. Because they are spinning in the opposite direction, the two circles have vorticity of opposite sign and thus are different colors. There is also a rectangle shown in each image. Its width represents the ejector diameter that was found experimentally to yield the highest thrust augmentation. It is apparent that the optimal ejector diameter is that which just "captures" the vortex: that is, the diameter bounding the outermost edge of the vortex structure. The exact mechanism behind the enhanced performance is unclear; however, it is believed to be related to the powerful vortex emitted with each pulse of the unsteady driver. As such, particle imaging velocimetry (PIV) measurements were obtained for three unsteady drivers: a pulsejet, a resonance tube, and a speaker-driven jet. All the drivers were tested with ejectors, and all exhibited performance enhancement over similarly sized steady drivers. The characteristic

  4. Making Professional Decisions in Research: Measurement and Key Predictors

    PubMed Central

    Antes, Alison L.; Chibnall, John T.; Baldwin, Kari A.; Tait, Raymond C.; Vander Wal, Jillon S.; DuBois, James M.

    2016-01-01

    The professional decision-making in research (PDR) measure was administered to 400 NIH-funded and industry-funded investigators, along with measures of cynicism, moral disengagement, compliance disengagement, impulsivity, work stressors, knowledge of responsible conduct of research (RCR), and socially desirable response tendencies. Negative associations were found for the PDR and measures of cynicism, moral disengagement, and compliance disengagement, while positive associations were found for the PDR and RCR knowledge and positive urgency, an impulsivity subscale. PDR scores were not related to socially desirable responding, or to measures of work stressors and the remaining impulsivity subscales. In a multivariate logistic regression analysis, lower moral disengagement scores, higher RCR knowledge, and identifying the United States as one’s nation of origin emerged as key predictors of stronger performance on the PDR. The implications of these findings for understanding the measurement of decision-making in research and future directions for research and RCR education are discussed. PMID:27093003

  5. Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution.

    PubMed

    Shivange, Amol V; Roccatano, Danilo; Schwaneberg, Ulrich

    2016-01-01

    Bacterial phytases have attracted industrial interest as animal feed supplement due to their high activity and sufficient thermostability (required for feed pelleting). We devised an approach named KeySIDE,  an iterative Key-residues interrogation of the wild type with Substitutions Identified in Directed Evolution for improving Yersinia mollaretii phytase (Ymphytase) thermostability by combining key beneficial substitutions and elucidating their individual roles. Directed evolution yielded in a discovery of nine positions in Ymphytase and combined iteratively to identify key positions. The "best" combination (M6: T77K, Q154H, G187S, and K289Q) resulted in significantly improved thermal resistance; the residual activity improved from 35 % (wild type) to 89 % (M6) at 58 °C and 20-min incubation. Melting temperature increased by 3 °C in M6 without a loss of specific activity. Molecular dynamics simulation studies revealed reduced flexibility in the loops located next to helices (B, F, and K) which possess substitutions (Helix-B: T77K, Helix-F: G187S, and Helix-K: K289E/Q). Reduced flexibility in the loops might be caused by strengthened hydrogen bonding network (e.g., G187S and K289E/K289Q) and a salt bridge (T77K). Our results demonstrate a promising approach to design phytases in food research, and we hope that the KeySIDE might become an attractive approach for understanding of structure-function relationships of enzymes.

  6. Research on Key Technologies of Cloud Computing

    NASA Astrophysics Data System (ADS)

    Zhang, Shufen; Yan, Hongcan; Chen, Xuebin

    With the development of multi-core processors, virtualization, distributed storage, broadband Internet and automatic management, a new type of computing mode named cloud computing is produced. It distributes computation task on the resource pool which consists of massive computers, so the application systems can obtain the computing power, the storage space and software service according to its demand. It can concentrate all the computing resources and manage them automatically by the software without intervene. This makes application offers not to annoy for tedious details and more absorbed in his business. It will be advantageous to innovation and reduce cost. It's the ultimate goal of cloud computing to provide calculation, services and applications as a public facility for the public, So that people can use the computer resources just like using water, electricity, gas and telephone. Currently, the understanding of cloud computing is developing and changing constantly, cloud computing still has no unanimous definition. This paper describes three main service forms of cloud computing: SAAS, PAAS, IAAS, compared the definition of cloud computing which is given by Google, Amazon, IBM and other companies, summarized the basic characteristics of cloud computing, and emphasized on the key technologies such as data storage, data management, virtualization and programming model.

  7. Tamper-proof secret image-sharing scheme for identifying cheated secret keys and shared images

    NASA Astrophysics Data System (ADS)

    Chen, Chien-Chang; Liu, Chong-An

    2013-01-01

    A (t,n) secret image-sharing scheme shares a secret image to n participants, and the t users recover the image. During the recovery procedure of a conventional secret image-sharing scheme, cheaters may use counterfeit secret keys or modified shared images to cheat other users' secret keys and shared images. A cheated secret key or shared image leads to an incorrect secret image. Unfortunately, the cheater cannot be identified. We present an exponent and modulus-based scheme to provide a tamper-proof secret image-sharing scheme for identifying cheaters on secret keys or shared images. The proposed scheme allows users to securely select their secret key. This assignment can be performed over networks. Modulus results of each shared image is calculated to recognize cheaters of a shared image. Experimental results indicate that the proposed scheme is excellent at identifying cheated secret keys and shared images.

  8. Pseudonymization of patient identifiers for translational research.

    PubMed

    Aamot, Harald; Kohl, Christian Dominik; Richter, Daniela; Knaup-Gregori, Petra

    2013-07-24

    The usage of patient data for research poses risks concerning the patients' privacy and informational self-determination. Next-generation-sequencing technologies and various other methods gain data from biospecimen, both for translational research and personalized medicine. If these biospecimen are anonymized, individual research results from genomic research, which should be offered to patients in a clinically relevant timeframe, cannot be associated back to the individual. This raises an ethical concern and challenges the legitimacy of anonymized patient samples. In this paper we present a new approach which supports both data privacy and the possibility to give feedback to patients about their individual research results. We examined previously published privacy concepts regarding a streamlined de-pseudonymization process and a patient-based pseudonym as applicable to research with genomic data and warehousing approaches. All concepts identified in the literature review were compared to each other and analyzed for their applicability to translational research projects. We evaluated how these concepts cope with challenges implicated by personalized medicine. Therefore, both person-centricity issues and a separation of pseudonymization and de-pseudonymization stood out as a central theme in our examination. This motivated us to enhance an existing pseudonymization method regarding a separation of duties. The existing concepts rely on external trusted third parties, making de-pseudonymization a multistage process involving additional interpersonal communication, which might cause critical delays in patient care. Therefore we propose an enhanced method with an asymmetric encryption scheme separating the duties of pseudonymization and de-pseudonymization. The pseudonymization service provider is unable to conclude the patient identifier from the pseudonym, but assigns this ability to an authorized third party (ombudsman) instead. To solve person-centricity issues, a

  9. Vulnerable Children's Access to Examinations at Key Stage 4. Research Report RR639

    ERIC Educational Resources Information Center

    Kendall, Sally; Johnson, Annie; Martin, Kerry; Kinder; Kay

    2005-01-01

    This research project was commissioned by the Department for Education and Skills (DfES) in 2004 to examine barriers to vulnerable children accessing examinations at the end of key stage 4 and to identify strategies employed to overcome these barriers. Key groups of vulnerable children identified by the DfES included: (1) Looked-after children;…

  10. Modelling Creativity: Identifying Key Components through a Corpus-Based Approach

    PubMed Central

    2016-01-01

    Creativity is a complex, multi-faceted concept encompassing a variety of related aspects, abilities, properties and behaviours. If we wish to study creativity scientifically, then a tractable and well-articulated model of creativity is required. Such a model would be of great value to researchers investigating the nature of creativity and in particular, those concerned with the evaluation of creative practice. This paper describes a unique approach to developing a suitable model of how creative behaviour emerges that is based on the words people use to describe the concept. Using techniques from the field of statistical natural language processing, we identify a collection of fourteen key components of creativity through an analysis of a corpus of academic papers on the topic. Words are identified which appear significantly often in connection with discussions of the concept. Using a measure of lexical similarity to help cluster these words, a number of distinct themes emerge, which collectively contribute to a comprehensive and multi-perspective model of creativity. The components provide an ontology of creativity: a set of building blocks which can be used to model creative practice in a variety of domains. The components have been employed in two case studies to evaluate the creativity of computational systems and have proven useful in articulating achievements of this work and directions for further research. PMID:27706185

  11. Modelling Creativity: Identifying Key Components through a Corpus-Based Approach.

    PubMed

    Jordanous, Anna; Keller, Bill

    2016-01-01

    Creativity is a complex, multi-faceted concept encompassing a variety of related aspects, abilities, properties and behaviours. If we wish to study creativity scientifically, then a tractable and well-articulated model of creativity is required. Such a model would be of great value to researchers investigating the nature of creativity and in particular, those concerned with the evaluation of creative practice. This paper describes a unique approach to developing a suitable model of how creative behaviour emerges that is based on the words people use to describe the concept. Using techniques from the field of statistical natural language processing, we identify a collection of fourteen key components of creativity through an analysis of a corpus of academic papers on the topic. Words are identified which appear significantly often in connection with discussions of the concept. Using a measure of lexical similarity to help cluster these words, a number of distinct themes emerge, which collectively contribute to a comprehensive and multi-perspective model of creativity. The components provide an ontology of creativity: a set of building blocks which can be used to model creative practice in a variety of domains. The components have been employed in two case studies to evaluate the creativity of computational systems and have proven useful in articulating achievements of this work and directions for further research.

  12. Novel screening cascade identifies MKK4 as key kinase regulating Tau phosphorylation at Ser422.

    PubMed

    Grueninger, Fiona; Bohrmann, Bernd; Christensen, Klaus; Graf, Martin; Roth, Doris; Czech, Christian

    2011-11-01

    Phosphorylation of Tau at serine 422 promotes Tau aggregation. The kinase that is responsible for this key phosphorylation event has so far not been identified but could be a potential drug target for Alzheimer's disease. We describe here an assay strategy to identify this kinase. Using a combination of screening a library of 65'000 kinase inhibitors and in vitro inhibitor target profiling of the screening hits using the Ambit kinase platform, MKK4 was identified as playing a key role in Tau-S422 phosphorylation in human neuroblastoma cells.

  13. GuiaTreeKey, a multi-access electronic key to identify tree genera in French Guiana

    PubMed Central

    Engel, Julien; Brousseau, Louise; Baraloto, Christopher

    2016-01-01

    Abstract The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines. The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550). PMID:27698572

  14. Health Insurance a Key to IVF Success, Researchers Say

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_164329.html Health Insurance a Key to IVF Success, Researchers Say At $ ... 2017 TUESDAY, March 28, 2017 (HealthDay News) -- Having health insurance that covers in vitro fertilization (IVF) boosts the ...

  15. Participatory Action Research with Older Adults: Key Principles in Practice

    ERIC Educational Resources Information Center

    Blair, Thomas; Minkler, Meredith

    2009-01-01

    Purpose: Although participatory action research (PAR) is increasingly viewed as an important complement to traditional investigator-driven research, relatively little PAR has taken place in which older adults have been prominent partners. This article provides a review of the literature on PAR in gerontology, highlighting key studies and their…

  16. Participatory Action Research with Older Adults: Key Principles in Practice

    ERIC Educational Resources Information Center

    Blair, Thomas; Minkler, Meredith

    2009-01-01

    Purpose: Although participatory action research (PAR) is increasingly viewed as an important complement to traditional investigator-driven research, relatively little PAR has taken place in which older adults have been prominent partners. This article provides a review of the literature on PAR in gerontology, highlighting key studies and their…

  17. Quantitative methods of identifying the key nodes in the illegal wildlife trade network

    PubMed Central

    Patel, Nikkita Gunvant; Rorres, Chris; Joly, Damien O.; Brownstein, John S.; Boston, Ray; Levy, Michael Z.; Smith, Gary

    2015-01-01

    Innovative approaches are needed to combat the illegal trade in wildlife. Here, we used network analysis and a new database, HealthMap Wildlife Trade, to identify the key nodes (countries) that support the illegal wildlife trade. We identified key exporters and importers from the number of shipments a country sent and received and from the number of connections a country had to other countries over a given time period. We used flow betweenness centrality measurements to identify key intermediary countries. We found the set of nodes whose removal from the network would cause the maximum disruption to the network. Selecting six nodes would fragment 89.5% of the network for elephants, 92.3% for rhinoceros, and 98.1% for tigers. We then found sets of nodes that would best disseminate an educational message via direct connections through the network. We would need to select 18 nodes to reach 100% of the elephant trade network, 16 nodes for rhinoceros, and 10 for tigers. Although the choice of locations for interventions should be customized for the animal and the goal of the intervention, China was the most frequently selected country for network fragmentation and information dissemination. Identification of key countries will help strategize illegal wildlife trade interventions. PMID:26080413

  18. Quantitative methods of identifying the key nodes in the illegal wildlife trade network.

    PubMed

    Patel, Nikkita Gunvant; Rorres, Chris; Joly, Damien O; Brownstein, John S; Boston, Ray; Levy, Michael Z; Smith, Gary

    2015-06-30

    Innovative approaches are needed to combat the illegal trade in wildlife. Here, we used network analysis and a new database, HealthMap Wildlife Trade, to identify the key nodes (countries) that support the illegal wildlife trade. We identified key exporters and importers from the number of shipments a country sent and received and from the number of connections a country had to other countries over a given time period. We used flow betweenness centrality measurements to identify key intermediary countries. We found the set of nodes whose removal from the network would cause the maximum disruption to the network. Selecting six nodes would fragment 89.5% of the network for elephants, 92.3% for rhinoceros, and 98.1% for tigers. We then found sets of nodes that would best disseminate an educational message via direct connections through the network. We would need to select 18 nodes to reach 100% of the elephant trade network, 16 nodes for rhinoceros, and 10 for tigers. Although the choice of locations for interventions should be customized for the animal and the goal of the intervention, China was the most frequently selected country for network fragmentation and information dissemination. Identification of key countries will help strategize illegal wildlife trade interventions.

  19. A matter of definition--key elements identified in a discourse analysis of definitions of palliative care.

    PubMed

    Pastrana, T; Jünger, S; Ostgathe, C; Elsner, F; Radbruch, L

    2008-04-01

    For more than 30 years, the term "palliative care" has been used. From the outset, the term has undergone a series of transformations in its definitions and consequently in its tasks and goals. There remains a lack of consensus on a definition. The aim of this article is to analyse the definitions of palliative care in the specialist literature and to identify the key elements of palliative care using discourse analysis: a qualitative methodology. The literature search focused on definitions of the term 'palliative medicine' and 'palliative care' in the World Wide Web and medical reference books in English and German. A total of 37 English and 26 German definitions were identified and analysed. Our study confirmed the lack of a consistent meaning concerning the investigated terms, reflecting on-going discussion about the nature of the field among palliative care practitioners. Several common key elements were identified. Four main categories emerged from the discourse analysis of the definition of palliative care: target groups, structure, tasks and expertise. In addition, the theoretical principles and goals of palliative care were discussed and found to be key elements, with relief and prevention of suffering and improvement of quality of life as main goals. The identified key elements can contribute to the definition of the concept 'palliative care'. Our study confirms the importance of semantic and ethical influences on palliative care that should be considered in future research on semantics in different languages.

  20. Qualitative research methods: key features and insights gained from use in infection prevention research.

    PubMed

    Forman, Jane; Creswell, John W; Damschroder, Laura; Kowalski, Christine P; Krein, Sarah L

    2008-12-01

    Infection control professionals and hospital epidemiologists are accustomed to using quantitative research. Although quantitative studies are extremely important in the field of infection control and prevention, often they cannot help us explain why certain factors affect the use of infection control practices and identify the underlying mechanisms through which they do so. Qualitative research methods, which use open-ended techniques, such as interviews, to collect data and nonstatistical techniques to analyze it, provide detailed, diverse insights of individuals, useful quotes that bring a realism to applied research, and information about how different health care settings operate. Qualitative research can illuminate the processes underlying statistical correlations, inform the development of interventions, and show how interventions work to produce observed outcomes. This article describes the key features of qualitative research and the advantages that such features add to existing quantitative research approaches in the study of infection control. We address the goal of qualitative research, the nature of the research process, sampling, data collection and analysis, validity, generalizability of findings, and presentation of findings. Health services researchers are increasingly using qualitative methods to address practical problems by uncovering interacting influences in complex health care environments. Qualitative research methods, applied with expertise and rigor, can contribute important insights to infection prevention efforts.

  1. Institutional Research: The Key to Successful Enrollment Management.

    ERIC Educational Resources Information Center

    Clagett, Craig A.

    Enrollment management includes the processes and activities that influence the size, shape, and characteristics of a student body by directing institutional efforts in marketing, recruitment, admissions, pricing, and financial aid. Institutional research plays an essential, if not the key, role in enrollment management. This report discusses the…

  2. Researchers Identify Early Sign of Pancreatic Cancer

    MedlinePlus

    ... study with Matthew Vander Heiden, MD, PhD , of MIT and Dana-Farber. “Detecting the disease earlier in ... the Koch Institute for Integrative Cancer Research at MIT. Their experiments showed that mice with newly formed ...

  3. A Provably Secure Revocable ID-Based Authenticated Group Key Exchange Protocol with Identifying Malicious Participants

    PubMed Central

    Tsai, Tung-Tso

    2014-01-01

    The existence of malicious participants is a major threat for authenticated group key exchange (AGKE) protocols. Typically, there are two detecting ways (passive and active) to resist malicious participants in AGKE protocols. In 2012, the revocable identity- (ID-) based public key system (R-IDPKS) was proposed to solve the revocation problem in the ID-based public key system (IDPKS). Afterwards, based on the R-IDPKS, Wu et al. proposed a revocable ID-based AGKE (RID-AGKE) protocol, which adopted a passive detecting way to resist malicious participants. However, it needs three rounds and cannot identify malicious participants. In this paper, we fuse a noninteractive confirmed computation technique to propose the first two-round RID-AGKE protocol with identifying malicious participants, which is an active detecting way. We demonstrate that our protocol is a provably secure AGKE protocol with forward secrecy and can identify malicious participants. When compared with the recently proposed ID/RID-AGKE protocols, our protocol possesses better performance and more robust security properties. PMID:24991641

  4. Identifying and Avoiding Bias in Research

    PubMed Central

    Pannucci, Christopher J.; Wilkins, Edwin G.

    2010-01-01

    This narrative review provides an overview on the topic of bias as part of Plastic and Reconstructive Surgery's series of articles on evidence-based medicine. Bias can occur in the planning, data collection, analysis, and publication phases of research. Understanding research bias allows readers to critically and independently review the scientific literature and avoid treatments which are suboptimal or potentially harmful. A thorough understanding of bias and how it affects study results is essential for the practice of evidence-based medicine. PMID:20679844

  5. Key informant views on biobanking and genomic research with Māori.

    PubMed

    Hudson, Maui; Southey, Kim; Uerata, Lynley; Beaton, Angela; Milne, Moe; Russell, Khyla; Smith, Barry; Wilcox, Phillip; Toki, Valmaine; Cheung, Melanie

    2016-12-16

    The aim of the Te Mata Ira project was to explore Māori views on biobanking and genomic research, and to identify ways to address Māori concerns over the collection and use of human tissue. Key informant interviews and workshops were conducted with Māori to identify Māori views in relation to biobanking and genomic research; and, informed by these views, interviews and workshops were conducted with Māori and non-Māori key informants (Indigenous Advisory Panel (IAP) members and science communities) to explore key issues in relation to Māori participation in biobanking and genomic research. Māori key informants identified the following as key deliberations: (1) the tension for Māori between previous well-publicised negative experiences with genomic research and the potential value for whānau and communities as technologies develop, (2) protection of Māori rights and interest, (3) focus on Māori health priorities, (4) control of samples and data, (5) expectations of consultation and consent and (6) a desire for greater feedback and communication. Māori and non-Māori key informants highlighted the need to enhance levels of Māori participation in the governance of genomic research and biobanking initiatives, and acknowledged that only by increasing the level of transparency and accountability in relation to these activities will Māori communities feel that their whakapapa, rights and interests are being appropriately protected.

  6. Identifying key performance indicators for nursing and midwifery care using a consensus approach.

    PubMed

    McCance, Tanya; Telford, Lorna; Wilson, Julie; Macleod, Olive; Dowd, Audrey

    2012-04-01

    The aim of this study was to gain consensus on key performance indicators that are appropriate and relevant for nursing and midwifery practice in the current policy context. There is continuing demand to demonstrate effectiveness and efficiency in health and social care and to communicate this at boardroom level. Whilst there is substantial literature on the use of clinical indicators and nursing metrics, there is less evidence relating to indicators that reflect the patient experience. A consensus approach was used to identify relevant key performance indicators. A nominal group technique was used comprising two stages: a workshop involving all grades of nursing and midwifery staff in two HSC trusts in Northern Ireland (n = 50); followed by a regional Consensus Conference (n = 80). During the workshop, potential key performance indicators were identified. This was used as the basis for the Consensus Conference, which involved two rounds of consensus. Analysis was based on aggregated scores that were then ranked. Stage one identified 38 potential indicators and stage two prioritised the eight top-ranked indicators as a core set for nursing and midwifery. The relevance and appropriateness of these indicators were confirmed with nurses and midwives working in a range of settings and from the perspective of service users. The eight indicators identified do not conform to the majority of other nursing metrics generally reported in the literature. Furthermore, they are strategically aligned to work on the patient experience and are reflective of the fundamentals of nursing and midwifery practice, with the focus on person-centred care. Nurses and midwives have a significant contribution to make in determining the extent to which these indicators are achieved in practice. Furthermore, measurement of such indicators provides an opportunity to evidence of the unique impact of nursing/midwifery care on the patient experience. © 2011 Blackwell Publishing Ltd.

  7. Gene expression analysis at multiple time-points identifies key genes for nerve regeneration.

    PubMed

    Pan, Bin; Liu, Yi; Yan, Jia-Yin; Wang, Yao; Yao, Xue; Zhou, Heng-Xing; Lu, Lu; Kong, Xiao-Hong; Feng, Shi-Qing

    2017-03-01

    The purpose of this study was to provide a comprehensive understanding of gene expression during Wallerian degeneration and axon regeneration after peripheral nerve injury. A microarray was used to detect gene expression in the distal nerve 0, 3, 7, and 14 days after sciatic nerve crush. Bioinformatic analysis was used to predict function of the differentially expressed mRNAs. Microarray results and the key pathways were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Differentially expressed mRNAs at different time-points (3, 7, and 14 days) after injury were identified and compared with a control group (0 day). Nine general trends of changes in gene expression were identified. Key signal pathways and 9 biological processes closely associated with nerve regeneration were identified and verified. Differentially expressed genes and biological processes and pathways associated with axonal regeneration may elucidate the molecular-biological mechanisms underlying peripheral nerve regeneration. Muscle Nerve 55: 373-383, 2017. © 2016 Wiley Periodicals, Inc.

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

    PubMed

    Moran, Lisa J; Spencer, Laura; Russell, Darryl L; Hull, Mary Louise; Robertson, Sarah A; Varcoe, Tamara J; Davies, Michael J; Brown, Hannah M; Rodgers, Raymond J

    2016-01-13

    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.

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

    PubMed Central

    Moran, Lisa J.; Spencer, Laura; Russell, Darryl L.; Hull, Mary Louise; Robertson, Sarah A.; Varcoe, Tamara J.; Davies, Michael J.; Brown, Hannah M.; Rodgers, Raymond J.

    2016-01-01

    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. PMID:26771633

  10. Differential pathway network analysis used to identify key pathways associated with pediatric pneumonia.

    PubMed

    Yang, Jun-Bo; Luo, Rong; Yan, Yan; Chen, Yan

    2016-12-01

    We aimed to identify key pathways to further explore the molecular mechanism underlying pediatric pneumonia using differential pathway network which integrated protein-protein interactions (PPI) data and pathway information. PPI data and pathway information were obtained from STRING and Reactome database, respectively. Next, pathway interactions were identified on the basis of constructing gene-gene interactions randomly, and a weight value computed using Spearman correlation coefficient was assigned to each pathway-pathway interaction, thereby to further detect differential pathway interactions. Subsequently, construction of differential pathway network was implemented using Cytoscope, following by network clustering analysis using ClusterONE. Finally, topological analysis for differential pathway network was performed to identify hub pathway which had top 5% degree distribution. Significantly, 901 pathways were identified to construct pathway interactions. After discarding the pathway interactions with weight value < 1.2, a differential pathway network was constructed, which contained 499 interactions and 347 pathways. Topological analysis showed 17 hub pathways (FGFR1 fusion mutants, molecules associated with elastic fibres, FGFR1 mutant receptor activation, and so on) were identified. Significantly, signaling by FGFR1 fusion mutants and FGFR1 mutant receptor activation simultaneously appeared in two clusters. Molecules associated with elastic fibres existed in one cluster. Accordingly, differential pathway network method might serve as a predictive tool to help us to further understand the development of pediatric pneumonia. FGFR1 fusion mutants, FGFR1 mutant receptor activation, and molecules associated with elastic fibres might play important roles in the progression of pediatric pneumonia.

  11. Identifying and characterizing key nodes among communities based on electrical-circuit networks.

    PubMed

    Zhu, Fenghui; Wang, Wenxu; Di, Zengru; Fan, Ying

    2014-01-01

    Complex networks with community structures are ubiquitous in the real world. Despite many approaches developed for detecting communities, we continue to lack tools for identifying overlapping and bridging nodes that play crucial roles in the interactions and communications among communities in complex networks. Here we develop an algorithm based on the local flow conservation to effectively and efficiently identify and distinguish the two types of nodes. Our method is applicable in both undirected and directed networks without a priori knowledge of the community structure. Our method bypasses the extremely challenging problem of partitioning communities in the presence of overlapping nodes that may belong to multiple communities. Due to the fact that overlapping and bridging nodes are of paramount importance in maintaining the function of many social and biological networks, our tools open new avenues towards understanding and controlling real complex networks with communities accompanied with the key nodes.

  12. Identifying and Characterizing Key Nodes among Communities Based on Electrical-Circuit Networks

    PubMed Central

    Zhu, Fenghui; Wang, Wenxu; Di, Zengru; Fan, Ying

    2014-01-01

    Complex networks with community structures are ubiquitous in the real world. Despite many approaches developed for detecting communities, we continue to lack tools for identifying overlapping and bridging nodes that play crucial roles in the interactions and communications among communities in complex networks. Here we develop an algorithm based on the local flow conservation to effectively and efficiently identify and distinguish the two types of nodes. Our method is applicable in both undirected and directed networks without a priori knowledge of the community structure. Our method bypasses the extremely challenging problem of partitioning communities in the presence of overlapping nodes that may belong to multiple communities. Due to the fact that overlapping and bridging nodes are of paramount importance in maintaining the function of many social and biological networks, our tools open new avenues towards understanding and controlling real complex networks with communities accompanied with the key nodes. PMID:24897125

  13. Systematically identify key genes in inflammatory and non-inflammatory breast cancer.

    PubMed

    Chai, Fan; Liang, Yan; Zhang, Fan; Wang, Minghao; Zhong, Ling; Jiang, Jun

    2016-01-10

    Although the gene expression in breast tumor stroma, playing a critical role in determining inflammatory breast cancer (IBC) phenotype, has been proved to be significantly different between IBC and non-inflammatory breast cancer (non-IBC), more effort needs to systematically investigate the gene expression profiles between tumor epithelium and stroma and to efficiently uncover the potential molecular networks and critical genes for IBC and non-IBC. Here, we comprehensively analyzed and compared the transcriptional profiles from IBC and non-IBC patients using hierarchical clustering, protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses, and identified PDGFRβ, SUMO1, COL1A1, FYN, CAV1, COL5A1 and MMP2 to be the key genes for breast cancer. Interestingly, PDGFRβ was found to be the hub gene in both IBC and non-IBC; SUMO1 and COL1A1 were respectively the key genes for IBC and non-IBC. These analysis results indicated that those key genes might play important role in IBC and non-IBC and provided some clues for future studies.

  14. Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph.

    PubMed

    Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

    2016-01-01

    In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks' price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds.

  15. Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph

    PubMed Central

    Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

    2016-01-01

    In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks’ price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds. PMID:27893780

  16. Key Stakeholders' Perceptions of Motivators for Research Participation Among Individuals Who Are Incarcerated.

    PubMed

    Hanson, Bridget L; Faulkner, Sherilyn A; Brems, Christiane; Corey, Staci L; Eldridge, Gloria D; Johnson, Mark E

    2015-10-01

    Understanding motivations of research participants is crucial for developing ethical research protocols, especially for research with vulnerable populations. Through interviews with 92 institutional review board members, prison administrators, research ethicists, and researchers, we explored key stakeholders' perceptions of what motivates incarcerated individuals to participate in research. Primary motivators identified were a desire to contribute to society, gaining knowledge and health care, acquiring incentives, and obtaining social support. The potential for undue influence or coercion were also identified as motivators. These results highlight the need for careful analysis of what motivates incarcerated individuals to participate in research as part of developing or reviewing ethically permissible and responsible research protocols. Future research should expand this line of inquiry to directly include perspectives of incarcerated individuals. © The Author(s) 2015.

  17. Key Stakeholders’ Perceptions of Motivators for Research Participation among Individuals who are Incarcerated

    PubMed Central

    Hanson, Bridget L.; Faulkner, Sherilyn A.; Brems, Christiane; Corey, Staci L.; Eldridge, Gloria D.; Johnson, Mark E.

    2015-01-01

    Understanding motivations of research participants is crucial for developing ethical research protocols, especially for research with vulnerable populations. Through interviews with 92 IRB members, prison administrators, research ethicists, and researchers, we explored key stakeholders’ perceptions of what motivates incarcerated individuals to participate in research. Primary motivators identified were a desire to contribute to society, gaining knowledge and healthcare, acquiring incentives, and obtaining social support. The potential for undue influence or coercion were also identified as motivators. These results highlight the need for careful analysis of what motivates incarcerated individuals to participate in research as part of developing or reviewing ethically permissible and responsible research protocols. Future research should expand this line of inquiry to directly include perspectives of incarcerated individuals. PMID:26283681

  18. A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18.

    PubMed

    Yang, Zhaoshou; Hou, Yongheng; Hao, Taofang; Rho, Hee-Sool; Wan, Jun; Luan, Yizhao; Gao, Xin; Yao, Jianping; Pan, Aihua; Xie, Zhi; Qian, Jiang; Liao, Wanqin; Zhu, Heng; Zhou, Xingwang

    2017-03-01

    Toxoplasma kinase ROP18 is a key molecule responsible for the virulence of Toxoplasma gondii; however, the mechanisms by which ROP18 exerts parasite virulence via interaction with host proteins remain limited to a small number of identified substrates. To identify a broader array of ROP18 substrates, we successfully purified bioactive mature ROP18 and used it to probe a human proteome array. Sixty eight new putative host targets were identified. Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. Among these proteins, four candidates, p53, p38, UBE2N, and Smad1, were further validated. We demonstrated that ROP18 targets p53, p38, UBE2N, and Smad1 for degradation. Importantly, we demonstrated that ROP18 phosphorylates Smad1 Ser-187 to trigger its proteasome-dependent degradation. Further functional characterization of the substrates of ROP18 may enhance understanding of the pathogenesis of Toxoplasma infection and provide new therapeutic targets. Similar strategies could be used to identify novel host targets for other microbial kinases functioning at the pathogen-host interface.

  19. Research on the architecture and key technologies of SIG

    NASA Astrophysics Data System (ADS)

    Fu, Zhongliang; Meng, Qingxiang; Huang, Yan; Liu, Shufan

    2007-06-01

    Along with the development of computer network, Grid has become one of the hottest issues of researches on sharing and cooperation of Internet resources throughout the world. This paper illustrates a new architecture of SIG-a five-hierarchy architecture (including Data Collecting Layer, Grid Layer, Service Layer, Application Layer and Client Layer) of SIG from the traditional three hierarchies (only including resource layer, service layer and client layer). In the paper, the author proposes a new mixed network mode of Spatial Information Grid which integrates CAG (Certificate Authority of Grid) and P2P (Peer to Peer) in the Grid Layer, besides, the author discusses some key technologies of SIG and analysis the functions of these key technologies.

  20. Identifying the key factors affecting warning message dissemination in VANET real urban scenarios.

    PubMed

    Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J; Cano, Juan-Carlos; Calafate, Carlos T; Manzoni, Pietro

    2013-04-19

    In recent years, new architectures and technologies have been proposed for Vehicular Ad Hoc networks (VANETs). Due to the cost and complexity of deploying such networks, most of these proposals rely on simulation. However, we find that most of the experiments made to validate these proposals tend to overlook the most important and representative factors. Moreover, the scenarios simulated tend to be very simplistic (highways or Manhattan-based layouts), which could seriously affect the validity of the obtained results. In this paper, we present a statistical analysis based on the 2k factorial methodology to determine the most representative factors affecting traffic safety applications under real roadmaps. Our purpose is to determine which are the key factors affecting Warning Message Dissemination in order to concentrate research tests on such parameters, thus avoiding unnecessary simulations and reducing the amount of simulation time required. Simulation results show that the key factors affecting warning messages delivery are the density of vehicles and the roadmap used. Based on this statistical analysis, we consider that VANET researchers must evaluate the benefits of their proposals using different vehicle densities and city scenarios, to obtain a broad perspective on the effectiveness of their solution. Finally, since city maps can be quite heterogeneous, we propose a roadmap profile classification to further reduce the number of cities evaluated.

  1. Identifying the Key Factors Affecting Warning Message Dissemination in VANET Real Urban Scenarios

    PubMed Central

    Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J.; Cano, Juan-Carlos; Calafate, Carlos T.; Manzoni, Pietro

    2013-01-01

    In recent years, new architectures and technologies have been proposed for Vehicular Ad Hoc networks (VANETs). Due to the cost and complexity of deploying such networks, most of these proposals rely on simulation. However, we find that most of the experiments made to validate these proposals tend to overlook the most important and representative factors. Moreover, the scenarios simulated tend to be very simplistic (highways or Manhattan-based layouts), which could seriously affect the validity of the obtained results. In this paper, we present a statistical analysis based on the 2k factorial methodology to determine the most representative factors affecting traffic safety applications under real roadmaps. Our purpose is to determine which are the key factors affecting Warning Message Dissemination in order to concentrate research tests on such parameters, thus avoiding unnecessary simulations and reducing the amount of simulation time required. Simulation results show that the key factors affecting warning messages delivery are the density of vehicles and the roadmap used. Based on this statistical analysis, we consider that VANET researchers must evaluate the benefits of their proposals using different vehicle densities and city scenarios, to obtain a broad perspective on the effectiveness of their solution. Finally, since city maps can be quite heterogeneous, we propose a roadmap profile classification to further reduce the number of cities evaluated. PMID:23604026

  2. Key-linked on-line databases for clinical research.

    PubMed

    Müller, Thomas H

    2012-01-01

    Separating patient identification data from clinical data and/or information about biomaterial samples is an effective data protection measure, especially in clinical research employing "on-line", i.e., web-based, data capture. In this paper, we show that this specialised technique can be generalised into a network architecture of interconnected on-line databases potentially serving a variety of purposes. The basic idea of this approach consists of maintaining logical links, i.e., common record keys, between corresponding data structures in pairs of databases while keeping the actual key values hidden from clients. For client systems, simultaneous access to corresponding records is mediated by temporary access tokens. At the relational level, these links are represented by arbitrary unique record keys common to both databases. This architecture allows for integration of related data in different databases without replicating or permanently sharing this data in one place. Each participating on-line database can determine the degree of integration by specifying linkage keys only for those data structures that may be logically connected to other data. Logical links can de designed for specific use cases. In addition, each database controls user access by enforcing its own authorisation scheme. Another advantage is that individual database owners retain considerable leeway in adapting to changing local requirements without compromising the integration into the network. Beyond protecting individual subject identification data, this architecture permits splitting a cooperatively used data pool to achieve many kinds of objectives. Application examples could be clinical registries needing subject contact information for follow-up, biomaterial banks with or without genetic information, and automatic or assisted integration of data from electronic medical records into research data.

  3. Quality of Dementia Care in the Community: Identifying Key Quality Assurance Components

    PubMed Central

    Heckman, George A.; Boscart, Veronique M.; Franco, Bryan B.; Hillier, Loretta; Crutchlow, Lauren; Lee, Linda; Molnar, Frank; Seitz, Dallas; Stolee, Paul

    2016-01-01

    Background Primary care-based memory clinics (PCMCs) have been established in several jurisdictions to improve the care for persons with Alzheimer’s disease and related dementias. We sought to identify key quality indicators (QIs), quality improvement mechanisms, and potential barriers and facilitators to the establishment of a quality assurance framework for PCMCs. Methods We employed a Delphi approach to obtain consensus from PCMC clinicians and specialist physicians on QIs and quality improvement mechanisms. Thirty-eight candidate QIs and 19 potential quality improvement mechanisms were presented to participants in two rounds of electronic Delphi surveys. Written comments were collected and descriptively analyzed. Results The response rate for the first and second rounds were 21.3% (n = 179) and 12.8% (n = 88), respectively. The majority of respondents were physicians. Fourteen QIs remained after the consensus process. Ten quality improvement mechanisms were selected with those characterized by specialist integration, such as case discussions and mentorships, being ranked highly. Written comments revealed three major themes related to potential barriers and facilitators to quality assurance: 1) perceived importance, 2) collaboration and role clarity, and 3) implementation process. Conclusion We successfully utilized a consultative process among primary and specialty providers to identify core QIs and quality improvement mechanisms for PCMCs. Identified quality improvement mechanisms highlight desire for multi-modal education. System integration and closer integration between PCMCs and specialists were emphasized as essential for the provision of high-quality dementia care in community settings. PMID:28050221

  4. Identifying key radiogenomic associations between DCE-MRI and micro-RNA expressions for breast cancer

    NASA Astrophysics Data System (ADS)

    Samala, Ravi K.; Chan, Heang-Ping; Hadjiiski, Lubomir; Helvie, Mark A.; Kim, Renaid

    2017-03-01

    Understanding the key radiogenomic associations for breast cancer between DCE-MRI and micro-RNA expressions is the foundation for the discovery of radiomic features as biomarkers for assessing tumor progression and prognosis. We conducted a study to analyze the radiogenomic associations for breast cancer using the TCGA-TCIA data set. The core idea that tumor etiology is a function of the behavior of miRNAs is used to build the regression models. The associations based on regression are analyzed for three study outcomes: diagnosis, prognosis, and treatment. The diagnosis group consists of miRNAs associated with clinicopathologic features of breast cancer and significant aberration of expression in breast cancer patients. The prognosis group consists of miRNAs which are closely associated with tumor suppression and regulation of cell proliferation and differentiation. The treatment group consists of miRNAs that contribute significantly to the regulation of metastasis thereby having the potential to be part of therapeutic mechanisms. As a first step, important miRNA expressions were identified and their ability to classify the clinical phenotypes based on the study outcomes was evaluated using the area under the ROC curve (AUC) as a figure-of-merit. The key mapping between the selected miRNAs and radiomic features were determined using least absolute shrinkage and selection operator (LASSO) regression analysis within a two-loop leave-one-out cross-validation strategy. These key associations indicated a number of radiomic features from DCE-MRI to be potential biomarkers for the three study outcomes.

  5. [Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

    PubMed

    Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

    2012-07-01

    In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

  6. Identifying Regional Key Eco-Space to Maintain Ecological Security Using GIS

    PubMed Central

    Xie, Hualin; Yao, Guanrong; Wang, Peng

    2014-01-01

    Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm2, accounting for 40% of the region’s total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability. PMID:24590051

  7. Identifying regional key eco-space to maintain ecological security using GIS.

    PubMed

    Xie, Hualin; Yao, Guanrong; Wang, Peng

    2014-02-28

    Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm(2), accounting for 40% of the region's total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability.

  8. A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas.

    PubMed

    Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti

    2011-01-01

    Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.

  9. Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies.

    PubMed

    Le Large, T Y S; Bijlsma, M F; Kazemier, G; van Laarhoven, H W M; Giovannetti, E; Jimenez, C R

    2017-06-01

    Pancreatic ductal adenocarcinoma (PDAC) is an extremely aggressive malignancy, characterized by a high metastatic burden, already at the time of diagnosis. The metastatic potential of PDAC is one of the main reasons for the poor outcome next to lack of significant improvement in effective treatments in the last decade. Key mutated driver genes, such as activating KRAS mutations, are concordantly expressed in primary and metastatic tumors. However, the biology behind the metastatic potential of PDAC is not fully understood. Recently, large-scale omic approaches have revealed new mechanisms by which PDAC cells gain their metastatic potency. In particular, genomic studies have shown that multiple heterogeneous subclones reside in the primary tumor with different metastatic potential. The development of metastases may be correlated to a more mesenchymal transcriptomic subtype. However, for cancer cells to survive in a distant organ, metastatic sites need to be modulated into pre-metastatic niches. Proteomic studies identified the influence of exosomes on the Kuppfer cells in the liver, which could function to prepare this tissue for metastatic colonization. Phosphoproteomics adds an extra layer to the established omic techniques by unravelling key functional signaling. Future studies integrating results from these large-scale omic approaches will hopefully improve PDAC prognosis through identification of new therapeutic targets and patient selection tools. In this article, we will review the current knowledge on the biology of PDAC metastasis unravelled by large scale multi-omic approaches. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  10. Diversity in research projects - A key to success?

    NASA Astrophysics Data System (ADS)

    Henkel, Daniela; Eisenhauer, Anton; Taubner, Isabelle

    2017-04-01

    According to demographers, psychologists, sociologists and economists diverse groups, which are groups of different race, ethnicity, gender and sexual orientation, are more innovative than homogeneous groups. This is also true for groups working together in research collaborations and international cooperation involving a culturally and functionally diverse mix of individuals who have to be integrated into an effective unit - a project team. If the goal is scientific excellence, diversity should be an essential ingredient to conduct science on high level productivity, quality and innovation. Effective teamwork is a key to project success and prime responsibilities of the project manager. Therefore, the project manager has to take into consideration different characteristics such as cultures, languages, and different values related to individual project partners. Here we show how diversity can affect the performance of a research project. Furthermore, the presentation indicates skills and abilities which are required for the management in order to deal also with the challenges of diversity in research projects. The presentation is based on insights experienced in the context of an Innovative Training Network (ITN) project within Marie Skłodowska-Curie Actions of the European HORIZON 2020 program and TRION a Collaborative Research Project in the Framework of the Trilateral Program of the German Research Foundation.

  11. WE-F-201-01: Identify Key Clinical Applications Needing Advanced Dose Calculation in Brachytherapy

    SciTech Connect

    Fulkerson, R.

    2015-06-15

    With the recent introduction of heterogeneity correction algorithms for brachytherapy, the AAPM community is still unclear on how to commission and implement these into clinical practice. The recently-published AAPM TG-186 report discusses important issues for clinical implementation of these algorithms. A charge of the AAPM-ESTRO-ABG Working Group on MBDCA in Brachytherapy (WGMBDCA) is the development of a set of well-defined test case plans, available as references in the software commissioning process to be performed by clinical end-users. In this practical medical physics course, specific examples on how to perform the commissioning process are presented, as well as descriptions of the clinical impact from recent literature reporting comparisons of TG-43 and heterogeneity-based dosimetry. Learning Objectives: Identify key clinical applications needing advanced dose calculation in brachytherapy. Review TG-186 and WGMBDCA guidelines, commission process, and dosimetry benchmarks. Evaluate clinical cases using commercially available systems and compare to TG-43 dosimetry.

  12. Key metabolites in tissue extracts of Elliptio complanata identified using (1)H nuclear magnetic resonance spectroscopy.

    PubMed

    Hurley-Sanders, Jennifer L; Levine, Jay F; Nelson, Stacy A C; Law, J M; Showers, William J; Stoskopf, Michael K

    2015-01-01

    We used (1)H nuclear magnetic resonance spectroscopy to describe key metabolites of the polar metabolome of the freshwater mussel, Elliptio complanata. Principal components analysis documented variability across tissue types and river of origin in mussels collected from two rivers in North Carolina (USA). Muscle, digestive gland, mantle and gill tissues yielded identifiable but overlapping metabolic profiles. Variation in digestive gland metabolic profiles between the two mussel collection sites was characterized by differences in mono- and disaccharides. Variation in mantle tissue metabolomes appeared to be associated with sex. Nuclear magnetic resonance spectroscopy is a sensitive means to detect metabolites in the tissues of E. complanata and holds promise as a tool for the investigation of freshwater mussel health and physiology.

  13. Key metabolites in tissue extracts of Elliptio complanata identified using 1H nuclear magnetic resonance spectroscopy

    PubMed Central

    Hurley-Sanders, Jennifer L.; Levine, Jay F.; Nelson, Stacy A. C.; Law, J. M.; Showers, William J.; Stoskopf, Michael K.

    2015-01-01

    We used 1H nuclear magnetic resonance spectroscopy to describe key metabolites of the polar metabolome of the freshwater mussel, Elliptio complanata. Principal components analysis documented variability across tissue types and river of origin in mussels collected from two rivers in North Carolina (USA). Muscle, digestive gland, mantle and gill tissues yielded identifiable but overlapping metabolic profiles. Variation in digestive gland metabolic profiles between the two mussel collection sites was characterized by differences in mono- and disaccharides. Variation in mantle tissue metabolomes appeared to be associated with sex. Nuclear magnetic resonance spectroscopy is a sensitive means to detect metabolites in the tissues of E. complanata and holds promise as a tool for the investigation of freshwater mussel health and physiology. PMID:27293708

  14. Identifying the key factors that affect the formation of humic substance during different materials composting.

    PubMed

    Wu, Junqiu; Zhao, Yue; Qi, Haishi; Zhao, Xinyu; Yang, Tianxue; Du, Yingqiu; Zhang, Hui; Wei, Zimin

    2017-11-01

    The aim of this work was to identify the factors which can affect humic substance (HS) formation. Composting periods, HS precursors, bacteria communities and environment factors were recognized as the key factors and few studies explored the potential relationships among them. During composting, HS precursors were mainly formed in the heating and thermophilic phases, but HS were polymerized in the cooling and mature phases. Moreover, bacterial species showed similar classification of community structure in the same composting period of different materials. Furthermore, structural equation model showed that NH4(-)-N and NO3(-)-N were the indirect environmental factors for regulating HS formation by the bacteria and precursors as the indirect and direct driver, respectively. Therefore, both environmental factors and HS precursors can be the regulating factors to promote HS formation. Given that, a new staging regulating method had been proposed to improve the amount of HS during different materials composting. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Exploring the effects of spatial autocorrelation when identifying key drivers of wildlife crop-raiding

    PubMed Central

    Songhurst, Anna; Coulson, Tim

    2014-01-01

    Few universal trends in spatial patterns of wildlife crop-raiding have been found. Variations in wildlife ecology and movements, and human spatial use have been identified as causes of this apparent unpredictability. However, varying spatial patterns of spatial autocorrelation (SA) in human–wildlife conflict (HWC) data could also contribute. We explicitly explore the effects of SA on wildlife crop-raiding data in order to facilitate the design of future HWC studies. We conducted a comparative survey of raided and nonraided fields to determine key drivers of crop-raiding. Data were subsampled at different spatial scales to select independent raiding data points. The model derived from all data was fitted to subsample data sets. Model parameters from these models were compared to determine the effect of SA. Most methods used to account for SA in data attempt to correct for the change in P-values; yet, by subsampling data at broader spatial scales, we identified changes in regression estimates. We consequently advocate reporting both model parameters across a range of spatial scales to help biological interpretation. Patterns of SA vary spatially in our crop-raiding data. Spatial distribution of fields should therefore be considered when choosing the spatial scale for analyses of HWC studies. Robust key drivers of elephant crop-raiding included raiding history of a field and distance of field to a main elephant pathway. Understanding spatial patterns and determining reliable socio-ecological drivers of wildlife crop-raiding is paramount for designing mitigation and land-use planning strategies to reduce HWC. Spatial patterns of HWC are complex, determined by multiple factors acting at more than one scale; therefore, studies need to be designed with an understanding of the effects of SA. Our methods are accessible to a variety of practitioners to assess the effects of SA, thereby improving the reliability of conservation management actions. PMID:25035800

  16. Identifying sensitive sources and key control handles for the reduction of greenhouse gas emissions from wastewater treatment.

    PubMed

    Sweetapple, Christine; Fu, Guangtao; Butler, David

    2014-10-01

    This research investigates the effects of adjusting control handle values on greenhouse gas emissions from wastewater treatment, and reveals critical control handles and sensitive emission sources for control through the combined use of local and global sensitivity analysis methods. The direction of change in emissions, effluent quality and operational cost resulting from variation of control handles individually is determined using one-factor-at-a-time sensitivity analysis, and corresponding trade-offs are identified. The contribution of each control handle to variance in model outputs, taking into account the effects of interactions, is then explored using a variance-based sensitivity analysis method, i.e., Sobol's method, and significant second order interactions are discovered. This knowledge will assist future control strategy development and aid an efficient design and optimisation process, as it provides a better understanding of the effects of control handles on key performance indicators and identifies those for which dynamic control has the greatest potential benefits. Sources with the greatest variance in emissions, and therefore the greatest need to monitor, are also identified. It is found that variance in total emissions is predominantly due to changes in direct N2O emissions and selection of suitable values for wastage flow rate and aeration intensity in the final activated sludge reactor is of key importance. To improve effluent quality, costs and/or emissions, it is necessary to consider the effects of adjusting multiple control handles simultaneously and determine the optimum trade-off.

  17. Transcriptional Profiling of Hmgb1-Induced Myocardial Repair Identifies a Key Role for Notch Signaling

    PubMed Central

    Limana, Federica; Esposito, Grazia; Fasanaro, Pasquale; Foglio, Eleonora; Arcelli, Diego; Voellenkle, Christine; Di Carlo, Anna; Avitabile, Daniele; Martelli, Fabio; Antonio Russo, Matteo; Pompilio, Giulio; Germani, Antonia; C Capogrossi, Maurizio

    2013-01-01

    Exogenous high-mobility group box 1 protein (HMGB1) administration to the mouse heart, during acute myocardial infarction (MI), results in cardiac regeneration via resident c-kit+ cell (CPC) activation. Aim of the present study was to identify the molecular pathways involved in HMGB1-induced heart repair. Gene expression profiling was performed to identify differentially expressed genes in the infarcted and bordering regions of untreated and HMGB1-treated mouse hearts, 3 days after MI. Functional categorization of the transcripts, accomplished using Ingenuity Pathway Analysis software (IPA), revealed that genes involved in tissue regeneration, that is, cardiogenesis, vasculogenesis and angiogenesis, were present both in the infarcted area and in the peri-infarct zone; HMGB1 treatment further increased the expression of these genes. IPA revealed the involvement of Notch signaling pathways in HMGB1-treated hearts. Importantly, HMGB1 determined a 35 and 58% increase in cardiomyocytes and CPCs expressing Notch intracellular cytoplasmic domain, respectively. Further, Notch inhibition by systemic treatment with the γ-secretase inhibitor DAPT, which blocked the proteolytic activation of Notch receptors, reduced the number of CPCs, their proliferative fraction, and cardiomyogenic differentiation in HMGB1-treated infarcted hearts. The present study gives insight into the molecular processes involved in HMGB1-mediated cardiac regeneration and indicates Notch signaling as a key player. PMID:23760446

  18. Key regulators in prostate cancer identified by co-expression module analysis.

    PubMed

    Jiang, Junfeng; Jia, Peilin; Zhao, Zhongming; Shen, Bairong

    2014-11-24

    Prostate cancer (PrCa) is the most commonly diagnosed cancer in men in the world. Despite the fact that a large number of its genes have been investigated, its etiology remains poorly understood. Furthermore, most PrCa candidate genes have not been rigorously replicated, and the methods by which they biologically function in PrCa remain largely unknown. Aiming to identify key players in the complex prostate cancer system, we reconstructed PrCa co-expressed modules within functional gene sets defined by the Gene Ontology (GO) annotation (biological process, GO_BP). We primarily identified 118 GO_BP terms that were well-preserved between two independent gene expression datasets and a consequent 55 conserved co-expression modules within them. Five modules were then found to be significantly enriched with PrCa candidate genes collected from expression Quantitative Trait Loci (eQTL), somatic copy number alteration (SCNA), somatic mutation data, or prognostic analyses. Specifically, two transcription factors (TFs) (NFAT and SP1) and three microRNAs (hsa-miR-19a, hsa-miR-15a, and hsa-miR-200b) regulating these five candidate modules were found to be critical to the development of PrCa. Collectively, our results indicated that genes with similar functions may play important roles in disease through co-expression, and modules with different functions could be regulated by similar genetic components, such as TFs and microRNAs, in a synergistic manner.

  19. An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.

    PubMed

    Walsh, Logan A; Alvarez, Mariano J; Sabio, Erich Y; Reyngold, Marsha; Makarov, Vladimir; Mukherjee, Suranjit; Lee, Ken-Wing; Desrichard, Alexis; Turcan, Şevin; Dalin, Martin G; Rajasekhar, Vinagolu K; Chen, Shuibing; Vahdat, Linda T; Califano, Andrea; Chan, Timothy A

    2017-08-15

    At the root of most fatal malignancies are aberrantly activated transcriptional networks that drive metastatic dissemination. Although individual metastasis-associated genes have been described, the complex regulatory networks presiding over the initiation and maintenance of metastatic tumors are still poorly understood. There is untapped value in identifying therapeutic targets that broadly govern coordinated transcriptional modules dictating metastatic progression. Here, we reverse engineered and interrogated a breast cancer-specific transcriptional interaction network (interactome) to define transcriptional control structures causally responsible for regulating genetic programs underlying breast cancer metastasis in individual patients. Our analyses confirmed established pro-metastatic transcription factors, and they uncovered TRIM25 as a key regulator of metastasis-related transcriptional programs. Further, in vivo analyses established TRIM25 as a potent regulator of metastatic disease and poor survival outcome. Our findings suggest that identifying and targeting keystone proteins, like TRIM25, can effectively collapse transcriptional hierarchies necessary for metastasis formation, thus representing an innovative cancer intervention strategy. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

    PubMed Central

    Luisier, Raphaëlle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik

    2014-01-01

    Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and β-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesis. PMID:24464994

  1. Identifying key areas for active interprofessional learning partnerships: A facilitated dialogue.

    PubMed

    Steven, Kathryn; Angus, Allyson; Breckenridge, Jenna; Davey, Peter; Tully, Vicki; Muir, Fiona

    2016-11-01

    Student and service user involvement is recognised as an important factor in creating interprofessional education (IPE) opportunities. We used a team-based learning approach to bring together undergraduate health professional students, early career professionals (ECPs), public partners, volunteers, and carers to explore learning partnerships. Influenced by evaluative inquiry, this qualitative study used a free text response to allow participants to give their own opinion. A total of 153 participants (50 public partners and 103 students and professionals representing 11 healthcare professions) took part. Participants were divided into mixed groups of six (n = 25) and asked to identify areas where students, professionals, and public could work together to improve health professional education. Each group documented their discussions by summarising agreed areas and next steps. Responses were collected and transcribed for inductive content analysis. Seven key themes (areas for joint working) were identified: communication, public as partners, standards of conduct, IPE, quality improvement, education, and learning environments. The team-based learning format enabled undergraduate and postgraduate health professionals to achieve consensus with public partners on areas for IPE and collaboration. Some of our results may be context-specific but the approach is generalisable to other areas.

  2. Identifying Key Performance Indicators for Holistic Hospital Management with a Modified DEMATEL Approach

    PubMed Central

    Si, Sheng-Li; You, Xiao-Yue; Huang, Jia

    2017-01-01

    Performance analysis is an important way for hospitals to achieve higher efficiency and effectiveness in providing services to their customers. The performance of the healthcare system can be measured by many indicators, but it is difficult to improve them simultaneously due to the limited resources. A feasible way is to identify the central and influential indicators to improve healthcare performance in a stepwise manner. In this paper, we propose a hybrid multiple criteria decision making (MCDM) approach to identify key performance indicators (KPIs) for holistic hospital management. First, through integrating evidential reasoning approach and interval 2-tuple linguistic variables, various assessments of performance indicators provided by healthcare experts are modeled. Then, the decision making trial and evaluation laboratory (DEMATEL) technique is adopted to build an interactive network and visualize the causal relationships between the performance indicators. Finally, an empirical case study is provided to demonstrate the proposed approach for improving the efficiency of healthcare management. The results show that “accidents/adverse events”, “nosocomial infection”, ‘‘incidents/errors”, “number of operations/procedures” are significant influential indicators. Also, the indicators of “length of stay”, “bed occupancy” and “financial measures” play important roles in performance evaluation of the healthcare organization. The proposed decision making approach could be considered as a reference for healthcare administrators to enhance the performance of their healthcare institutions. PMID:28825613

  3. Identifying key parameters to differentiate groundwater flow systems using multifactorial analysis

    NASA Astrophysics Data System (ADS)

    Menció, Anna; Folch, Albert; Mas-Pla, Josep

    2012-11-01

    SummaryMultivariate techniques are useful in hydrogeological studies to reduce the complexity of large-scale data sets, and provide more understandable insight into the system hydrology. In this study, principal component analysis (PCA) has been used as an exploratory method to identify the key parameters that define distinct flow systems in the Selva basin (NE Spain). In this statistical analysis, all the information obtained in hydrogeological studies (that is, hydrochemical and isotopic data, but also potentiometric data) is used. Additionally, cluster analysis, based on PCA results, allows the associations between samples to be identified, and thus, corroborates the occurrence of different groundwater fluxes. PCA and cluster analysis reveal that two main groundwater flow systems exist in the Selva basin, each with distinct hydrochemical, isotopic, and potentiometric features. Regional groundwater fluxes are associated with high F- contents, and confined aquifer layers; while local fluxes are linked to nitrate polluted unconfined aquifers with a different recharge rates. In agreement with previous hydrogeological studies, these statistical methods stand as valid screening tools to highlight the fingerprint variables that can be used as indicators to facilitate further, more arduous, analytical approaches and a feasible interpretation of the whole data set.

  4. Identifying Key Performance Indicators for Holistic Hospital Management with a Modified DEMATEL Approach.

    PubMed

    Si, Sheng-Li; You, Xiao-Yue; Liu, Hu-Chen; Huang, Jia

    2017-08-19

    Performance analysis is an important way for hospitals to achieve higher efficiency and effectiveness in providing services to their customers. The performance of the healthcare system can be measured by many indicators, but it is difficult to improve them simultaneously due to the limited resources. A feasible way is to identify the central and influential indicators to improve healthcare performance in a stepwise manner. In this paper, we propose a hybrid multiple criteria decision making (MCDM) approach to identify key performance indicators (KPIs) for holistic hospital management. First, through integrating evidential reasoning approach and interval 2-tuple linguistic variables, various assessments of performance indicators provided by healthcare experts are modeled. Then, the decision making trial and evaluation laboratory (DEMATEL) technique is adopted to build an interactive network and visualize the causal relationships between the performance indicators. Finally, an empirical case study is provided to demonstrate the proposed approach for improving the efficiency of healthcare management. The results show that "accidents/adverse events", "nosocomial infection", ''incidents/errors", "number of operations/procedures" are significant influential indicators. Also, the indicators of "length of stay", "bed occupancy" and "financial measures" play important roles in performance evaluation of the healthcare organization. The proposed decision making approach could be considered as a reference for healthcare administrators to enhance the performance of their healthcare institutions.

  5. Key research questions of global importance for cetacean conservation

    NASA Astrophysics Data System (ADS)

    Parsons, E. C. M.

    2016-02-01

    Limited resources and increasing environmental concerns have prompted calls to identify the critical questions that most need to be answered to advance conservation, thereby providing an agenda for scientific research priorities. Cetaceans are often keystone indicator species but also high profile, charismatic flagship taxa that capture public and media attention as well as political interest. A dedicated workshop was held at the conference of the Society for Marine Mammalogy (December 2013, New Zealand) to identify where lack of data was hindering cetacean conservation and which questions need to be addressed most urgently. This paper summarizes 15 themes and component questions prioritized during the workshop. We hope this list will encourage cetacean conservation-orientated research and help agencies and policy makers to prioritize funding and future activities. This will ultimately remove some of the current obstacles to science-based cetacean conservation.

  6. Identifying Research Priorities for School Improvement in the Developing World

    ERIC Educational Resources Information Center

    Read, Robyn; Fernandez-Hermosilla, Magdalena; Anderson, Stephen; Mundy, Karen

    2016-01-01

    This paper discusses a research agenda setting project conducted for an international non-governmental organization which aims to help create a regionally relevant, high-quality knowledge base on key education issues of policy and practice. Specifically, we illustrate how our team adapted the Child Health and Nutrition Research Initiative (CHRNI)…

  7. Good Clinical Practice Training: Identifying Key Elements and Strategies for Increasing Training Efficiency.

    PubMed

    Arango, Jaime; Chuck, Tina; Ellenberg, Susan S; Foltz, Bridget; Gorman, Colleen; Hinrichs, Heidi; McHale, Susan; Merchant, Kunal; Seltzer, Jonathan; Shapley, Stephanie; Wild, Gretchen

    2016-07-01

    Good Clinical Practice (GCP) is an international standard for the design, conduct, performance, monitoring, auditing, recording, analyses, and reporting of clinical trials. The goal of GCP is to ensure the protection of the rights, integrity, and confidentiality of clinical trial participants and to ensure the credibility and accuracy of data and reported results. In the United States, trial sponsors generally require investigators to complete GCP training prior to participating in each clinical trial to foster GCP and as a method to meet regulatory expectations (ie, sponsor's responsibility to select qualified investigators per 21 CFR 312.50 and 312.53(a) for drugs and biologics and 21 CFR 812.40 and 812.43(a) for medical devices). This training requirement is often extended to investigative site staff, as deemed relevant by the sponsor, institution, or investigator. Those who participate in multiple clinical trials are often required by sponsors to complete repeated GCP training, which is unnecessarily burdensome. The Clinical Trials Transformation Initiative convened a multidisciplinary project team involving partners from academia, industry, other researchers and research staff, and government to develop recommendations for streamlining current GCP training practices. Recommendations drafted by the project team, including the minimum key training elements, frequency, format, and evidence of training completion, were presented to a broad group of experts to foster discussion of the current issues and to seek consensus on proposed solutions.

  8. Framework for Identifying Key Environmental Concerns in Marine Renewable Energy Projects- Appendices

    SciTech Connect

    Kramer, Sharon; Previsic, Mirko; Nelson, Peter; Woo, Sheri

    2010-06-17

    Marine wave and tidal energy technology could interact with marine resources in ways that are not well understood. As wave and tidal energy conversion projects are planned, tested, and deployed, a wide range of stakeholders will be engaged; these include developers, state and federal regulatory agencies, environmental groups, tribal governments, recreational and commercial fishermen, and local communities. Identifying stakeholders’ environmental concerns in the early stages of the industry’s development will help developers address and minimize potential environmental effects. Identifying important concerns will also assist with streamlining siting and associated permitting processes, which are considered key hurdles by the industry in the U.S. today. In September 2008, RE Vision consulting, LLC was selected by the Department of Energy (DoE) to conduct a scenario-based evaluation of emerging hydrokinetic technologies. The purpose of this evaluation is to identify and characterize environmental impacts that are likely to occur, demonstrate a process for analyzing these impacts, identify the “key” environmental concerns for each scenario, identify areas of uncertainty, and describe studies that could address that uncertainty. This process is intended to provide an objective and transparent tool to assist in decision-making for siting and selection of technology for wave and tidal energy development. RE Vision worked with H. T. Harvey & Associates, to develop a framework for identifying key environmental concerns with marine renewable technology. This report describes the results of this study. This framework was applied to varying wave and tidal power conversion technologies, scales, and locations. The following wave and tidal energy scenarios were considered: 4 wave energy generation technologies 3 tidal energy generation technologies 3 sites: Humboldt coast, California (wave); Makapu’u Point, Oahu, Hawaii (wave); and the Tacoma Narrows, Washington (tidal

  9. Transcriptome Analysis Identifies Key Candidate Genes Mediating Purple Ovary Coloration in Asiatic Hybrid Lilies

    PubMed Central

    Xu, Leifeng; Yang, Panpan; Yuan, Suxia; Feng, Yayan; Xu, Hua; Cao, Yuwei; Ming, Jun

    2016-01-01

    Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic “Tiny Padhye”. Comparative transcriptome analysis revealed 4228 differentially expressed genes. Differential expression analysis revealed that ten unigenes including four CHS genes, one CHI gene, one F3H gene, one F3′H gene, one DFR gene, one UFGT gene, and one 3RT gene were significantly up-regulated in purple ovaries. One MYB gene, LhMYB12-Lat, was identified as a key transcription factor determining the distribution of anthocyanins in Asiatic hybrid lily ovaries. Further qPCR results showed unigenes related to anthocyanin biosynthesis were highly expressed in purple ovaries of three purple-ovaried Asiatic hybrid lilies at stages 2 and 3, while they showed an extremely low level of expression in ovaries of three green-ovaried Asiatic hybrid lilies during all developmental stages. In addition, shading treatment significantly decreased pigment accumulation by suppressing the expression of several unigenes related to anthocyanin biosynthesis in ovaries of Asiatic “Tiny Padhye”. Lastly, a total of 15,048 Simple Sequence Repeats (SSRs) were identified in 13,710 sequences, and primer pairs for SSRs were designed. The results could further our understanding of the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. PMID:27879624

  10. Identifying key interactions stabilizing DOF zinc finger-DNA complexes using in silico approaches.

    PubMed

    Hamzeh-Mivehroud, Maryam; Moghaddas-Sani, Hakimeh; Rahbar-Shahrouziasl, Mahdieh; Dastmalchi, Siavoush

    2015-10-07

    DOF (DNA-binding with one finger) proteins, a family of DNA-binding transcription factors, are members of zinc fingers unique to plants. They are associated with different plant specific phenomena including germination, dormancy, light and defense responses. Until now, there is no report of experimentally solved structure for DOF proteins, making empirical investigation of DOF-DNA interaction more challenging. It has been shown that comparative modeling can be used to reliably predict the three-dimensional (3D) model of structurally unknown proteins whenever a suitable template is available. Furthermore, current molecular mechanics force fields allow prediction of interaction energies for macromolecular complexes. Therefore, the approaches considered in this work were to model the 3D structures of DOF zinc fingers (ZFs) from Arabidopsis thaliana complexed with DNA molecule, to calculate their binding energies, to identify key interactions established between ZFs and DNA, and to determine the impact of the different interactions on the binding energies. The results were used to predict the binding affinities for the novel designed ZFs and may be used in engineering DNA binding proteins.

  11. The CD10 enzyme is a key player to identify and regulate human mammary stem cells.

    PubMed

    Bachelard-Cascales, Elodie; Chapellier, Marion; Delay, Emmanuel; Pochon, Gaetan; Voeltzel, Thibault; Puisieux, Alain; Caron de Fromentel, Claude; Maguer-Satta, Véronique

    2010-06-01

    The major components of the mammary ductal tree are an inner layer of luminal cells, an outer layer of myoepithelial cells, and a basement membrane that separates the ducts from the underlying stroma. Cells in the outer layer express CD10, a zinc-dependent metalloprotease that regulates the growth of the ductal tree during mammary gland development. To define the steps in the human mammary lineage at which CD10 acts, we have developed an in vitro assay for human mammary lineage progression. We show that sorting for CD10 and EpCAM cleanly separates progenitors from differentiated luminal cells and that the CD10-high EpCAM-low population is enriched for early common progenitor and mammosphere-forming cells. We also show that sorting for CD10 enriches sphere-forming cells from other tissue types, suggesting that it may provide a simple tool to identify stem or progenitor populations in tissues for which lineage studies are not currently possible. We demonstrate that the protease activity of CD10 and the adhesion function of beta1-integrin are required to prevent differentiation of mammary progenitors. Taken together, our data suggest that integrin-mediated contact with the basement membrane and cleavage of signaling factors by CD10 are key elements in the niche that maintains the progenitor and stem cell pools in the mammary lineage.

  12. Experimental Infections with Mycoplasma agalactiae Identify Key Factors Involved in Host-Colonization

    PubMed Central

    Baranowski, Eric; Bergonier, Dominique; Sagné, Eveline; Hygonenq, Marie-Claude; Ronsin, Patricia; Berthelot, Xavier; Citti, Christine

    2014-01-01

    Mechanisms underlying pathogenic processes in mycoplasma infections are poorly understood, mainly because of limited sequence similarities with classical, bacterial virulence factors. Recently, large-scale transposon mutagenesis in the ruminant pathogen Mycoplasma agalactiae identified the NIF locus, including nifS and nifU, as essential for mycoplasma growth in cell culture, while dispensable in axenic media. To evaluate the importance of this locus in vivo, the infectivity of two knock-out mutants was tested upon experimental infection in the natural host. In this model, the parental PG2 strain was able to establish a systemic infection in lactating ewes, colonizing various body sites such as lymph nodes and the mammary gland, even when inoculated at low doses. In these PG2-infected ewes, we observed over the course of infection (i) the development of a specific antibody response and (ii) dynamic changes in expression of M. agalactiae surface variable proteins (Vpma), with multiple Vpma profiles co-existing in the same animal. In contrast and despite a sensitive model, none of the knock-out mutants were able to survive and colonize the host. The extreme avirulent phenotype of the two mutants was further supported by the absence of an IgG response in inoculated animals. The exact role of the NIF locus remains to be elucidated but these data demonstrate that it plays a key role in the infectious process of M. agalactiae and most likely of other pathogenic mycoplasma species as many carry closely related homologs. PMID:24699671

  13. Experimental infections with Mycoplasma agalactiae identify key factors involved in host-colonization.

    PubMed

    Baranowski, Eric; Bergonier, Dominique; Sagné, Eveline; Hygonenq, Marie-Claude; Ronsin, Patricia; Berthelot, Xavier; Citti, Christine

    2014-01-01

    Mechanisms underlying pathogenic processes in mycoplasma infections are poorly understood, mainly because of limited sequence similarities with classical, bacterial virulence factors. Recently, large-scale transposon mutagenesis in the ruminant pathogen Mycoplasma agalactiae identified the NIF locus, including nifS and nifU, as essential for mycoplasma growth in cell culture, while dispensable in axenic media. To evaluate the importance of this locus in vivo, the infectivity of two knock-out mutants was tested upon experimental infection in the natural host. In this model, the parental PG2 strain was able to establish a systemic infection in lactating ewes, colonizing various body sites such as lymph nodes and the mammary gland, even when inoculated at low doses. In these PG2-infected ewes, we observed over the course of infection (i) the development of a specific antibody response and (ii) dynamic changes in expression of M. agalactiae surface variable proteins (Vpma), with multiple Vpma profiles co-existing in the same animal. In contrast and despite a sensitive model, none of the knock-out mutants were able to survive and colonize the host. The extreme avirulent phenotype of the two mutants was further supported by the absence of an IgG response in inoculated animals. The exact role of the NIF locus remains to be elucidated but these data demonstrate that it plays a key role in the infectious process of M. agalactiae and most likely of other pathogenic mycoplasma species as many carry closely related homologs.

  14. Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

    PubMed

    Sweetapple, Christine; Fu, Guangtao; Butler, David

    2013-09-01

    This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality.

  15. An integrated analysis identifies STAT4 as a key regulator of ovarian cancer metastasis.

    PubMed

    Zhao, L; Ji, G; Le, X; Luo, Z; Wang, C; Feng, M; Xu, L; Zhang, Y; Lau, W B; Lau, B; Yang, Y; Lei, L; Yang, H; Xuan, Y; Chen, Y; Deng, X; Yi, T; Yao, S; Zhao, X; Wei, Y; Zhou, S

    2017-06-15

    Epithelial ovarian cancer (EOC) is one of the most common gynecological cancers, with diagnosis often at a late stage. Metastasis is a major cause of death in patients with EOC, but the underlying molecular mechanisms remain obscure. Here, we utilized an integrated approach to find potential key transcription factors involved in ovarian cancer metastasis and identified STAT4 as a critical player in ovarian cancer metastasis. We found that activated STAT4 was overexpressed in epithelial cells of ovarian cancer and STAT4 overexpression was associated with poor outcome of ovarian cancer patients, which promoted metastasis of ovarian cancer in both in vivo and in vitro. Although STAT4 mediated EOC metastasis via inducing epithelial-to-mesenchymal transition (EMT) of ovarian cancer cells in vivo, STAT4 failed to induce EMT directly in vitro, suggesting that STAT4 might mediate EMT process via cancer-stroma interactions. Further functional analysis revealed that STAT4 overexpression induced normal omental fibroblasts and adipose- and bone marrow-derived mesenchymal stem cells to obtain cancer-associated fibroblasts (CAF)-like features via induction of tumor-derived Wnt7a. Reciprocally, increased production of CAF-induced CXCL12, IL6 and VEGFA within tumor microenvironment could enable peritoneal metastasis of ovarian cancer via induction of EMT program. In summary, our study established a model that STAT4 promotes ovarian cancer metastasis via tumor-derived Wnt7a-induced activation of CAFs.

  16. Identifying fruitful connections between and among researchers and practitioners

    NASA Technical Reports Server (NTRS)

    Feather, Martin S.; Menzies, Tim; Connelly, Judith R.

    2003-01-01

    Many organizations look to research to yield new and improved products and practices. Connecting practitioners who have the need for research results to the researchers producing those results is important to guiding research and utilizing its results. Likewise, connecting researchers working on related topics to one another, and connecting practitioners with related needs to one another, is important to establishing communities of shared interests. We present an approach that helps identify fruitful such connections.

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

    PubMed

    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.

  18. Vitamin D and the brain: key questions for future research.

    PubMed

    Cui, Xiaoying; Gooch, Helen; Groves, Natalie J; Sah, Pankaj; Burne, Thomas H; Eyles, Darryl W; McGrath, John J

    2015-04-01

    Over the last decade a convergent body of evidence has emerged from epidemiology, animal experiments and clinical trials which links low vitamin D status with a range of adverse neuropsychiatric outcomes. This research demonstrates that the timing of exposure to low vitamin D influences the nature of brain phenotypes, as exposures during gestation versus adulthood result in different phenotypes. With respect to early life exposures, there is robust evidence from rodent experiments indicating that transient developmental vitamin D (DVD) deficiency is associated with changes in brain structure, neurochemistry, gene and protein expression and behavior. In particular, DVD deficiency is associated with alterations in the dopaminergic neurotransmitter systems. In contrast, recently published animal experiments indicate that adult vitamin D (AVD) deficiency is associated with more subtle neurochemical and behavioral phenotypes. This paper explores key issues that need to be addressed in future research. There is a need to define the timing and duration of the 'critical window' during which low vitamin D status is associated with differential and adverse brain outcomes. We discuss the role for 'two-hit hypotheses', which propose that adult vitamin D deficiency leaves the brain more vulnerable to secondary adverse exposures, and thus may exacerbate disease progression. Finally, we explore the evidence implicating a role for vitamin D in rapid, non-genomic mechanisms that may involve L-type calcium channels and brain function. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.

  19. Research on key technology of space laser communication network

    NASA Astrophysics Data System (ADS)

    Chang, Chengwu; Huang, Huiming; Liu, Hongyang; Gao, Shenghua; Cheng, Liyu

    2016-10-01

    Since the 21st century, Spatial laser communication has made a breakthrough development. Europe, the United States, Japan and other space powers have carried out the test of spatial laser communication technology on-orbit, and put forward a series of plans. In 2011, China made the first technology demonstration of satellite-ground laser communication carried by HY-2 satellite. Nowadays, in order to improve the transmission rate of spatial network, the topic of spatial laser communication network is becoming a research hotspot at home and abroad. This thesis, from the basic problem of spatial laser communication network to solve, analyzes the main difference between spatial network and ground network, which draws forth the key technology of spatial laser communication backbone network, and systematically introduces our research on aggregation, addressing, architecture of spatial network. From the perspective of technology development status and trends, the thesis proposes the development route of spatial laser communication network in stages. So as to provide reference about the development of spatial laser communication network in China.

  20. Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation.

    PubMed

    Servetas, Stephanie L; Carpenter, Beth M; Haley, Kathryn P; Gilbreath, Jeremy J; Gaddy, Jennifer A; Merrell, D Scott

    2016-09-15

    Helicobacter pylori must be able to rapidly respond to fluctuating conditions within the stomach. Despite this need for constant adaptation, H. pylori encodes few regulatory proteins. Of the identified regulators, the ferric uptake regulator (Fur), the nickel response regulator (NikR), and the two-component acid response system (ArsRS) are each paramount to the success of this pathogen. While numerous studies have individually examined these regulatory proteins, little is known about their combined effect. Therefore, we constructed a series of isogenic mutant strains that contained all possible single, double, and triple regulatory mutations in Fur, NikR, and ArsS. A growth curve analysis revealed minor variation in growth kinetics across the strains; these were most pronounced in the triple mutant and in strains lacking ArsS. Visual analysis showed that strains lacking ArsS formed large aggregates and a biofilm-like matrix at the air-liquid interface. Biofilm quantification using crystal violet assays and visualization via scanning electron microscopy (SEM) showed that all strains lacking ArsS or containing a nonphosphorylatable form of ArsR (ArsR-D52N mutant) formed significantly more biofilm than the wild-type strain. Molecular characterization of biofilm formation showed that strains containing mutations in the ArsRS pathway displayed increased levels of cell aggregation and adherence, both of which are key to biofilm development. Furthermore, SEM analysis revealed prevalent coccoid cells and extracellular matrix formation in the ArsR-D52N, ΔnikR ΔarsS, and Δfur ΔnikR ΔarsS mutant strains, suggesting that these strains may have an exacerbated stress response that further contributes to biofilm formation. Thus, H. pylori ArsRS has a previously unrecognized role in biofilm formation. Despite a paucity of regulatory proteins, adaptation is key to the survival of H. pylori within the stomach. While prior studies have focused on individual regulatory proteins

  1. Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation

    PubMed Central

    Servetas, Stephanie L.; Carpenter, Beth M.; Haley, Kathryn P.; Gilbreath, Jeremy J.; Gaddy, Jennifer A.

    2016-01-01

    ABSTRACT Helicobacter pylori must be able to rapidly respond to fluctuating conditions within the stomach. Despite this need for constant adaptation, H. pylori encodes few regulatory proteins. Of the identified regulators, the ferric uptake regulator (Fur), the nickel response regulator (NikR), and the two-component acid response system (ArsRS) are each paramount to the success of this pathogen. While numerous studies have individually examined these regulatory proteins, little is known about their combined effect. Therefore, we constructed a series of isogenic mutant strains that contained all possible single, double, and triple regulatory mutations in Fur, NikR, and ArsS. A growth curve analysis revealed minor variation in growth kinetics across the strains; these were most pronounced in the triple mutant and in strains lacking ArsS. Visual analysis showed that strains lacking ArsS formed large aggregates and a biofilm-like matrix at the air-liquid interface. Biofilm quantification using crystal violet assays and visualization via scanning electron microscopy (SEM) showed that all strains lacking ArsS or containing a nonphosphorylatable form of ArsR (ArsR-D52N mutant) formed significantly more biofilm than the wild-type strain. Molecular characterization of biofilm formation showed that strains containing mutations in the ArsRS pathway displayed increased levels of cell aggregation and adherence, both of which are key to biofilm development. Furthermore, SEM analysis revealed prevalent coccoid cells and extracellular matrix formation in the ArsR-D52N, ΔnikR ΔarsS, and Δfur ΔnikR ΔarsS mutant strains, suggesting that these strains may have an exacerbated stress response that further contributes to biofilm formation. Thus, H. pylori ArsRS has a previously unrecognized role in biofilm formation. IMPORTANCE Despite a paucity of regulatory proteins, adaptation is key to the survival of H. pylori within the stomach. While prior studies have focused on individual

  2. Identifying key features of early stressful experiences that produce stress vulnerability and resilience in primates.

    PubMed

    Parker, Karen J; Maestripieri, Dario

    2011-06-01

    This article examines the complex role of early stressful experiences in producing both vulnerability and resilience to later stress-related psychopathology in a variety of primate models of human development. Two types of models are reviewed: Parental Separation Models (e.g., isolate-rearing, peer-rearing, parental separations, and stress inoculation) and Maternal Behavior Models (e.g., foraging demands, variation in maternal style, and maternal abuse). Based on empirical evidence, it is argued that early life stress exposure does not increase adult vulnerability to stress-related psychopathology as a linear function, as is generally believed, but instead reflects a quadratic function. Features of early stress exposure including the type, duration, frequency, ecological validity, sensory modality, and developmental timing, within and between species, are identified to better understand how early stressful experiences alter neurobiological systems to produce such diverse developmental outcomes. This article concludes by identifying gaps in our current knowledge, providing directions for future research, and discussing the translational implications of these primate models for human development and psychopathology. Copyright © 2010 Elsevier Ltd. All rights reserved.

  3. Identifying key features of early stressful experiences that produce stress vulnerability and resilience in primates

    PubMed Central

    Parker, Karen J.; Maestripieri, Dario

    2010-01-01

    This article examines the complex role of early stressful experiences in producing both vulnerability and resilience to later stress-related psychopathology in a variety of primate models of human development. Two types of models are reviewed: Parental Separation Models (e.g., isolate-rearing, peer-rearing, parental separations, and stress inoculation) and Maternal Behavior Models (e.g., foraging demands, variation in maternal style, and maternal abuse). Based on empirical evidence, it is argued that early life stress exposure does not increase adult vulnerability to stress-related psychopathology as a linear function, as is generally believed, but instead reflects a quadratic function. Features of early stress exposure including the type, duration, frequency, ecological validity, sensory modality, and developmental timing, within and between species, are identified to better understand how early stressful experiences alter neurobiological systems to produce such diverse developmental outcomes. This article concludes by identifying gaps in our current knowledge, providing directions for future research, and discussing the translational implications of these primate models for human development and psychopathology. PMID:20851145

  4. European Society of Gastrointestinal Endoscopy - Establishing the key unanswered research questions within gastrointestinal endoscopy.

    PubMed

    Rees, Colin J; Ngu, Wee Sing; Regula, Jaroslaw; Bisschops, Raf; Saftoiu, Adrian; Dekker, Evelien; Gralnek, Ian; Ciocirlan, Mihai; Dinis-Ribeiro, Mario; Jover, Rodrigo; Meisner, Søren; Spada, Cristiano; Hassan, Cesare; Valori, Roland; Hucl, Tomas; Le Moine, Olivier; Domagk, Dirk; Kaminski, Michal F; Bretthauer, Michael; Rutter, Matthew D; Aabakken, Lars; Ponchon, Thierry; Fockens, Paul; Siersema, Peter D

    2016-10-01

    Background and study aim: Gastrointestinal endoscopy is a rapidly evolving research field. The European Society of Gastrointestinal Endoscopy (ESGE) plays a key role in shaping opinion and endoscopy activity throughout Europe and further afield. Establishing key unanswered questions within the field of endoscopy and prioritizing those that are important enables researchers and funders to appropriately allocate resources. Methods: Over 2 years, the ESGE Research Committee gathered information on research priorities and refined them through a modified Delphi approach. Consultations were held with the ESGE Governing Board and Quality Improvement Committee to identify important unanswered questions. Research workshops were held at the 21st United European Gastroenterology Week. Research questions were refined by the ESGE Research Committee and Governing Board, compiled into an online survey, and distributed to all ESGE members, who were invited to rank each question by priority. Results: The final questionnaire yielded 291 responses from over 60 countries. The three countries with the highest response rates were Spain, Italy, and United Kingdom. Most responders were from teaching hospitals (62 %) and were specialist endoscopists (51 %). Responses were analyzed with weighted rankings, resulting in prioritization of 26 key unanswered questions. The top ranked generic questions were: 1) How do we define the correct surveillance interval following endoscopic diagnosis? 2) How do we correctly utilize advanced endoscopic imaging? 3) What are the best markers of endoscopy quality? Conclusion: Following this comprehensive process, the ESGE has identified and ranked the key unanswered questions within the field of gastrointestinal endoscopy. Researchers, funders, and journals should prioritize studies that seek to answer these important questions. © Georg Thieme Verlag KG Stuttgart · New York.

  5. Identifying same-cell contours in image stacks: a key step in making 3D reconstructions.

    PubMed

    Leung, Tony Kin Shun; Veldhuis, Jim H; Krens, S F Gabby; Heisenberg, C P; Brodland, G Wayne

    2011-02-01

    Identification of contours belonging to the same cell is a crucial step in the analysis of confocal stacks and other image sets in which cell outlines are visible, and it is central to the making of 3D cell reconstructions. When the cells are close packed, the contour grouping problem is more complex than that found in medical imaging, for example, because there are multiple regions of interest, the regions are not separable from each other by an identifiable background and regions cannot be distinguished by intensity differences. Here, we present an algorithm that uses three primary metrics-overlap of contour areas in adjacent images, co-linearity of the centroids of these areas across three images in a stack, and cell taper-to assign cells to groups. Decreasing thresholds are used to successively assign contours whose membership is less obvious. In a final step, remaining contours are assigned to existing groups by setting all thresholds to zero and groups having strong hour-glass shapes are partitioned. When applied to synthetic data from isotropic model aggregates, a curved model epithelium in which the long axes of the cells lie at all possible angles to the transection plane, and a confocal image stack, algorithm assignments were between 97 and 100% accurate in sets having at least four contours per cell. The algorithm is not particularly sensitive to the thresholds used, and a single set of parameters was used for all of the tests. The algorithm, which could be extended to time-lapse data, solves a key problem in the translation of image data into cell information.

  6. The "Key" Method of Identifying Igneous and Metamorphic Rocks in Introductory Laboratory.

    ERIC Educational Resources Information Center

    Eves, Robert Leo; Davis, Larry Eugene

    1987-01-01

    Proposes that identification keys provide an orderly strategy for the identification of igneous and metamorphic rocks in an introductory geology course. Explains the format employed in the system and includes the actual key guides for both igneous and metamorphic rocks. (ML)

  7. The "Key" Method of Identifying Igneous and Metamorphic Rocks in Introductory Laboratory.

    ERIC Educational Resources Information Center

    Eves, Robert Leo; Davis, Larry Eugene

    1987-01-01

    Proposes that identification keys provide an orderly strategy for the identification of igneous and metamorphic rocks in an introductory geology course. Explains the format employed in the system and includes the actual key guides for both igneous and metamorphic rocks. (ML)

  8. Identifying Key Issues and Potential Solutions for Integrated Arrival, Departure, Surface Operations by Surveying Stakeholder Preferences

    NASA Technical Reports Server (NTRS)

    Aponso, Bimal; Coppenbarger, Richard A.; Jung, Yoon; Quon, Leighton; Lohr, Gary; O’Connor, Neil; Engelland, Shawn

    2015-01-01

    NASA's Aeronautics Research Mission Directorate (ARMD) collaborates with the FAA and industry to provide concepts and technologies that enhance the transition to the next-generation air-traffic management system (NextGen). To facilitate this collaboration, ARMD has a series of Airspace Technology Demonstration (ATD) sub-projects that develop, demonstrate, and transitions NASA technologies and concepts for implementation in the National Airspace System (NAS). The second of these sub-projects, ATD-2, is focused on the potential benefits to NAS stakeholders of integrated arrival, departure, surface (IADS) operations. To determine the project objectives and assess the benefits of a potential solution, NASA surveyed NAS stakeholders to understand the existing issues in arrival, departure, and surface operations, and the perceived benefits of better integrating these operations. NASA surveyed a broad cross-section of stakeholders representing the airlines, airports, air-navigation service providers, and industry providers of NAS tools. The survey indicated that improving the predictability of flight times (schedules) could improve efficiency in arrival, departure, and surface operations. Stakeholders also mentioned the need for better strategic and tactical information on traffic constraints as well as better information sharing and a coupled collaborative planning process that allows stakeholders to coordinate IADS operations. To assess the impact of a potential solution, NASA sketched an initial departure scheduling concept and assessed its viability by surveying a select group of stakeholders for a second time. The objective of the departure scheduler was to enable flights to move continuously from gate to cruise with minimal interruption in a busy metroplex airspace environment using strategic and tactical scheduling enhanced by collaborative planning between airlines and service providers. The stakeholders agreed that this departure concept could improve schedule

  9. Engaging basic scientists in translational research: identifying opportunities, overcoming obstacles

    PubMed Central

    2012-01-01

    This report is based on the Federation of American Societies for Experimental Biology’s symposium, “Engaging basic Scientists in Translational Research: Identifying Opportunities, Overcoming Obstacles,” held in Chevy Chase, MD, March 24–25, 2011. Meeting participants examined the benefits of engaging basic scientists in translational research, the challenges to their participation in translational research, and the roles that research institutions, funding organizations, professional societies, and scientific publishers can play to address these challenges. PMID:22500917

  10. Key aspects of melatonin physiology: thirty years of research.

    PubMed

    Di Bella, Luigi; Gualano, Luciano

    2006-08-01

    Numerous studies of melatonin, by now widely acknowledged as a circadian rhythm-affecting neurohormone, also describe its anti-oxidant, anti-cytotoxic or immune-modulating activity. While emphasizing the multifunctional aspect of melatonin action, this review presents the results of our thirty years of research, which point to the following conclusions: melatonin is capable of promoting platelet production by megakaryocytes, of acting on the latter's ion channels by way of the outward currents, and of performing a physiological anti-aggregation function thus lengthening platelet life span. Melatonin can be transported everywhere by platelets and, thanks to its lipophilicity, can cross cellular membranes easily, thus regulating blood-tissue exchanges and ensuring an improved haematic crisis. It interacts with endothelial cells by regulating their release of both relaxing-factor and contracting-factor, and with platelets by affecting their discharge of dense-body components. Finally, platelets could behave as mobile and itinerant serotonergic and/or melatonergic elements, a function comparable to the release of neurotransmitters by neurons of the central nervous system. This dynamism in melatonin physiology could prove to be a key in approaching tumour aetiopathogenesis.

  11. Key characters for identifying Aedes bahamensis and Aedes albopictus in North America, north of Mexico.

    PubMed

    Darsie, R F

    1992-09-01

    Aedes bahamensis, a species recently introduced into southern Florida represents the first member of the subgenus Howardina to be found in the United States. Its separation from all other Nearctic Aedes is the subject of this work, integrating it into the North American mosquito keys (Darsie and Ward 1981). The key revisions presented are expanded to include the other exotic species now found in the United States, Aedes albopictus.

  12. Research to Identify Effective Antifungal Agents, 1991 Annual Report.

    SciTech Connect

    Schreck, Carl

    1991-09-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990). The objectives of the present study was to evaluate up to 10 candidate fungicides.

  13. Research to Identify Effective Antifungal Agents, 1993 Annual Report.

    SciTech Connect

    Schreck, Carl

    1993-10-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990, 1991, and 1992). The objectives of the present study were to select and evaluate candidate fungicides.

  14. Pharmacy patronage: identifying key factors in the decision making process using the determinant attribute approach.

    PubMed

    Franic, Duska M; Haddock, Sarah M; Tucker, Leslie Tootle; Wooten, Nathan

    2008-01-01

    To use the determinant attribute approach, a research method commonly used in marketing to identify the wants of various consumer groups, to evaluate consumer pharmacy choice when having a prescription order filled in different pharmacy settings. Cross sectional. Community independent, grocery store, community chain, and discount store pharmacies in Georgia between April 2005 and April 2006. Convenience sample of adult pharmacy consumers (n = 175). Survey measuring consumer preferences on 26 attributes encompassing general pharmacy site features (16 items), pharmacist characteristics (5 items), and pharmacy staff characteristics (5 items). 26 potential determinant attributes for pharmacy selection. 175 consumers were surveyed at community independent (n = 81), grocery store (n = 44), community chain (n = 27), or discount store (n = 23) pharmacy settings. The attributes of pharmacists and staff at all four pharmacy settings were shown to affect pharmacy patronage motives, although consumers frequenting non-community independent pharmacies were also motivated by secondary convenience factors, e.g., hours of operation, and prescription coverage. Most consumers do not perceive pharmacies as merely prescription-distribution centers that vary only by convenience. Prescriptions are not just another economic good. Pharmacy personnel influence pharmacy selection; therefore, optimal staff selection and training is likely the greatest asset and most important investment for ensuring pharmacy success.

  15. Identifying mental health nursing research priorities: A Delphi study.

    PubMed

    Wynaden, Dianne; Heslop, Karen; Omari, Omar Al; Nelson, Deborah; Osmond, Bernadette; Taylor, Monica; Gee, Trevor

    2014-01-01

    Abstract Engaging in research and using evidence based practice are essential for mental health nurses to provide quality nursing care to consumers and families. This paper reports on a Delphi study that identified the top 10 mental health nursing research priorities at one area health service in Australia servicing a population of 840,000 people. Initially 390 research questions were identified by nurses and these were then reduced to 56 broader questions. Finally, the top 10 questions were ranked in order of importance. The priority questions were clinically and professionally focussed and included research into the delivery and organisation of mental health services and the need to design and evaluate new practice paradigms for nurses in the primary care setting. The mental health knowledge and skill set of graduates from Australian comprehensive nursing programmes along with improved recruitment and retention of graduates in mental health were also identified priority areas for research.

  16. De-identified genomic data sharing: the research participant perspective.

    PubMed

    Goodman, Deborah; Johnson, Catherine O; Bowen, Deborah; Smith, Megan; Wenzel, Lari; Edwards, Karen

    2017-04-05

    Combining datasets into larger and separate datasets is becoming increasingly common, and personal identifiers are often removed in order to maintain participant anonymity. Views of research participants on the use of de-identified data in large research datasets are important for future projects, such as the Precision Medicine Initiative and Cancer Moonshot Initiative. This quantitative study set in the USA examines participant preferences and evaluates differences by demographics and cancer history. Study participants were recruited from the Northwest Cancer Genetics Registry and included cancer patients, their relatives, and controls. A secure online survey was administered to 450 participants. While the majority participants were not concerned about personal identification when participating in a genetic study using de-identified data, they expressed their concern that researchers protect their privacy and information. Most participants expressed a desire that their data should be available for as many research studies as possible, and in doing so, they would increase their chance of receiving personal health information. About 20% of participants felt that a link should not be maintained between the participant and their de-identified data. Reasons to maintain a link included an ability to return individual health results and an ability to support further research. Knowledge of participants' attitudes regarding the use of data into a research repository and the maintenance of a link to de-identified data is critical to the success of recruitment into future genomic research projects.

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

    ERIC Educational Resources Information Center

    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…

  18. The Use of Citation Counting to Identify Research Trends

    ERIC Educational Resources Information Center

    Rothman, Harry; Woodhead, Michael

    1971-01-01

    The analysis and application of manpower statistics to identify some long-term international research trends in economic entomology and pest conrol are described. Movements in research interests, particularly towards biological methods of control, correlations between these sectors, and the difficulties encountered in the construction of a…

  19. The Use of Citation Counting to Identify Research Trends

    ERIC Educational Resources Information Center

    Rothman, Harry; Woodhead, Michael

    1971-01-01

    The analysis and application of manpower statistics to identify some long-term international research trends in economic entomology and pest conrol are described. Movements in research interests, particularly towards biological methods of control, correlations between these sectors, and the difficulties encountered in the construction of a…

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

    ERIC Educational Resources Information Center

    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. Key success factors of health research centers: A mixed method study

    PubMed Central

    Tofighi, Shahram; Teymourzadeh, Ehsan; Heydari, Majid

    2017-01-01

    Background In order to achieve success in future goals and activities, health research centers are required to identify their key success factors. Objective This study aimed to extract and rank the factors affecting the success of research centers at one of the medical universities in Iran. Methods This study is a mixed method (qualitative-quantitative) study, which was conducted between May to October in 2016. The study setting was 22 health research centers. In qualitative phase, we extracted the factors affecting the success in research centers through purposeful interviews with 10 experts of centers, and classified them into themes and sub-themes. In the quantitative phase, we prepared a questionnaire and scored and ranked the factors recognized by 54 of the study samples by Friedman test. Results Nine themes and 42 sub-themes were identified. Themes included: strategic orientation, management, human capital, support, projects, infrastructure, communications and collaboration, paradigm and innovation and they were rated respectively as components of success in research centers. Among the 42 identified factors, 10 factors were ranked respectively as the key factors of success, and included: science and technology road map, strategic plan, evaluation indexes, committed human resources, scientific evaluation of members and centers, innovation in research and implementation, financial support, capable researchers, equipment infrastructure and teamwork. Conclusion According to the results, the strategic orientation was the most important component in the success of research centers. Therefore, managers and authorities of research centers should pay more attention to strategic areas in future planning, including the science and technology road map and strategic plan.

  2. Roots and Research. Key Stage 3 English. Key Stage 3: National Strategy.

    ERIC Educational Resources Information Center

    Harrison, Colin

    In 1998, Roger Beard of the University of Leeds wrote an account of the research underpinning the emerging National Literacy Strategy (NLS). Since Beard published his review, there have been developments both in terms of age groups covered and within the field of literacy research. This document attempts a fresh review of the relationship between…

  3. Identifying Key Features of Student Performance in Educational Video Games and Simulations through Cluster Analysis

    ERIC Educational Resources Information Center

    Kerr, Deirdre; Chung, Gregory K. W. K.

    2012-01-01

    The assessment cycle of "evidence-centered design" (ECD) provides a framework for treating an educational video game or simulation as an assessment. One of the main steps in the assessment cycle of ECD is the identification of the key features of student performance. While this process is relatively simple for multiple choice tests, when…

  4. Identifying Key Features of Student Performance in Educational Video Games and Simulations through Cluster Analysis

    ERIC Educational Resources Information Center

    Kerr, Deirdre; Chung, Gregory K. W. K.

    2012-01-01

    The assessment cycle of "evidence-centered design" (ECD) provides a framework for treating an educational video game or simulation as an assessment. One of the main steps in the assessment cycle of ECD is the identification of the key features of student performance. While this process is relatively simple for multiple choice tests, when…

  5. Identifying Key Features of Effective Active Learning: The Effects of Writing and Peer Discussion

    ERIC Educational Resources Information Center

    Linton, Debra L.; Pangle, Wiline M.; Wyatt, Kevin H.; Powell, Karli N.; Sherwood, Rachel E.

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between…

  6. Identifying Key Features of Effective Active Learning: The Effects of Writing and Peer Discussion

    ERIC Educational Resources Information Center

    Linton, Debra L.; Pangle, Wiline M.; Wyatt, Kevin H.; Powell, Karli N.; Sherwood, Rachel E.

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between…

  7. Identifying and controlling emerging foodborne pathogens: research needs.

    PubMed

    Buchanan, R L

    1997-01-01

    Systems for managing the risks associated with foodborne pathogens are based on detailed knowledge of the microorganisms and the foods with which they are associated--known hazards. An emerging pathogen, however, is an unknown hazard; therefore, to control it, key data must be acquired to convert the pathogen from an unknown to a known hazard. The types of information required are similar despite the identity of the new agent. The key to rapid control is rapid mobilization of research capabilities targeted at addressing critical knowledge gaps. In addition, longer-term research is needed to improve our ability to respond quickly to new microbial threats and help us become more proactive at anticipating and preventing emergence. The type of contingency planning used by the military in anticipating new threats serves as a useful framework for planning for new emergence.

  8. Identifying and Tracing Persistent Identifiers of Research Resources : Automation, Metrics and Analytics

    NASA Astrophysics Data System (ADS)

    Maull, K. E.; Hart, D.; Mayernik, M. S.

    2015-12-01

    Formal and informal citations and acknowledgements for research infrastructures, such as data collections, software packages, and facilities, are an increasingly important function of attribution in scholarly literature. While such citations provide the appropriate links, even if informally, to their origins, they are often done so inconsistently, making such citations hard to analyze. While significant progress has been made in the past few years in the development of recommendations, policies, and procedures for creating and promoting citable identifiers, progress has been mixed in tracking how data sets and other digital infrastructures have actually been identified and cited in the literature. Understanding the full extent and value of research infrastructures through the lens of scholarly literature requires significant resources, and thus, we argue must rely on automated approaches that mine and track persistent identifiers to scientific resources. Such automated approaches, however, face a number of unique challenges, from the inconsistent and informal referencing practices of authors, to unavailable, embargoed or hard-to-obtain full-text resources for text analytics, to inconsistent and capricious impact metrics. This presentation will discuss work to develop and evaluate tools for automating the tracing of research resource identification and referencing in the research literature via persistent citable identifiers. Despite the impediments, automated processes are of considerable importance in enabling these traceability efforts to scale, as the numbers of identifiers being created for unique scientific resources continues to grow rapidly. Such efforts, if successful, should improve the ability to answer meaningful questions about research resources as they continue to grow as a target of advanced analyses in research metrics.

  9. What are the key organisational capabilities that facilitate research use in public health policy?

    PubMed

    Huckel Schneider, Carmen; Campbell, Danielle; Milat, Andrew; Haynes, Abby; Quinn, Emma

    2014-11-28

    Literature about research use suggests that certain characteristics or capabilities may make policy agencies more evidence attuned. This study sought to determine policy makers' perceptions of a suite of organisational capabilities identified from the literature as potentially facilitating research uptake in policy decision making. A literature scan identified eight key organisational capabilities that support research use in policy making. To determine whether these capabilities were relevant, practical and applicable in real world policy settings, nine Australian health policy makers were consulted in September 2011. We used an open-ended questionnaire asking what facilitates the use of research in policy and program decision making, followed by specific questions rating the proposed capabilities. Interviews were transcribed and the content analysed. There was general agreement that the capabilities identified from the literature were relevant to real world contexts. However, interviewees varied in whether they could provide examples of experiences with the capabilities, how essential they considered the different capabilities to be and how difficult they considered the capabilities were to achieve. Efforts to improve the use of research in policy decision making are likely to benefit from targeting multiple organisational capabilities, including staff skills and competence, tools such as templates and checklists to aid evidence use and leadership support for the use of research in policy development. However, such efforts should be guided by an understanding of how policy agencies use evidence and how they view their roles, and external factors such as resource constraints and availability of appropriate research.

  10. Research Ethics Review: Identifying Public Policy and Program Gaps

    PubMed Central

    Strosberg, Martin A.; Gefenas, Eugenijus; Famenka, Andrei

    2014-01-01

    We present an analytical frame-work for use by fellows of the Fogarty International Center–sponsored Advanced Certificate Program in Research Ethics for Central and Eastern Europe to identify gaps in the public policies establishing research ethics review systems that impede them from doing their job of protecting human research subjects. The framework, illustrated by examples from post-Communist countries, employs a logic model based on the public policy and public management literature. This paper is part of a collection of papers analyzing the Fogarty International Center’s International Research Ethics Education and Curriculum program. PMID:24782068

  11. Comparing classification performance of several types of significant genes to identify key genes in uremia.

    PubMed

    Ying, X-X; Zhou, C-X

    2016-06-01

    End-stage renal failure has profound changes in human gene expressions, but the molecular causation of these pleomorphic effects termed uremia is poorly understood. The purpose of this study was to explore key genes in uremia by comparing classification performance of five kinds of significant genes based on the support vector machines (SVM) model. The five kinds of genes were differentially expressed genes (DEGs), differential pathway genes (DPGs), common differential genes between DEGs and DPGs (CDGs), hub genes (HUGs) and common genes of hub genes and DEGs (CHDGs). In detailed, DEGs were detected by linear models for microarray data (Limma) package. Attract method was utilized to capture DPGs from differential pathways. HUGs were determined according to topological centrality analysis of mutual information network (MIN). Subsequently, SVM model was implemented to assess the classification performance of DEGs, DPGs, CDGs, HUGs and CHDGs, depending on its induces the area under the receiver operating characteristics curve (AUC), true negative rate (TNR), true positive rate (TPR) and the Matthews coefficient correlation classification (MCC). A total of 166 DEGs, 597 DPGs, 13 CDGs, 29 HUGs and 10 CHDGs were obtained in uremia. By assessing the SVM model classification analysis, CHDGs had the best performance of all with AUC = 0.99, TNR = 1.00, TPR = 0.97 and MCC = 0.95. Hence, we considered the CHDGs as key genes in uremia. Key genes concluded in this investigation might provide vital insights into uremia progression and new therapies.

  12. Key influences identified by first year undergraduate nursing students as impacting on the quality of clinical placement: A qualitative study.

    PubMed

    Cooper, John; Courtney-Pratt, Helen; Fitzgerald, Mary

    2015-09-01

    Despite the fact that high quality clinical placement is an integral component of pre-registration nursing education for the development of the future nursing workforce, the literature identifies an ongoing struggle to 'get it right'. To examine qualitative data gathered through the Quality Clinical Placements Evaluation project to identify what pre-registration nursing students deemed helpful and not helpful influences on their first year Professional Experience Placement. A total of 553 first year undergraduate nursing students from 2010 to 2012 were enrolled in the programme and all were invited to complete a validated survey to measure the quality of their first clinical placement. A total of 361 completed surveys were returned. This paper examines the data provided through open-ended questions within the survey related to most helpful and least helpful aspects of their clinical experience. An inductive analysis approach using NVIVO allowed inherent areas to emerge from the raw data forming three key themes that influenced the experience of students. Feeling welcomed, individual versus team attitudes, and student expectations of supervising ward nurses were the themes identified that were perceived by the student as important to the success of learning and the quality of the experience overall. The findings echo previous research into the student experience of clinical placement; however the focus regarding the need for students to have a quality relationship with the supervising nurse is an area that warrants further exploration. Furthermore, we argue that students should be purposely engaged in the tertiary sector and provided guidance and strategies related to forming and maintaining relationships with those that supervise their clinical placement, in order to ensure consistent positive experiences. The outcomes from this study suggest that a missing component is teaching undergraduates how to manage relationships in clinical settings. Copyright © 2015

  13. Construction of a Comprehensive Protein-Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach.

    PubMed

    Malhotra, Anvita Gupta; Jha, Mohit; Singh, Sudha; Pandey, Khushhali M

    2017-03-13

    Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters. The existing research data helped us in collating 215 proteins involved in vitiligo onset or progression. Interaction study of these proteins leads to a comprehensive vitiligo map with 4845 protein nodes linked with 107,416 edges. Based on centrality measures, a backbone network with 500 nodes has been derived. This has presented a clear overview of the proteins and processes involved and the crosstalk between them. Clustering backbone proteins revealed densely connected regions inferring major molecular interaction modules essential for vitiligo. Finally, a list of top order proteins that play a key role in the disease pathomechanism has been formulated. This includes SUMO2, ESR1, COPS5, MYC, SMAD3, and Cullin proteins. While this list is in fair agreement with the available literature, it also introduces new candidate proteins that can be further explored. A subnetwork of 64 vitiligo core proteins was built by analyzing the backbone and seed protein networks. Our finding suggests that the topology, along with functional clustering, provides a deep insight into the behavior of proteins. This in turn aids in the illustration of disease condition and discovery of significant proteins involved in vitiligo.

  14. Developing Intuition: The Key to Creative Futures Research.

    ERIC Educational Resources Information Center

    Southern, Stephen; Domzalski, Suzanne

    Futures research involves speculation about alternative developments based upon existing data and potential choices. Effective futures research requires creativity in scientific practice rather than an overemphasis on reason. In discussing the important role of intuition in futures research, characteristics of creative scientists are reviewed and…

  15. Key Lessons about Induction for Policy Makers and Researchers

    ERIC Educational Resources Information Center

    Wayne, Andrew J.

    2012-01-01

    The purpose of this chapter is to digest the core chapters of this volume, which draws together some of the most sophisticated thinking on new teacher induction from the last decade. This chapter attends to five key understandings about induction programs, including their context, design, implementation, and outcomes. These understandings emerge…

  16. Educational Evaluation: Key Characteristics. ACER Research Series No. 102.

    ERIC Educational Resources Information Center

    Maling-Keepes, Jillian

    A set of 13 key characteristics is presented as a framework for educational evaluation studies: (1) program's stage of development when evaluator is appointed; (2) program's openness to revision; (3) program uniformity from site to site; (4) specificity of program objectives; (5) evaluator's independence; (6) evaluator's orientation to value…

  17. The genome-wide transcriptional response to neonatal hyperoxia identifies Ahr as a key regulator

    PubMed Central

    Bhattacharya, Soumyaroop; Zhou, Zhongyang; Yee, Min; Chu, Chin-Yi; Lopez, Ashley M.; Lunger, Valerie A.; Solleti, Siva Kumar; Resseguie, Emily; Buczynski, Bradley; O'Reilly, Michael A.

    2014-01-01

    Premature infants requiring supplemental oxygen are at increased risk for developing bronchopulmonary dysplasia (BPD). Rodent models involving neonatal exposure to excessive oxygen concentrations (hyperoxia) have helped to identify mechanisms of BPD-associated pathology. Genome-wide assessments of the effects of hyperoxia in neonatal mouse lungs could identify novel BPD-related genes and pathways. Newborn C57BL/6 mice were exposed to 100% oxygen for 10 days, and whole lung tissue RNA was used for high-throughput, sequencing-based transcriptomic analysis (RNA-Seq). Significance Analysis of Microarrays and Ingenuity Pathway Analysis were used to identify genes and pathways affected. Expression patterns for selected genes were validated by qPCR. Mechanistic relationships between genes were further tested in cultured mouse lung epithelial cells. We identified 300 genes significantly and substantially affected following acute neonatal hyperoxia. Canonical pathways dysregulated in hyperoxia lungs included nuclear fctor (erythryoid-derived-2)-like 2-mediated oxidative stress signaling, p53 signaling, eNOS signaling, and aryl hydrocarbon receptor (Ahr) pathways. Cluster analysis identified Ccnd1, Cdkn1a, and Ahr as critical regulatory nodes in the response to hyperoxia, with Ahr serving as the major effector node. A mechanistic role for Ahr was assessed in lung epithelial cells, and we confirmed its ability to regulate the expression of multiple hyperoxia markers, including Cdkn1a, Pdgfrb, and A2m. We conclude that a global assessment of gene regulation in the acute neonatal hyperoxia model of BPD-like pathology has identified Ahr as one driver of gene dysregulation. PMID:25150061

  18. The Promise of Virtual Teams: Identifying Key Factors in Effectiveness and Failure

    ERIC Educational Resources Information Center

    Horwitz, Frank M.; Bravington, Desmond; Silvis, Ulrik

    2006-01-01

    Purpose: The aim of the investigation is to identify enabling and disenabling factors in the development and operation of virtual teams; to evaluate the importance of factors such as team development, cross-cultural variables, leadership, communication and social cohesion as contributors to virtual team effectiveness. Design/methodology/approach:…

  19. The Promise of Virtual Teams: Identifying Key Factors in Effectiveness and Failure

    ERIC Educational Resources Information Center

    Horwitz, Frank M.; Bravington, Desmond; Silvis, Ulrik

    2006-01-01

    Purpose: The aim of the investigation is to identify enabling and disenabling factors in the development and operation of virtual teams; to evaluate the importance of factors such as team development, cross-cultural variables, leadership, communication and social cohesion as contributors to virtual team effectiveness. Design/methodology/approach:…

  20. Identifying the Key Factors Affecting the Chance of Passing Vocational Education and Training Subjects

    ERIC Educational Resources Information Center

    John, David

    2004-01-01

    This report identifies student characteristics--demographic and life-stage factors--which influence successful completion of vocational education and training (VET) subjects. It finds the likelihood of passing is significantly reduced for people who are Indigenous, have a disability, are of non-English speaking background, are unemployed or are…

  1. Research to Identify Effective Antifungal Agents, 1992 Annual Report.

    SciTech Connect

    Schreck, Carl

    1993-03-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990 and Schreck et al. 1991). The objectives of the present study were to select and evaluate up to 10 candidate fungicides.

  2. Faculty Use of Author Identifiers and Researcher Networking Tools

    ERIC Educational Resources Information Center

    Tran, Clara Y.; Lyon, Jennifer A.

    2017-01-01

    This cross-sectional survey focused on faculty use and knowledge of author identifiers and researcher networking systems, and professional use of social media, at a large state university. Results from 296 completed faculty surveys representing all disciplines (9.3% response rate) show low levels of awareness and variable resource preferences. The…

  3. Microarray analysis identifies candidate genes for key roles in coral development.

    PubMed

    Grasso, Lauretta C; Maindonald, John; Rudd, Stephen; Hayward, David C; Saint, Robert; Miller, David J; Ball, Eldon E

    2008-11-14

    Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development - when skeletogenesis is initiated, and symbionts are first acquired. Of 5081 unique peptide coding genes, 1084 were differentially expressed (P key developmental transitions. Genes of likely relevance to the processes of settlement, metamorphosis, calcification and interaction with symbionts were characterised further and their spatial expression patterns investigated using whole-mount in situ hybridization. This study is the first large-scale investigation of developmental gene expression for any cnidarian, and has provided candidate genes for key roles in many aspects of coral biology, including calcification, metamorphosis and symbiont uptake. One surprising finding is that some of these genes have clear counterparts in higher animals but are not present in the closely-related sea anemone Nematostella. Secondly, coral-specific processes (i.e. traits which distinguish corals from their close relatives) may be analogous to similar processes in distantly related organisms. This first large-scale application of microarray analysis demonstrates the potential of this approach for investigating many aspects of coral biology, including the effects of stress and disease.

  4. Microarray analysis identifies candidate genes for key roles in coral development

    PubMed Central

    Grasso, Lauretta C; Maindonald, John; Rudd, Stephen; Hayward, David C; Saint, Robert; Miller, David J; Ball, Eldon E

    2008-01-01

    Background Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development – when skeletogenesis is initiated, and symbionts are first acquired. Results Of 5081 unique peptide coding genes, 1084 were differentially expressed (P ≤ 0.05) in comparisons between four different stages of coral development, spanning key developmental transitions. Genes of likely relevance to the processes of settlement, metamorphosis, calcification and interaction with symbionts were characterised further and their spatial expression patterns investigated using whole-mount in situ hybridization. Conclusion This study is the first large-scale investigation of developmental gene expression for any cnidarian, and has provided candidate genes for key roles in many aspects of coral biology, including calcification, metamorphosis and symbiont uptake. One surprising finding is that some of these genes have clear counterparts in higher animals but are not present in the closely-related sea anemone Nematostella. Secondly, coral-specific processes (i.e. traits which distinguish corals from their close relatives) may be analogous to similar processes in distantly related organisms. This first large-scale application of microarray analysis demonstrates the potential of this approach for investigating many aspects of coral biology, including the effects of stress and disease. PMID:19014561

  5. Research on Key Technology and Applications for Internet of Things

    NASA Astrophysics Data System (ADS)

    Chen, Xian-Yi; Jin, Zhi-Gang

    The Internet of Things (IOT) has been paid more and more attention by the academe, industry, and government all over the world. The concept of IOT and the architecture of IOT are discussed. The key technologies of IOT, including Radio Frequency Identification technology, Electronic Product Code technology, and ZigBee technology are analyzed. The framework of digital agriculture application based on IOT is proposed.

  6. Indemnificatory research on key services of survivable networks

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoquan; Zhang, Jihong; Xu, Peng

    2012-01-01

    Survivable network refers to the system that can continue to fulfill the basic services set in advance when the system faces some threats, such as external attacks and intrusions, interior errors and confusions and so on, until the system backs to normal. The most significant feature of survivable network lies in that the key services of the system can keep on running when the system is in a desperate environment. Therefore, in a survivable network, how to ensure the nonstop running of the key services becomes very important. As a technology, apart from the basic features of Agent, such as response, autonomy and target-oriented, Mobile Agent also has its own unique feature--mobility. Based on the analysis of the survivability theory and the features of Mobile Agent, this paper proposes MESMMA (A Model for Essential Services Mobility Based on Mobile Agent), a Mobile Agent mobility-based model used to ensure the nonstop running of key services of survivable networks. Besides, this paper deeply discusses the structure design, running process and various Mobile Agent functions of the MESMMA system.

  7. Indemnificatory research on key services of survivable networks

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoquan; Zhang, Jihong; Xu, Peng

    2011-12-01

    Survivable network refers to the system that can continue to fulfill the basic services set in advance when the system faces some threats, such as external attacks and intrusions, interior errors and confusions and so on, until the system backs to normal. The most significant feature of survivable network lies in that the key services of the system can keep on running when the system is in a desperate environment. Therefore, in a survivable network, how to ensure the nonstop running of the key services becomes very important. As a technology, apart from the basic features of Agent, such as response, autonomy and target-oriented, Mobile Agent also has its own unique feature--mobility. Based on the analysis of the survivability theory and the features of Mobile Agent, this paper proposes MESMMA (A Model for Essential Services Mobility Based on Mobile Agent), a Mobile Agent mobility-based model used to ensure the nonstop running of key services of survivable networks. Besides, this paper deeply discusses the structure design, running process and various Mobile Agent functions of the MESMMA system.

  8. Separating the Wheat from the Chaff: Identifying Key Elements in the NLA .AU Domain Harvest

    ERIC Educational Resources Information Center

    Fellows, Geoff; Harvey, Ross; Lloyd, Annemaree; Pymm, Bob; Wallis, Jake

    2008-01-01

    In 2005 and 2006 the National Library of Australia (NLA) carried out two whole-domain web harvests which complement the selective web archiving approach taken by PANDORA. Web harvests of this size pose significant challenges to their use. Despite these challenges, such harvests present fascinating research opportunities. The NLA has provided…

  9. Separating the Wheat from the Chaff: Identifying Key Elements in the NLA .AU Domain Harvest

    ERIC Educational Resources Information Center

    Fellows, Geoff; Harvey, Ross; Lloyd, Annemaree; Pymm, Bob; Wallis, Jake

    2008-01-01

    In 2005 and 2006 the National Library of Australia (NLA) carried out two whole-domain web harvests which complement the selective web archiving approach taken by PANDORA. Web harvests of this size pose significant challenges to their use. Despite these challenges, such harvests present fascinating research opportunities. The NLA has provided…

  10. Identifying emerging research collaborations and networks: Method development

    PubMed Central

    Dozier, Ann M.; Martina, Camille A.; O’Dell, Nicole L.; Fogg, Thomas T.; Lurie, Stephen J.; Rubinstein, Eric P.; Pearson, Thomas A.

    2014-01-01

    Clinical and translational research is a multidisciplinary, collaborative team process. To evaluate this process, we developed a method to document emerging research networks and collaborations in our medical center to describe their productivity and viability over time. Using an email survey, sent to 1,620 clinical and basic science full-and part-time faculty members, respondents identified their research collaborators. Initial analyses, using Pajek software, assessed the feasibility of using social network analysis (SNA) methods with these data. Nearly 400 respondents identified 1,594 collaborators across 28 medical center departments resulting in 309 networks with 5 or more collaborators. This low-burden approach yielded a rich dataset useful for evaluation using SNA to: a) assess networks at several levels of the organization, including intrapersonal (individuals), interpersonal (social), organizational/institutional leadership (tenure and promotion), and physical/environmental (spatial proximity) and b) link with other data to assess the evolution of these networks. PMID:24019209

  11. Identifying emerging research collaborations and networks: method development.

    PubMed

    Dozier, Ann M; Martina, Camille A; O'Dell, Nicole L; Fogg, Thomas T; Lurie, Stephen J; Rubinstein, Eric P; Pearson, Thomas A

    2014-03-01

    Clinical and translational research is a multidisciplinary, collaborative team process. To evaluate this process, we developed a method to document emerging research networks and collaborations in our medical center to describe their productivity and viability over time. Using an e-mail survey, sent to 1,620 clinical and basic science full- and part-time faculty members, respondents identified their research collaborators. Initial analyses, using Pajek software, assessed the feasibility of using social network analysis (SNA) methods with these data. Nearly 400 respondents identified 1,594 collaborators across 28 medical center departments resulting in 309 networks with 5 or more collaborators. This low-burden approach yielded a rich data set useful for evaluation using SNA to: (a) assess networks at several levels of the organization, including intrapersonal (individuals), interpersonal (social), organizational/institutional leadership (tenure and promotion), and physical/environmental (spatial proximity) and (b) link with other data to assess the evolution of these networks.

  12. Criticisms of Educational Research: Key Topics and Levels of Analysis

    ERIC Educational Resources Information Center

    Oancea, Alis

    2005-01-01

    The article is an exploration of the meanings and worthiness of criticism as a significant phenomenon in the evolution of educational research during the 1990s. While drawing on an overview of the vast amount of documents expressing criticisms of educational research in the UK, western and eastern continental Europe and the USA, it summarises the…

  13. Key Institutions in Business and Management Education Research

    ERIC Educational Resources Information Center

    Fornaciari, Charles J.; Arbaugh, J. B.; Asarta, Carlos J.; Bento, Regina F.; Hwang, Alvin; Lund Dean, Kathy

    2017-01-01

    The authors investigate institutional productivity in business and management education (BME) research based on the analysis of 4,464 articles published by 7,210 authors across 17 BME journals over a 10-year period, involving approximately 1,900 schools worldwide. Departing from traditional disciplinary silos, they examine the BME research field…

  14. Hurricane Sandy: An Educational Bibliography of Key Research Studies

    ERIC Educational Resources Information Center

    Piotrowski, Chris

    2013-01-01

    There, undoubtedly, will be a flurry of research activity in the "Superstorm" Sandy impact area on a myriad of disaster-related topics, across academic disciplines. The purpose of this study was to review the disaster research related specifically to hurricanes in the educational and social sciences that would best serve as a compendium…

  15. Identifying Signs of Tinea Pedis: A Key to Understanding Clinical Variables.

    PubMed

    Canavan, Theresa N; Elewski, Boni E

    2015-10-01

    Tinea pedis is a frequently encountered dermatophytosis affecting the superficial skin of the feet, primarily of adults. The prevalence of tinea pedis has increased over the last several decades due to an increase in multiple risk factors. Infection from dermatophytes is most common, but infection from other fungi can also result in tinea pedis. Four distinct clinical presentations occur: interdigital, moccasin, vesicular, and acute ulcerative types. A variety of physical exam findings can help the clinician identify patients with tinea pedis.

  16. Identifying key parent-reported symptoms for detecting depression in high risk adolescents.

    PubMed

    Thapar, Ajay K; Hood, Kerenza; Collishaw, Stephan; Hammerton, Gemma; Mars, Becky; Sellers, Ruth; Potter, Robert; Craddock, Nick; Thapar, Anita; Rice, Frances

    2016-08-30

    Adolescent offspring of depressed parents are at particularly heightened risk of developing early onset Major Depressive Disorder (MDD) yet are unlikely to access services. We therefore aimed to identify a parsimonious combination of parent-reported symptoms that accurately detected offspring MDD. We used a multi-sample study comprising a development sample of 335 offspring of adults with recurrent MDD assessed on three occasions (mean age 12.4-14.8 years) and an independent validation sub-sample of 807 adolescents from a general population cohort (mean age 13.1 years). Parent ratings of psychiatric symptoms in adolescent offspring were assessed using established questionnaires. The best performing four-item combination of symptoms was identified. Accuracy in detecting concurrent DSM-IV MDD diagnosis, assessed by direct adolescent and parent interviews, was compared to the well-established 13-item short Moods and Feelings Questionnaire (sMFQ) using ROC curve analysis. The combination identified (concentration problems, anhedonia, worrying excessively and feeling unloved) performed equivalently to the sMFQ both in the development dataset and in the validation dataset. We concluded that a combination of four parent-reported mental health items performs equivalently to an established, longer depression questionnaire measure in detecting a diagnosis of adolescent major depressive disorder among offspring of parents with recurrent MDD and needs further evaluation.

  17. A practical guideline for identifying research intent with projects that collect private, identifiable health information.

    PubMed

    Amdur, Robert J; Speers, Marjorie A

    2003-06-01

    Radiation oncologists frequently engage in activities that involve the collection and analysis of data from medical records. Access to health information is an ethical issue because, if not done according to appropriate guidelines, it constitutes an invasion of privacy or breach in confidentiality. To protect patients for the social harm that may result from medical record review, our society has established laws and regulations that apply to projects that require medical record review. A major branch point in the guidelines for such projects is whether private information will be collected for research or nonresearch purposes. However, a problem with discussing privacy protection in terms of a research versus nonresearch model is that it is difficult to make this distinction for many kinds of projects. The purpose of this paper is to establish a practical guideline that can be used to decide if a project that involves analysis of private, identifiable medical information should be considered research from the regulatory standpoint.

  18. Identifying key features of effective active learning: the effects of writing and peer discussion.

    PubMed

    Linton, Debra L; Pangle, Wiline M; Wyatt, Kevin H; Powell, Karli N; Sherwood, Rachel E

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between three sections taught by three different instructors in a full factorial design. The data set was analyzed by generalized linear mixed-effect models with three independent variables: student aptitude, treatment, and instructor, and three dependent (assessment) variables: change in score on pre- and postactivity clicker questions, and coding scores on in-class writing and exam essays. All independent variables had significant effects on student performance for at least one of the dependent variables. Students with higher aptitude scored higher on all assessments. Student scores were higher on exam essay questions when the activity was implemented with a writing component compared with peer discussion only. There was a significant effect of instructor, with instructors showing different degrees of effectiveness with active-learning techniques. We suggest that individual writing should be implemented as part of active learning whenever possible and that instructors may need training and practice to become effective with active learning.

  19. Identifying Key Features of Effective Active Learning: The Effects of Writing and Peer Discussion

    PubMed Central

    Pangle, Wiline M.; Wyatt, Kevin H.; Powell, Karli N.; Sherwood, Rachel E.

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between three sections taught by three different instructors in a full factorial design. The data set was analyzed by generalized linear mixed-effect models with three independent variables: student aptitude, treatment, and instructor, and three dependent (assessment) variables: change in score on pre- and postactivity clicker questions, and coding scores on in-class writing and exam essays. All independent variables had significant effects on student performance for at least one of the dependent variables. Students with higher aptitude scored higher on all assessments. Student scores were higher on exam essay questions when the activity was implemented with a writing component compared with peer discussion only. There was a significant effect of instructor, with instructors showing different degrees of effectiveness with active-learning techniques. We suggest that individual writing should be implemented as part of active learning whenever possible and that instructors may need training and practice to become effective with active learning. PMID:25185230

  20. Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer

    PubMed Central

    Yao, Xin; Conley, Sarah; Zhong, Haihong; Liu, Zheng; Brohawn, Philip; Shen, Dong; Wu, Song; Ge, Xiaoxiao; Jiang, Yue; Zhao, Yizhuo; Lou, Yuqing; Morehouse, Chris; Zhu, Wei; Sebastian, Yinong; Czapiga, Meggan; Oganesyan, Vaheh; Fu, Haihua; Niu, Yanjie; Zhang, Wei; Streicher, Katie; Tice, David; Zhao, Heng; Zhu, Meng; Xu, Lin; Herbst, Ronald; Su, Xinying; Gu, Yi; Li, Shyoung; Huang, Lihua; Gu, Jianren; Han, Baohui; Jallal, Bahija; Shen, Hongbing; Yao, Yihong

    2016-01-01

    Small cell lung cancer (SCLC) is an aggressive disease with poor survival. A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC, however, much still remains unknown, particularly in the Asian patient population. Here we conducted whole exome sequencing (WES) and transcriptomic sequencing of primary tumors from 99 Chinese SCLC patients. Dysregulation of tumor suppressor genes TP53 and RB1 was observed in 82% and 62% of SCLC patients, respectively, and more than half of the SCLC patients (62%) harbored TP53 and RB1 mutation and/or copy number loss. Additionally, Serine/Arginine Splicing Factor 1 (SRSF1) DNA copy number gain and mRNA over-expression was strongly associated with poor survival using both discovery and validation patient cohorts. Functional studies in vitro and in vivo demonstrate that SRSF1 is important for tumorigenicity of SCLC and may play a key role in DNA repair and chemo-sensitivity. These results strongly support SRSF1 as a prognostic biomarker in SCLC and provide a rationale for personalized therapy in SCLC. PMID:27093186

  1. A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis

    PubMed Central

    Kou, Yan; McGrath, Kathleen; Nowak, Roberta; Catherman, Seana; Bigarella, Carolina L.; Rimmelé, Pauline; Zhang, Xin; Gnanapragasam, Merlin Nithya; Bieker, James J.; Papatsenko, Dmitri; Ma’ayan, Avi; Bresnick, Emery; Fowler, Velia; Palis, James; Ghaffari, Saghi

    2015-01-01

    Circulating red blood cells (RBCs) are essential for tissue oxygenation and homeostasis. Defective terminal erythropoiesis contributes to decreased generation of RBCs in many disorders. Specifically, ineffective nuclear expulsion (enucleation) during terminal maturation is an obstacle to therapeutic RBC production in vitro. To obtain mechanistic insights into terminal erythropoiesis we focused on FOXO3, a transcription factor implicated in erythroid disorders. Using an integrated computational and experimental systems biology approach, we show that FOXO3 is essential for the correct temporal gene expression during terminal erythropoiesis. We demonstrate that the FOXO3-dependent genetic network has critical physiological functions at key steps of terminal erythropoiesis including enucleation and mitochondrial clearance processes. FOXO3 loss deregulated transcription of genes implicated in cell polarity, nucleosome assembly and DNA packaging-related processes and compromised erythroid enucleation. Using high-resolution confocal microscopy and imaging flow cytometry we show that cell polarization is impaired leading to multilobulated Foxo3 -/- erythroblasts defective in nuclear expulsion. Ectopic FOXO3 expression rescued Foxo3 -/- erythroblast enucleation-related gene transcription, enucleation defects and terminal maturation. Remarkably, FOXO3 ectopic expression increased wild type erythroblast maturation and enucleation suggesting that enhancing FOXO3 activity may improve RBCs production. Altogether these studies uncover FOXO3 as a novel regulator of erythroblast enucleation and terminal maturation suggesting FOXO3 modulation might be therapeutic in disorders with defective erythroid maturation. PMID:26452208

  2. RNA-Seq Identifies Key Reproductive Gene Expression Alterations in Response to Cadmium Exposure

    PubMed Central

    Hu, Hanyang; Lu, Xing; Cen, Xiang; Chen, Xiaohua; Li, Feng; Zhong, Shan

    2014-01-01

    Cadmium is a common toxicant that is detrimental to many tissues. Although a number of transcriptional signatures have been revealed in different tissues after cadmium treatment, the genes involved in the cadmium caused male reproductive toxicity, and the underlying molecular mechanism remains unclear. Here we observed that the mice treated with different amount of cadmium in their rodent chow for six months exhibited reduced serum testosterone. We then performed RNA-seq to comprehensively investigate the mice testicular transcriptome to further elucidate the mechanism. Our results showed that hundreds of genes expression altered significantly in response to cadmium treatment. In particular, we found several transcriptional signatures closely related to the biological processes of regulation of hormone, gamete generation, and sexual reproduction, respectively. The expression of several testosterone synthetic key enzyme genes, such as Star, Cyp11a1, and Cyp17a1, were inhibited by the cadmium exposure. For better understanding of the cadmium-mediated transcriptional regulatory mechanism of the genes, we computationally analyzed the transcription factors binding sites and the mircoRNAs targets of the differentially expressed genes. Our findings suggest that the reproductive toxicity by cadmium exposure is implicated in multiple layers of deregulation of several biological processes and transcriptional regulation in mice. PMID:24982889

  3. Co-extinction in a host-parasite network: identifying key hosts for network stability.

    PubMed

    Dallas, Tad; Cornelius, Emily

    2015-08-17

    Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

  4. Defining hybrid poplar (Populus deltoides x Populus trichocarpa) tolerance to ozone: identifying key parameters.

    PubMed

    Ryan, A; Cojocariu, C; Possell, M; Davies, W J; Hewitt, C N

    2009-01-01

    This study examined whether two genotypes of hybrid poplar (Populus deltoides x Populus trichocarpa), previously classified as ozone tolerant and ozone sensitive, had differing physiological and biochemical responses when fumigated with 120 nL L(-1) ozone for 6 h per day for eight consecutive days. Isoprene emission rate, ozone uptake and a number of physiological and biochemical parameters were investigated before, during and after fumigation with ozone. Previous studies have shown that isoprene protects plants against oxidative stress. Therefore, it was hypothesized that these two genotypes would differ in either their basal isoprene emission rates or in the response of isoprene to fumigation by ozone. Our results showed that the basal emission rates of isoprene, physiological responses and ozone uptake rates were all similar. However, significant differences were found in visible damage, carotenoids, hydrogen peroxide (H(2)O(2)), thiobarbituric acid reactions (TBARS) and post-fumigation isoprene emission rates. It is shown that, although the classification of ozone tolerance or sensitivity had been previously clearly and carefully defined using one particular set of parameters, assessment of other key variables does not necessarily lead to the same conclusions. Thus, it may be necessary to reconsider the way in which plants are classified as ozone tolerant or sensitive.

  5. Transcriptome analyses identify key cellular factors associated with HIV-1 associated neuropathogenesis in infected men

    PubMed Central

    Venkatachari, Narasimhan J.; Jain, Siddhartha; Walker, Leah; Bivalkar-Mehla, Shalmali; Chattopadhyay, Ansuman; Bar-Joseph, Ziv; Rinaldo, Charles; Ragin, Ann; Seaberg, Eric; Levine, Andrew; Becker, James; Martin, Eileen; Sacktor, Ned; Ayyavoo, Velpandi

    2017-01-01

    Objective HIV-1 viral proteins and host inflammatory factors have a direct role in neuronal toxicity in in vitro, however, the contribution of these factors in vivo in HIV-1 associated neurocognitive disorder (HAND) is not fully understood. We applied novel Systems Biology approaches to identify specific cellular and viral factors and their related pathways that are associated with different stages of HAND. Design A cross-sectional study of individuals enrolled in the Multicenter AIDS Cohort Study (MACS) including HIV-1 seronegative (N=36) and HIV-1 seropositive individuals without neurocognitive symptoms (N=16), or with mild neurocognitive disorder (MND) (N=8) or HIV-associated dementia (HAD) (N=16). Methods A systematic evaluation of global transcriptome of peripheral blood mononuclear cells (PBMCs) obtained from HIV-1 seronegative individuals and from HIV-1 positive men without neurocognitive symptoms, or MND or HAD was performed. Results MND and HAD were associated with specific changes in mRNA transcripts and miRNAs in PBMCs. Comparison of upstream regulators and TimePath analyses identified specific cellular factors associated with MND and HAD, while HIV-1 viral proteins played a greater role in HAD. Additionally, expression of specific microRNAs – miR-let-7a, miR-124, miR-15a and others were found to correlate with mRNA gene expression and may have a potential protective role in asymptomatic HIV-1 seropositive individuals by regulating cellular signal transduction pathways downstream of chemokines and cytokines. Conclusions These results identify signature transcriptome changes in PBMCs associated with stages of HAND and shed light on the potential contribution of host cellular factors and viral proteins in HAND development. PMID:28005686

  6. Identifying Key Components for an Effective Case Report Poster: An Observational Study

    PubMed Central

    Paranjape, Anuradha; Estrada, Carlos

    2008-01-01

    BACKGROUND Residents demonstrate scholarly activity by presenting posters at academic meetings. Although recommendations from national organizations are available, evidence identifying which components are most important is not. OBJECTIVE To develop and test an evaluation tool to measure the quality of case report posters and identify the specific components most in need of improvement. DESIGN Faculty evaluators reviewed case report posters and provided on-site feedback to presenters at poster sessions of four annual academic general internal medicine meetings. A newly developed ten-item evaluation form measured poster quality for specific components of content, discussion, and format (5-point Likert scale, 1 = lowest, 5 = highest). Main outcome measure(s): Evaluation tool performance, including Cronbach alpha and inter-rater reliability, overall poster scores, differences across meetings and evaluators and specific components of the posters most in need of improvement. RESULTS Forty-five evaluators from 20 medical institutions reviewed 347 posters. Cronbach’s alpha of the evaluation form was 0.84 and inter-rater reliability, Spearman’s rho 0.49 ( < 0.001). The median score was 4.1 (Q1 -Q3, 3.7-4.6)(Q1 = 25th, Q3 = 75th percentile). The national meeting median score was higher than the regional meetings (4.4 vs, 4.0,  < 0.001). We found no difference in faculty scores. The following areas were identified as most needing improvement: clearly state learning objectives, tie conclusions to learning objectives, and use appropriate amount of words. CONCLUSIONS Our evaluation tool provides empirical data to guide trainees as they prepare posters for presentation which may improve poster quality and enhance their scholarly productivity. PMID:19089510

  7. Identifying key components for an effective case report poster: an observational study.

    PubMed

    Willett, Lisa L; Paranjape, Anuradha; Estrada, Carlos

    2009-03-01

    Residents demonstrate scholarly activity by presenting posters at academic meetings. Although recommendations from national organizations are available, evidence identifying which components are most important is not. To develop and test an evaluation tool to measure the quality of case report posters and identify the specific components most in need of improvement. Faculty evaluators reviewed case report posters and provided on-site feedback to presenters at poster sessions of four annual academic general internal medicine meetings. A newly developed ten-item evaluation form measured poster quality for specific components of content, discussion, and format (5-point Likert scale, 1 = lowest, 5 = highest). Evaluation tool performance, including Cronbach alpha and inter-rater reliability, overall poster scores, differences across meetings and evaluators and specific components of the posters most in need of improvement. Forty-five evaluators from 20 medical institutions reviewed 347 posters. Cronbach's alpha of the evaluation form was 0.84 and inter-rater reliability, Spearman's rho 0.49 (p < 0.001). The median score was 4.1 (Q1 -Q3, 3.7-4.6)(Q1 = 25th, Q3 = 75th percentile). The national meeting median score was higher than the regional meetings (4.4 vs, 4.0, P < 0.001). We found no difference in faculty scores. The following areas were identified as most needing improvement: clearly state learning objectives, tie conclusions to learning objectives, and use appropriate amount of words. Our evaluation tool provides empirical data to guide trainees as they prepare posters for presentation which may improve poster quality and enhance their scholarly productivity.

  8. Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

    PubMed

    Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

    2017-08-01

    This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  9. Appropriate disclosure of a diagnosis of dementia: identifying the key behaviours of 'best practice'.

    PubMed

    Lecouturier, Jan; Bamford, Claire; Hughes, Julian C; Francis, Jillian J; Foy, Robbie; Johnston, Marie; Eccles, Martin P

    2008-05-01

    Despite growing evidence that many people with dementia want to know their diagnosis, there is wide variation in attitudes of professionals towards disclosure. The disclosure of the diagnosis of dementia is increasingly recognised as being a process rather than a one-off behaviour. However, the different behaviours that contribute to this process have not been comprehensively defined. No intervention studies to improve diagnostic disclosure in dementia have been reported to date. As part of a larger study to develop an intervention to promote appropriate disclosure, we sought to identify important disclosure behaviours and explore whether supplementing a literature review with other methods would result in the identification of new behaviours. To identify a comprehensive list of behaviours in disclosure we conducted a literature review, interviewed people with dementia and informal carers, and used a consensus process involving health and social care professionals. Content analysis of the full list of behaviours was carried out. Interviews were conducted with four people with dementia and six informal carers. Eight health and social care professionals took part in the consensus panel. From the interviews, consensus panel and literature review 220 behaviours were elicited, with 109 behaviours over-lapping. The interviews and consensus panel elicited 27 behaviours supplementary to the review. Those from the interviews appeared to be self-evident but highlighted deficiencies in current practice and from the panel focused largely on balancing the needs of people with dementia and family members. Behaviours were grouped into eight categories: preparing for disclosure; integrating family members; exploring the patient's perspective; disclosing the diagnosis; responding to patient reactions; focusing on quality of life and well-being; planning for the future; and communicating effectively. This exercise has highlighted the complexity of the process of disclosing a

  10. Appropriate disclosure of a diagnosis of dementia: identifying the key behaviours of 'best practice'

    PubMed Central

    Lecouturier, Jan; Bamford, Claire; Hughes, Julian C; Francis, Jillian J; Foy, Robbie; Johnston, Marie; Eccles, Martin P

    2008-01-01

    Background Despite growing evidence that many people with dementia want to know their diagnosis, there is wide variation in attitudes of professionals towards disclosure. The disclosure of the diagnosis of dementia is increasingly recognised as being a process rather than a one-off behaviour. However, the different behaviours that contribute to this process have not been comprehensively defined. No intervention studies to improve diagnostic disclosure in dementia have been reported to date. As part of a larger study to develop an intervention to promote appropriate disclosure, we sought to identify important disclosure behaviours and explore whether supplementing a literature review with other methods would result in the identification of new behaviours. Methods To identify a comprehensive list of behaviours in disclosure we conducted a literature review, interviewed people with dementia and informal carers, and used a consensus process involving health and social care professionals. Content analysis of the full list of behaviours was carried out. Results Interviews were conducted with four people with dementia and six informal carers. Eight health and social care professionals took part in the consensus panel. From the interviews, consensus panel and literature review 220 behaviours were elicited, with 109 behaviours over-lapping. The interviews and consensus panel elicited 27 behaviours supplementary to the review. Those from the interviews appeared to be self-evident but highlighted deficiencies in current practice and from the panel focused largely on balancing the needs of people with dementia and family members. Behaviours were grouped into eight categories: preparing for disclosure; integrating family members; exploring the patient's perspective; disclosing the diagnosis; responding to patient reactions; focusing on quality of life and well-being; planning for the future; and communicating effectively. Conclusion This exercise has highlighted the complexity

  11. Clinical Trials: A Crucial Key to Human Health Research

    MedlinePlus

    ... that work in people, and there are clinical trials going on all the time in virtually every area of medical research. People who volunteer to take part in clinical trials do so for several reasons, including the chance ...

  12. Writing implementation research grant proposals: ten key ingredients

    PubMed Central

    2012-01-01

    Background All investigators seeking funding to conduct implementation research face the challenges of preparing a high-quality proposal and demonstrating their capacity to conduct the proposed study. Applicants need to demonstrate the progressive nature of their research agenda and their ability to build cumulatively upon the literature and their own preliminary studies. Because implementation science is an emerging field involving complex and multilevel processes, many investigators may not feel equipped to write competitive proposals, and this concern is pronounced among early stage implementation researchers. Discussion This article addresses the challenges of preparing grant applications that succeed in the emerging field of dissemination and implementation. We summarize ten ingredients that are important in implementation research grants. For each, we provide examples of how preliminary data, background literature, and narrative detail in the application can strengthen the application. Summary Every investigator struggles with the challenge of fitting into a page-limited application the research background, methodological detail, and information that can convey the project’s feasibility and likelihood of success. While no application can include a high level of detail about every ingredient, addressing the ten ingredients summarized in this article can help assure reviewers of the significance, feasibility, and impact of the proposed research. PMID:23062065

  13. Writing implementation research grant proposals: ten key ingredients.

    PubMed

    Proctor, Enola K; Powell, Byron J; Baumann, Ana A; Hamilton, Ashley M; Santens, Ryan L

    2012-10-12

    All investigators seeking funding to conduct implementation research face the challenges of preparing a high-quality proposal and demonstrating their capacity to conduct the proposed study. Applicants need to demonstrate the progressive nature of their research agenda and their ability to build cumulatively upon the literature and their own preliminary studies. Because implementation science is an emerging field involving complex and multilevel processes, many investigators may not feel equipped to write competitive proposals, and this concern is pronounced among early stage implementation researchers. This article addresses the challenges of preparing grant applications that succeed in the emerging field of dissemination and implementation. We summarize ten ingredients that are important in implementation research grants. For each, we provide examples of how preliminary data, background literature, and narrative detail in the application can strengthen the application. Every investigator struggles with the challenge of fitting into a page-limited application the research background, methodological detail, and information that can convey the project's feasibility and likelihood of success. While no application can include a high level of detail about every ingredient, addressing the ten ingredients summarized in this article can help assure reviewers of the significance, feasibility, and impact of the proposed research.

  14. Integrative genome analyses identify key somatic driver mutations of small cell lung cancer

    PubMed Central

    Peifer, Martin; Fernández-Cuesta, Lynnette; Sos, Martin L; George, Julie; Seidel, Danila; Kasper, Lawryn H; Plenker, Dennis; Leenders, Frauke; Sun, Ruping; Zander, Thomas; Menon, Roopika; Koker, Mirjam; Dahmen, Ilona; Müller, Christian; Di Cerbo, Vincenzo; Schildhaus, Hans-Ulrich; Altmüller, Janine; Baessmann, Ingelore; Becker, Christian; de Wilde, Bram; Vandesompele, Jo; Böhm, Diana; Ansén, Sascha; Gabler, Franziska; Wilkening, Ines; Heynck, Stefanie; Heuckmann, Johannes M; Lu, Xin; Carter, Scott L; Cibulskis, Kristian; Banerji, Shantanu; Getz, Gad; Park, Kwon-Sik; Rauh, Daniel; Grütter, Christian; Fischer, Matthias; Pasqualucci, Laura; Wright, Gavin; Wainer, Zoe; Russell, Prudence; Petersen, Iver; Chen, Yuan; Stoelben, Erich; Ludwig, Corinna; Schnabel, Philipp; Hoffmann, Hans; Muley, Thomas; Brockmann, Michael; Engel-Riedel, Walburga; Muscarella, Lucia A; Fazio, Vito M; Groen, Harry; Timens, Wim; Sietsma, Hannie; Thunnissen, Erik; Smit, Egbert; Heideman, Daniëlle AM; Snijders, Peter JF; Cappuzzo, Federico; Ligorio, Claudia; Damiani, Stefania; Field, John; Solberg, Steinar; Brustugun, Odd Terje; Lund-Iversen, Marius; Sänger, Jörg; Clement, Joachim H; Soltermann, Alex; Moch, Holger; Weder, Walter; Solomon, Benjamin; Soria, Jean-Charles; Validire, Pierre; Besse, Benjamin; Brambilla, Elisabeth; Brambilla, Christian; Lantuejoul, Sylvie; Lorimier, Philippe; Schneider, Peter M; Hallek, Michael; Pao, William; Meyerson, Matthew; Sage, Julien; Shendure, Jay; Schneider, Robert; Büttner, Reinhard; Wolf, Jürgen; Nürnberg, Peter; Perner, Sven; Heukamp, Lukas C; Brindle, Paul K; Haas, Stefan; Thomas, Roman K

    2016-01-01

    Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor survival1–3. We sequenced 29 SCLC exomes, two genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million basepairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in histone-modifying genes, CREBBP, EP300, and MLL. Furthermore, we observed mutations in PTEN, in SLIT2, and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from p53/Rb1-deficient mice4. Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genome alterations, and provides a generalizable framework for identification of biologically relevant genes in the context of high mutational background. PMID:22941188

  15. Identifying Key Proteins in Hg Methylation Pathways of Desulfovibrio by Global Proteomics, Final Technical Report

    SciTech Connect

    Summers, Anne O.; Miller, Susan M.; Wall, Judy; Lipton, Mary

    2016-06-18

    Elemental mercury, Hg(0) is a contaminant at many DOE sites, especially at Oak Ridge National Laboratory (ORNL) where the spread of spilled Hg and its effects on microbial populations have been monitored for decades. To explore the microbial interactions with Hg, we have devised a global proteomic approach capable of directly detecting Hg-adducts of proteins. This technique developed in the facultative anaerobe, Escherichia coli, allows us to identify the proteins most vulnerable to acute exposure to organomercurials phenyl- and ethyl-mercury (as surrogates for the highly neurotoxic methyl-Hg) (Polacco, et al, 2011). We have found >300 such proteins in all metabolic functional groups and cellular compartments; most are highly conserved and can serve as markers for acute Hg exposure (Zink, et al. 2016, in preparation). We have also discovered that acute Hg exposure severely disrupts thiol, iron and redox homeostases, and electrolyte balance (LaVoie, et al., 2015) Thus, we proposed to bring these techniques to bear on the central problem of identifying the cellular proteins involved in bacterial uptake and methylation of mercury and its release from the cell.

  16. What is big data? A consensual definition and a review of key research topics

    NASA Astrophysics Data System (ADS)

    De Mauro, Andrea; Greco, Marco; Grimaldi, Michele

    2015-02-01

    Although Big Data is a trending buzzword in both academia and the industry, its meaning is still shrouded by much conceptual vagueness. The term is used to describe a wide range of concepts: from the technological ability to store, aggregate, and process data, to the cultural shift that is pervasively invading business and society, both drowning in information overload. The lack of a formal definition has led research to evolve into multiple and inconsistent paths. Furthermore, the existing ambiguity among researchers and practitioners undermines an efficient development of the subject. In this paper we have reviewed the existing literature on Big Data and analyzed its previous definitions in order to pursue two results: first, to provide a summary of the key research areas related to the phenomenon, identifying emerging trends and suggesting opportunities for future development; second, to provide a consensual definition for Big Data, by synthesizing common themes of existing works and patterns in previous definitions.

  17. A Chemical Screening Approach to Identify Novel Key Mediators of Erythroid Enucleation.

    PubMed

    Wölwer, Christina B; Pase, Luke B; Pearson, Helen B; Gödde, Nathan J; Lackovic, Kurt; Huang, David C S; Russell, Sarah M; Humbert, Patrick O

    2015-01-01

    Erythroid enucleation is critical for terminal differentiation of red blood cells, and involves extrusion of the nucleus by orthochromatic erythroblasts to produce reticulocytes. Due to the difficulty of synchronizing erythroblasts, the molecular mechanisms underlying the enucleation process remain poorly understood. To elucidate the cellular program governing enucleation, we utilized a novel chemical screening approach whereby orthochromatic cells primed for enucleation were enriched ex vivo and subjected to a functional drug screen using a 324 compound library consisting of structurally diverse, medicinally active and cell permeable drugs. Using this approach, we have confirmed the role of HDACs, proteasomal regulators and MAPK in erythroid enucleation and introduce a new role for Cyclin-dependent kinases, in particular CDK9, in this process. Importantly, we demonstrate that when coupled with imaging analysis, this approach provides a powerful means to identify and characterize rate limiting steps involved in the erythroid enucleation process.

  18. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming gene

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Li, Hu; Collins, James; Mehta, Pankaj

    2013-03-01

    A common metaphor for describing development is a rugged epigenetic landscape where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from physics, specifically Hopfield neural networks. Each cell fate is a dynamic attractor, yet cells can change fate in response to external signals. Our model suggests that partially reprogrammed cells (cells found in reprogramming experiments but not in vivo) are a natural consequence of high-dimensional landscapes and predicts that partially reprogrammed cells should be hybrids that coexpress genes from multiple cell fates. We verify this prediction by reanalyzing existing data sets. Our model reproduces known reprogramming protocols and identifies candidate transcription factors for reprogramming to novel cell fates, suggesting epigenetic landscapes are a powerful paradigm for understanding cellular identity.

  19. Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

    PubMed Central

    Lang, Alex H.; Li, Hu; Collins, James J.; Mehta, Pankaj

    2014-01-01

    A common metaphor for describing development is a rugged “epigenetic landscape” where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from spin-glass physics. Each cell fate is a dynamic attractor, yet cells can change fate in response to external signals. Our model suggests that partially reprogrammed cells are a natural consequence of high-dimensional landscapes, and predicts that partially reprogrammed cells should be hybrids that co-express genes from multiple cell fates. We verify this prediction by reanalyzing existing datasets. Our model reproduces known reprogramming protocols and identifies candidate transcription factors for reprogramming to novel cell fates, suggesting epigenetic landscapes are a powerful paradigm for understanding cellular identity. PMID:25122086

  20. Identifying keys to success in clinical learning: a study of two interprofessional learning environments.

    PubMed

    Laksov, Klara Bolander; Boman, Lena Engqvist; Liljedahl, Matilda; Björck, Erik

    2015-03-01

    The aim of this study was to study the intrinsic system behind interprofessional clinical learning environments. Two health care units were selected on the basis of having received a reward for best clinical learning organization. Interviews were carried out with health care staff/clinical supervisors from different professions. The interviews were transcribed and analysed according to qualitative content analysis, and categories and themes were identified. Analysis revealed two different systems of clinical learning environments. In one, the interplay between the structural aspects dominated, and in the other, the interplay between the cultural aspects dominated. An important similarity between the environments was that a defined role for students in the organization and interprofessional teamwork around supervision across professional borders was emphasized.

  1. Transdisciplinary research for complex One Health issues: a scoping review of key concepts.

    PubMed

    Min, B; Allen-Scott, L K; Buntain, B

    2013-11-01

    In order to address the complexity inherent in researching One Health (OH) issues, we support the concept that researchers must transcend individual disciplinary and non-disciplinary boundaries, and move into the realm of transdisciplinary (TD) research approaches. For the purposes of this paper we use the term OH and the concept that OH research is conducted to solve complex health challenges at the animal-human--human-ecosystem interface. TD goes beyond interdisciplinary research to engages disciplines and communities through a unified conceptual framework. In this scoping review we investigated key concepts, definitions and themes in OH and TD based on the peer reviewed literature. We identified nine emerging themes in TD research: (1) education, (2) conflict amongst disciplines, (3) effective communication, (4) shared conceptual framework, (5) leadership, (6) perceived power differentials, (7) community-based methodologies, (8) support for TD research and (9) time and effort. This review provides a synthesized knowledge base that describes the nature, extent of evidence and challenges of engaging in TD initiatives. This knowledge base further provides a foundation for those interested in developing improved strategies for TD collaborative and cross-sectoral research in OH.

  2. Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments.

    PubMed

    Noto, Jennifer M; Chopra, Abha; Loh, John T; Romero-Gallo, Judith; Piazuelo, M Blanca; Watson, Mark; Leary, Shay; Beckett, Amber C; Wilson, Keith T; Cover, Timothy L; Mallal, Simon; Israel, Dawn A; Peek, Richard M

    2017-09-18

    Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease. Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed. A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034). These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  3. Organizing patient safety research to identify risks and hazards

    PubMed Central

    Battles, J; Lilford, R

    2003-01-01

    Patient safety has become an international priority with major research programmes being carried out in the USA, UK, and elsewhere. The challenge is how to organize research efforts that will produce the greatest yield in making health care safer for patients. Patient safety research initiatives can be considered in three different stages: (1) identification of the risks and hazards; (2) design, implementation, and evaluation of patient safety practices; and (3) maintaining vigilance to ensure that a safe environment continues and patient safety cultures remain in place. Clearly, different research methods and approaches are needed at each of the different stages of the continuum. A number of research approaches can be used at stage 1 to identify risks and hazards including the use of medical records and administrative record review, event reporting, direct observation, process mapping, focus groups, probabilistic risk assessment, and safety culture assessment. No single method can be universally applied to identify risks and hazards in patient safety. Rather, multiple approaches using combinations of these methods should be used to increase identification of risks and hazards of health care associated injury or harm to patients. PMID:14645888

  4. Tracing Scientific Facilities through the Research Literature Using Persistent Identifiers

    NASA Astrophysics Data System (ADS)

    Mayernik, M. S.; Maull, K. E.

    2016-12-01

    Tracing persistent identifiers to their source publications is an easy task when authors use them, since it is a simple matter of matching the persistent identifier to the specific text string of the identifier. However, trying to understand if a publication uses the resource behind an identifier when such identifier is not referenced explicitly is a harder task. In this research, we explore the effectiveness of alternative strategies of associating publications with uses of the resource referenced by an identifier when it may not be explicit. This project is explored within the context of the NCAR supercomputer, where we are broadly interesting in the science that can be traced to the usage of the NCAR supercomputing facility, by way of the peer-reviewed research publications that utilize and reference it. In this project we explore several ways of drawing linkages between publications and the NCAR supercomputing resources. Identifying and compiling peer-reviewed publications related to NCAR supercomputer usage are explored via three sources: 1) User-supplied publications gathered through a community survey, 2) publications that were identified via manual searching of the Google scholar search index, and 3) publications associated with National Science Foundation (NSF) grants extracted from a public NSF database. These three sources represent three styles of collecting information about publications that likely imply usage of the NCAR supercomputing facilities. Each source has strengths and weaknesses, thus our discussion will explore how our publication identification and analysis methods vary in terms of accuracy, reliability, and effort. We will also discuss strategies for enabling more efficient tracing of research impacts of supercomputing facilities going forward through the assignment of a persistent web identifier to the NCAR supercomputer. While this solution has potential to greatly enhance our ability to trace the use of the facility through

  5. Key challenges in future Li-battery research.

    PubMed

    Tarascon, J-M

    2010-07-28

    Batteries are a major technological challenge in this new century as they are a key method to make more efficient use of energy. Although today's Li-ion technology has conquered the portable electronic markets and is still improving, it falls short of meeting the demands dictated by the powering of both hybrid electric vehicles and electric vehicles or by the storage of renewable energies (wind, solar). There is room for optimism as long as we pursue paradigm shifts while keeping in mind the concept of materials sustainability. Some of these concepts, relying on new ways to prepare electrode materials via eco-efficient processes, on the use of organic rather than inorganic materials or new chemistries will be discussed. Achieving these concepts will require the inputs of multiple disciplines.

  6. Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD

    PubMed Central

    Yoo, Seungyeul; Takikawa, Sachiko; Geraghty, Patrick; Argmann, Carmen; Campbell, Joshua; Lin, Luan; Huang, Tao; Tu, Zhidong; Feronjy, Robert; Spira, Avrum; Schadt, Eric E.; Powell, Charles A.; Zhu, Jun

    2015-01-01

    Chronic Obstructive Pulmonary Disease (COPD) is a complex disease. Genetic, epigenetic, and environmental factors are known to contribute to COPD risk and disease progression. Therefore we developed a systematic approach to identify key regulators of COPD that integrates genome-wide DNA methylation, gene expression, and phenotype data in lung tissue from COPD and control samples. Our integrative analysis identified 126 key regulators of COPD. We identified EPAS1 as the only key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms of methylation profile and downstream target genes. Genes predicted to be regulated by EPAS1 were enriched for biological processes including signaling, cell communications, and system development. We confirmed that EPAS1 protein levels are lower in human COPD lung tissue compared to non-disease controls and that Epas1 gene expression is reduced in mice chronically exposed to cigarette smoke. As EPAS1 downstream genes were significantly enriched for hypoxia responsive genes in endothelial cells, we tested EPAS1 function in human endothelial cells. EPAS1 knockdown by siRNA in endothelial cells impacted genes that significantly overlapped with EPAS1 downstream genes in lung tissue including hypoxia responsive genes, and genes associated with emphysema severity. Our first integrative analysis of genome-wide DNA methylation and gene expression profiles illustrates that not only does DNA methylation play a ‘causal’ role in the molecular pathophysiology of COPD, but it can be leveraged to directly identify novel key mediators of this pathophysiology. PMID:25569234

  7. Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD.

    PubMed

    Yoo, Seungyeul; Takikawa, Sachiko; Geraghty, Patrick; Argmann, Carmen; Campbell, Joshua; Lin, Luan; Huang, Tao; Tu, Zhidong; Foronjy, Robert F; Feronjy, Robert; Spira, Avrum; Schadt, Eric E; Powell, Charles A; Zhu, Jun

    2015-01-01

    Chronic Obstructive Pulmonary Disease (COPD) is a complex disease. Genetic, epigenetic, and environmental factors are known to contribute to COPD risk and disease progression. Therefore we developed a systematic approach to identify key regulators of COPD that integrates genome-wide DNA methylation, gene expression, and phenotype data in lung tissue from COPD and control samples. Our integrative analysis identified 126 key regulators of COPD. We identified EPAS1 as the only key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms of methylation profile and downstream target genes. Genes predicted to be regulated by EPAS1 were enriched for biological processes including signaling, cell communications, and system development. We confirmed that EPAS1 protein levels are lower in human COPD lung tissue compared to non-disease controls and that Epas1 gene expression is reduced in mice chronically exposed to cigarette smoke. As EPAS1 downstream genes were significantly enriched for hypoxia responsive genes in endothelial cells, we tested EPAS1 function in human endothelial cells. EPAS1 knockdown by siRNA in endothelial cells impacted genes that significantly overlapped with EPAS1 downstream genes in lung tissue including hypoxia responsive genes, and genes associated with emphysema severity. Our first integrative analysis of genome-wide DNA methylation and gene expression profiles illustrates that not only does DNA methylation play a 'causal' role in the molecular pathophysiology of COPD, but it can be leveraged to directly identify novel key mediators of this pathophysiology.

  8. Commentary on collaboration: the key to interdisciplinary research.

    PubMed

    Clarke-Tasker, Veronica A

    2009-01-01

    Researchers seeking federal and other sources of funding for their proposed studies have found the request for applications are for those developed by multidisciplinary teams including but not limited faith based and grass root organizations. Nurses, pharmacist, physicians, allied health providers, students, clergy and lay organizations are working together to decrease health disparities. Academic settings have the infrastructure and human resources that can promote interdisciplinary opportunities for partnerships across campus, within their school, colleges and community. The author provides recommendations for building a multidisciplinary research team.

  9. Student as Communication Skills Trainer: From Research to "Concept Keys"

    ERIC Educational Resources Information Center

    Bodie, Graham D.

    2008-01-01

    Although textbooks are filled with practical communication advice, many students overlook the importance of basing practical advice about communication on quality research. This oversight is important for two reasons. First, given the explosion of self-help remedies focused on communication, students should learn to distinguish between…

  10. Student as Communication Skills Trainer: From Research to "Concept Keys"

    ERIC Educational Resources Information Center

    Bodie, Graham D.

    2008-01-01

    Although textbooks are filled with practical communication advice, many students overlook the importance of basing practical advice about communication on quality research. This oversight is important for two reasons. First, given the explosion of self-help remedies focused on communication, students should learn to distinguish between…

  11. Gene expression profiling in Entamoeba histolytica identifies key components in iron uptake and metabolism.

    PubMed

    Hernández-Cuevas, Nora Adriana; Weber, Christian; Hon, Chung-Chau; Guillen, Nancy

    2014-01-01

    Entamoeba histolytica is an ameboid parasite that causes colonic dysentery and liver abscesses in humans. The parasite encounters dramatic changes in iron concentration during its invasion of the host, with relatively low levels in the intestinal lumen and then relatively high levels in the blood and liver. The liver notably contains sources of iron; therefore, the parasite's ability to use these sources might be relevant to its survival in the liver and thus the pathogenesis of liver abscesses. The objective of the present study was to identify factors involved in iron uptake, use and storage in E. histolytica. We compared the respective transcriptomes of E. histolytica trophozoites grown in normal medium (containing around 169 µM iron), low-iron medium (around 123 µM iron), iron-deficient medium (around 91 µM iron), and iron-deficient medium replenished with hemoglobin. The differentially expressed genes included those coding for the ATP-binding cassette transporters and major facilitator transporters (which share homology with bacterial siderophores and heme transporters) and genes involved in heme biosynthesis and degradation. Iron deficiency was associated with increased transcription of genes encoding a subset of cell signaling molecules, some of which have previously been linked to adaptation to the intestinal environment and virulence. The present study is the first to have assessed the transcriptome of E. histolytica grown under various iron concentrations. Our results provide insights into the pathways involved in iron uptake and metabolism in this parasite.

  12. Gene Expression Profiling in Entamoeba histolytica Identifies Key Components in Iron Uptake and Metabolism

    PubMed Central

    Hernández-Cuevas, Nora Adriana; Weber, Christian; Hon, Chung-Chau; Guillen, Nancy

    2014-01-01

    Entamoeba histolytica is an ameboid parasite that causes colonic dysentery and liver abscesses in humans. The parasite encounters dramatic changes in iron concentration during its invasion of the host, with relatively low levels in the intestinal lumen and then relatively high levels in the blood and liver. The liver notably contains sources of iron; therefore, the parasite's ability to use these sources might be relevant to its survival in the liver and thus the pathogenesis of liver abscesses. The objective of the present study was to identify factors involved in iron uptake, use and storage in E. histolytica. We compared the respective transcriptomes of E. histolytica trophozoites grown in normal medium (containing around 169 µM iron), low-iron medium (around 123 µM iron), iron-deficient medium (around 91 µM iron), and iron-deficient medium replenished with hemoglobin. The differentially expressed genes included those coding for the ATP-binding cassette transporters and major facilitator transporters (which share homology with bacterial siderophores and heme transporters) and genes involved in heme biosynthesis and degradation. Iron deficiency was associated with increased transcription of genes encoding a subset of cell signaling molecules, some of which have previously been linked to adaptation to the intestinal environment and virulence. The present study is the first to have assessed the transcriptome of E. histolytica grown under various iron concentrations. Our results provide insights into the pathways involved in iron uptake and metabolism in this parasite. PMID:25210888

  13. An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis

    PubMed Central

    Zhao, Min; Li, Zhe; Qu, Hong

    2015-01-01

    Metastasis suppressor genes (MS genes) are genes that play important roles in inhibiting the process of cancer metastasis without preventing growth of the primary tumor. Identification of these genes and understanding their functions are critical for investigation of cancer metastasis. Recent studies on cancer metastasis have identified many new susceptibility MS genes. However, the comprehensive illustration of diverse cellular processes regulated by metastasis suppressors during the metastasis cascade is lacking. Thus, the relationship between MS genes and cancer risk is still unclear. To unveil the cellular complexity of MS genes, we have constructed MSGene (http://MSGene.bioinfo-minzhao.org/), the first literature-based gene resource for exploring human MS genes. In total, we manually curated 194 experimentally verified MS genes and mapped to 1448 homologous genes from 17 model species. Follow-up functional analyses associated 194 human MS genes with epithelium/tissue morphogenesis and epithelia cell proliferation. In addition, pathway analysis highlights the prominent role of MS genes in activation of platelets and coagulation system in tumor metastatic cascade. Moreover, global mutation pattern of MS genes across multiple cancers may reveal common cancer metastasis mechanisms. All these results illustrate the importance of MSGene to our understanding on cell development and cancer metastasis. PMID:26486520

  14. Physiologically-based toxicokinetic models help identifying the key factors affecting contaminant uptake during flood events.

    PubMed

    Brinkmann, Markus; Eichbaum, Kathrin; Kammann, Ulrike; Hudjetz, Sebastian; Cofalla, Catrina; Buchinger, Sebastian; Reifferscheid, Georg; Schüttrumpf, Holger; Preuss, Thomas; Hollert, Henner

    2014-07-01

    As a consequence of global climate change, we will be likely facing an increasing frequency and intensity of flood events. Thus, the ecotoxicological relevance of sediment re-suspension is of growing concern. It is vital to understand contaminant uptake from suspended sediments and relate it to effects in aquatic biota. Here we report on a computational study that utilizes a physiologically based toxicokinetic model to predict uptake, metabolism and excretion of sediment-borne pyrene in rainbow trout (Oncorhynchus mykiss). To this end, data from two experimental studies were compared with the model predictions: (a) batch re-suspension experiments with constant concentration of suspended particulate matter at two different temperatures (12 and 24°C), and (b) simulated flood events in an annular flume. The model predicted both the final concentrations and the kinetics of 1-hydroxypyrene secretion into the gall bladder of exposed rainbow trout well. We were able to show that exhaustive exercise during exposure in simulated flood events can lead to increased levels of biliary metabolites and identified cardiac output and effective respiratory volume as the two most important factors for contaminant uptake. The results of our study clearly demonstrate the relevance and the necessity to investigate uptake of contaminants from suspended sediments under realistic exposure scenarios.

  15. Identifying key factors in homeowner's adoption of water quality best management practices.

    PubMed

    Brehm, Joan M; Pasko, Danielle K; Eisenhauer, Brian W

    2013-07-01

    The recognition of the significance of the residential environment in contributing to non-point source (NPS) pollution and the inherently dispersed nature of NPS pollution itself that presents significant challenges to effective regulation has led to the creation and dissemination of best management practices (BMPs) that can reduce the impacts of NPS pollution (Environmental Protection Agency US, Protecting water quality from urban runoff, http://www.epa.gov/npdes/pubs/nps_urban-facts_final.pdf , 2003). However, very few studies have examined the factors that influence the adoption of BMPs by residential homeowners, despite the fact that residential environments have been identified as one of the most significant contributors to NPS pollution. Given this need, the purpose of this project was to explore how demographic and knowledge-based factors predict adoption of residential BMPs in an urbanizing watershed in Northern Illinois using statistical analyses of survey data collected as part of a watershed planning process. The findings indicate that broad knowledge of BMPs is the strongest predictor of use for a specific BMP. Knowledge of BMPs is strongly correlated with their use, which reinforces the need for educational programs, even among those assumed to be knowledgeable about BMPs.

  16. An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis.

    PubMed

    Zhao, Min; Li, Zhe; Qu, Hong

    2015-10-21

    Metastasis suppressor genes (MS genes) are genes that play important roles in inhibiting the process of cancer metastasis without preventing growth of the primary tumor. Identification of these genes and understanding their functions are critical for investigation of cancer metastasis. Recent studies on cancer metastasis have identified many new susceptibility MS genes. However, the comprehensive illustration of diverse cellular processes regulated by metastasis suppressors during the metastasis cascade is lacking. Thus, the relationship between MS genes and cancer risk is still unclear. To unveil the cellular complexity of MS genes, we have constructed MSGene (http://MSGene.bioinfo-minzhao.org/), the first literature-based gene resource for exploring human MS genes. In total, we manually curated 194 experimentally verified MS genes and mapped to 1448 homologous genes from 17 model species. Follow-up functional analyses associated 194 human MS genes with epithelium/tissue morphogenesis and epithelia cell proliferation. In addition, pathway analysis highlights the prominent role of MS genes in activation of platelets and coagulation system in tumor metastatic cascade. Moreover, global mutation pattern of MS genes across multiple cancers may reveal common cancer metastasis mechanisms. All these results illustrate the importance of MSGene to our understanding on cell development and cancer metastasis.

  17. Identifying key soil cyanobacteria easy to isolate and culture for arid soil restoration

    NASA Astrophysics Data System (ADS)

    Roncero-Ramos, Beatriz; Ángeles Muñoz-Martín, M.; Chamizo, Sonia; Román, Raúl; Rodriguez-Caballero, Emilio; Mateo, Pilar; Cantón, Yolanda

    2017-04-01

    Drylands represent an important fraction of the Earth land's surface. Low cover of vascular plants characterizes these regions, and the large open areas among plants are often colonized by cyanobacteria, mosses, lichens, algae, bryophytes, bacteria and fungi, known as biocrusts. Because these communities are on or within the soil surface, they contribute to improve physicochemical properties of the uppermost soil layers and have important effects on soil fertility and stability, so they could play an important role on soil restoration. Cyanobacteria appear to be a cross component of biocrusts and they have been demonstrated to enhance water availability, soil fertility (fixing atmospheric C and N), and soil aggregation (thanks to their filamentous morphology and the exopolysaccharides they excrete), and significantly reduce water and wind erosion. Besides, they are able to tolerate high temperatures and UV radiation. All these features convert cyanobacteria in pioneer organisms capable of colonizing degraded soils and may be crucial in facilitating the succession of more developed organisms such as vascular plants. Therefore, the use of native cyanobacteria, already adapted to site environmental conditions, could guarantee a successful restoration approach of degraded soils. However, previous to their application for soil restoration, the most representative species inhabiting these soils should be identified. The objective of this study was to identify (morphologically and genetically) and isolate representative native cyanobacteria species from arid soils in SE Spain, characterized for being easily isolated and cultured with the aim of using them to inoculate degraded arid soil. We selected two study areas in Almería, SE Spain, where biocrust cover most of the open spaces between plants: El Cautivo experimental site located in the Tabernas desert and a limestone quarry located at the southeastern edge of the Gádor massif. The first site is characterized by

  18. Fragmentation patterns of evergreen oak woodlands in Southwestern Iberia: identifying key spatial indicators.

    PubMed

    Costa, Augusta; Madeira, Manuel; Lima Santos, José; Plieninger, Tobias; Seixas, Júlia

    2014-01-15

    Mediterranean evergreen oak woodlands (composed of Quercus suber L. and Quercus rotundifolia Lam.) are becoming increasingly fragmented in the human-modified landscapes of Southwestern Portugal and Spain. Previous studies have largely neglected to assess the spatial changes of oak woodlands in relation to their surrounding landscape matrix, and to characterize and quantify woodland boundaries and edges. The present study aims to fill this gap by analyzing fragmentation patterns of oak woodlands over a 50-year period (1958-2007) in three landscapes. Using archived aerial imagery from 1958, 1995 and 2007, for two consecutive periods (1958-1995 and 1995-2007), we calculated a set of landscape metrics to compare woodland fragmentation over time. Our results indicated a continuous woodland fragmentation characterized by their edge dynamics. From 1958 to 2007, the replacement of open farmland by shrubland and by new afforestation areas in the oak woodland landscape surrounding matrix, led to the highest values for edge contrast length trends of 5.0 and 12.3, respectively. Linear discriminant analysis was performed to delineate fragmented woodland structures and identify metric variables that characterize woodland spatial configuration. The edge contrast length with open farmland showed a strong correlation with F1 (correlations ranging between 0.55 and 0.98) and may be used as a proxy for oak woodland mixedness in landscape matrix. The edge dynamics of oak woodlands may result in different patterns of oak recruitment and therefore, its study may be helpful in highlighting future baselines for the sustainable management of oak woodlands. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

    PubMed Central

    Dixit, Anshuman; Verkhivker, Gennady M.

    2012-01-01

    Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based “conformational selection” of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters

  20. Identifying key drivers of sea surface variability from satellite altimetry in the North-East Atlantic

    NASA Astrophysics Data System (ADS)

    Sterlini, Paul; de Vries, Hylke

    2015-04-01

    Sea surface height variability (SSV) operates in varying temporal and spatial scales and acts as a source of noise when trying to perform long term trend analysis on the sea surface height (SSH). SSV can be removed through a simple running average process but this approach takes no account of individual contributors to the SSV. This study seeks to identify (and ultimately remove) the major contributing components of the SSV in the North-East Atlantic to expose the underlying changes in the SSH signal. This allows a trend analysis on the "cleaned" SSH for an accurate determination of sea level rise. Observations of sea level anomalies (SLA) are taken from 21 years of satellite altimeter data and are used to estimate the SSV in the North-East Atlantic. Seasonal signals are removed and monthly means calculated. The SSV is decomposed into global, regional and local components and a simple multiple linear regression model is constructed on the basis of these components to model the explained SSV. Initial results show that a region of high SSV exists off the west coast of Denmark and can be well represented with a regression model which uses local wind and global temperature as primary regressors. The same model does not capture a more diffuse region of high SSV in the Atlantic Ocean which suggests that the SSV is driven by other physical processes and highlights the need for specific spatial analyses when seeking to model SSV. This work will help in understanding regional sea level change over the past 21 years and to provide a foundation for estimates of local sea level change in the near future.

  1. Identifying plant traits: a key aspect for suitable species selection in ecological restoration of semiarid slopes

    NASA Astrophysics Data System (ADS)

    Bochet, Esther; García-Fayos, Patricio

    2017-04-01

    In the context of ecological restoration, one of the greatest challenges for practitioners and scientists is to select suitable species for revegetation purposes. In semiarid environments where restoration projects often fail, little attention has been paid so far to the contribution of plant traits to species success. The objective of this study was to (1) identify plant traits associated with species success on four roadside situations along an erosion-productivity gradient, and (2) to provide an ecological framework for selecting suitable species on the basis of their morphological and functional traits, applied to semiarid environments. We analyzed the association of 10 different plant traits with species success of 296 species surveyed on the four roadside situations in a semiarid region (Valencia, Spain). Plant traits included general plant traits (longevity, woodiness) and more specific root-, seed- and leaf-related traits (root type, sprouting ability, seed mucilage, seed mass, seed susceptibility to removal, specific leaf area and leaf dry matter content). All of them were selected according to the prevailing limiting ecogeomorphological processes acting along the erosion-productivity gradient. We observed strong shifts along the erosion-productivity gradient in the traits associated to species success. At the harshest end of the gradient, the most intensely eroded and driest one, species success was mainly associated to seed resistance to removal by runoff and to resistance to drought. At the opposite end of the gradient, the most productive one, species success was associated to a competitive-ruderal plant strategy (herbaceous successful species with high specific leaf area and low leaf dry matter content). Our study provides an ecologically-based approach for selecting suitable native species on the basis or their morphological and functional traits and supports a differential trait-based selection of species as regards roadslope type and aspect. In

  2. Dynamic height: A key variable for identifying the spawning habitat of small pelagic fishes

    NASA Astrophysics Data System (ADS)

    Asch, Rebecca G.; Checkley, David M., Jr.

    2013-01-01

    Small pelagic fishes off southern California exhibit interannual variations in the regions they occupy. An enhanced understanding of these fluctuations could improve fisheries management and predictions of fish's responses to climate change. We investigated dynamic height as a variable for identifying the spawning habitat of northern anchovy (Engraulis mordax), Pacific sardine (Sardinops sagax), and jack mackerel (Trachurus symmetricus). During cruises between 1998 and 2004, dynamic height was calculated from temperature and salinity profiles, while fish egg concentration was measured with obliquely towed bongo nets and the Continuous, Underway Fish Egg Sampler. Dynamic height ranged between 68 and 108 cm, with values increasing offshore. The greatest probability of encountering anchovy, sardine, and jack mackerel eggs occurred at dynamic heights of 79-83 cm, 84-89 cm, and 89-99 cm, respectively. Four mechanisms were proposed to explain how dynamic height affects egg distribution: (1) dynamic height is a proxy for upper water column temperature and salinity, which are known to influence spawning habitat. (2) Low dynamic heights are indicative of coastal upwelling, which increases primary and secondary productivity. (3) Egg concentration is greater at dynamic heights coincident with geostrophic currents that transport larvae to favorable habitats. (4) Eddies delineated by dynamic height contours retain eggs in productive habitats. To evaluate these mechanisms, a generalized linear model was constructed using dynamic height, temperature, salinity, chlorophyll, zooplankton volume, geostrophic currents, and eddies as independent variables. Dynamic height explained more variance than any other variable in models of sardine and anchovy spawning habitat. Together temperature, salinity, and chlorophyll accounted for 80-95% of the dynamic height effect, emphasizing the importance of the first two mechanisms. However, dynamic height remained statistically significant in the

  3. The phenotypic patterns of essential hypertension are the key to identifying "high blood pressure" genes.

    PubMed

    Korner, P I

    2010-01-01

    hypertension provide targets for identifying high BP genes. Reading the genome from the phenotype will require new approaches, such as those used in developmental genetics. In addition, transgenic technology may help verify hypotheses and examine whether an observed effect is through single or multiple mechanisms. To obtain answers will require substantial collaborative efforts between physiologists and geneticists.

  4. A multivariate and stochastic approach to identify key variables to rank dairy farms on profitability.

    PubMed

    Atzori, A S; Tedeschi, L O; Cannas, A

    2013-05-01

    The economic efficiency of dairy farms is the main goal of farmers. The objective of this work was to use routinely available information at the dairy farm level to develop an index of profitability to rank dairy farms and to assist the decision-making process of farmers to increase the economic efficiency of the entire system. A stochastic modeling approach was used to study the relationships between inputs and profitability (i.e., income over feed cost; IOFC) of dairy cattle farms. The IOFC was calculated as: milk revenue + value of male calves + culling revenue - herd feed costs. Two databases were created. The first one was a development database, which was created from technical and economic variables collected in 135 dairy farms. The second one was a synthetic database (sDB) created from 5,000 synthetic dairy farms using the Monte Carlo technique and based on the characteristics of the development database data. The sDB was used to develop a ranking index as follows: (1) principal component analysis (PCA), excluding IOFC, was used to identify principal components (sPC); and (2) coefficient estimates of a multiple regression of the IOFC on the sPC were obtained. Then, the eigenvectors of the sPC were used to compute the principal component values for the original 135 dairy farms that were used with the multiple regression coefficient estimates to predict IOFC (dRI; ranking index from development database). The dRI was used to rank the original 135 dairy farms. The PCA explained 77.6% of the sDB variability and 4 sPC were selected. The sPC were associated with herd profile, milk quality and payment, poor management, and reproduction based on the significant variables of the sPC. The mean IOFC in the sDB was 0.1377 ± 0.0162 euros per liter of milk (€/L). The dRI explained 81% of the variability of the IOFC calculated for the 135 original farms. When the number of farms below and above 1 standard deviation (SD) of the dRI were calculated, we found that 21

  5. For research on climate change, past is key to future

    NASA Astrophysics Data System (ADS)

    Oldfield, Frank

    One of the major challenges for predicting future climate change is determining the specific causes of past and present changes. Greenhouse gases are not alone in influencing climate; changes in solar irradiance and major volcanic eruptions also play important roles. Recent research findings complement and reinforce evidence for human-induced warming based on theory, computer models, and the growing number of observations that claim to detect a “fingerprint” signal of the greenhouse effect. They do not deny the importance of solar influences on climate and especially cloud variability, but they do point to a broader picture.

  6. Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation.

    PubMed

    Pürzer, Andreas; Grassmann, Felix; Birzer, Dietmar; Merkl, Rainer

    2011-03-04

    Deducing common properties or degrees of phylogenetic relationship by analyzing a grouping or clustering of sequence sets is a frequently used technique in computational biology. If interpreted by means of visual inspection, the conclusions depend for many of these applications on meaningful names for the input data. In accordance with the aim of the analysis, the sequences should be provided with names indicating the function of the genes or gene-products, the phylogenetic position or other properties characterizing the contributing species. However, sequences extracted from databases are most often annotated with identifiers which only implicitly contain the desired information. To solve this problem, we have designed and implemented a tool named Key2Ann, which replaces in multiple fasta files the database keys with short terms indicating the taxonomic position or other features like the gene name or the EC-number. In addition, properties like habitat, growth temperature or the degree of pathogenicity can be coded for microbial species. To allow for highest flexibility, the user can control the composition of the names by means of command line parameters. Key2Ann is written in Java and can be downloaded via http://www-bioinf.uni-regensburg.de/downl/Key2Ann.zip. We demonstrate the usage of Key2Ann by discussing three typical examples of phylogenetic analysis.

  7. Key observations from the NHLBI Asthma Clinical Research Network.

    PubMed

    Szefler, Stanley J; Chinchilli, Vernon M; Israel, Elliot; Denlinger, Loren Clark; Lemanske, Robert F; Calhoun, William; Peters, Stephen P

    2012-05-01

    The National Heart, Lung and Blood Institute (NHLBI) Asthma Clinical Research Network (ACRN) recently completed its work after 20 years of collaboration as a multicentre clinical trial network. When formed, its stated mission was to perform multiple controlled clinical trials for treating patients with asthma by dispassionately examining new and existing therapies, and to rapidly communicate its findings to the medical community. The ACRN conducted 15 major clinical trials. In addition, clinical data, manual of operations, protocols and template informed consents from all ACRN trials are available via NHLBI BioLINCC (https://biolincc.nhlbi.nih.gov/studies/). This network contributed major insights into the use of inhaled corticosteroids, short-acting and long-acting ß-adrenergic agonists, leukotriene receptor antagonists, and novel agents (tiotropium, colchicine and macrolide antibiotics). They also pioneered studies of the variability in drug response, predictors of treatment response and pharmacogenetics. This review highlights the major research observations from the ACRN that have impacted the current management of asthma.

  8. Using social network analysis to identify key child care center staff for obesity prevention interventions: a pilot study.

    PubMed

    Marks, Jennifer; Barnett, Lisa M; Foulkes, Chad; Hawe, Penelope; Allender, Steven

    2013-01-01

    Interest has grown in how systems thinking could be used in obesity prevention. Relationships between key actors, represented by social networks, are an important focus for considering intervention in systems. Two long day care centers were selected in which previous obesity prevention programs had been implemented. Measures showed ways in which physical activity and dietary policy are conversations and actions transacted through social networks (interrelationships) within centers, via an eight item closed-ended social network questionnaire. Questionnaire data were collected from (17/20; response rate 85%) long day care center staff. Social network density and centrality statistics were calculated, using UCINET social network software, to examine the role of networks in obesity prevention. "Degree" (influence) and "betweeness" (gatekeeper) centrality measures of staff inter-relationships about physical activity, dietary, and policy information identified key players in each center. Network density was similar and high on some relationship networks in both centers but markedly different in others, suggesting that the network tool identified unique center social dynamics. These differences could potentially be the focus of future team capacity building. Social network analysis is a feasible and useful method to identify existing obesity prevention networks and key personnel in long day care centers.

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

    PubMed

    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

  10. A method for identifying research priorities for health systems research on health and aging.

    PubMed

    Sivananthan, Saskia N; Chambers, Larry W

    2013-01-01

    A rapid and feasible priority-setting method conducted within a limited budget was used to identify research topics that would have an influence on health services for older adults. Health and aging researchers, policy makers, and caregivers were recruited to complete Delphi surveys that generated and ranked topics and identified other potential researchers. An interdisciplinary team of researchers was selected to produce and submit a proposal to a peer-review-granting agency. This method can be adapted by organizations to determine the focus of their research agenda and to engage individuals for collaboration on future research projects.

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

    PubMed

    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".

  12. Key Competencies and Characteristics for Innovative Teaching among Secondary School Teachers: A Mixed-Methods Research

    ERIC Educational Resources Information Center

    Zhu, Chang; Wang, Di

    2014-01-01

    This research aims to understand the key competencies and characteristics for innovative teaching as perceived by Chinese secondary teachers. A mixed-methods research was used to investigate secondary teachers' views. First, a qualitative study was conducted with interviews of teachers to understand the perceived key competencies and…

  13. Key Competencies and Characteristics for Innovative Teaching among Secondary School Teachers: A Mixed-Methods Research

    ERIC Educational Resources Information Center

    Zhu, Chang; Wang, Di

    2014-01-01

    This research aims to understand the key competencies and characteristics for innovative teaching as perceived by Chinese secondary teachers. A mixed-methods research was used to investigate secondary teachers' views. First, a qualitative study was conducted with interviews of teachers to understand the perceived key competencies and…

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

    PubMed

    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

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

    PubMed Central

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

    2014-01-01

    Objectives 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). Setting The UK. Participants 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. Methods 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. Results 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. Conclusions These research priorities identify crucial gaps in the existing evidence to

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

    PubMed

    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.

  17. The Practical Integration of Action Research into Building Climate Literacy and Partnership with Key Influentials

    NASA Astrophysics Data System (ADS)

    Estrada, M.

    2015-12-01

    Climate Education Partners (CEP) has been using an action research approach to build climate literacy and partnership with key influential (KI) leaders in the San Diego community. After identifying 6 key sectors that either (a) could reduce green house gas emissions and adapt to impacts, or (b) would be highly vulnerable to the impacts of climate change, we conducted 89 interviews with KIs from the San Diego region -- including elected officials, academics, laborers, and representatives from local businesses, non-profits, ethnic and cultural communities, faith-based groups, and special interest groups -- to assess their science knowledge and opinions about climate change and the impacts of climate change. Other questions asked were about KIs' personal efficacy, identity, values and engagement in pro-environmental behaviors related to climate change. The results of the interviews contributed to CEP's action research approach in two ways: 1) it provided critical data regarding which leaders wanted further engagement with CEP and what that engagement should entail (e.g., being a connector to other leaders, a spokesperson, or a participant in future educational activities), and 2) it provided key information about the extent to which "knowledge deficit" is related to use of climate change knowledge to inform engagement in mitigation and adaptive behaviors. Practically, the results were used to create a database that is being used to inform the contact and education of KIs. We were able to show, consistent with previous research and identity theory, that liberal leaders were more likely than conservatives to believe in, feel concern for, and be knowledgeable about climate change. However, engagement in mitigation behaviors- specifically making decisions that would reduce electricity, gas, or water use- were similar for both groups. These results are being used to create resources and direct climate education activities going forward.

  18. 76 FR 44593 - Identifying the Center for Drug Evaluation and Research's Science and Research Needs...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-26

    ... Science and Research Needs; Availability of a Draft Report; Request for Comments AGENCY: Food and Drug... announcing the availability of a draft report entitled ``Identifying CDER's Science and Research Needs... efforts. Through external communication of the science and research needs outlined in the report,...

  19. Research fronts analysis : A bibliometric to identify emerging fields of research

    NASA Astrophysics Data System (ADS)

    Miwa, Sayaka; Ando, Satoko

    Research fronts analysis identifies emerging areas of research through observing co-clustering in highly-cited papers. This article introduces the concept of research fronts analysis, explains its methodology and provides case examples. It also demonstrates developing research fronts in Japan by looking at the past winners of Thomson Reuters Research Fronts Awards. Research front analysis is currently being used by the Japanese government to determine new trends in science and technology. Information professionals can also utilize this bibliometric as a research evaluation tool.

  20. Identifying Priorities for International Arctic Research and Policy

    NASA Astrophysics Data System (ADS)

    Rachold, V.; Hik, D.; Barr, S.

    2015-12-01

    Participants. This paper presents an overview of IASC´s efforts and achievements in terms of identifying Arctic research priorities and providing scientific expertise to policy makers and people who live in or near the Arctic.

  1. Identifying Multiple Submissions in Internet Research: Preserving Data Integrity

    PubMed Central

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

    2008-01-01

    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”. PMID:18240015

  2. Perspectives of survivors, families and researchers on key outcomes for research in acute respiratory failure.

    PubMed

    Dinglas, Victor D; Chessare, Caroline M; Davis, Wesley E; Parker, Ann; Friedman, Lisa Aronson; Colantuoni, Elizabeth; Bingham, Clifton O; Turnbull, Alison E; Needham, Dale M

    2017-07-29

    There is heterogeneity among the outcomes evaluated in studies of survivors of acute respiratory failure (ARF). To evaluate the importance of specific outcome domains to acute respiratory distress syndrome (ARDS) survivors, their family members and clinical researchers. Nineteen outcome domains were identified from the National Institutes of Health's Patient Reported Outcomes Measurement Information System; WHO's International Classification of Functioning, Disability, and Health; Society of Critical Care Medicine's Post-Intensive Care Syndrome (PICS); as well as patient, clinician and researcher input. We surveyed ARDS survivors, family members and critical care researchers, 279 respondents in total, using a 5-point scale (strongly disagree, disagree, neutral, agree and strongly agree) to rate the importance of measuring each domain in studies of ARF survivors' postdischarge outcomes. At least 80% of patients and family members supported (ie, rated 'agree' or 'strongly agree') that 15 of the 19 domains should be measured in all future studies. Among researchers, 6 of 19 domains were supported, with researchers less supportive for all domains, except survival (95% vs 72% support). Overall, four domains were supported by all groups: physical function, cognitive function, return to work or prior activities and mental health. Patient, family and researcher groups supported inclusion of outcome domains that fit within the PICS framework. Patients and family members also supported many additional domains, emphasising the importance of including patients/family, along with researchers, in consensus processes to select core outcome domains for future research studies. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  3. Engaging patients in health research: identifying research priorities through community town halls.

    PubMed

    Etchegary, Holly; Bishop, Lisa; Street, Catherine; Aubrey-Bassler, Kris; Humphries, Dale; Vat, Lidewij Eva; Barrett, Brendan

    2017-03-11

    The vision of Canada's Strategy for Patient-Oriented Research is that patients be actively engaged as partners in health research. Support units have been created across Canada to build capacity in patient-oriented research and facilitate its conduct. This study aimed to explore patients' health research priorities in the province of Newfoundland and Labrador (NL). Eight town halls were held with members of the general public in rural and urban settings across the province. Sessions were a hybrid information-consultation event, with key questions about health research priorities and outcomes guiding the discussion. Sixty eight members of the public attended town hall sessions. A broad range of health experiences in the healthcare system were recounted. Key priorities for the public included access and availability of providers and services, disease prevention and health promotion, and follow-up support and community care. In discussing their health research priorities, participants spontaneously raised a broad range of suggestions for improving the healthcare system in our jurisdiction. Public research priorities and suggestions for improving the provision of healthcare provide valuable information to guide Support Units' planning and priority-setting processes. A range of research areas were raised as priorities for patients that are likely comparable to other healthcare systems. These create a number of health research questions that would be in line with public priorities. Findings also provide lessons learned for others and add to the evidence base on patient engagement methods.

  4. A proteomics approach to identifying key protein targets involved in VEGF inhibitor mediated attenuation of bleomycin-induced pulmonary fibrosis

    PubMed Central

    Kulkarni, Yogesh M.; Dutta, Sucharita; Iyer, Anand Krishnan V.; Venkatadri, Rajkumar; Kaushik, Vivek; Ramesh, Vani; Wright, Clayton A.; Semmes, Oliver John; Yakisich, Juan S.; Azad, Neelam

    2015-01-01

    Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a life expectancy of less than 5 years post diagnosis for most patients. Poor molecular characterization of IPF has led to insufficient understanding of the pathogenesis of the disease, resulting in lack of effective therapies. In this study, we have integrated a label-free LC-MS based approach with systems biology to identify signaling pathways and regulatory nodes within protein interaction networks that govern phenotypic changes that may lead to IPF. Ingenuity Pathway Analysis of proteins modulated in response to bleomycin treatment identified PI3K/Akt and Wnt signaling as the most significant profibrotic pathways. Similar analysis of proteins modulated in response to vascular endothelial growth factor (VEGF) inhibitor (CBO-P11) treatment identified natural killer cell signaling and PTEN signaling as the most significant antifibrotic pathways. Mechanistic/mammalian target of rapamycin (mTOR) and extracellular signal-regulated kinase (ERK) were identified to be key mediators of pro- and antifibrotic response, where bleomycin (BLM) treatment resulted in increased expression and VEGF inhibitor treatment attenuated expression of mTOR and ERK. Using a BLM mouse model of pulmonary fibrosis and VEGF inhibitor CBO-P11 as a therapeutic measure, we identified a comprehensive set of signaling pathways and proteins that contribute to the pathogenesis of pulmonary fibrosis that can be targeted for therapy against this fatal disease. PMID:26425798

  5. Using Range-Wide Abundance Modeling to Identify Key Conservation Areas for the Micro-Endemic Bolson Tortoise (Gopherus flavomarginatus)

    PubMed Central

    Ureña-Aranda, Cinthya A.; Rojas-Soto, Octavio; Martínez-Meyer, Enrique; Yáñez-Arenas, Carlos; Landgrave Ramírez, Rosario; Espinosa de los Monteros, Alejandro

    2015-01-01

    A widespread biogeographic pattern in nature is that population abundance is not uniform across the geographic range of species: most occurrence sites have relatively low numbers, whereas a few places contain orders of magnitude more individuals. The Bolson tortoise Gopherus flavomarginatus is endemic to a small region of the Chihuahuan Desert in Mexico, where habitat deterioration threatens this species with extinction. In this study we combined field burrows counts and the approach for modeling species abundance based on calculating the distance to the niche centroid to obtain range-wide abundance estimates. For the Bolson tortoise, we found a robust, negative relationship between observed burrows abundance and distance to the niche centroid, with a predictive capacity of 71%. Based on these results we identified four priority areas for the conservation of this microendemic and threatened tortoise. We conclude that this approach may be a useful approximation for identifying key areas for sampling and conservation efforts in elusive and rare species. PMID:26115482

  6. Using Range-Wide Abundance Modeling to Identify Key Conservation Areas for the Micro-Endemic Bolson Tortoise (Gopherus flavomarginatus).

    PubMed

    Ureña-Aranda, Cinthya A; Rojas-Soto, Octavio; Martínez-Meyer, Enrique; Yáñez-Arenas, Carlos; Landgrave Ramírez, Rosario; Espinosa de los Monteros, Alejandro

    2015-01-01

    A widespread biogeographic pattern in nature is that population abundance is not uniform across the geographic range of species: most occurrence sites have relatively low numbers, whereas a few places contain orders of magnitude more individuals. The Bolson tortoise Gopherus flavomarginatus is endemic to a small region of the Chihuahuan Desert in Mexico, where habitat deterioration threatens this species with extinction. In this study we combined field burrows counts and the approach for modeling species abundance based on calculating the distance to the niche centroid to obtain range-wide abundance estimates. For the Bolson tortoise, we found a robust, negative relationship between observed burrows abundance and distance to the niche centroid, with a predictive capacity of 71%. Based on these results we identified four priority areas for the conservation of this microendemic and threatened tortoise. We conclude that this approach may be a useful approximation for identifying key areas for sampling and conservation efforts in elusive and rare species.

  7. Fasciola and fasciolosis in ruminants in Europe: Identifying research needs.

    PubMed

    Beesley, N J; Caminade, C; Charlier, J; Flynn, R J; Hodgkinson, J E; Martinez-Moreno, A; Martinez-Valladeres, M; Perez, J; Rinaldi, L; Williams, D J L

    2017-10-06

    Fasciola hepatica is a trematode parasite with a global distribution, which is responsible for considerable disease and production losses in a range of food producing species. It is also identified by WHO as a re-emerging neglected tropical disease associated with endemic and epidemic outbreaks of disease in human populations. In Europe, F. hepatica is mostly associated with disease in sheep, cattle and goats. This study reviews the most recent advances in our understanding of the transmission, diagnosis, epidemiology and the economic impact of fasciolosis. We also focus on the impact of the spread of resistance to anthelmintics used to control F. hepatica and consider how vaccines might be developed and applied in the context of the immune-modulation driven by the parasite. Several major research gaps are identified which, when addressed, will contribute to providing focussed and where possible, bespoke, advice for farmers on how to integrate stock management and diagnosis with vaccination and/or targeted treatment to more effectively control the parasite in the face of increasing the prevalence of infection and spread of anthelmintic resistance that are likely to be exacerbated by climate change. © 2017 Blackwell Verlag GmbH.

  8. Psychological Therapies for Auditory Hallucinations (Voices): Current Status and Key Directions for Future Research

    PubMed Central

    Thomas, Neil; Hayward, Mark; Peters, Emmanuelle; van der Gaag, Mark; Bentall, Richard P.; Jenner, Jack; Strauss, Clara; Sommer, Iris E.; Johns, Louise C.; Varese, Filippo; García-Montes, José Manuel; Waters, Flavie; Dodgson, Guy; McCarthy-Jones, Simon

    2014-01-01

    This report from the International Consortium on Hallucinations Research considers the current status and future directions in research on psychological therapies targeting auditory hallucinations (hearing voices). Therapy approaches have evolved from behavioral and coping-focused interventions, through formulation-driven interventions using methods from cognitive therapy, to a number of contemporary developments. Recent developments include the application of acceptance- and mindfulness-based approaches, and consolidation of methods for working with connections between voices and views of self, others, relationships and personal history. In this article, we discuss the development of therapies for voices and review the empirical findings. This review shows that psychological therapies are broadly effective for people with positive symptoms, but that more research is required to understand the specific application of therapies to voices. Six key research directions are identified: (1) moving beyond the focus on overall efficacy to understand specific therapeutic processes targeting voices, (2) better targeting psychological processes associated with voices such as trauma, cognitive mechanisms, and personal recovery, (3) more focused measurement of the intended outcomes of therapy, (4) understanding individual differences among voice hearers, (5) extending beyond a focus on voices and schizophrenia into other populations and sensory modalities, and (6) shaping interventions for service implementation. PMID:24936081

  9. Onchocerciasis, an undiagnosed disease in Mozambique: identifying research opportunities.

    PubMed

    Noormahomed, Emilia V; Akrami, Kevan; Mascaró-Lazcano, Carmen

    2016-03-31

    The objective of this paper is to summarise and critically review the available data about onchocerciasis in Mozambique, in order to report epidemiological and clinical aspects related to the disease and identify gaps in knowledge. The paper is intended to raise awareness of the existence and importance of this disease and to define research priorities. We examined the scarce epidemiological data at our disposal: two diagnostic studies in 1997 and 1998 (first reports on the existence of onchocerciasis in Mozambique), and two Rapid Epidemiological Mapping of Onchocerciasis (REMO) surveys in 2001 and 2007. We examined differences in study designs and methodologies as well as the differing geographical locations to explain the divergence in findings among the studies. Evidence indicates that onchocerciasis is hypoendemic in Mozambique (with national and imported cases), but still largely remains an undiagnosed illness. There is no awareness of the clinical aspects of the disease and nor of the differential diagnosis with lepromatous leprosy and dermatitis caused by Scabies spp. The use of skin biopsy and a symptom screening questionnaire, combined with nodule rate, in the first two studies may have captured even atypical or subacute presentations. Both REMO surveys relied solely on nodule detection and in the six years between the two studies, the prevalence of nodules detected more than doubled. The epidemiology and clinical aspects of the disease are unknown in Mozambique. Since the last REMO took place in 2007 and since the population is subject to large-scale movement and displacement, it is important to develop tools to identify and analyse populations that are at high risk for onchocerciasis. Cases of onchocerciasis may be misdiagnosed as leprosy or scabies that fail to improve despite being subjected to treatment against leprosy. Techniques to enable a differential diagnosis need to be established by training health professionals on the recognition of this

  10. Researchers identify potential therapeutic targets for a rare childhood cancer | Center for Cancer Research

    Cancer.gov

    CCR researchers have identified the mechanism behind a rare but extremely aggressive childhood cancer called alveolar rhabdomyosarcoma (ARMS) and have pinpointed a potential drug target for its treatment. Learn more...

  11. Global analysis of SUMO-binding proteins identifies SUMOylation as a key regulator of the INO80 chromatin remodeling complex.

    PubMed

    Cox, Eric; Hwang, Woochang; Uzoma, Ijeoma; Hu, Jianfei; Guzzo, Catherine; Jeong, Junseop; Matunis, Michael; Qian, Jiang; Zhu, Heng; Blackshaw, Seth

    2017-03-02

    SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo. We then demonstrated a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo. By demonstrating a key role for SUMOylation in regulating the INO80 chromatin-remodeling complex, this work illustrates the power of integrated analysis of large datasets in predicting novel biological phenomena.

  12. Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase.

    PubMed

    Li, Zhengyi; Chang, Siping; Ye, Shuting; Chen, Mingyue; Lin, Li; Li, Yuanyuan; Li, Shuying; An, Qianli

    2015-10-01

    1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase.

  13. Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma

    PubMed Central

    Jin, Xiang; Li, Xiaodan; Guan, Yinghui

    2016-01-01

    Introduction. Lung adenocarcinoma (LAC) is the most frequent type of lung cancer and has a high metastatic rate at an early stage. This study is aimed at identifying LAC-associated genes. Materials and Methods. GSE62950 downloaded from Gene Expression Omnibus included a DNA methylation dataset and an mRNA expression profiles dataset, both of which included 28 LAC tissue samples and 28 adjacent normal tissue samples. The differentially expressed genes (DEGs) were screened by Limma package in R, and their functions were predicted by enrichment analysis using TargetMine online tool. Then, protein-protein interaction (PPI) network was constructed using STRING and Cytoscape. Finally, LAC-associated methylation sites were identified by CpGassoc package in R and mapped to the DEGs to obtain LAC-associated DEGs. Results. Total 913 DEGs were identified in LAC tissues. In the PPI networks, MAD2L1, AURKB, CCNB2, CDC20, and WNT3A had higher degrees, and the first four genes might be involved in LAC through interaction. Total 8856 LAC-associated methylation sites were identified and mapped to the DEGs. And there were 29 LAC-associated methylation sites located in 27 DEGs (e.g., SH3GL2, BAI3, CDH13, JAM2, MT1A, LHX6, and IGFBP3). Conclusions. These key genes might play a role in pathogenesis of LAC. PMID:27610375

  14. Identifying health problems and health research priorities in developing countries.

    PubMed

    Feachem, R G; Graham, W J; Timaeus, I M

    1989-06-01

    Section 5, we draw these strands together and, having reviewed current approaches to prioritizing health problems and suggested some ways in which they could be improved, in Section 6 identify several research priorities, emphasizing the need for methodological research. This paper was commissioned in March 1987; prepared in draft and presented to a meeting at Chateau de Bossey, Geneva, Switzerland during 15-17 July; and revised and completed in September 1987. It is in no sense definitive or final.(ABSTRACT TRUNCATED AT 400 WORDS)

  15. Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  16. Integrated analysis of mutation data from various sources identifies key genes and signaling pathways in hepatocellular carcinoma.

    PubMed

    Zhang, Yuannv; Qiu, Zhaoping; Wei, Lin; Tang, Ruqi; Lian, Baofeng; Zhao, Yingjun; He, Xianghuo; Xie, Lu

    2014-01-01

    Recently, a number of studies have performed genome or exome sequencing of hepatocellular carcinoma (HCC) and identified hundreds or even thousands of mutations in protein-coding genes. However, these studies have only focused on a limited number of candidate genes, and many important mutation resources remain to be explored. In this study, we integrated mutation data obtained from various sources and performed pathway and network analysis. We identified 113 pathways that were significantly mutated in HCC samples and found that the mutated genes included in these pathways contained high percentages of known cancer genes, and damaging genes and also demonstrated high conservation scores, indicating their important roles in liver tumorigenesis. Five classes of pathways that were mutated most frequently included (a) proliferation and apoptosis related pathways, (b) tumor microenvironment related pathways, (c) neural signaling related pathways, (d) metabolic related pathways, and (e) circadian related pathways. Network analysis further revealed that the mutated genes with the highest betweenness coefficients, such as the well-known cancer genes TP53, CTNNB1 and recently identified novel mutated genes GNAL and the ADCY family, may play key roles in these significantly mutated pathways. Finally, we highlight several key genes (e.g., RPS6KA3 and PCLO) and pathways (e.g., axon guidance) in which the mutations were associated with clinical features. Our workflow illustrates the increased statistical power of integrating multiple studies of the same subject, which can provide biological insights that would otherwise be masked under individual sample sets. This type of bioinformatics approach is consistent with the necessity of making the best use of the ever increasing data provided in valuable databases, such as TCGA, to enhance the speed of deciphering human cancers.

  17. Integrated Analysis of Mutation Data from Various Sources Identifies Key Genes and Signaling Pathways in Hepatocellular Carcinoma

    PubMed Central

    Wei, Lin; Tang, Ruqi; Lian, Baofeng; Zhao, Yingjun; He, Xianghuo; Xie, Lu

    2014-01-01

    Background Recently, a number of studies have performed genome or exome sequencing of hepatocellular carcinoma (HCC) and identified hundreds or even thousands of mutations in protein-coding genes. However, these studies have only focused on a limited number of candidate genes, and many important mutation resources remain to be explored. Principal Findings In this study, we integrated mutation data obtained from various sources and performed pathway and network analysis. We identified 113 pathways that were significantly mutated in HCC samples and found that the mutated genes included in these pathways contained high percentages of known cancer genes, and damaging genes and also demonstrated high conservation scores, indicating their important roles in liver tumorigenesis. Five classes of pathways that were mutated most frequently included (a) proliferation and apoptosis related pathways, (b) tumor microenvironment related pathways, (c) neural signaling related pathways, (d) metabolic related pathways, and (e) circadian related pathways. Network analysis further revealed that the mutated genes with the highest betweenness coefficients, such as the well-known cancer genes TP53, CTNNB1 and recently identified novel mutated genes GNAL and the ADCY family, may play key roles in these significantly mutated pathways. Finally, we highlight several key genes (e.g., RPS6KA3 and PCLO) and pathways (e.g., axon guidance) in which the mutations were associated with clinical features. Conclusions Our workflow illustrates the increased statistical power of integrating multiple studies of the same subject, which can provide biological insights that would otherwise be masked under individual sample sets. This type of bioinformatics approach is consistent with the necessity of making the best use of the ever increasing data provided in valuable databases, such as TCGA, to enhance the speed of deciphering human cancers. PMID:24988079

  18. The Key Role of Educational Research in the Development and Evaluation of the National Numeracy Strategy

    ERIC Educational Resources Information Center

    Brown, Margaret; Askew, Mike; Millett, Alison; Rhodes, Valerie

    2003-01-01

    The authors contest a politician's claim that the National Numeracy Strategy (NNS) in English primary schools has been an undisputed success with no contribution from educational researchers. First, the key role of researchers and research in the development of the NNS is outlined. Then there is a description of the Leverhulme Numeracy Research…

  19. A simple technique to identify key recruitment issues in randomised controlled trials: Q-QAT - Quanti-Qualitative Appointment Timing.

    PubMed

    Paramasivan, Sangeetha; Strong, Sean; Wilson, Caroline; Campbell, Bruce; Blazeby, Jane M; Donovan, Jenny L

    2015-03-11

    Recruitment to pragmatic randomised controlled trials (RCTs) is acknowledged to be difficult, and few interventions have proved to be effective. Previous qualitative research has consistently revealed that recruiters provide imbalanced information about RCT treatments. However, qualitative research can be time-consuming to apply. Within a programme of research to optimise recruitment and informed consent in challenging RCTs, we developed a simple technique, Q-QAT (Quanti-Qualitative Appointment Timing), to systematically investigate and quantify the imbalance to help identify and address recruitment difficulties. The Q-QAT technique comprised: 1) quantification of time spent discussing the RCT and its treatments using transcripts of audio-recorded recruitment appointments, 2) targeted qualitative research to understand the obstacles to recruitment and 3) feedback to recruiters on opportunities for improvement. This was applied to two RCTs with different clinical contexts and recruitment processes. Comparisons were made across clinical centres, recruiters and specialties. In both RCTs, the Q-QAT technique first identified considerable variations in the time spent by recruiters discussing the RCT and its treatments. The patterns emerging from this initial quantification of recruitment appointments then enabled targeted qualitative research to understand the issues and make suggestions to improve recruitment. In RCT1, presentation of the treatments was balanced, but little time was devoted to describing the RCT. Qualitative research revealed patients would have considered participation, but lacked awareness of the RCT. In RCT2, the balance of treatment presentation varied by specialists and centres. Qualitative research revealed difficulties with equipoise and confidence among recruiters presenting the RCT. The quantitative and qualitative findings were well-received by recruiters and opportunities to improve information provision were discussed. A blind coding

  20. The use of social networking platforms for sexual health promotion: identifying key strategies for successful user engagement.

    PubMed

    Veale, Hilary J; Sacks-Davis, Rachel; Weaver, Emma Rn; Pedrana, Alisa E; Stoové, Mark A; Hellard, Margaret E

    2015-02-06

    Online social networking platforms such as Facebook and Twitter have grown rapidly in popularity, with opportunities for interaction enhancing their health promotion potential. Such platforms are being used for sexual health promotion but with varying success in reaching and engaging users. We aimed to identify Facebook and Twitter profiles that were able to engage large numbers of users, and to identify strategies used to successfully attract and engage users in sexual health promotion on these platforms. We identified active Facebook (n = 60) and Twitter (n = 40) profiles undertaking sexual health promotion through a previous systematic review, and assessed profile activity over a one-month period. Quantitative measures of numbers of friends and followers (reach) and social media interactions were assessed, and composite scores used to give profiles an 'engagement success' ranking. Associations between host activity, reach and interaction metrics were explored. Content of the top ten ranked Facebook and Twitter profiles was analysed using a thematic framework and compared with five poorly performing profiles to identify strategies for successful user engagement. Profiles that were able to successfully engage large numbers of users were more active and had higher levels of interaction per user than lower-ranked profiles. Strategies used by the top ten ranked profiles included: making regular posts/tweets (median 46 posts or 124 tweets/month for top-ranked profiles versus six posts or six tweets for poorly-performing profiles); individualised interaction with users (85% of top-ranked profiles versus 0% for poorly-performing profiles); and encouraging interaction and conversation by posing questions (100% versus 40%). Uploading multimedia material (80% versus 30%) and highlighting celebrity involvement (70% versus 10%) were also key strategies. Successful online engagement on social networking platforms can be measured through quantitative (user numbers and

  1. Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death

    PubMed Central

    Welsbie, Derek S.; Yang, Zhiyong; Ge, Yan; Mitchell, Katherine L.; Zhou, Xinrong; Martin, Scott E.; Berlinicke, Cynthia A.; Hackler, Laszlo; Fuller, John; Fu, Jie; Cao, Li-hui; Han, Bing; Auld, Douglas; Xue, Tian; Hirai, Syu-ichi; Germain, Lucie; Simard-Bisson, Caroline; Blouin, Richard; Nguyen, Judy V.; Davis, Chung-ha O.; Enke, Raymond A.; Boye, Sanford L.; Merbs, Shannath L.; Marsh-Armstrong, Nicholas; Hauswirth, William W.; DiAntonio, Aaron; Nickells, Robert W.; Inglese, James; Hanes, Justin; Yau, King-Wai; Quigley, Harry A.; Zack, Donald J.

    2013-01-01

    Glaucoma, a major cause of blindness worldwide, is a neurodegenerative optic neuropathy in which vision loss is caused by loss of retinal ganglion cells (RGCs). To better define the pathways mediating RGC death and identify targets for the development of neuroprotective drugs, we developed a high-throughput RNA interference screen with primary RGCs and used it to screen the full mouse kinome. The screen identified dual leucine zipper kinase (DLK) as a key neuroprotective target in RGCs. In cultured RGCs, DLK signaling is both necessary and sufficient for cell death. DLK undergoes robust posttranscriptional up-regulation in response to axonal injury in vitro and in vivo. Using a conditional knockout approach, we confirmed that DLK is required for RGC JNK activation and cell death in a rodent model of optic neuropathy. In addition, tozasertib, a small molecule protein kinase inhibitor with activity against DLK, protects RGCs from cell death in rodent glaucoma and traumatic optic neuropathy models. Together, our results establish a previously undescribed drug/drug target combination in glaucoma, identify an early marker of RGC injury, and provide a starting point for the development of more specific neuroprotective DLK inhibitors for the treatment of glaucoma, nonglaucomatous forms of optic neuropathy, and perhaps other CNS neurodegenerations. PMID:23431148

  2. Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma.

    PubMed

    Kreher, Stephan; Bouhlel, M Amine; Cauchy, Pierre; Lamprecht, Björn; Li, Shuang; Grau, Michael; Hummel, Franziska; Köchert, Karl; Anagnostopoulos, Ioannis; Jöhrens, Korinna; Hummel, Michael; Hiscott, John; Wenzel, Sören-Sebastian; Lenz, Peter; Schneider, Markus; Küppers, Ralf; Scheidereit, Claus; Giefing, Maciej; Siebert, Reiner; Rajewsky, Klaus; Lenz, Georg; Cockerill, Peter N; Janz, Martin; Dörken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2014-10-21

    Deregulated transcription factor (TF) activities are commonly observed in hematopoietic malignancies. Understanding tumorigenesis therefore requires determining the function and hierarchical role of individual TFs. To identify TFs central to lymphomagenesis, we identified lymphoma type-specific accessible chromatin by global mapping of DNaseI hypersensitive sites and analyzed enriched TF-binding motifs in these regions. Applying this unbiased approach to classical Hodgkin lymphoma (HL), a common B-cell-derived lymphoma with a complex pattern of deregulated TFs, we discovered interferon regulatory factor (IRF) sites among the top enriched motifs. High-level expression of the proinflammatory TF IRF5 was specific to HL cells and crucial for their survival. Furthermore, IRF5 initiated a regulatory cascade in human non-Hodgkin B-cell lines and primary murine B cells by inducing the TF AP-1 and cooperating with NF-κB to activate essential characteristic features of HL. Our strategy efficiently identified a lymphoma type-specific key regulator and uncovered a tumor promoting role of IRF5.

  3. Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma

    PubMed Central

    Kreher, Stephan; Bouhlel, M. Amine; Cauchy, Pierre; Lamprecht, Björn; Li, Shuang; Grau, Michael; Hummel, Franziska; Köchert, Karl; Anagnostopoulos, Ioannis; Jöhrens, Korinna; Hummel, Michael; Hiscott, John; Wenzel, Sören-Sebastian; Lenz, Peter; Schneider, Markus; Küppers, Ralf; Scheidereit, Claus; Giefing, Maciej; Siebert, Reiner; Rajewsky, Klaus; Lenz, Georg; Cockerill, Peter N.; Janz, Martin; Dörken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2014-01-01

    Deregulated transcription factor (TF) activities are commonly observed in hematopoietic malignancies. Understanding tumorigenesis therefore requires determining the function and hierarchical role of individual TFs. To identify TFs central to lymphomagenesis, we identified lymphoma type-specific accessible chromatin by global mapping of DNaseI hypersensitive sites and analyzed enriched TF-binding motifs in these regions. Applying this unbiased approach to classical Hodgkin lymphoma (HL), a common B-cell–derived lymphoma with a complex pattern of deregulated TFs, we discovered interferon regulatory factor (IRF) sites among the top enriched motifs. High-level expression of the proinflammatory TF IRF5 was specific to HL cells and crucial for their survival. Furthermore, IRF5 initiated a regulatory cascade in human non-Hodgkin B-cell lines and primary murine B cells by inducing the TF AP-1 and cooperating with NF-κB to activate essential characteristic features of HL. Our strategy efficiently identified a lymphoma type-specific key regulator and uncovered a tumor promoting role of IRF5. PMID:25288773

  4. Linking Researchers with their Research: Persistent identifiers, registries, and interoperability standards

    NASA Astrophysics Data System (ADS)

    Haak, Laurel; Bryant, Rebecca

    2014-03-01

    While in some scientific disciplines researcher identification and data citation is an established community norm, lack of interoperability between identification systems for research works on the one hand and ambiguity of contributor names on the other remains a major hurdle. Improving the ease by which researchers are uniquely and unambiguously associated with their research contributions across systems and disciplines can support citability and in turn provide incentives to share works and datasets. This in turn can facilitate information flow and enable data re-use. In this presentation, we will illustrate the potential of coordinating persistent identifier initiatives across e-infrastructures using ORCID and the ODIN Project. ORCID is a community-driven organization that provides a registry of unique and persistent identifiers for researchers. The ORCID registry connects together existing but fragmented researcher identifiers, and stores persistent connections to publications, datasets, grants, and current and past affiliations. ODIN--the ORCID and DataCite Interoperability Framework--is a two-year EC project with the goal of connecting existing identifiers across multiple services and infrastructures. Together, these two efforts have supported improvements in the way author and contributor information is collected for publications and datasets that go a long way to addressing name ambiguity and citability problems in research communication.

  5. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb.

    PubMed

    Zhao, Liang; Glazov, Evgeny A; Pattabiraman, Diwakar R; Al-Owaidi, Faisal; Zhang, Ping; Brown, Matthew A; Leo, Paul J; Gonda, Thomas J

    2011-06-01

    To gain insight into the mechanisms by which the Myb transcription factor controls normal hematopoiesis and particularly, how it contributes to leukemogenesis, we mapped the genome-wide occupancy of Myb by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) in ERMYB myeloid progenitor cells. By integrating the genome occupancy data with whole genome expression profiling data, we identified a Myb-regulated transcriptional program. Gene signatures for leukemia stem cells, normal hematopoietic stem/progenitor cells and myeloid development were overrepresented in 2368 Myb regulated genes. Of these, Myb bound directly near or within 793 genes. Myb directly activates some genes known critical in maintaining hematopoietic stem cells, such as Gfi1 and Cited2. Importantly, we also show that, despite being usually considered as a transactivator, Myb also functions to repress approximately half of its direct targets, including several key regulators of myeloid differentiation, such as Sfpi1 (also known as Pu.1), Runx1, Junb and Cebpb. Furthermore, our results demonstrate that interaction with p300, an established coactivator for Myb, is unexpectedly required for Myb-mediated transcriptional repression. We propose that the repression of the above mentioned key pro-differentiation factors may contribute essentially to Myb's ability to suppress differentiation and promote self-renewal, thus maintaining progenitor cells in an undifferentiated state and promoting leukemic transformation.

  6. A core human primary tumor angiogenesis signature identifies the endothelial orphan receptor ELTD1 as a key regulator of angiogenesis.

    PubMed

    Masiero, Massimo; Simões, Filipa Costa; Han, Hee Dong; Snell, Cameron; Peterkin, Tessa; Bridges, Esther; Mangala, Lingegowda S; Wu, Sherry Yen-Yao; Pradeep, Sunila; Li, Demin; Han, Cheng; Dalton, Heather; Lopez-Berestein, Gabriel; Tuynman, Jurriaan B; Mortensen, Neil; Li, Ji-Liang; Patient, Roger; Sood, Anil K; Banham, Alison H; Harris, Adrian L; Buffa, Francesca M

    2013-08-12

    Limited clinical benefits derived from anti-VEGF therapy have driven the identification of new targets involved in tumor angiogenesis. Here, we report an integrative meta-analysis to define the transcriptional program underlying angiogenesis in human cancer. This approach identified ELTD1, an orphan G-protein-coupled receptor whose expression is induced by VEGF/bFGF and repressed by DLL4 signaling. Extensive analysis of multiple cancer types demonstrates significant upregulation of ELTD1 in tumor-associated endothelial cells, with a higher expression correlating with favorable prognosis. Importantly, ELTD1 silencing impairs endothelial sprouting and vessel formation in vitro and in vivo, drastically reducing tumor growth and greatly improving survival. Collectively, these results provide insight into the regulation of tumor angiogenesis and highlight ELTD1 as key player in blood vessel formation. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  7. A Delphi survey of research priorities and identified areas for collaborative research in health sector library and information services UK.

    PubMed

    Dwyer, M

    1999-09-01

    The survey aims were to determine research priorities in the Health Library and Information Services sector in the United Kingdom as to their perceived value for the professional and impact on user needs and to identify areas suitable for collaborative research. A 34-member panel consisting of the Chairs of professional groups, journal editors, educationalists, key organizations and representatives from the Health Libraries Group, Libraries for Nursing and University Health Science Libraries professional groups, participated in a three-round postal questionnaire survey using the Delphi Technique. Consensus was achieved for a final set of 20 research priorities. The priorities and their category groups are discussed in the context of (i) the current R&D scene, and (ii) the health information environment. Six developmental recommendations are provided.

  8. TCGA researchers identify 4 subtypes of stomach cancer

    Cancer.gov

    Stomach cancers fall into four distinct molecular subtypes, researchers with The Cancer Genome Atlas (TCGA) Network have found. Scientists report that this discovery could change how researchers think about developing treatments for stomach cancer, also c

  9. Identifiability and privacy in pluripotent stem cell research.

    PubMed

    Isasi, Rosario; Andrews, Peter W; Baltz, Jay M; Bredenoord, Annelien L; Burton, Paul; Chiu, Ing-Ming; Hull, Sara Chandros; Jung, Ji-Won; Kurtz, Andreas; Lomax, Geoffrey; Ludwig, Tenneille; McDonald, Michael; Morris, Clive; Ng, Huck Hui; Rooke, Heather; Sharma, Alka; Stacey, Glyn N; Williams, Clare; Zeng, Fanyi; Knoppers, Bartha Maria

    2014-04-03

    Data sharing is an essential element of research; however, recent scientific and social developments have challenged conventional methods for protecting privacy. Here we provide guidance for determining data sharing thresholds for human pluripotent stem cell research aimed at a wide range of stakeholders, including research consortia, biorepositories, policy-makers, and funders.

  10. Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease.

    PubMed

    Carpanini, Sarah M; Wishart, Thomas M; Gillingwater, Thomas H; Manson, Jean C; Summers, Kim M

    2017-04-01

    The incidence of neurodegenerative diseases in the developed world has risen over the last century, concomitant with an increase in average human lifespan. A major challenge is therefore to identify genes that control neuronal health and viability with a view to enhancing neuronal health during ageing and reducing the burden of neurodegeneration. Analysis of gene expression data has recently been used to infer gene functions for a range of tissues from co-expression networks. We have now applied this approach to transcriptomic datasets from the mammalian nervous system available in the public domain. We have defined the genes critical for influencing neuronal health and disease in different neurological cell types and brain regions. The functional contribution of genes in each co-expression cluster was validated using human disease and knockout mouse phenotypes, pathways and gene ontology term annotation. Additionally a number of poorly annotated genes were implicated by this approach in nervous system function. Exploiting gene expression data available in the public domain allowed us to validate key nervous system genes and, importantly, to identify additional genes with minimal functional annotation but with the same expression pattern. These genes are thus novel candidates for a role in neurological health and disease and could now be further investigated to confirm their function and regulation during ageing and neurodegeneration.

  11. Temporal retinal transcriptome and systems biology analysis identifies key pathways and hub genes in Staphylococcus aureus endophthalmitis.

    PubMed

    Rajamani, Deepa; Singh, Pawan Kumar; Rottmann, Bruce G; Singh, Natasha; Bhasin, Manoj K; Kumar, Ashok

    2016-02-11

    Bacterial endophthalmitis remains a devastating inflammatory condition associated with permanent vision loss. Hence, assessing the host response in this disease may provide new targets for intervention. Using a mouse model of Staphylococcus aureus (SA) endophthalmitis and performing retinal transcriptome analysis, we discovered progressive changes in the expression of 1,234 genes. Gene ontology (GO) and pathway analyses revealed the major pathways impacted in endophthalmitis includes: metabolism, inflammatory/immune, antimicrobial, cell trafficking, and lipid biosynthesis. Among the immune/inflammation pathways, JAK/Stat and IL-17A signaling were the most significantly affected. Interactive network-based analyses identified 13 focus hub genes (IL-6, IL-1β, CXCL2, STAT3, NUPR1, Jun, CSF1, CYR61, CEBPB, IGF-1, EGFR1, SPP1, and TGM2) within these important pathways. The expression of hub genes confirmed by qRT-PCR, ELISA (IL-6, IL-1β, and CXCL2), and Western blot or immunostaining (CEBP, STAT3, NUPR1, and IGF1) showed strong correlation with transcriptome data. Since TLR2 plays an important role in SA endophthalmitis, counter regulation analysis of TLR2 ligand pretreated retina or the use of retinas from TLR2 knockout mice showed the down-regulation of inflammatory regulatory genes. Collectively, our study provides, for the first time, a comprehensive analysis of the transcriptomic response and identifies key pathways regulating retinal innate responses in staphylococcal endophthalmitis.

  12. Microarray identifies ADAM family members as key responders to TGF-beta1 in alveolar epithelial cells.

    PubMed

    Keating, Dominic T; Sadlier, Denise M; Patricelli, Andrea; Smith, Sinead M; Walls, Dermot; Egan, Jim J; Doran, Peter P

    2006-09-01

    The molecular mechanisms of Idiopathic Pulmonary Fibrosis (IPF) remain elusive. Transforming Growth Factor beta 1(TGF-beta1) is a key effector cytokine in the development of lung fibrosis. We used microarray and computational biology strategies to identify genes whose expression is significantly altered in alveolar epithelial cells (A549) in response to TGF-beta1, IL-4 and IL-13 and Epstein Barr virus. A549 cells were exposed to 10 ng/ml TGF-beta1, IL-4 and IL-13 at serial time points. Total RNA was used for hybridisation to Affymetrix Human Genome U133A microarrays. Each in vitro time-point was studied in duplicate and an average RMA value computed. Expression data for each time point was compared to control and a signal log ratio of 0.6 or greater taken to identify significant differential regulation. Using normalised RMA values and unsupervised Average Linkage Hierarchical Cluster Analysis, a list of 312 extracellular matrix (ECM) proteins or modulators of matrix turnover was curated via Onto-Compare and Gene-Ontology (GO) databases for baited cluster analysis of ECM associated genes. Interrogation of the dataset using ontological classification focused cluster analysis revealed coordinate differential expression of a large cohort of extracellular matrix associated genes. Of this grouping members of the ADAM (A disintegrin and Metalloproteinase domain containing) family of genes were differentially expressed. ADAM gene expression was also identified in EBV infected A549 cells as well as IL-13 and IL-4 stimulated cells. We probed pathologenomic activities (activation and functional activity) of ADAM19 and ADAMTS9 using siRNA and collagen assays. Knockdown of these genes resulted in diminished production of collagen in A549 cells exposed to TGF-beta1, suggesting a potential role for these molecules in ECM accumulation in IPF.

  13. Integrating Transcriptome and Genome Re-Sequencing Data to Identify Key Genes and Mutations Affecting Chicken Eggshell Qualities

    PubMed Central

    Liu, Long; Zheng, Chuan Wei; Wang, De He; Hou, Zhuo Cheng; Ning, Zhong Hua

    2015-01-01

    Eggshell damages lead to economic losses in the egg production industry and are a threat to human health. We examined 49-wk-old Rhode Island White hens (Gallus gallus) that laid eggs having shells with significantly different strengths and thicknesses. We used HiSeq 2000 (Illumina) sequencing to characterize the chicken transcriptome and whole genome to identify the key genes and genetic mutations associated with eggshell calcification. We identified a total of 14,234 genes expressed in the chicken uterus, representing 89% of all annotated chicken genes. A total of 889 differentially expressed genes were identified by comparing low eggshell strength (LES) and normal eggshell strength (NES) genomes. The DEGs are enriched in calcification-related processes, including calcium ion transport and calcium signaling pathways as reveled by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Some important matrix proteins, such as OC-116, LTF and SPP1, were also expressed differentially between two groups. A total of 3,671,919 single-nucleotide polymorphisms (SNPs) and 508,035 Indels were detected in protein coding genes by whole-genome re-sequencing, including 1775 non-synonymous variations and 19 frame-shift Indels in DEGs. SNPs and Indels found in this study could be further investigated for eggshell traits. This is the first report to integrate the transcriptome and genome re-sequencing to target the genetic variations which decreased the eggshell qualities. These findings further advance our understanding of eggshell calcification in the chicken uterus. PMID:25974068

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

    PubMed

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

    2016-03-31

    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.

  15. Identifying and prioritizing uncertainties: patient and clinician engagement in the identification of research questions.

    PubMed

    Elwyn, Glyn; Crowe, Sally; Fenton, Mark; Firkins, Lester; Versnel, Jenny; Walker, Samantha; Cook, Ivor; Holgate, Stephen; Higgins, Bernard; Gelder, Colin

    2010-06-01

    To arrive at an agreed, prioritized ranking of treatment uncertainties in asthma that need further research, by developing a collaboration of patients, carers and clinicians, facilitated by the James Lind Alliance Working Partnership between Asthma UK and the British Thoracic Society. A four-step procedure: (1) establish a collaborative Working Partnership; (2) identify and collect treatment uncertainties by using a patient survey and analysing existing systematic reviews, clinical guidelines and query-answering services; (3) categorize uncertainties; and (4) convene a workshop using a nominal group process to establish a ranked prioritization of treatment uncertainties in asthma. Agreement and rankings were reached for 10 treatment uncertainties. The highest was given to the uncertainty surrounding the adverse effects of inhaled and oral steroids. The top three priorities dealt with clinical management issues, where uncertainties still exist, namely concerns about the side effects of inhaled and oral steroids, how to manage asthma when other illnesses exist or how to rely on personal decisions in an ever-changing illness (self-management). The key outcome is the generation of a prioritized list of treatment uncertainties in asthma, agreed by a collaboration of patients and health professionals, to inform the commissioning of new research. Such a large number of patient-identified treatment uncertainties had not previously been identified in the literature, an indication perhaps that asthma self-management is a neglected research area. Whether the results have an influence of research funding decisions is not yet known.

  16. A comparison of the performance of seven key bibliographic databases in identifying all relevant systematic reviews of interventions for hypertension.

    PubMed

    Rathbone, John; Carter, Matt; Hoffmann, Tammy; Glasziou, Paul

    2016-02-09

    Bibliographic databases are the primary resource for identifying systematic reviews of health care interventions. Reliable retrieval of systematic reviews depends on the scope of indexing used by database providers. Therefore, searching one database may be insufficient, but it is unclear how many need to be searched. We sought to evaluate the performance of seven major bibliographic databases for the identification of systematic reviews for hypertension. We searched seven databases (Cochrane library, Database of Abstracts of Reviews of Effects (DARE), Excerpta Medica Database (EMBASE), Epistemonikos, Medical Literature Analysis and Retrieval System Online (MEDLINE), PubMed Health and Turning Research Into Practice (TRIP)) from 2003 to 2015 for systematic reviews of any intervention for hypertension. Citations retrieved were screened for relevance, coded and checked for screening consistency using a fuzzy text matching query. The performance of each database was assessed by calculating its sensitivity, precision, the number of missed reviews and the number of unique records retrieved. Four hundred systematic reviews were identified for inclusion from 11,381 citations retrieved from seven databases. No single database identified all the retrieved systematic reviews for hypertension. EMBASE identified the most reviews (sensitivity 69 %) but also retrieved the most irrelevant citations with 7.2 % precision (Pr). The sensitivity of the Cochrane library was 60 %, DARE 57 %, MEDLINE 57 %, PubMed Health 53 %, Epistemonikos 49 % and TRIP 33 %. EMBASE contained the highest number of unique records (n = 43). The Cochrane library identified seven unique records and had the highest precision (Pr = 30 %), followed by Epistemonikos (n = 2, Pr = 19 %). No unique records were found in PubMed Health (Pr = 24 %) DARE (Pr = 21 %), TRIP (Pr = 10 %) or MEDLINE (Pr = 10 %). Searching EMBASE and the Cochrane library identified 88 % of all systematic reviews in the reference set, and

  17. The Identification, Definition, and Measurement of Key Variables in Wait Time Research.

    ERIC Educational Resources Information Center

    Gooding, C. Thomas; And Others

    Wait time, or the pauses between questions and responses, has been demonstrated to be an important factor influencing classroom learning. This paper reviews the key variables that have emerged in wait time research over the past 20 years. Progress in defining and measuring wait time has resulted in improved methodology for wait time research.…

  18. What Makes a Teacher Effective? A Summary of Key Research Findings on Teacher Preparation

    ERIC Educational Resources Information Center

    National Council for Accreditation of Teacher Education (NJ1), 2006

    2006-01-01

    This report presents current research findings on teacher preparation and effectiveness. While some critics question the role of teacher preparation as a key to teacher effectiveness, this report contends that available research supports the importance of high quality teacher preparation. Well prepared teachers outperform those who are not…

  19. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed

    Ferris, Todd A; Garrison, Gregory M; Lowe, Henry J

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers.

  20. [Research progress on key technology of power and signal transmission in neuroprosthetic].

    PubMed

    Wang, Xing; Peng, Chenglin; Liu, Tao; Wang, Rui; Hou, Wensheng; Zheng, Xiaolin; Zheng, Erxin

    2011-10-01

    The power and signal transmission technology is one of the key technologies in neuroprosthetic research. This paper proposes firstly the related theory of power and signal transmission technology in neuroprosthetic, then summarizes the three key aspects of the power and signal transmission technology in neuroprosthetic. After analyzed the development of the inductive wireless power harvesting technology, the wireless telemetry technology and the wireless power harvesting telemetry technology, the emphasis on research contents will be proposed and discussed, which will help accelerate the further research of prosthetic.

  1. Research strategy for developing key information on bromate's mode of action.

    PubMed

    Bull, Richard J; Cottruvo, Joseph A

    2006-04-17

    metabolism of bromate and to associate these with key events for the induction of cancer and develop an initial pharmacokinetic (PK) model based on preliminary studies. Phase II will be implemented if it appears that there is a linear relationship between external dose and key event responses and is designed to gather carcinogenesis data in female rats in the absence of alpha2u-globulin-induced nephropathy which the workgroup concluded was a probable contributor to the responses observed in the male rats for which detailed dose-response data were collected. If the key events and external dosimetry are found not to be linear in Phase I, Phase III is initiated with a screening study of the auditory toxicity of bromate to determine if it is likely to be exacerbated by chronic exposure. If this occurs, auditory toxicity will be further evaluated in Phase IV. If auditory toxicity is determined unlikely to occur, an alternative chronic study in female rats to the one identified in Phase II will be implemented to include exposure in utero. This was recommended to address the possibility that the fetus may be more susceptible. One of the three options are to be implemented in Phase IV depending upon whether preliminary data indicated that chronic auditory toxicity, reproductive and/or developmental toxicities, or a combination of these outcomes is necessary to characterize the toxicology of low dose exposures to bromate. Each phase of the research will be accompanied by further development of pharmacokinetic models to guide collection of appropriate data to meet the needs of the more sophisticated studies. It is suggested that a Bayesian approach be utilized to develop a final risk model based upon measurement of prior observations from the Phase I studies and the set of posterior observations that would be obtained from whichever chronic study is conducted.

  2. Key Principles of Community-Based Natural Resource Management: A Synthesis and Interpretation of Identified Effective Approaches for Managing the Commons

    NASA Astrophysics Data System (ADS)

    Gruber, James S.

    2010-01-01

    This article examines recent research on approaches to community-based environmental and natural resource management and reviews the commonalities and differences between these interdisciplinary and multistakeholder initiatives. To identify the most effective characteristics of Community-based natural resource management (CBNRM), I collected a multiplicity of perspectives from research teams and then grouped findings into a matrix of organizational principles and key characteristics. The matrix was initially vetted (or “field tested”) by applying numerous case studies that were previously submitted to the World Bank International Workshop on CBNRM. These practitioner case studies were then compared and contrasted with the findings of the research teams. It is hoped that the developed matrix may be useful to researchers in further focusing research, understanding core characteristics of effective and sustainable CBNRM, providing practitioners with a framework for developing new CBNRM initiatives for managing the commons, and providing a potential resource for academic institutions during their evaluation of their practitioner-focused environmental management and leadership curriculum.

  3. Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex.

    PubMed

    Holinski, Alexandra; Heyn, Kristina; Merkl, Rainer; Sterner, Reinhard

    2017-02-01

    It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. ‘Geo’chemical research: A key building block for nuclear waste disposal safety cases

    NASA Astrophysics Data System (ADS)

    Altmann, Scott

    2008-12-01

    Disposal of high level radioactive waste in deep underground repositories has been chosen as solution by several countries. Because of the special status this type waste has in the public mind, national implementation programs typically mobilize massive R&D efforts, last decades and are subject to extremely detailed and critical social-political scrutiny. The culminating argument of each program is a 'Safety Case' for a specific disposal concept containing, among other elements, the results of performance assessment simulations whose object is to model the release of radionuclides to the biosphere. Public and political confidence in performance assessment results (which generally show that radionuclide release will always be at acceptable levels) is based on their confidence in the quality of the scientific understanding in the processes included in the performance assessment model, in particular those governing radionuclide speciation and mass transport in the geological host formation. Geochemistry constitutes a core area of research in this regard. Clay-mineral rich formations are the subjects of advanced radwaste programs in several countries (France, Belgium, Switzerland…), principally because of their very low permeabilities and demonstrated capacities to retard by sorption most radionuclides. Among the key processes which must be represented in performance assessment models are (i) radioelement speciation (redox state, speciation, reactions determining radionuclide solid-solution partitioning) and (ii) diffusion-driven transport. The safety case must therefore demonstrate a detailed understanding of the physical-chemical phenomena governing the effects of these two aspects, for each radionuclide, within the geological barrier system. A wide range of coordinated (and internationally collaborated) research has been, and is being, carried out in order to gain the detailed scientific understanding needed for constructing those parts of the Safety Case

  5. 'Geo'chemical research: a key building block for nuclear waste disposal safety cases.

    PubMed

    Altmann, Scott

    2008-12-12

    Disposal of high level radioactive waste in deep underground repositories has been chosen as solution by several countries. Because of the special status this type waste has in the public mind, national implementation programs typically mobilize massive R&D efforts, last decades and are subject to extremely detailed and critical social-political scrutiny. The culminating argument of each program is a 'Safety Case' for a specific disposal concept containing, among other elements, the results of performance assessment simulations whose object is to model the release of radionuclides to the biosphere. Public and political confidence in performance assessment results (which generally show that radionuclide release will always be at acceptable levels) is based on their confidence in the quality of the scientific understanding in the processes included in the performance assessment model, in particular those governing radionuclide speciation and mass transport in the geological host formation. Geochemistry constitutes a core area of research in this regard. Clay-mineral rich formations are the subjects of advanced radwaste programs in several countries (France, Belgium, Switzerland...), principally because of their very low permeabilities and demonstrated capacities to retard by sorption most radionuclides. Among the key processes which must be represented in performance assessment models are (i) radioelement speciation (redox state, speciation, reactions determining radionuclide solid-solution partitioning) and (ii) diffusion-driven transport. The safety case must therefore demonstrate a detailed understanding of the physical-chemical phenomena governing the effects of these two aspects, for each radionuclide, within the geological barrier system. A wide range of coordinated (and internationally collaborated) research has been, and is being, carried out in order to gain the detailed scientific understanding needed for constructing those parts of the Safety Case

  6. Multiplexed autoantigen microarrays identify HLA as a key driver of anti-desmoglein and -non-desmoglein reactivities in pemphigus

    PubMed Central

    Sajda, Thomas; Hazelton, Julian; Patel, Milan; Seiffert-Sinha, Kristina; Steinman, Lawrence; Robinson, William; Haab, Brian B.; Sinha, Animesh A.

    2016-01-01

    Patients with pemphigus vulgaris (PV) harbor antibodies reactive against self-antigens expressed at the surface of keratinocytes, primarily desmoglein (Dsg) 3 and, to a lesser extent, Dsg1. Conventionally, only antibodies targeting these molecules have been thought to contribute to disease pathogenesis. This notion has been challenged by a growing pool of evidence that suggests that antibodies toward additional targets may play a role in disease. The aims of this study were to (i) establish high-throughput protein microarray technology as a method to investigate traditional and putative autoantibodies (autoAbs) in PV and (ii) use multiplexed protein array technology to define the scope and specificity of the autoAb response in PV. Our analysis demonstrated significant IgG reactivity in patients with PV toward the muscarinic acetylcholine receptor subtypes 3, 4, and 5 as well as thyroid peroxidase. Furthermore, we found that healthy first- and second-degree relatives of patients with PV express autoAbs toward desmoglein and non-Dsg targets. Our analysis also identified genetic elements, particularly HLA, as key drivers of autoAb expression. Finally, we show that patients with PV exhibit significantly reduced IgM reactivity toward disease-associated antigens relative to controls. The use of protein microarrays to profile the autoAb response in PV advanced the current understanding of disease and provided insight into the complex relationship between genetics and disease development. PMID:26831096

  7. Genomic profiling of Sézary Syndrome identifies alterations of key T-cell signaling and differentiation genes

    PubMed Central

    Wang, Linghua; Ni, Xiao; Covington, Kyle R.; Yang, Betty Y.; Shiu, Jessica; Zhang, Xiang; Xi, Liu; Meng, Qingchang; Langridge, Timothy; Drummond, Jennifer; Donehower, Lawrence A.; Doddapaneni, Harshavardhan; Muzny, Donna M.; Gibbs, Richard A.; Wheeler, David A.; Duvic, Madeleine

    2016-01-01

    Sézary Syndrome is a rare leukemic form of cutaneous T-cell lymphoma defined as erythroderma, adenopathy, and circulating atypical T-lymphocytes. It is rarely curable with poor prognosis. Here we present a multi-platform genomic analysis of 37 Sézary Syndrome patients that implicates dysregulation of the cell cycle checkpoint and T-cell signaling. Frequent somatic alterations were identified in TP53, CARD11, CCR4, PLCG1, CDKN2A, ARID1A, RPS6KA1, and ZEB1. Activating CCR4 and CARD11 mutations were detected in nearly a third of patients. ZEB1, a transcription repressor essential for T-cell differentiation, was deleted in over half of patients. IL32 and IL2RG were over-expressed in nearly all cases. Analysis of T-cell receptor Vβ and Vα expression revealed ongoing rearrangement of the receptors after the expansion of a malignant clone in one third of subjects. Our results demonstrate profound disruption of key signaling pathways in Sézary Syndrome and suggest potential targets for novel therapies. PMID:26551670

  8. Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis.

    PubMed

    Wei, Chengguo; Li, Li; Menon, Madhav C; Zhang, Weijia; Fu, Jia; Kidd, Brian; Keung, Karen L; Woytovich, Christopher; Greene, Ilana; Xiao, Wenzhen; Salem, Fadi; Yi, Zhengzi; He, John Cijiang; Dudley, Joel T; Murphy, Barbara

    2016-12-07

    Renal fibrosis is the common pathway of progression for patients with CKD and chronic renal allograft injury (CAI), but the underlying mechanisms remain obscure. We performed a meta-analysis in human kidney biopsy specimens with CAI, incorporating data available publicly and from our Genomics of Chronic Renal Allograft Rejection study. We identified an Src family tyrosine kinase, hematopoietic cell kinase (Hck), as upregulated in allografts in CAI. Querying the Kinase Inhibitor Resource database revealed that dasatinib, a Food and Drug Administration-approved drug, potently binds Hck with high selectivity. In vitro, Hck overexpression activated the TGF-β/Smad3 pathway, whereas HCK knockdown inhibited it. Treatment of tubular cells with dasatinib reduced the expression of Col1a1 Dasatinib also reduced proliferation and α-SMA expression in fibroblasts. In a murine model with unilateral ureteric obstruction, pretreatment with dasatinib significantly reduced the upregulation of profibrotic markers, phosphorylation of Smad3, and renal fibrosis observed in kidneys pretreated with vehicle alone. Dasatinib treatment also improved renal function, reduced albuminuria, and inhibited expression of profibrotic markers in animal models with lupus nephritis and folic acid nephropathy. These data suggest that Hck is a key mediator of renal fibrosis and dasatinib could be developed as an antifibrotic drug.

  9. Multiplexed autoantigen microarrays identify HLA as a key driver of anti-desmoglein and -non-desmoglein reactivities in pemphigus.

    PubMed

    Sajda, Thomas; Hazelton, Julian; Patel, Milan; Seiffert-Sinha, Kristina; Steinman, Lawrence; Robinson, William; Haab, Brian B; Sinha, Animesh A

    2016-02-16

    Patients with pemphigus vulgaris (PV) harbor antibodies reactive against self-antigens expressed at the surface of keratinocytes, primarily desmoglein (Dsg) 3 and, to a lesser extent, Dsg1. Conventionally, only antibodies targeting these molecules have been thought to contribute to disease pathogenesis. This notion has been challenged by a growing pool of evidence that suggests that antibodies toward additional targets may play a role in disease. The aims of this study were to (i) establish high-throughput protein microarray technology as a method to investigate traditional and putative autoantibodies (autoAbs) in PV and (ii) use multiplexed protein array technology to define the scope and specificity of the autoAb response in PV. Our analysis demonstrated significant IgG reactivity in patients with PV toward the muscarinic acetylcholine receptor subtypes 3, 4, and 5 as well as thyroid peroxidase. Furthermore, we found that healthy first- and second-degree relatives of patients with PV express autoAbs toward desmoglein and non-Dsg targets. Our analysis also identified genetic elements, particularly HLA, as key drivers of autoAb expression. Finally, we show that patients with PV exhibit significantly reduced IgM reactivity toward disease-associated antigens relative to controls. The use of protein microarrays to profile the autoAb response in PV advanced the current understanding of disease and provided insight into the complex relationship between genetics and disease development.

  10. TCGA researchers identify potential drug targets, markers for leukemia risk

    Cancer.gov

    Investigators for The Cancer Genome Atlas (TCGA) Research Network have detailed and broadly classified the genomic alterations that frequently underlie the development of acute myeloid leukemia (AML), a deadly cancer of the blood and bone marrow. Their wo

  11. Identifying Future Scientists: Predicting Persistence into Research Training

    PubMed Central

    2007-01-01

    This study used semistructured interviews and grounded theory to look for characteristics among college undergraduates that predicted persistence into Ph.D. and M.D./Ph.D. training. Participants in the summer undergraduate and postbaccalaureate research programs at the Mayo Clinic College of Medicine were interviewed at the start, near the end, and 8–12 months after their research experience. Of more than 200 themes considered, five characteristics predicted those students who went on to Ph.D. and M.D./Ph.D. training or to M.D. training intending to do research: 1) Curiosity to discover the unknown, 2) Enjoyment of problem solving, 3) A high level of independence, 4) The desire to help others indirectly through research, and 5) A flexible, minimally structured approach to the future. Web-based surveys with different students confirmed the high frequency of curiosity and/or problem solving as the primary reason students planned research careers. No evidence was found for differences among men, women, and minority and nonminority students. Although these results seem logical compared with successful scientists, their constancy, predictive capabilities, and sharp contrast to students who chose clinical medicine were striking. These results provide important insights into selection and motivation of potential biomedical scientists and the early experiences that will motivate them toward research careers. PMID:18056303

  12. Identifying future scientists: predicting persistence into research training.

    PubMed

    McGee, Richard; Keller, Jill L

    2007-01-01

    This study used semistructured interviews and grounded theory to look for characteristics among college undergraduates that predicted persistence into Ph.D. and M.D./Ph.D. training. Participants in the summer undergraduate and postbaccalaureate research programs at the Mayo Clinic College of Medicine were interviewed at the start, near the end, and 8-12 months after their research experience. Of more than 200 themes considered, five characteristics predicted those students who went on to Ph.D. and M.D./Ph.D. training or to M.D. training intending to do research: 1) Curiosity to discover the unknown, 2) Enjoyment of problem solving, 3) A high level of independence, 4) The desire to help others indirectly through research, and 5) A flexible, minimally structured approach to the future. Web-based surveys with different students confirmed the high frequency of curiosity and/or problem solving as the primary reason students planned research careers. No evidence was found for differences among men, women, and minority and nonminority students. Although these results seem logical compared with successful scientists, their constancy, predictive capabilities, and sharp contrast to students who chose clinical medicine were striking. These results provide important insights into selection and motivation of potential biomedical scientists and the early experiences that will motivate them toward research careers.

  13. Designing a knowledge transfer and exchange strategy for the Alberta Depression Initiative: contributions of qualitative research with key stakeholders

    PubMed Central

    Mitton, Craig; Adair, Carol E; McKenzie, Emily; Patten, Scott; Waye-Perry, Brenda; Smith, Neale

    2009-01-01

    Background Depressive disorders are highly prevalent and of significant societal burden. In fall 2004, the 'Alberta Depression Initiative' (ADI) research program was formed with a mission to enhance the mental health of the Alberta population. A key expectation of the ADI is that research findings will be effectively translated to appropriate research users. To help ensure this, one of the initiatives funded through the ADI focused specifically on knowledge transfer and exchange (KTE). The objectives of this project were first to examine the state of the KTE literature, and then based on this review and a set of key informant interviews, design a KTE strategy for the ADI. Methods Face to face interviews were conducted with 15 key informants familiar with KTE and/or mental health policy and programs in Alberta. Interviews were transcribed and analyzed using the constant comparison method. Results This paper reports on findings from the qualitative interviews. Respondents were familiar with the barriers to and facilitators of KTE as identified in the existing literature. Four key themes related to the nature of effective KTE were identified in the data analysis: personal relationships, cultivating champions, supporting communities of practice, and building receptor capacity. These recommendations informed the design of a contextually appropriate KTE strategy for the ADI. The three-phased strategy involves preliminary research, public workshops, on-going networking and linkage activities and rigorous evaluation against pre-defined and mutually agreed outcome measures. Conclusion Interest in KTE on the part of ADI has led to the development of a strategy for engaging decision makers, researchers, and other mental health stakeholders in an on-going network related to depression programs and policy. A similarly engaged process might benefit other policy areas. PMID:19523226

  14. Perceptions of graduating students from eight medical schools in Vietnam on acquisition of key skills identified by teachers

    PubMed Central

    Hoat, Luu Ngoc; Son, Nguyen Minh; Wright, E Pamela

    2008-01-01

    Background The eight main Vietnamese medical schools recently cooperated to produce a book listing the knowledge, attitudes and skills expected of a graduate, including specification of the required level for each skill. The teaching program should ensure that students can reach that level. The objective of this study was to determine the perception of graduating students on whether they had achieved the level set for a selection of clinical and public health skills as a guide for the schools to adjust either the levels or the teaching. Methods From all eight schools, 1136 of the 1528 final year students completed questionnaires just before completed all the requirements for graduation, a response rate of 87% overall (ranging from 74–99% per school). They rated their own competence on a scale of 0–5 for 129 skills selected from the 557 skills listed in the book, and reported where they thought they had learned them. The scores that the students gave themselves were then compared to the levels proposed by the teachers for each skill. The proportions of the self-assessed achievement to the levels expected by the teachers, means self-assessed scores and the coefficients of variation were calculated to make comparisons among disciplines, among schools and among learning sites. Results Most students felt they had learned most of the skills for key clinical departments to the required level; this varied little among the schools. Self-assessed skill acquisition in public health and minor clinical disciplines was lower and varied more. Sites outside the classroom were especially important for learning skills. The results revealed key similarities and differences between the teachers and the students in their perception about what could be learned and where Conclusion Revising a curriculum for medical schools demands inputs from all stakeholders. Graduating class students can provide valuable feedback on what they have learned in the existing system. Learning objectives

  15. Identifying reasons for failure in biomedical research and publishing.

    PubMed

    Bousfield, D

    2009-07-01

    The regular assessment of Brazilian scientific output means that individual university departments need to constantly improve the quantity and quality of their scientific output. A significant proportion of this output involves the work of Master's and Doctoral students, but getting this work published in a suitable journal can often prove to be a challenge. Although students' lack of fluency in English is a contributing factor, many of the problems observed have an early origin in the formulation of the research problem and its relevance to current research trends in the international literature. In short, more time needs to be spent in the library and less in the laboratory, and more effort needs to be made in teaching students basic research skills such as the effective use of bibliographic databases like PubMed, Web of Science and Scopus.

  16. Identifying Vasopressor and Inotrope Use for Health Services Research

    PubMed Central

    Fawzy, Ashraf; Bradford, Mark; Lindenauer, Peter K.

    2016-01-01

    Rationale: Identifying vasopressor and inotrope (vasopressor) use from administrative claims data may provide an important resource to study the epidemiology of shock. Objectives: Determine accuracy of identifying vasopressor use using International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) coding. Methods: Using administrative data enriched with pharmacy billing files (Premier, Inc., Charlotte, NC), we identified two cohorts: adult patients admitted with a diagnosis of sepsis from 2010 to 2013 or pulmonary embolism (PE) from 2008 to 2011. Vasopressor administration was obtained using pharmacy billing files (dopamine, dobutamine, epinephrine, milrinone, norepinephrine, phenylephrine, vasopressin) and compared with ICD-9-CM procedure code for vasopressor administration (00.17). We estimated performance characteristics of the ICD-9-CM code and compared patients’ characteristics and mortality rates according to vasopressor identification method. Measurements and Main Results: Using either pharmacy data or the ICD-9-CM procedure code, 29% of 541,144 patients in the sepsis cohort and 5% of 81,588 patients in the PE cohort were identified as receiving a vasopressor. In the sepsis cohort, the ICD-9-CM procedure code had low sensitivity (9.4%; 95% confidence interval, 9.2–9.5), which increased over time. Results were similar in the PE cohort (sensitivity, 5.8%; 95% confidence interval, 5.1–6.6). The ICD-9-CM code exhibited high specificity in the sepsis (99.8%) and PE (100%) cohorts. However, patients identified as receiving vasopressors by ICD-9-CM code had significantly higher unadjusted in-hospital mortality, had more acute organ failures, and were more likely hospitalized in the Northeast and West. Conclusions: The ICD-9-CM procedure code for vasopressor administration has low sensitivity and selects for higher severity of illness in studies of shock. Temporal changes in sensitivity would likely make longitudinal shock

  17. Obstructive Lung Diseases in HIV: A Clinical Review and Identification of Key Future Research Needs

    PubMed Central

    Drummond, M. Bradley; Kunisaki, Ken M.; Huang, Laurence

    2016-01-01

    HIV infection has shifted from what was once a disease directly impacting short-term mortality to what is now a chronic illness controllable in the era of effective combination antiretroviral therapy (ART). In this setting, life expectancy for HIV-infected individual is nearly comparable to that of individuals without HIV. Subsequent to this increase in life expectancy, there has been recognition of increased multimorbidity among HIV-infected persons, with prevalence of comorbid chronic illnesses now approaching 65%. Obstructive lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma, are prevalent conditions associated with substantial morbidity and mortality in the United States. There is overlap in risk factors for HIV acquisition and chronic lung diseases, including lower socioeconomic status and the use of tobacco and illicit drugs. Objectives of this review are to (1) summarize the current state of knowledge regarding COPD and asthma among HIV-infected persons, (2) highlight implications for clinicians caring for patients with these combined comorbidities, and (3) identify key research initiatives to reduce the burden of obstructive lung diseases among HIV-infected persons. PMID:26974304

  18. Traumatic brain injury in the US military: epidemiology and key clinical and research programs.

    PubMed

    Helmick, Katherine M; Spells, Cynthia A; Malik, Saafan Z; Davies, Cathleen A; Marion, Donald W; Hinds, Sidney R

    2015-09-01

    Traumatic brain injury (TBI), and particularly concussion, is a major concern for the U.S. Military because of the associated short term disability, long term cognitive and pain symptoms suffered by some, and risk of prolonged or permanent neurologic injury if the Service member incurs a second TBI before full recovery from the first. Concussions were seen more often during the recent conflicts in Afghanistan and Iraq than in prior conflicts, such as the Vietnam War, because of the use of improvised explosive devices that typically caused non-penetrating closed head injury. Since 2000 more than 300,000 Service members were diagnosed with TBI, of which more than 80 % were concussions. Improved TBI screening tools also have identified a higher than expected incidence of concussions occurring in garrison. In this review we summarize current epidemiologic data for TBI in the Military, and describe contemporary Military procedures and strategies for TBI prevention, identification, evaluation, and acute and chronic care. Key TBI clinical research priorities and programs are described, and innovative organizational plans to address future TBI needs are summarized.

  19. RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album

    PubMed Central

    Zhang, Xinhua; Berkowitz, Oliver; Teixeira da Silva, Jaime A.; Zhang, Muhan; Ma, Guohua; Whelan, James; Duan, Jun

    2015-01-01

    Santalum album (sandalwood) is one of the economically important plant species in the Santalaceae for its production of highly valued perfume oils. Sandalwood is also a hemiparasitic tree that obtains some of its water and simple nutrients by tapping into other plants through haustoria which are highly specialized organs in parasitic angiosperms. However, an understanding of the molecular mechanisms involved in haustorium development is limited. In this study, RNA sequencing (RNA-seq) analyses were performed to identify changes in gene expression and metabolic pathways associated with the development of the S. album haustorium. A total of 56,011 non-redundant contigs with a mean contig size of 618 bp were obtained by de novo assembly of the transcriptome of haustoria and non-haustorial seedling roots. A substantial number of the identified differentially expressed genes were involved in cell wall metabolism and protein metabolism, as well as mitochondrial electron transport functions. Phytohormone-mediated regulation might play an important role during haustorial development. Especially, auxin signaling is likely to be essential for haustorial initiation, and genes related to cytokinin and gibberellin biosynthesis and metabolism are involved in haustorial development. Our results suggest that genes encoding nodulin-like proteins may be important for haustorial morphogenesis in S. album. The obtained sequence data will become a rich resource for future research in this interesting species. This information improves our understanding of haustorium development in root hemiparasitic species and will allow further exploration of the detailed molecular mechanisms underlying plant parasitism. PMID:26388878

  20. Identifying Data-Driven Instructional Systems. Research to Practice Brief

    ERIC Educational Resources Information Center

    Lawrence, K. S.

    2016-01-01

    The study summarized in this research to practice brief, "Creating data-driven instructional systems in school: The new instructional leadership," Halverson, R., Grigg, J., Pritchett, R., & Thomas, C. (2015), "Journal of School Leadership," 25. 447-481, investigated whether student outcome improvements were linked to the…

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

    ERIC Educational Resources Information Center

    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…

  2. Identifying Future Scientists: Predicting Persistence into Research Training

    ERIC Educational Resources Information Center

    McGee, Richard; Keller, Jill L.

    2007-01-01

    This study used semistructured interviews and grounded theory to look for characteristics among college undergraduates that predicted persistence into Ph.D. and M.D./Ph.D. training. Participants in the summer undergraduate and postbaccalaureate research programs at the Mayo Clinic College of Medicine were interviewed at the start, near the end,…

  3. Identifying and preventing medical errors in patients with limited English proficiency: key findings and tools for the field.

    PubMed

    Wasserman, Melanie; Renfrew, Megan R; Green, Alexander R; Lopez, Lenny; Tan-McGrory, Aswita; Brach, Cindy; Betancourt, Joseph R

    2014-01-01

    Since the 1999 Institute of Medicine (IOM) report To Err is Human, progress has been made in patient safety, but few efforts have focused on safety in patients with limited English proficiency (LEP). This article describes the development, content, and testing of two new evidence-based Agency for Healthcare Research and Quality (AHRQ) tools for LEP patient safety. In the content development phase, a comprehensive mixed-methods approach was used to identify common causes of errors for LEP patients, high-risk scenarios, and evidence-based strategies to address them. Based on our findings, Improving Patient Safety Systems for Limited English Proficient Patients: A Guide for Hospitals contains recommendations to improve detection and prevention of medical errors across diverse populations, and TeamSTEPPS Enhancing Safety for Patients with Limited English Proficiency Module trains staff to improve safety through team communication and incorporating interpreters in the care process. The Hospital Guide was validated with leaders in quality and safety at diverse hospitals, and the TeamSTEPPS LEP module was field-tested in varied settings within three hospitals. Both tools were found to be implementable, acceptable to their audiences, and conducive to learning. Further research on the impact of the combined use of the guide and module would shed light on their value as a multifaceted intervention. © 2014 National Association for Healthcare Quality.

  4. Research in Online and Blended Learning in the Business Disciplines: Key Findings and Possible Future Directions

    ERIC Educational Resources Information Center

    Arbaugh, J. B.; Godfrey, Michael R.; Johnson, Marianne; Pollack, Birgit Leisen; Niendorf, Bruce; Wresch, William

    2009-01-01

    In this literature review, we examine and assess the state of research of online and blended learning in the business disciplines with the intent of assessing the state of the field and identifying opportunities for meaningful future research. We review research from business disciplines such as Accounting, Economics, Finance, Information Systems…

  5. Research in Online and Blended Learning in the Business Disciplines: Key Findings and Possible Future Directions

    ERIC Educational Resources Information Center

    Arbaugh, J. B.; Godfrey, Michael R.; Johnson, Marianne; Pollack, Birgit Leisen; Niendorf, Bruce; Wresch, William

    2009-01-01

    In this literature review, we examine and assess the state of research of online and blended learning in the business disciplines with the intent of assessing the state of the field and identifying opportunities for meaningful future research. We review research from business disciplines such as Accounting, Economics, Finance, Information Systems…

  6. How Can Book Reading Close the Word Gap? Five Key Practices from Research

    ERIC Educational Resources Information Center

    Snell, Emily K.; Hindman, Annemarie H.; Wasik, Barbara A.

    2015-01-01

    Vocabulary development is critical for children's ability to learn to read and their success at school. Vocabulary has also been identified as a key factor in the achievement gap, with children from low-income families knowing significantly fewer words when they enter school. Although book reading has long been celebrated as an effective way for…

  7. How Can Book Reading Close the Word Gap? Five Key Practices from Research

    ERIC Educational Resources Information Center

    Snell, Emily K.; Hindman, Annemarie H.; Wasik, Barbara A.

    2015-01-01

    Vocabulary development is critical for children's ability to learn to read and their success at school. Vocabulary has also been identified as a key factor in the achievement gap, with children from low-income families knowing significantly fewer words when they enter school. Although book reading has long been celebrated as an effective way for…

  8. A key hydrophobic patch identified in an AAA⁺ protein essential for its in trans inhibitory regulation.

    PubMed

    Zhang, Nan; Simpson, Timothy; Lawton, Edward; Uzdavinys, Povilas; Joly, Nicolas; Burrows, Patricia; Buck, Martin

    2013-08-09

    Bacterial enhancer binding proteins (bEBPs) are a subclass of the AAA(+) (ATPases Associated with various cellular Activities) protein family. They are responsible for σ(54)-dependent transcription activation during infection and function under many stressful growth conditions. The majority of bEBPs are regulated in their formation of ring-shaped hexameric self-assemblies via an amino-terminal domain through its phosphorylation or ligand binding. In contrast, the Escherichia coli phage shock protein F (PspF) is negatively regulated in trans by phage shock protein A (PspA). Up to six PspA subunits suppress PspF hexamer action. Here, we present biochemical evidence that PspA engages across the side of a PspF hexameric ring. We identify three key binding determinants located in a surface-exposed 'W56 loop' of PspF, which form a tightly packed hydrophobic cluster, the 'YLW' patch. We demonstrate the profound impact of the PspF W56 loop residues on ATP hydrolysis, the σ(54) binding loop 1, and the self-association interface. We infer from single-chain studies that for complete PspF inhibition to occur, more than three PspA subunits need to bind a PspF hexamer with at least two binding to adjacent PspF subunits. By structural modelling, we propose that PspA binds to PspF via its first two helical domains. After PspF binding-induced conformational changes, PspA may then share structural similarities with a bEBP regulatory domain.

  9. Heat tolerance around flowering in wheat identified as a key trait for increased yield potential in Europe under climate change

    PubMed Central

    Stratonovitch, Pierre; Semenov, Mikhail A.

    2015-01-01

    To deliver food security for the 9 billon population in 2050, a 70% increase in world food supply will be required. Projected climatic and environmental changes emphasize the need for breeding strategies that delivers both a substantial increase in yield potential and resilience to extreme weather events such as heat waves, late frost, and drought. Heat stress around sensitive stages of wheat development has been identified as a possible threat to wheat production in Europe. However, no estimates have been made to assess yield losses due to increased frequency and magnitude of heat stress under climate change. Using existing experimental data, the Sirius wheat model was refined by incorporating the effects of extreme temperature during flowering and grain filling on accelerated leaf senescence, grain number, and grain weight. This allowed us, for the first time, to quantify yield losses resulting from heat stress under climate change. The model was used to optimize wheat ideotypes for CMIP5-based climate scenarios for 2050 at six sites in Europe with diverse climates. The yield potential for heat-tolerant ideotypes can be substantially increased in the future (e.g. by 80% at Seville, 100% at Debrecen) compared with the current cultivars by selecting an optimal combination of wheat traits, e.g. optimal phenology and extended duration of grain filling. However, at two sites, Seville and Debrecen, the grain yields of heat-sensitive ideotypes were substantially lower (by 54% and 16%) and more variable compared with heat-tolerant ideotypes, because the extended grain filling required for the increased yield potential was in conflict with episodes of high temperature during flowering and grain filling. Despite much earlier flowering at these sites, the risk of heat stress affecting yields of heat-sensitive ideotypes remained high. Therefore, heat tolerance in wheat is likely to become a key trait for increased yield potential and yield stability in southern Europe in the

  10. A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model

    SciTech Connect

    Caruso, Joseph A.; Stemmer, Paul M.; Dombkowski, Alan; Caruthers, Nicholas J.; Gill, Randall; Rosenspire, Allen J.

    2014-04-01

    Network and protein–protein interaction analyses of proteins undergoing Hg{sup 2+}-induced phosphorylation and dephosphorylation in Hg{sup 2+}-intoxicated mouse WEHI-231 B cells identified Lyn as the most interconnected node. Lyn is a Src family protein tyrosine kinase known to be intimately involved in the B cell receptor (BCR) signaling pathway. Under normal signaling conditions the tyrosine kinase activity of Lyn is controlled by phosphorylation, primarily of two well known canonical regulatory tyrosine sites, Y-397 and Y-508. However, Lyn has several tyrosine residues that have not yet been determined to play a major role under normal signaling conditions, but are potentially important sites for phosphorylation following mercury exposure. In order to determine how Hg{sup 2+} exposure modulates the phosphorylation of additional residues in Lyn, a targeted MS assay was developed. Initial mass spectrometric surveys of purified Lyn identified 7 phosphorylated tyrosine residues. A quantitative assay was developed from these results using the multiple reaction monitoring (MRM) strategy. WEHI-231 cells were treated with Hg{sup 2+}, pervanadate (a phosphatase inhibitor), or anti-Ig antibody (to stimulate the BCR). Results from these studies showed that the phosphoproteomic profile of Lyn after exposure of the WEHI-231 cells to a low concentration of Hg{sup 2+} closely resembled that of anti-Ig antibody stimulation, whereas exposure to higher concentrations of Hg{sup 2+} led to increases in the phosphorylation of Y-193/Y-194, Y-501 and Y-508 residues. These data indicate that mercury can disrupt a key regulatory signal transduction pathway in B cells and point to phospho-Lyn as a potential biomarker for mercury exposure. - Highlights: • Inorganic mercury (Hg{sup 2+}) induces changes in the WEHI-231 B cell phosphoproteome. • The B cell receptor (BCR) signaling pathway was the pathway most affected by Hg{sup 2+}. • The Src family phosphoprotein kinase Lyn was the

  11. Industry-identified combustion research needs: Special study

    SciTech Connect

    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.

  12. Mentoring international research ethics trainees: identifying best practices.

    PubMed

    Loue, Sana; Loff, Bebe

    2013-12-01

    Mentoring is an important component of training in the basic and clinical sciences due to the increasing complexities associated with establishing a career. Data relating to 466 long-term trainees in research ethics training programs were obtained from the Fogarty International Center's database. Data were supplemented with survey data (n = 17) and telephone interviews (n = 10) of the 21 principal investigators whose programs offered long-term training. The programs most successful with mentoring involved (1) the provision of an orientation for the trainees at the commencement of training; (2) a highly structured process of mentoring that required regular meetings and task achievement timelines; (3) intensive, frequent contact with the PI; and (4) support with personal issues that were troublesome to trainees. This paper is part of a collection of papers analyzing the Fogarty International Center's International Research Ethics Education and Curriculum Development program.

  13. CCR researchers identify pathway critical for preventing premature aging | Center for Cancer Research

    Cancer.gov

    Hutchinson-Gilford progeria syndrome (HGPS) is a rare, fatal disease in which patients age prematurely. To identify primary HGPS driver mechanisms, Nard Kubben, Ph.D., a Research Fellow in the laboratory of Tom Misteli, Ph.D., in CCR’s Laboratory of Receptor Biology and Gene Expression, and colleagues in the NCI High-throughput Imaging Facility developed an imaging-based high-throughput small interfering RNA (siRNA) screen.

  14. The current structure of key actors involved in research on land and soil degradation

    NASA Astrophysics Data System (ADS)

    Escadafal, Richard; Barbero, Celia; Exbrayat, Williams; Marques, Maria Jose; Ruiz, Manuel; El Haddadi, Anass; Akhtar-Schuster, Mariam

    2013-04-01

    Land and soil conservation topics, the final mandate of the United Convention to Combat desertification in drylands, have been diagnosed as still suffering from a lack of guidance. On the contrary, climate change and biodiversity issues -the other two big subjects of the Rio Conventions- seem to progress and may benefit from the advice of international panels. Arguably the weakness of policy measures and hence the application of scientific knowledge by land users and stakeholders could be the expression of an inadequate research organization and a lack of ability to channel their findings. In order to better understand the size, breadth and depth of the scientific communities involved in providing advice to this convention and to other bodies, this study explores the corpus of international publications dealing with land and/or with soils. A database of several thousands records including a significant part of the literature published so far was performed using the Web of Science and other socio-economic databases such as FRANCIS and CAIRN. We extracted hidden information using bibliometric methods and data mining applied to these scientific publications to map the key actors (laboratories, teams, institutions) involved in research on land and on soils. Several filters were applied to the databases in combination with the word "desertification". The further use of Tetralogie software merges databases, analyses similarities and differences between keywords, disciplines, authors and regions and identifies obvious clusters. Assessing their commonalities and differences, the visualisation of links and gaps between scientists, organisations, policymakers and other stakeholders is possible. The interpretation of the 'clouds' of disciplines, keywords, and techniques will enhance the understanding of interconnections between them; ultimately this will allow diagnosing some of their strengths and weaknesses. This may help explain why land and soil degradation remains a

  15. [Translational research in geriatrics? A plea based on current biomedical key publications].

    PubMed

    Bollheimer, L C; Volkert, D; Bertsch, T; Bauer, J; Klucken, J; Sieber, C C; Büttner, R

    2013-08-01

    Contemporary geriatric research focuses mainly on observational clinical studies and epidemiological surveys and the translation of basic scientific results from biogerontology into a clinical context is often neglected. Following a definition of translational research the article gives an overview of recent key publications in experimental biogerontology with a special emphasis on their relevance for clinical geriatrics. The topics dealt with include age-induced loss of skeletal muscle (sarcopenia), the aging immune system (immunosenescence) and neurodegenerative disorders (Alzheimer's and Parkinson's disease).

  16. Identifying and Leveraging Trust as a Key Element in the Development, Implementation and Sustainment of the Salt Lake City Fire Department’s Intelligence Program

    DTIC Science & Technology

    2014-09-01

    LEVERAGING TRUST AS A KEY ELEMENT IN THE DEVELOPMENT, IMPLEMENTATION AND SUSTAINMENT OF THE SALT LAKE CITY FIRE DEPARTMENT’S INTELLIGENCE PROGRAM by...IDENTIFYING AND LEVERAGING TRUST AS A KEY ELEMENT IN THE DEVELOPMENT, IMPLEMENTATION AND SUSTAINMENT OF THE SALT LAKE CITY FIRE DEPARTMENT’S INTELLIGENCE...reestablishment of the Salt Lake City Fire Department’s intelligence program requires several steps: Establishing a need; identifying the stakeholders

  17. Some Key Issues in Creativity Research and Evaluation as Seen from a Psychological Perspective

    ERIC Educational Resources Information Center

    Fryer, Marilyn

    2012-01-01

    This article explores a number of key issues with regard to the measurement of creativity in the course of conducting psychological research or when applying various evaluation measures. It is argued that, although creativity is a fuzzy concept, it is no more difficult to investigate than other fuzzy concepts people tend to take for granted. At…

  18. Key Events and Lessons for Managers in a Diverse Workforce: A Report on Research and Findings.

    ERIC Educational Resources Information Center

    Douglas, Christina A.

    The research documented in this report builds on earlier work in the 1980s in the area of on-the-job experiences in developing effective leaders. The current study was designed to answer the following: (1) What are the significant events from which African American managers learn and develop? (2) Are the key events and lessons learned different…

  19. Good Research and Faculty Buy-in: 2 Keys to Effective Marketing

    ERIC Educational Resources Information Center

    Blumenstyk, Goldie

    2008-01-01

    Effective marketing requires more than a sleek new logo. This article presents excerpts of an online discussion on the dos and don'ts of college marketing with Mary R. Stagaman, associate vice president for external relations at the University of Cincinnati. In this discussion, she noted that good research and faculty buy-in are the two keys to…

  20. Training: Who Needs It? Research Report 1995. Key Issues for Providers.

    ERIC Educational Resources Information Center

    Hotel and Catering Training Co., London (England).

    Aimed at all those involved in the supply of training and vocational education for the hospitality industry, this report summarizes findings of the research report, "Training Who Needs It?" It draws out and explores in more detail key issues relating to the provision of training, support, and related initiatives for the industry. Section…

  1. Some Key Issues in Creativity Research and Evaluation as Seen from a Psychological Perspective

    ERIC Educational Resources Information Center

    Fryer, Marilyn

    2012-01-01

    This article explores a number of key issues with regard to the measurement of creativity in the course of conducting psychological research or when applying various evaluation measures. It is argued that, although creativity is a fuzzy concept, it is no more difficult to investigate than other fuzzy concepts people tend to take for granted. At…

  2. Building and Strengthening Policy Research Capacity: Key Issues in Canadian Higher Education

    ERIC Educational Resources Information Center

    Jones, Glen A.

    2014-01-01

    Given the importance of higher education in social and economic development, governments need to build a strong higher education data and policy research infrastructure to support informed decision-making, provide policy advice, and offer a critical assessment of key trends and issues. The author discusses the decline of higher education policy…

  3. Building and Strengthening Policy Research Capacity: Key Issues in Canadian Higher Education

    ERIC Educational Resources Information Center

    Jones, Glen A.

    2014-01-01

    Given the importance of higher education in social and economic development, governments need to build a strong higher education data and policy research infrastructure to support informed decision-making, provide policy advice, and offer a critical assessment of key trends and issues. The author discusses the decline of higher education policy…

  4. Using Research: A Key to Elementary School Mathematics, The Research from 1970: What Did It Add?

    ERIC Educational Resources Information Center

    Suydam, Marilyn N.; Weaver, J. Fred

    A review of research reported in 1970, which might be used by the elementary teacher in facilitating mathematics learning is presented. There are 16 basic categories of research included: teaching mathematical operations; children's perception of geometric representation; curriculum sequencing; teaching of non-decimal numeration; variables which…

  5. Sourcing Program: To identify outstanding women and ethnic minorities in research and research management

    SciTech Connect

    Nissen, S.H.

    1991-08-01

    To meet the challenges of the changing demographics and a projected shortage of technically trained workers in the 21st century, Lawrence Livermore National (LLNL) is increasing its commitment to develop a diverse work force with the abilities to carry out the Laboratory's missions. In addition to the recruitment programs already established at LLNL, a sourcing program to identify outstanding women and minorities in research and research management was initiated in the summer of 1990. A research methodology, time table, selection criteria, and data generation strategy were designed and implemented for this program. Through extensive contacts with R D facilities, women's and minority professional organizations, national research councils, technical professional societies and universities, other sourcing programs were investigated and evaluated and a network of contacts and resources was developed. This report describes the design and implementation of the sourcing program targeting outstanding women and minorities in science and engineering. It details the investigation and evaluation of sourcing programs in other R D facilities and provides information regarding methods and sources used to identify potential candidates. Conclusions and recommendations are presented. 10 refs., 5 tabs.

  6. EMSODEV and EPOS-IP: key findings for effective management of EU research infrastructure projects

    NASA Astrophysics Data System (ADS)

    Materia, Paola; Bozzoli, Sabrina; Beranzoli, Laura; Cocco, Massimo; Favali, Paolo; Freda, Carmela; Sangianantoni, Agata

    2017-04-01

    -2019) is a project of 47 partners, 6 associate partners and several international organizations for a total of 25 countries involved. EPOS IP is a key step in EPOS' mission of a pan-European Earth science integrated platform. It will deliver not only a suite of domain-specific and multidisciplinary data and services in one platform, but also the legal, governance and financial frameworks to ensure the infrastructure future operation and sustainability (EPOS ERIC). INGV experience over the years indicates that effective management of EU RIs projects should contain 5 basic elements: 1.Defined life cycle and milestones: Map of phases, deliverables, key milestones and sufficiency criteria for each group involved in the project using project management tools and software. 2.Shared organization, systems, roles: Defined roles for team members and responsibilities for functional managers are crucial. Similarly, a system of communication and team involvement is essential to success. Leadership and interpersonal/organizational skills are also important. 3.Quality assurance: Quality dimension should be aligned to the project objectives and specific criteria should be identified for each phase of the project. 4.Tracking and variance analysis: Regular reports and periodic meetings of the teams are crucial to identify when things are off target. Schedule slips, cost overruns, open issues, new risks and problems must be dealt with as early as possible. 5.Impact assessment by monitoring the achievement of results and socio-economic impact.

  7. Heat tolerance around flowering in wheat identified as a key trait for increased yield potential in Europe under climate change.

    PubMed

    Stratonovitch, Pierre; Semenov, Mikhail A

    2015-06-01

    To deliver food security for the 9 billon population in 2050, a 70% increase in world food supply will be required. Projected climatic and environmental changes emphasize the need for breeding strategies that delivers both a substantial increase in yield potential and resilience to extreme weather events such as heat waves, late frost, and drought. Heat stress around sensitive stages of wheat development has been identified as a possible threat to wheat production in Europe. However, no estimates have been made to assess yield losses due to increased frequency and magnitude of heat stress under climate change. Using existing experimental data, the Sirius wheat model was refined by incorporating the effects of extreme temperature during flowering and grain filling on accelerated leaf senescence, grain number, and grain weight. This allowed us, for the first time, to quantify yield losses resulting from heat stress under climate change. The model was used to optimize wheat ideotypes for CMIP5-based climate scenarios for 2050 at six sites in Europe with diverse climates. The yield potential for heat-tolerant ideotypes can be substantially increased in the future (e.g. by 80% at Seville, 100% at Debrecen) compared with the current cultivars by selecting an optimal combination of wheat traits, e.g. optimal phenology and extended duration of grain filling. However, at two sites, Seville and Debrecen, the grain yields of heat-sensitive ideotypes were substantially lower (by 54% and 16%) and more variable compared with heat-tolerant ideotypes, because the extended grain filling required for the increased yield potential was in conflict with episodes of high temperature during flowering and grain filling. Despite much earlier flowering at these sites, the risk of heat stress affecting yields of heat-sensitive ideotypes remained high. Therefore, heat tolerance in wheat is likely to become a key trait for increased yield potential and yield stability in southern Europe in the

  8. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed Central

    Ferris, Todd A.; Garrison, Gregory M.; Lowe, Henry J.

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers. PMID:12463824

  9. Research on Self-Determination in Physical Education: Key Findings and Proposals for Future Research

    ERIC Educational Resources Information Center

    Van den Berghe, Lynn; Vansteenkiste, Maarten; Cardon, Greet; Kirk, David; Haerens, Leen

    2014-01-01

    Background: During the last 30 years, several theories of motivation have generated insights into the motives underlying learners' behavior in physical education. Self-determination theory (SDT), a general theory on social development and motivation, has enjoyed increasing popularity in physical education research during the past decade. SDT…

  10. Key Features of Research Portal for Stimulating Research in Institutions of Higher Technical Education

    ERIC Educational Resources Information Center

    Agarwal, Parul Dharmani; Kiran, Ravi; Verma, Anil Kumar

    2012-01-01

    Problem Statement: The current higher learning institutions in developed countries have adapted to their changing role in a knowledge-based society It is time for developing countries like India to focus on Knowledge Management thus, the current study presents research undertaken in understanding the implication of Knowledge Management in the…

  11. Research on Self-Determination in Physical Education: Key Findings and Proposals for Future Research

    ERIC Educational Resources Information Center

    Van den Berghe, Lynn; Vansteenkiste, Maarten; Cardon, Greet; Kirk, David; Haerens, Leen

    2014-01-01

    Background: During the last 30 years, several theories of motivation have generated insights into the motives underlying learners' behavior in physical education. Self-determination theory (SDT), a general theory on social development and motivation, has enjoyed increasing popularity in physical education research during the past decade. SDT…

  12. Using key informant methods in organizational survey research: assessing for informant bias.

    PubMed

    Hughes, L C; Preski, S

    1997-02-01

    Specification of variables that reflect organizational processes can add an important dimension to the investigation of outcomes. However, many contextual variables are conceptualized at a macro unit of analysis and may not be amenable to direct measurement. In these situations, proxy measurement is obtained by treating organizational members as key informants who report about properties of the work group or organization. Potential sources of bias when using key informant methods in organizational survey research are discussed. Statistical procedures for assessment of rater-trait interaction as a type of informant bias are illustrated using data from a study in which multiple key informants were sampled to obtain proxy measurement of the organizational climate for caring among baccalaureate schools of nursing.

  13. Setting health research priorities using the CHNRI method: IV. Key conceptual advances

    PubMed Central

    Rudan, Igor

    2016-01-01

    Introduction Child Health and Nutrition Research Initiative (CHNRI) started as an initiative of the Global Forum for Health Research in Geneva, Switzerland. Its aim was to develop a method that could assist priority setting in health research investments. The first version of the CHNRI method was published in 2007–2008. The aim of this paper was to summarize the history of the development of the CHNRI method and its key conceptual advances. Methods The guiding principle of the CHNRI method is to expose the potential of many competing health research ideas to reduce disease burden and inequities that exist in the population in a feasible and cost–effective way. Results The CHNRI method introduced three key conceptual advances that led to its increased popularity in comparison to other priority–setting methods and processes. First, it proposed a systematic approach to listing a large number of possible research ideas, using the “4D” framework (description, delivery, development and discovery research) and a well–defined “depth” of proposed research ideas (research instruments, avenues, options and questions). Second, it proposed a systematic approach for discriminating between many proposed research ideas based on a well–defined context and criteria. The five “standard” components of the context are the population of interest, the disease burden of interest, geographic limits, time scale and the preferred style of investing with respect to risk. The five “standard” criteria proposed for prioritization between research ideas are answerability, effectiveness, deliverability, maximum potential for disease burden reduction and the effect on equity. However, both the context and the criteria can be flexibly changed to meet the specific needs of each priority–setting exercise. Third, it facilitated consensus development through measuring collective optimism on each component of each research idea among a larger group of experts using a simple

  14. [Research on finger key-press gesture recognition based on surface electromyographic signals].

    PubMed

    Cheng, Juan; Chen, Xiang; Lu, Zhiyuan; Zhang, Xu; Zhao, Zhangyan

    2011-04-01

    This article reported researches on the pattern recognition of finger key-press gestures based on surface electromyographic (SEMG) signals. All the gestures were defined referring to the PC standard keyboard, and totally 16 sorts of key-press gestures relating to the right hand were defined. The SEMG signals were collected from the forearm of the subjects by 4 sensors. And two kinds of pattern recognition experiments were designed and implemented for exploring the feasibility and repeatability of the key-press gesture recognition based on SEMG signals. The results from 6 subjects showed, by using the same-day templates, that the average classification rates of 16 defined key-press gestures reached above 75.8%. Moreover, when the training samples added up to 5 days, the recognition accuracies approached those obtained with the same-day templates. The experimental results confirm the feasibility and repeatability of SEMG-based key-press gestures classification, which is meaningful for the implementation of myoelectric control-based virtual keyboard interaction.

  15. Research capacity and culture of the Victorian public health allied health workforce is influenced by key research support staff and location.

    PubMed

    Williams, Cylie; Miyazaki, Koki; Borkowski, Donna; McKinstry, Carol; Cotchet, Matthew; Haines, Terry

    2015-06-01

    The aim of the present study was to identify and understand the self-rated research capacity and culture of the allied health workforce. METHODS. The present study was a cross-sectional survey. The Research Capacity and Culture tool was disseminated to all Victorian public health allied health departments. General demographic data were also collected, including the presence of an organisational allied health research lead. Five hundred and twenty fully completed surveys were returned by participants; all allied health disciplines and all grades were represented. One hundred and eighty-six participants had an organisational allied health research lead and 432 were located in a metropolitan-based health service. There were significant differences (P < 0.05) within all organisational and team research skills between those with and without a research lead, together with those in different service locations (metropolitan vs non-metropolitan). Higher self-ratings in individual research skills (P < 0.05) were primarily associated with more senior and metropolitan-located clinicians. The allied health workforce identifies as a group that is ready to build the evidence to support clinical practice yet requires a whole-systems approach to do so. The results of the present study suggest that the development of key people to build capacity at a higher organisational level has a flow-down effect on research capacity and culture.

  16. Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling

    PubMed Central

    Grad, Yonatan H.; Goldstein, Edward; Lipsitch, Marc; White, Peter J.

    2016-01-01

    The rise in gonococcal antibiotic resistance and the threat of untreatable infection are focusing attention on strategies to limit the spread of drug-resistant gonorrhea. Mathematical models provide a framework to link the natural history of infection and patient behavior to epidemiological outcomes and can be used to guide research and enhance the public health impact of interventions. While limited knowledge of key disease parameters and networks of spread has impeded development of operational models of gonococcal transmission, new tools in gonococcal surveillance may provide useful data to aid tracking and modeling. Here, we highlight critical questions in the management of gonorrhea that can be addressed by mathematical models and identify key data needs. Our overarching aim is to articulate a shared agenda across gonococcus-related fields from microbiology to epidemiology that will catalyze a comprehensive evidence-based clinical and public health strategy for management of gonococcal infections and antimicrobial resistance. PMID:26518045

  17. Recommendations for sex/gender neuroimaging research: key principles and implications for research design, analysis, and interpretation

    PubMed Central

    Rippon, Gina; Jordan-Young, Rebecca; Kaiser, Anelis; Fine, Cordelia

    2014-01-01

    Neuroimaging (NI) technologies are having increasing impact in the study of complex cognitive and social processes. In this emerging field of social cognitive neuroscience, a central goal should be to increase the understanding of the interaction between the neurobiology of the individual and the environment in which humans develop and function. The study of sex/gender is often a focus for NI research, and may be motivated by a desire to better understand general developmental principles, mental health problems that show female-male disparities, and gendered differences in society. In order to ensure the maximum possible contribution of NI research to these goals, we draw attention to four key principles—overlap, mosaicism, contingency and entanglement—that have emerged from sex/gender research and that should inform NI research design, analysis and interpretation. We discuss the implications of these principles in the form of constructive guidelines and suggestions for researchers, editors, reviewers and science communicators. PMID:25221493

  18. Recommendations for sex/gender neuroimaging research: key principles and implications for research design, analysis, and interpretation.

    PubMed

    Rippon, Gina; Jordan-Young, Rebecca; Kaiser, Anelis; Fine, Cordelia

    2014-01-01

    Neuroimaging (NI) technologies are having increasing impact in the study of complex cognitive and social processes. In this emerging field of social cognitive neuroscience, a central goal should be to increase the understanding of the interaction between the neurobiology of the individual and the environment in which humans develop and function. The study of sex/gender is often a focus for NI research, and may be motivated by a desire to better understand general developmental principles, mental health problems that show female-male disparities, and gendered differences in society. In order to ensure the maximum possible contribution of NI research to these goals, we draw attention to four key principles-overlap, mosaicism, contingency and entanglement-that have emerged from sex/gender research and that should inform NI research design, analysis and interpretation. We discuss the implications of these principles in the form of constructive guidelines and suggestions for researchers, editors, reviewers and science communicators.

  19. Swift residue-screening identifies key N-glycosylated asparagines sufficient for surface expression of neuroglycoprotein Lingo-1.

    PubMed

    Zhong, Xiaotian; Pocas, Jennifer; Liu, Yan; Wu, Paul W; Mosyak, Lidia; Somers, Will; Kriz, Ron

    2009-03-18

    Advances in genomics and proteomics have generated the needs for the efficient identification of key residues for structure and function of target proteins. Here we report the utilization of a new residue-screening approach, which combines a mammalian high-throughput transient expression system with a PCR-based expression cassette, for the study of the post-translational modification. Applying this approach results in a quick identification of essential N-glycosylation sites of a heavily glycosylated neuroglycoprotein Lingo-1, which are sufficient for the support of its surface expression. These key N-glycosylated sites uniquely locate on the concave surface of the elongated arc-shape structure of the leucine-rich repeat domain. The swift residue-screening approach may provide a new strategy for structural and functional analysis.

  20. An informatics research agenda to support precision medicine: seven key areas

    PubMed Central

    Avillach, Paul; Benham-Hutchins, Marge; Breitenstein, Matthew K; Crowgey, Erin L; Hoffman, Mark A; Jiang, Xia; Madhavan, Subha; Mattison, John E; Nagarajan, Radhakrishnan; Ray, Bisakha; Shin, Dmitriy; Visweswaran, Shyam; Zhao, Zhongming; Freimuth, Robert R

    2016-01-01

    The recent announcement of the Precision Medicine Initiative by President Obama has brought precision medicine (PM) to the forefront for healthcare providers, researchers, regulators, innovators, and funders alike. As technologies continue to evolve and datasets grow in magnitude, a strong computational infrastructure will be essential to realize PM’s vision of improved healthcare derived from personal data. In addition, informatics research and innovation affords a tremendous opportunity to drive the science underlying PM. The informatics community must lead the development of technologies and methodologies that will increase the discovery and application of biomedical knowledge through close collaboration between researchers, clinicians, and patients. This perspective highlights seven key areas that are in need of further informatics research and innovation to support the realization of PM. PMID:27107452

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

    PubMed

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

    2005-07-01

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

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

    PubMed Central

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

    2005-01-01

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

  3. Your next clinical cancer research project: preparation in a multidisciplinary environment is key

    PubMed Central

    Van Hemelrijck, Mieke; Bosco, Cecilia

    2017-01-01

    For clinical cancer research to have an impact, careful planning in a multidisciplinary translational setting is required. Once your multidisciplinary research team is established, the first step is to define an answerable research question, followed by planning the study design and identifying the study population—allowing for appropriate statistical analyses of high-quality data, whether patient or lab-based. Finally, interpretation of the results also requires multidisciplinary discussions and academic writing in a clear and concise way. This editorial is designed to give you some helpful tips and structure when planning your next clinical cancer research project. PMID:28386300

  4. Translating research for evidence-based public health: key concepts and future directions.

    PubMed

    Rychetnik, Lucie; Bauman, Adrian; Laws, Rachel; King, Lesley; Rissel, Chris; Nutbeam, Don; Colagiuri, Stephen; Caterson, Ian

    2012-12-01

    Applying research to guide evidence-based practice is an ongoing and significant challenge for public health. Developments in the emerging field of 'translation' have focused on different aspects of the problem, resulting in competing frameworks and terminology. In this paper the scope of 'translation' in public health is defined, and four related but conceptually different 'translation processes' that support evidence-based practice are outlined: (1) reviewing the transferability of evidence to new settings, (2) translation research, (3) knowledge translation, and (4) knowledge translation research. Finally, an integrated framework is presented to illustrate the relationship between these domains, and priority areas for further development and empirical research are identified.

  5. Key considerations for logic model development in research partnerships: a Canadian case study.

    PubMed

    Fielden, Sarah J; Rusch, Melanie L; Masinda, Mambo Tabu; Sands, Jim; Frankish, Jim; Evoy, Brian

    2007-05-01

    Community-academic partnership research is a fairly new genre of community-based participatory research. It has arisen in part, from recognition of the potential role of alliances in the development and translation of applied knowledge and the elimination of health disparities. This paper reports on the learning process of academic and community members who worked together in developing a logic model for a research program focusing on partnerships with vulnerable populations. The Partners in Community Health Research is a 6-year training program that seeks to combine research, training, and practice through the work of its "learning clusters". As these types of partnerships proliferate, the articulation and exploration of clear models will assist in their implementation. The authors, coming from both academia and community agencies, present a logic model meant to facilitate program management. Key considerations in the model's development are discussed in the context of an ongoing research partnership; namely, the complexity of the research partnership, power and accountability, alignment with health promotion policy, and the iterative nature of program design. Recommendations challenge academics, policy-makers, service providers, and community members to reflect on the elements needed to support and manage research partnerships and the tools necessary to ensure continued collaboration.

  6. EUFAR the key portal and network for airborne research in Europe

    NASA Astrophysics Data System (ADS)

    Gérard, Elisabeth; Brown, Philip

    2017-04-01

    will contribute substantially toward broadening the user base of existing airborne research facilities in Europe and mobilising additional resources to this end. EUFAR AISBL will be the most appropriate organisation for the (i) coordination of joint activities among the European institutions involved in airborne research, and also (ii) coordination of projects funded by the European Commission or other bodies for supporting activities beyond the self-financing perimeter of the AISBL (transnational access projects, education and training events, joint research activities, etc.). This will confirm EUFAR's position as the key portal for airborne research in Europe. This central position opens the way for further collaboration with other communities (UAS, etc.) and environmental research infrastructures (IAGOS, ACTRIS, ENVRIplus, EUROFLEETS, etc.) to ensure the mutual benefit of joint efforts in addressing future science challenges in a multi-disciplinary approach to the study of the Earth system.

  7. The Prevalence of Stalking among College Students: The Disparity between Researcher- and Self-Identified Victimization

    ERIC Educational Resources Information Center

    McNamara, Corinne L.; Marsil, Dorothy F.

    2012-01-01

    Objective: Researchers examined the prevalence of self-identified and researcher-identified stalking victimization among college students. Participants and Methods: A representative sample of 1,573 (70.1% female; 29.9% male) student respondents completed an online stalking questionnaire. Results: Overall, 12% self-identified as having been…

  8. Identifying psychological distress at key stages of the cancer illness trajectory: a systematic review of validated self-report measures.

    PubMed

    Ziegler, Lucy; Hill, Kate; Neilly, Liz; Bennett, Michael I; Higginson, Irene J; Murray, Scott A; Stark, Dan

    2011-03-01

    To enable study of psychological distress along the cancer journey, we need to be able to select and map validated measures through the cancer trajectory. To examine the performance of self-report measures for identifying clinically significant levels of psychological distress across the cancer patient trajectory. Electronic searches of Medline, PsychInfo, CINAHL, EmBase, The Cochrane Library, AMED, BNI, ASSIA, and Web of Science were undertaken. Only studies of self-report measures that used validated diagnostic tools for psychiatric diagnosis as the criterion measure were included. We then further limited our focus to those papers that specified a trajectory stage. Forty-eight different self-report measures were reported in the 85 papers identified. The Hospital Anxiety and Depression Scale (HADS) was the most frequently reported measure (23 times). Several other measures were reported between two and four times, but most (37) measures were reported only once. Twenty-two of the 85 included papers reported measure performance by trajectory stage. Best performing measures based on validation data available could be identified for each trajectory stage: for pretreatment, the HADS for identifying depression; during treatment, the HADS and Mental Health Inventory-5 (MHI-5) together for identifying clinically significant distress; post-treatment, the HADS for identifying depression; and at recurrence and during the palliative phase, the Brief Edinburgh Depression Scale (BEDS) for identifying depression. No single measure had evidence to support use throughout the illness trajectory in a longitudinal study, but the HADS, in combination with the MHI-5, was supported during the cancer treatment phase, and BEDS in the palliative care phase. Copyright © 2011 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

  9. Organizational participatory research: a systematic mixed studies review exposing its extra benefits and the key factors associated with them.

    PubMed

    Bush, Paula L; Pluye, Pierre; Loignon, Christine; Granikov, Vera; Wright, Michael T; Pelletier, Jean-François; Bartlett-Esquilant, Gillian; Macaulay, Ann C; Haggerty, Jeannie; Parry, Sharon; Repchinsky, Carol

    2017-10-10

    In health, organizational participatory research (OPR) refers to health organization members participating in research decisions, with university researchers, throughout a study. This non-academic partner contribution to the research may take the form of consultation or co-construction. A drawback of OPR is that it requires more time from all those involved, compared to non-participatory research approaches; thus, understanding the added value of OPR, if any, is important. Thus, we sought to assess whether the OPR approach leads to benefits beyond what could be achieved through traditional research. We identified, selected, and appraised OPR health literature, and at each stage, two team members independently reviewed and coded the literature. We used quantitative content analysis to transform textual data into reliable numerical codes and conducted a logistic regression to test the hypothesis that a co-construction type OPR study yields extra benefits with a greater likelihood than consultation-type OPR studies. From 8873 abstracts and 992 full text papers, we distilled a sample of 107 OPR studies. We found no difference between the type of organization members' participation and the likelihood of exhibiting an extra benefit. However, the likelihood of an OPR study exhibiting at least one extra benefit is quadrupled when the impetus for the study comes from the organization, rather than the university researcher(s), or the organization and the university researcher(s) together (OR = 4.11, CI = 1.12-14.01). We also defined five types of extra benefits. This review describes the types of extra benefits OPR can yield and suggests these benefits may occur if the organization initiates the OPR. Further, this review exposes a need for OPR authors to more clearly describe the type of non-academic partner participation in key research decisions throughout the study. Detailed descriptions will benefit others conducting OPR and allow for a re-examination of the

  10. Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm

    PubMed Central

    Teh, Chee-Keng; Ong, Ai-Ling; Kwong, Qi-Bin; Apparow, Sukganah; Chew, Fook-Tim; Mayes, Sean; Mohamed, Mohaimi; Appleton, David; Kulaveerasingam, Harikrishna

    2016-01-01

    GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10−4) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential. PMID:26743827

  11. Understanding price elasticities to inform public health research and intervention studies: key issues.

    PubMed

    Nghiem, Nhung; Wilson, Nick; Genç, Murat; Blakely, Tony

    2013-11-01

    Pricing policies such as taxes and subsidies are important tools in preventing and controlling a range of threats to public health. This is particularly so in tobacco and alcohol control efforts and efforts to change dietary patterns and physical activity levels as a means of addressing increases in noncommunicable diseases. To understand the potential impact of pricing policies, it is critical to understand the nature of price elasticities for consumer products. For example, price elasticities are key parameters in models of any food tax or subsidy that aims to quantify health impacts and cost-effectiveness. We detail relevant terms and discuss key issues surrounding price elasticities to inform public health research and intervention studies.

  12. Key-problem analysis and experimental research of stereo HMD used in augmented reality

    NASA Astrophysics Data System (ADS)

    Gao, Wei-Qing; Zhou, Shi-E.; Lv, Guo-Qiang; Ming, Hai

    2009-11-01

    The key problems to be solved in stereo HMD (Head-Mounted Display) used in augmented reality are analyzed, such as brightness of image, fusion of virtual and real scene, binocular rivalry, occlusion, distortion, stereo vision and tracking of head and line of sight. An experimental platform of HMD is developed by discrete elements to research the key problems. The problem of fusion of virtual and real scene can be solved effectively by replacing the common beam splitter with polarization beam splitter in combiner. The variations of HMD vision effects including binocular rivalry with binocular overlapped range are investigated, and the results indicate that the optimal effect is achieved when the binocular overlapped range is 33~50% of the monocular field of view (FOV). At last, stereo vision is realized in HMD by the stereo image pairs made up according to the parallax theory.

  13. Understanding Price Elasticities to Inform Public Health Research and Intervention Studies: Key Issues

    PubMed Central

    Nghiem, Nhung; Genç, Murat; Blakely, Tony

    2013-01-01

    Pricing policies such as taxes and subsidies are important tools in preventing and controlling a range of threats to public health. This is particularly so in tobacco and alcohol control efforts and efforts to change dietary patterns and physical activity levels as a means of addressing increases in noncommunicable diseases. To understand the potential impact of pricing policies, it is critical to understand the nature of price elasticities for consumer products. For example, price elasticities are key parameters in models of any food tax or subsidy that aims to quantify health impacts and cost-effectiveness. We detail relevant terms and discuss key issues surrounding price elasticities to inform public health research and intervention studies. PMID:24028228

  14. Identifying Key Factors in Implementing and Sustaining Response to Intervention: A Comparison of Schools Currently Implementing RtI

    ERIC Educational Resources Information Center

    Schwierjohn, Carrie Ann

    2011-01-01

    Since the reauthorization of IDEIA in 2004, school leaders across America have labored toward implementing a new process or model called Response to Intervention, in the hopes of lowering the high rates of students identified as Learning Disabled and increasing overall student achievement, by providing skilled interventions to struggling students.…

  15. Identifying key stage-specific genes and transcription factors for gastric cancer based on RNA-sequencing data

    PubMed Central

    Wang, Yan

    2017-01-01

    Abstract Background: To identify gastric cancer (GC)-associated genes and transcription factors (TFs) using RNA-sequencing (RNA-seq) data of Asians. Materials and methods: The RNA-seq data (GSE36968) were downloaded from Gene Expression Omnibus database, including 6 noncancerous gastric tissue samples, 5 stage I GC samples, 5 stage II GC samples, 8 stage III GC samples, and 6 stage IV GC samples. The gene expression values in each sample were calculated using Cuffdiff. Following, stage-specific genes were identified by 1-way analysis of variance and hierarchical clustering analysis. Upstream TFs were identified using Seqpos. Besides, functional enrichment analysis of stage-specific genes was performed by DAVID. In addition, the underlying protein–protein interactions (PPIs) information among stage IV-specific genes were extracted from STRING database and PPI network was constructed using Cytoscape software. Results: A total of 3576 stage-specific genes were identified, including 813 specifically up-regulated genes in the normal gastric tissues, 2224 stage I and II-specific genes, and 539 stage IV-specific genes. Also, a total of 9 and 11 up-regulated TFs were identified for the stage I and II-specific genes and stage IV-specific genes, respectively. Functional enrichment showed SPARC, MMP17, and COL6A3 were related to extracellular matrix. Notably, 2 regulatory pathways HOXA4-GLI3-RUNX2-FGF2 and HMGA2-PRKCA were obtained from the PPI network for stage IV-specific genes. In the PPI network, TFs HOXA4 and HMGA2 might function via mediating other genes. Conclusion: These stage-specific genes and TFs might act in the pathogenesis of GC in Asians. PMID:28121923

  16. Academic detailing can play a key role in assessing and implementing comparative effectiveness research findings.

    PubMed

    Fischer, Michael A; Avorn, Jerry

    2012-10-01

    Comparative effectiveness research evaluates the relative effectiveness, safety, and value of competing treatment options in clinically realistic settings. Such evaluations can be methodologically complex and difficult to interpret. There will be a growing need for critical evaluation of comparative effectiveness studies to assess the adequacy of their design and to put new information into a broader context. Equally important, this knowledge will have to be communicated to clinicians in a way that will actually change practice. We identify three challenges to effective dissemination of comparative effectiveness research findings: the difficulty of interpreting comparative effectiveness research data, the need for trusted sources of information, and the challenge of turning research results into clinical action. We suggest that academic detailing-direct outreach education that gives clinicians an accurate and unbiased synthesis of the best evidence for practice in a given clinical area-can translate comparative effectiveness research findings into actions that improve health care decision making and patient outcomes.

  17. Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal - a case study from health science.

    PubMed

    Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

    2016-01-01

    Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become

  18. Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal – a case study from health science

    PubMed Central

    Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

    2016-01-01

    Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become

  19. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.

    PubMed

    Ariani, Andrea; Di Baccio, Daniela; Romeo, Stefania; Lombardi, Lara; Andreucci, Andrea; Lux, Alexander; Horner, David Stephen; Sebastiani, Luca

    2015-01-01

    Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.

  20. Gene expression profiling identifies novel key players involved in the cytotoxic effect of Artesunate on pancreatic cancer cells.

    PubMed

    Youns, Mahmoud; Efferth, Thomas; Reichling, Jürgen; Fellenberg, Kurt; Bauer, Andrea; Hoheisel, Jörg D

    2009-08-01

    Pancreatic cancer is one of the most aggressive human malignancies, with an extremely poor prognosis. The paucity of curative therapies has translated into an overall 5-year survival rate of less than 5%, underscoring a desperate need for new therapeutic options. Artesunate (ART), clinically used as anti-malarial agent, has recently revealed remarkable anti-tumor activity. However, the mechanisms underlying those activities in pancreatic cancer are not yet known. Here we evaluated the anti-tumor activity of Artesunate and the possible underlying mechanisms in pancreatic cancer. MiaPaCa-2 (poorly differentiated) and BxPC-3 (moderately differentiated) pancreatic cancer cell lines were treated with Artesunate and the effect was monitored by a tetrazolium-based assay (MTS) for evaluating cell viability and by flow cytometry and caspase 3/7 activation for apoptosis evaluation. In addition cDNA arrays were used to identify differentially expressed genes. The microarray data were then validated by RT-PCR and Western blotting. Moreover, pathways associated with these expression changes were identified using the Ingenuity Pathway Analysis. The expression analysis identified a common set of genes that were regulated by Artesunate in pancreatic cancer. Our results provide the first in vitro evidence for the therapeutic utility of Artesunate in pancreatic cancer. Moreover, we identified Artesunate as a novel topoisomerase IIalpha inhibitor that inhibits pancreatic cancer growth through modulation of multiple signaling pathways. The present analysis is a starting point for the generation of hypotheses on candidate genes and for a more detailed dissection of the functional role of individual genes for the activity of Artesunate in tumor cells.

  1. How to identify the key factors that affect driver perception of accident risk. A comparison between Italian and Spanish driver behavior.

    PubMed

    de Oña, Juan; de Oña, Rocio; Eboli, Laura; Forciniti, Carmen; Mazzulla, Gabriella

    2014-12-01

    Road crashes can be caused by different factors, including infrastructure, vehicles, and human variables. Many research studies have focused solely on identifying the key factors that cause road crashes. From these studies, it emerged that human factors have the most relevant impact on accident severity. More specifically, accident severity depends on several factors related directly to the driver, i.e., driving experience, driver's socio-economic characteristics, and driving behavior and attitudes. In this paper, we investigate driver behaviors and attitudes while driving and specifically focus on different methods for identifying the factors that most affect the driver's perception of accident risk. To this end, we designed and conducted a survey in two different European contexts: the city of Cosenza, which is located in the south of Italy, and the city of Granada, which is located in the south of Spain. Samples of drivers were contacted for their opinions on certain aspects of driving rules and attitudes while driving, and different types of questions were addressed to the drivers to assess their judgments of these aspects. Consequently, different methods of data analysis were applied to determine the aspects that heavily influence driver perception of accident risk. An experiment based on the stated preferences (SP) was carried out with the drivers, and the SP data were analyzed using an ordered probit (OP) model. Interesting findings emerged from different analyses of the data and from the comparisons among the data collected in the two different territorial contexts. We found that both Italian and Spanish drivers consider driving in an altered psychophysical state and violating the overtaking rules to be the most risky behaviors.

  2. Self-transcendence: Lonergan's key to integration of nursing theory, research, and practice.

    PubMed

    Perry, Donna J

    2004-04-01

    This paper proposes that the philosophy of Bernard Lonergan can provide insight into the challenge of integrating nursing theory, research and practice. The author discusses Lonergan's work in regard to reflective understanding, authenticity and the human person as a subject of consciously developing unity. This is followed by a discussion of two key elements in Lonergan's work that relate to nursing: the subject-object challenge of nursing inquiry and common sense vs. scientific knowledge. The author suggests that integration of nursing theory, science and practice may be achieved through self-transcendence.

  3. Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii

    PubMed Central

    Mahamad Maifiah, Mohd Hafidz; Cheah, Soon-Ee; Johnson, Matthew D.; Han, Mei-Ling; Boyce, John D.; Thamlikitkul, Visanu; Forrest, Alan; Kaye, Keith S.; Hertzog, Paul; Purcell, Anthony W.; Song, Jiangning; Velkov, Tony; Creek, Darren J.; Li, Jian

    2016-01-01

    Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and polymyxin-resistant A. baumannii using untargeted metabolomics. The metabolome of each A. baumannii strain was measured using liquid chromatography-mass spectrometry. Multivariate and univariate statistics and pathway analyses were employed to elucidate metabolic differences between the polymyxin-susceptible and -resistant A. baumannii strains. Significant differences were identified between the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii strains. The lipopolysaccharide (LPS) deficient, polymyxin-resistant 19606R showed perturbation in specific amino acid and carbohydrate metabolites, particularly pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle intermediates. Levels of nucleotides were lower in the LPS-deficient 19606R. Furthermore, 19606R exhibited a shift in its glycerophospholipid profile towards increased abundance of short-chain lipids compared to the parent polymyxin-susceptible ATCC 19606. In contrast, in a pair of clinical isolates 03–149.1 (polymyxin-susceptible) and 03–149.2 (polymyxin-resistant, due to modification of lipid A), minor metabolic differences were identified. Notably, peptidoglycan biosynthesis metabolites were significantly depleted in both of the aforementioned polymyxin-resistant strains. This is the first comparative untargeted metabolomics study to show substantial differences in the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii. PMID:26924392

  4. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants

    PubMed Central

    Jin, Ying; Andersen, Genevieve; Yorgov, Daniel; Ferrara, Tracey M; Ben, Songtao; Brownson, Kelly M; Holland, Paulene J; Birlea, Stanca A; Siebert, Janet; Hartmann, Anke; Lienert, Anne; van Geel, Nanja; Lambert, Jo; Luiten, Rosalie M; Wolkerstorfer, Albert; van der Veen, JP Wietze; Bennett, Dorothy C; Taïeb, Alain; Ezzedine, Khaled; Kemp, E Helen; Gawkrodger, David J; Weetman, Anthony P; Kõks, Sulev; Prans, Ele; Kingo, Külli; Karelson, Maire; Wallace, Margaret R; McCormack, Wayne T; Overbeck, Andreas; Moretti, Silvia; Colucci, Roberta; Picardo, Mauro; Silverberg, Nanette B; Olsson, Mats; Valle, Yan; Korobko, Igor; Böhm, Markus; Lim, Henry W.; Hamzavi, Iltefat; Zhou, Li; Mi, Qing-Sheng; Fain, Pamela R.; Santorico, Stephanie A; Spritz, Richard A

    2016-01-01

    Vitiligo is an autoimmune disease in which depigmented skin results from destruction of melanocytes1, with epidemiologic association with other autoimmune diseases2. In previous linkage and genome-wide association studies (GWAS1, GWAS2), we identified 27 vitiligo susceptibility loci in patients of European (EUR) ancestry. We carried out a third GWAS (GWAS3) in EUR subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new loci and 7 suggestive loci, most encoding immune and apoptotic regulators, some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some corresponding to eQTL at these loci. Together, the identified genes provide a framework for vitiligo genetic architecture and pathobiology, highlight relationships to other autoimmune diseases and melanoma, and offer potential targets for treatment. PMID:27723757

  5. Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii.

    PubMed

    Maifiah, Mohd Hafidz Mahamad; Cheah, Soon-Ee; Johnson, Matthew D; Han, Mei-Ling; Boyce, John D; Thamlikitkul, Visanu; Forrest, Alan; Kaye, Keith S; Hertzog, Paul; Purcell, Anthony W; Song, Jiangning; Velkov, Tony; Creek, Darren J; Li, Jian

    2016-02-29

    Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and polymyxin-resistant A. baumannii using untargeted metabolomics. The metabolome of each A. baumannii strain was measured using liquid chromatography-mass spectrometry. Multivariate and univariate statistics and pathway analyses were employed to elucidate metabolic differences between the polymyxin-susceptible and -resistant A. baumannii strains. Significant differences were identified between the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii strains. The lipopolysaccharide (LPS) deficient, polymyxin-resistant 19606R showed perturbation in specific amino acid and carbohydrate metabolites, particularly pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle intermediates. Levels of nucleotides were lower in the LPS-deficient 19606R. Furthermore, 19606R exhibited a shift in its glycerophospholipid profile towards increased abundance of short-chain lipids compared to the parent polymyxin-susceptible ATCC 19606. In contrast, in a pair of clinical isolates 03-149.1 (polymyxin-susceptible) and 03-149.2 (polymyxin-resistant, due to modification of lipid A), minor metabolic differences were identified. Notably, peptidoglycan biosynthesis metabolites were significantly depleted in both of the aforementioned polymyxin-resistant strains. This is the first comparative untargeted metabolomics study to show substantial differences in the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii.

  6. Screening in planarians identifies MORN2 as a key component in LC3-associated phagocytosis and resistance to bacterial infection.

    PubMed

    Abnave, Prasad; Mottola, Giovanna; Gimenez, Gregory; Boucherit, Nicolas; Trouplin, Virginie; Torre, Cedric; Conti, Filippo; Ben Amara, Amira; Lepolard, Catherine; Djian, Benjamin; Hamaoui, Daniel; Mettouchi, Amel; Kumar, Atul; Pagnotta, Sophie; Bonatti, Stefano; Lepidi, Hubert; Salvetti, Alessandra; Abi-Rached, Laurent; Lemichez, Emmanuel; Mege, Jean-Louis; Ghigo, Eric

    2014-09-10

    Dugesia japonica planarian flatworms are naturally exposed to various microbes but typically survive this challenge. We show that planarians eliminate bacteria pathogenic to Homo sapiens, Caenorhabditis elegans, and/or Drosophila melanogaster and thus represent a model to identify innate resistance mechanisms. Whole-transcriptome analysis coupled with RNAi screening of worms infected with Staphylococcus aureus or Legionella pneumophila identified 18 resistance genes with nine human orthologs, of which we examined the function of MORN2. Human MORN2 facilitates phagocytosis-mediated restriction of Mycobacterium tuberculosis, L. pneumophila, and S. aureus in macrophages. MORN2 promotes the recruitment of LC3, an autophagy protein also involved in phagocytosis, to M. tuberculosis-containing phagosomes and subsequent maturation to degradative phagolysosomes. MORN2-driven trafficking of M. tuberculosis to single-membrane, LC3-positive compartments requires autophagy-related proteins Atg5 and Beclin-1, but not Ulk-1 and Atg13, highlighting the importance of MORN2 in LC3-associated phagocytosis. These findings underscore the value of studying planarian defenses to identify immune factors. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Identifying a key physical factor sensitive to the performance of Madden-Julian oscillation simulation in climate models

    NASA Astrophysics Data System (ADS)

    Kim, Go-Un; Seo, Kyong-Hwan

    2017-03-01

    A key physical factor in regulating the performance of Madden-Julian oscillation (MJO) simulation is examined by using 26 climate model simulations from the World Meteorological Organization's Working Group for Numerical Experimentation/Global Energy and Water Cycle Experiment Atmospheric System Study (WGNE and MJO-Task Force/GASS) global model comparison project. For this, intraseasonal moisture budget equation is analyzed and a simple, efficient physical quantity is developed. The result shows that MJO skill is most sensitive to vertically integrated intraseasonal zonal wind convergence (ZC). In particular, a specific threshold value of the strength of the ZC can be used as distinguishing between good and poor models. An additional finding is that good models exhibit the correct simultaneous convection and large-scale circulation phase relationship. In poor models, however, the peak circulation response appears 3 days after peak rainfall, suggesting unfavorable coupling between convection and circulation. For an improving simulation of the MJO in climate models, we propose that this delay of circulation in response to convection needs to be corrected in the cumulus parameterization scheme.

  8. Involuntary Memories and Dissociative Amnesia: Assessing Key Assumptions in PTSD Research

    PubMed Central

    Berntsen, Dorthe; Rubin, David C.

    2014-01-01

    Autobiographical memories of trauma victims are often described as disturbed in two ways. First, the trauma is frequently re-experienced in the form of involuntary, intrusive recollections. Second, the trauma is difficult to recall voluntarily (strategically); important parts may be totally or partially inaccessible—a feature known as dissociative amnesia. These characteristics are often mentioned by PTSD researchers and are included as PTSD symptoms in the DSM-IV-TR (American Psychiatric Association, 2000). In contrast, we show that both involuntary and voluntary recall are enhanced by emotional stress during encoding. We also show that the PTSD symptom in the diagnosis addressing dissociative amnesia, trouble remembering important aspects of the trauma is less well correlated with the remaining PTSD symptoms than the conceptual reversal of having trouble forgetting important aspects of the trauma. Our findings contradict key assumptions that have shaped PTSD research over the last 40 years. PMID:25309832

  9. Key Challenges and New Trends in Battery Research (2011 EFRC Forum)

    ScienceCinema

    Tarascon, Jean Marie (University de Picardie Jules Verne, France)

    2016-07-12

    Jean-Marie Tarascon, Professor at the University de Picardie Jules Verne, France, was the fourth speaker in the May 26, 2011 EFRC Forum session, "Global Perspectives on Frontiers in Energy Research." In his presentation, Professor Tarascon recounted European basic research activates in electrical energy storage. The 2011 EFRC Summit and Forum brought together the EFRC community and science and policy leaders from universities, national laboratories, industry and government to discuss "Science for our Nation's Energy Future." In August 2009, the Office of Science established 46 Energy Frontier Research Centers. The EFRCs are collaborative research efforts intended to accelerate high-risk, high-reward fundamental research, the scientific basis for transformative energy technologies of the future. These Centers involve universities, national laboratories, nonprofit organizations, and for-profit firms, singly or in partnerships, selected by scientific peer review. They are funded at $2 to $5 million per year for a total planned DOE commitment of $777 million over the initial five-year award period, pending Congressional appropriations. These integrated, multi-investigator Centers are conducting fundamental research focusing on one or more of several “grand challenges” and use-inspired “basic research needs” recently identified in major strategic planning efforts by the scientific community. The purpose of the EFRCs is to integrate the talents and expertise of leading scientists in a setting designed to accelerate research that transforms the future of energy and the environment.

  10. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

    PubMed Central

    Guichard, Cécile; Amaddeo, Giuliana; Imbeaud, Sandrine; Ladeiro, Yannick; Pelletier, Laura; Maad, Ichrafe Ben; Calderaro, Julien; Bioulac-Sage, Paulette; Letexier, Mélanie; Degos, Françoise; Clément, Bruno; Balabaud, Charles; Chevet, Eric; Laurent, Alexis; Couchy, Gabrielle; Letouzé, Eric; Calvo, Fabien; Zucman-Rossi, Jessica

    2012-01-01

    Hepatocellular carcinoma (HCC) is the most common primary liver malignancy. High-resolution copy number analysis of 125 tumors of which 24 were subjected to whole-exome sequencing identified 135 homozygous deletions and 994 somatic gene mutations with predicted functional consequences. We identified new recurrent alterations in 6 genes (ARID1A, RPS6KA3, NFE2L2, IRF2, CDH8 and PROKR2) not previously described in HCC. Functional analyses demonstrated tumor suppressor properties for IRF2 whose inactivation, exclusively found in hepatitis B virus related tumors, leads to impaired TP53 function. Alternatively, inactivation of proteins involved in chromatin remodeling was frequent and predominant in alcohol related tumors. Moreover, activation of the oxidative stress metabolism and inactivation of RPS6KA3 were new pathways associated with WNT/β-catenin activation, thereby suggesting a cooperative effect in tumorigenesis. This study shows the dramatic somatic genetic diversity in HCC, it reveals interactions between oncogene and tumor suppressor gene mutations markedly related to specific risk factors. PMID:22561517

  11. Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals.

    PubMed

    Quirós, Pedro M; Prado, Miguel A; Zamboni, Nicola; D'Amico, Davide; Williams, Robert W; Finley, Daniel; Gygi, Steven P; Auwerx, Johan

    2017-07-03

    Mitochondrial stress activates a mitonuclear response to safeguard and repair mitochondrial function and to adapt cellular metabolism to stress. Using a multiomics approach in mammalian cells treated with four types of mitochondrial stressors, we identify activating transcription factor 4 (ATF4) as the main regulator of the stress response. Surprisingly, canonical mitochondrial unfolded protein response genes mediated by ATF5 are not activated. Instead, ATF4 activates the expression of cytoprotective genes, which reprogram cellular metabolism through activation of the integrated stress response (ISR). Mitochondrial stress promotes a local proteostatic response by reducing mitochondrial ribosomal proteins, inhibiting mitochondrial translation, and coupling the activation of the ISR with the attenuation of mitochondrial function. Through a trans-expression quantitative trait locus analysis, we provide genetic evidence supporting a role for Fh1 in the control of Atf4 expression in mammals. Using gene expression data from mice and humans with mitochondrial diseases, we show that the ATF4 pathway is activated in vivo upon mitochondrial stress. Our data illustrate the value of a multiomics approach to characterize complex cellular networks and provide a versatile resource to identify new regulators of mitochondrial-related diseases. © 2017 Quirós et al.

  12. Monitoring oxidative and nitrative modification of cellular proteins; a paradigm for identifying key disease related markers of oxidative stress.

    PubMed

    Murray, James; Oquendo, C Elisa; Willis, John H; Marusich, Michael F; Capaldi, Roderick A

    2008-01-01

    High levels of free radicals produced by the mitochondrial respiratory chain, with subsequent damage to mitochondria have been implicated in a large and growing number of diseases. The underlying pathology of these diseases is oxidative damage to mitochondrial DNA, lipids and proteins which accumulate over time to produce a metabolic deficiency. We are developing an antibody based immunocapture array for many important mitochondrial proteins involved in free radical production, detoxification and mitochondrial energy production. Our array is capable of a multi-parameter measurement including enzyme activity, quantity, and oxidative protein modifications. Here we demonstrate the use of this array by analyzing the proteomic differences in OXPHOS (oxidative phosphorylation) enzymes between human heart and liver tissues, cells grown in media promoting aerobic versus anaerobic metabolism, and the catalytic/proteomic effects of mitochondria exposed to oxidative stress. Protein oxidation is identified as carbonyl formation arising from reactive oxygen species and 3-nitrotyrosine as a marker of reactive nitrogen species. Several identified modifications are confirmed by electrophoresis and mass spectrometry of immunocaptured material. We continue to expand this array as antibodies for enzyme isolation and detection become available.

  13. Transcript profiling identifies novel key players mediating the growth inhibitory effect of NS-398 on human pancreatic cancer cells.

    PubMed

    Youns, Mahmoud; Efferth, Thomas; Hoheisel, Jörg D

    2011-01-10

    Pancreatic cancer is one of the most aggressive human malignancies with an increasing incidence worldwide. Despite an increase in the number of systemic treatments available for pancreatic cancer, the impact of therapy on the clinical course of the disease has been modest, underscoring an urgent need for new therapeutic options. Although selective cyclooxygenase-2 inhibitors have been demonstrated to have cancer-preventive effects, the mechanism of their effects is not clearly known. Moreover, there have been no unbiased studies to identify novel molecular targets of NS-398 regarding pancreatic cancer. Here we undertook a gene expression profiling study to identify novel molecular targets modulating the growth inhibitory effects of NS-398 on pancreatic cancer cell lines. Our mRNA-based gene expression results showed that the growth inhibitory effect of NS-398 was accompanied with an activation of G1/S and G2/M cell cycle regulation, P53 signalling, apoptotic, aryl hydrocarbon receptor and death receptor signalling pathways. Moreover, we reported, for the first time, that the growth inhibitory effect of NS-398 is mediated by down-regulation of RRM2, CTGF, MCM2 and PCNA and up-regulation of NAG-1 in all cell lines.

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

    PubMed

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

    2016-04-01

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

  15. Cerebrospinal fluid metabolomics identifies a key role of isocitrate dehydrogenase in bipolar disorder: evidence in support of mitochondrial dysfunction hypothesis

    PubMed Central

    Yoshimi, N; Futamura, T; Bergen, S E; Iwayama, Y; Ishima, T; Sellgren, C; Ekman, C J; Jakobsson, J; Pålsson, E; Kakumoto, K; Ohgi, Y; Yoshikawa, T; Landén, M; Hashimoto, K

    2016-01-01

    Although evidence for mitochondrial dysfunction in the pathogenesis of bipolar disorder (BD) has been reported, the precise biological basis remains unknown, hampering the search for novel biomarkers. In this study, we performed metabolomics of cerebrospinal fluid (CSF) from male BD patients (n=54) and age-matched male healthy controls (n=40). Subsequently, post-mortem brain analyses, genetic analyses, metabolomics of CSF samples from rats treated with lithium or valproic acid were also performed. After multivariate logistic regression, isocitric acid (isocitrate) levels were significantly higher in the CSF from BD patients than healthy controls. Furthermore, gene expression of two subtypes (IDH3A and IDH3B) of isocitrate dehydrogenase (IDH) in the dorsolateral prefrontal cortex from BD patients was significantly lower than that of controls, although the expression of other genes including, aconitase (ACO1, ACO2), IDH1, IDH2 and IDH3G, were not altered. Moreover, protein expression of IDH3A in the cerebellum from BD patients was higher than that of controls. Genetic analyses showed that IDH genes (IDH1, IDH2, IDH3A, IDH3B) and ACO genes (ACO1, ACO2) were not associated with BD. Chronic (4 weeks) treatment with lithium or valproic acid in rats did not alter CSF levels of isocitrate, and mRNA levels of Idh3a, Idh3b, Aco1 and Aco2 genes in the rat brain. These findings suggest that abnormality in the metabolism of isocitrate by IDH3A in the mitochondria plays a key role in the pathogenesis of BD, supporting the mitochondrial dysfunction hypothesis of BD. Therefore, IDH3 in the citric acid cycle could potentially be a novel therapeutic target for BD. PMID:26782057

  16. Analysis of gene expression profiles between apical papilla tissues, stem cells from apical papilla and cell sheet to identify the key modulators in MSCs niche.

    PubMed

    Diao, Shu; Lin, Xiao; Wang, Liping; Dong, Rui; Du, Juan; Yang, Dongmei; Fan, Zhipeng

    2017-06-01

    The microenvironmental niche plays the key role for maintaining the cell functions. The stem cells from apical papilla (SCAPs) are important for tooth development and regeneration. However, there is limited knowledge about the key factors in niche for maintaining the function of SCAPs. In this study, we analyse the gene expression profiles between apical papilla tissues, SCAPs and SCAPs cell sheet to identify the key genes in SCAPs niche. Microarray assays and bioinformatic analysis were performed to screen the differential genes between apical papilla tissues and SCAPs, and SCAPs and SCAPs cell sheet. Recombinant human BMP6 protein was used in SCAPs. Then CCK-8 assay, CFSE assay, alkaline phosphatase activity, alizarin red staining, quantitative calcium analysis and real-time reverse transcriptase-polymerase chain reaction were performed to investigate the cell proliferation and differentiation potentials of SCAPs. Microarray analysis found that 846 genes were up-regulated and 1203 genes were down-regulated in SCAPs compared with apical papilla tissues. While 240 genes were up-regulated and 50 genes were down-regulated in SCAPs compared to in SCAPs cell sheet. Moreover, only 31 gene expressions in apical papilla tissues were recovered in cell sheet compared with SCAPs. Bioinformatic analysis identified that TGF-β, WNT and MAPK signalling pathways may play an important role in SCAPs niche. Based on the analysis, we identified one key growth factor in niche, BMP6, which could enhance the cell proliferation, the osteo/dentinogenic, neurogenic and angiogenic differentiation potentials of SCAPs. Our results provided insight into the mechanisms of the microenvironmental niche which regulate the function of SCAPs, and identified the key candidate genes in niche to promote mesenchymal stem cells-mediated dental tissue regeneration. © 2017 John Wiley & Sons Ltd.

  17. A Video Analysis of Intra- and Interprofessional Leadership Behaviors Within "The Burns Suite": Identifying Key Leadership Models.

    PubMed

    Sadideen, Hazim; Weldon, Sharon-Marie; Saadeddin, Munir; Loon, Mark; Kneebone, Roger

    2016-01-01

    Leadership is particularly important in complex highly interprofessional health care contexts involving a number of staff, some from the same specialty (intraprofessional), and others from different specialties (interprofessional). The authors recently published the concept of "The Burns Suite" (TBS) as a novel simulation tool to deliver interprofessional and teamwork training. It is unclear which leadership behaviors are the most important in an interprofessional burns resuscitation scenario, and whether they can be modeled on to current leadership theory. The purpose of this study was to perform a comprehensive video analysis of leadership behaviors within TBS. A total of 3 burns resuscitation simulations within TBS were recorded. The video analysis was grounded-theory inspired. Using predefined criteria, actions/interactions deemed as leadership behaviors were identified. Using an inductive iterative process, 8 main leadership behaviors were identified. Cohen's κ coefficient was used to measure inter-rater agreement and calculated as κ = 0.7 (substantial agreement). Each video was watched 4 times, focusing on 1 of the 4 team members per viewing (senior surgeon, senior nurse, trainee surgeon, and trainee nurse). The frequency and types of leadership behavior of each of the 4 team members were recorded. Statistical significance to assess any differences was assessed using analysis of variance, whereby a p < 0.05 was taken to be significant. Leadership behaviors were triangulated with verbal cues and actions from the videos. All 3 scenarios were successfully completed. The mean scenario length was 22 minutes. A total of 362 leadership behaviors were recorded from the 12 participants. The most evident leadership behaviors of all team members were adhering to guidelines (which effectively equates to following Advanced Trauma and Life Support/Emergency Management of Severe Burns resuscitation guidelines and hence "maintaining standards"), followed by making

  18. Analysis of Nicotiana tabacum PIN genes identifies NtPIN4 as a key regulator of axillary bud growth.

    PubMed

    Xie, Xiaodong; Qin, Guangyong; Si, Ping; Luo, Zhaopeng; Gao, Junping; Chen, Xia; Zhang, Jianfeng; Wei, Pan; Xia, Qingyou; Lin, Fucheng; Yang, Jun

    2017-01-27

    The plant-specific PIN-FORMED (PIN) auxin efflux proteins have been well characterized in many plant species, where they are crucial in the regulation of auxin transport in various aspects of plant development. However, little is known about the exact roles of the PIN genes during plant development in Nicotiana species. This study investigated the PIN genes in tobacco (N. tabacum) and in two ancestral species (N. sylvestris and N. tomentosiformis). Genome-wide analysis of the N. tabacum genome identified 20 genes of the PIN family. An in-depth phylogenetic analysis of the PIN genes of N. tabacum, N. sylvestris and N. tomentosiformis was conducted. NtPIN4 expression was strongly induced by the application of exogenous IAA, but was downregulated by the application of ABA, a strigolactone analogue, and cytokinin, as well as by decapitation treatments, suggesting that the NtPIN4 expression level is likely positively regulated by auxin. Expression analysis indicated that NtPIN4 was highly expressed in tobacco stems and shoots, which was further validated through analysis of the activity of the NtPIN4 promoter. We used CRISPR-Cas9 technology to generate mutants for NtPIN4 and observed that both T0 and T1 plants had a significantly increased axillary bud growth phenotype, as compared with the wild-type plants. Therefore, NtPIN4 offers an opportunity for studying auxin-dependent branching processes.

  19. A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation

    PubMed Central

    Westerman, Bart A.; Braat, A. Koen; Taub, Nicole; Potman, Marko; Vissers, Joseph H.A.; Blom, Marleen; Verhoeven, Els; Stoop, Hans; Gillis, Ad; Velds, Arno; Nijkamp, Wouter; Beijersbergen, Roderick; Huber, Lukas A.; Looijenga, Leendert H.J.

    2011-01-01

    Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. We used a genome-wide short hairpin RNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3 or Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation, and promoted proliferation. Fibroblast growth factor 4 (FGF4) signaling is required for initial fate commitment of ES cells. Knockdown of Mp1 inhibited FGF4-induced differentiation but did not alter FGF4-driven proliferation. This uncoupling of differentiation and proliferation was also observed when oncogenic Ras isoforms were overexpressed in ES cells. Knockdown of Mp1 redirected FGF4 signaling from differentiation toward pluripotency and up-regulated the pluripotency-related genes Esrrb, Rex1, Tcl1, and Sox2. We also found that human germ cell tumors (GCTs) express low amounts of Mp1 in the invasive embryonic carcinoma and seminoma histologies and higher amounts of Mp1 in the noninvasive carcinoma in situ precursor and differentiated components. Knockdown of Mp1 in invasive GCT cells resulted in resistance to differentiation, thereby showing a functional role for Mp1 both in normal differentiation of ES cells and in germ cell cancer. PMID:22143885

  20. Using a structured review of the literature to identify key factors associated with the current nursing shortage.

    PubMed

    Duvall, Judy J; Andrews, Diane Randall

    2010-01-01

    The current population of nurses is aging and rapidly approaching retirement, and graduation of new nurses is not expected to meet demand. Multiple reports have offered information regarding the pending shortage and made recommendations regarding interventions. It is important that suggested interventions be based upon current evidence. An integrated review of literature was undertaken, searching CINAHL, PubMed, Academic Search Premier, Medline, and PsychInfo. Studies were limited to those conducted in the United States and published in English between 2000 and 2007. Search terms were nursing shortage, job satisfaction in nursing, stress in nursing, nursing turnover, nursing image, nursing work environment, physical demands of nursing, and nursing faculty shortage. The identified reasons for nurses leaving hospital practice were management issues, job design, job stress, physical demands, and the failure to nurture new nurses. The education issues include a lack of qualified faculty and clinical sites to allow for more students to be accepted into the programs. These are issues that can be addressed; and changes, implemented. Steps must be taken immediately to resolve these issues in an effort to keep an adequate supply of nurses at the bedside.

  1. A Drosophila in vivo screen identifies store-operated calcium entry as a key regulator of adiposity.

    PubMed

    Baumbach, Jens; Hummel, Petra; Bickmeyer, Iris; Kowalczyk, Katarzyna M; Frank, Martina; Knorr, Konstantin; Hildebrandt, Anja; Riedel, Dietmar; Jäckle, Herbert; Kühnlein, Ronald P

    2014-02-04

    To unravel the evolutionarily conserved genetic network underlying energy homeostasis, we performed a systematic in vivo gene knockdown screen in Drosophila. We used a transgenic RNAi library enriched for fly orthologs of human genes to functionally impair about half of all Drosophila genes specifically in adult fat storage tissue. This approach identified 77 genes, which affect the body fat content of the fly, including 58 previously unknown obesity-associated genes. These genes function in diverse biological processes such as lipid metabolism, vesicle-mediated trafficking, and the universal store-operated calcium entry (SOCE). Impairment of the SOCE core component Stromal interaction molecule (Stim), as well as other components of the pathway, causes adiposity in flies. Acute Stim dysfunction in the fat storage tissue triggers hyperphagia via remote control of the orexigenic short neuropeptide F in the brain, which in turn affects the coordinated lipogenic and lipolytic gene regulation, resulting in adipose tissue hypertrophy. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Inflammatory and fibrotic proteins proteomically identified as key protein constituents in urine and stone matrix of patients with kidney calculi.

    PubMed

    Boonla, Chanchai; Tosukhowong, Piyaratana; Spittau, Björn; Schlosser, Andreas; Pimratana, Chaowat; Krieglstein, Kerstin

    2014-02-15

    To uncover whether urinary proteins are incorporated into stones, the proteomic profiles of kidney stones and urine collected from the same patients have to be explored. We employed 1D-PAGE and nanoHPLC-ESI-MS/MS to analyze the proteomes of kidney stone matrix (n=16), nephrolithiatic urine (n=14) and healthy urine (n=3). We identified 62, 66 and 22 proteins in stone matrix, nephrolithiatic urine and healthy urine, respectively. Inflammation- and fibrosis-associated proteins were frequently detected in the stone matrix and nephrolithiatic urine. Eighteen proteins were exclusively found in the stone matrix and nephrolithiatic urine, considered as candidate biomarkers for kidney stone formation. S100A8 and fibronectin, representatives of inflammation and fibrosis, respectively, were up-regulated in nephrolithiasis renal tissues. S100A8 was strongly expressed in infiltrated leukocytes. Fibronectin was over-expressed in renal tubular cells. S100A8 and fibronectin were immunologically confirmed to exist in nephrolithiatic urine and stone matrix, but in healthy urine they were undetectable. Conclusion, both kidney stones and urine obtained from the same patients greatly contained inflammatory and fibrotic proteins. S100A8 and fibronectin were up-regulated in stone-baring kidneys and nephrolithiatic urine. Therefore, inflammation and fibrosis are suggested to be involved in the formation of kidney calculi.

  3. Stepwise organization of the β-structure identifies key regions essential for the propagation and cytotoxicity of insulin amyloid fibrils.

    PubMed

    Chatani, Eri; Imamura, Hiroshi; Yamamoto, Naoki; Kato, Minoru

    2014-04-11

    Amyloid fibrils are supramolecular assemblies, the deposition of which is associated with many serious diseases including Alzheimer, prion, and Huntington diseases. Several smaller aggregates such as oligomers and protofibrils have been proposed to play a role in early stages of the fibrillation process; however, little is known about how these species contribute to the formation of mature amyloid fibrils with a rigid cross-β structure. Here, we identified a new pathway for the formation of insulin amyloid fibrils at a high concentration of salt in which mature fibrils were formed in a stepwise manner via a prefibrillar intermediate: minute prefibrillar species initially accumulated, followed by the subsequent formation of thicker amyloid fibrils. Fourier transform infrared spectra suggested the sequential formation of two types of β-sheets with different strength hydrogen bonds, one of which was developed concomitantly with the mutual assembly of the prefibrillar intermediate to form mature fibrils. Interestingly, fibril propagation and cellular toxicity appeared only after the later step of structural organization, and a comparison of β-sheet regions between the prefibrillar intermediate and mature fibrils using proteolysis led to the proposal of specific regions essential for manifestation of these properties.

  4. A framework for identifying public research priorities: an application in forestry research.

    Treesearch

    Glenn Fox

    1986-01-01

    Discusses attempts to model and measure the relationship between research and development activity and the rate and nature of technological change in recent decades. Reviews efforts to model optimal research resource allocation, and presents a model for southern pine forestry research.

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

    PubMed

    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

  6. Statistical study to identify the key factors governing ground water recharge in the watersheds of the arid Central Asia.

    PubMed

    Zhu, Binq-Qi; Wang, Yue-Ling

    2016-01-01

    Understanding the source and recharge of ground waters is of great significance to our knowledge in hydrological cycles in arid environments over the world. Northern Xinjiang in northwestern China is a significant repository of information relating to the hydrological evolution and climatic changes in central Asia. In this study, two multivariate statistical techniques, hierarchical cluster analysis (HCA) and principal component analysis (PCA), were used to assess the ground water recharge and its governing factors, with the principal idea of exploring the above techniques to utilize all available hydrogeochemical variables in the quality assessment, which are not considered in the conventional techniques like Stiff and Piper diagrams. Q-mode HCA and R-mode PCA were combined to partition the water samples into seven major water clusters (C1-C7) and three principal components (PC1-PC3, PC1 salinity, PC2 hydroclimate, PC3 contaminant). The water samples C1 + C4 were classified as recharge area waters (Ca-HCO3 water), C2 + C3 as transitional zone waters (Ca-Mg-HCO3-SO4 water), and C5 + C6 + C7 as discharge area waters (Na-SO4 water). Based on the Q-mode PCA scores, three groups of geochemical processes influencing recharge regimes were identified: geogenic (i.e., caused by natural geochemical processes), geomorphoclimatic (caused by topography and climate), and anthropogenic (caused by ground water contamination). It is proposed that differences in recharge mechanism and ground water evolution, and possible bedrock composition difference, are responsible for the chemical genesis of these waters. These will continue to influence the geochemistry of the northern Xinjiang drainage system for a long time due to its steady tectonics and arid climate. This study proved that the chemistry differentiation of ground water can effectively support the identification of ground water recharge and evolution patterns.

  7. The theory research of multi-user quantum access network with Measurement Device Independent quantum key distribution

    NASA Astrophysics Data System (ADS)

    Ji, Yi-Ming; Li, Yun-Xia; Shi, Lei; Meng, Wen; Cui, Shu-Min; Xu, Zhen-Yu

    2015-10-01

    Quantum access network can't guarantee the absolute security of multi-user detector and eavesdropper can get access to key information through time-shift attack and other ways. Measurement-device-independent quantum key distribution is immune from all the detection attacks, and accomplishes the safe sharing of quantum key. In this paper, that Measurement-device-independent quantum key distribution is used in the application of multi-user quantum access to the network is on the research. By adopting time-division multiplexing technology to achieve the sharing of multiuser detector, the system structure is simplified and the security of quantum key sharing is acquired.

  8. Different animal welfare orientations towards some key research areas of current relevance to pastoral dairy farming in New Zealand.

    PubMed

    Webster, J R; Schütz, K E; Sutherland, M A; Stewart, M; Mellor, D J

    2015-01-01

    The New Zealand dairy industry needs to meet public expectations regarding animal welfare in order to retain the freedom to operate and achieve market success. Three key orientations towards animal welfare assessment have been identified, namely biological functioning, affective state and natural living, the last two of which are more recent foci for societal concern. Biological functioning was the first and most-studied aspect of animal welfare and continues to be important, but now the contribution of affective state to animal well-being is emphasised much more. Natural living, or naturalness, has received relatively less attention from animal welfare science. It is proposed that increasing the use of naturalness as a contextual reference point for considering species-specific behavioural expressions of affective state will enhance its inclusion in animal welfare assessment. Nevertheless, all three orientations need to be considered in order to evaluate the significance of welfare research findings. On this basis, five key aspects of the New Zealand dairy industry that have been the subject of recent research, due to the risk of them not meeting public expectations, are highlighted and discussed. The aspects are provision of shade and shelter, meeting targets for body condition, provision of comfortable surfaces for rearing calves, and for adult cows while off pasture, and pain relief for disbudding of calves. Research evidence indicates that the industry guidelines on body condition score, if met, would satisfy public expectations across the three orientations to animal welfare, whereas further work is needed on the other aspects. It is concluded that considering these three orientations to animal welfare when planning research and then evaluating the outcomes will help to promote the market success of the dairy industry in New Zealand.

  9. Identifying key hydrological and biochemical processes for predicting field scale nitrate and ammonia export in agricultural cold regions

    NASA Astrophysics Data System (ADS)

    Costa, D.; Pomeroy, J. W.; Wheater, H. S.

    2016-12-01

    Nutrient runoff from agricultural cold regions such as the Canadian Prairies is impairing the ecological function of regional lakes and contributing to massive algal blooms such as found in Lake Winnipeg. Improving catchment model predictions of nutrient export in cold regions requires a better understanding and representation of the main processes controlling nutrient exports at multiple scales. Popular state-of-the-art models often have deficient representation of processes at smaller scales and lack the temporal resolution required to capture important solute transport phenomena, such as preferential elution of ions from the melting snowpack, solute infiltration to frozen soils, and transport during rain-on-snow events. Important processes in the Canadian Prairies that are often neglected are wind redistributed snowpacks and the impacts of their heterogeneous snowcover depletion on nutrient transport. In this research, physical evidence from high frequency field measurements were used to develop a process-based nutrient model for field-scale prediction of nitrate-nitrite (NO3-NO2) and ammonia (NH3) concentrations in both spring snowmelt and summer rainfall driven runoff. The process-based, modular Cold Regions Hydrological Model (CRHM) was used to simulate the main hydrological drivers such as snow redistribution, snowmelt, infiltration into frozen and unfrozen soils, evapotranspiration and subsurface and surface runoff generation. Field observations and a model application to the South Tobacco Creek sub-basin of the Red River in Manitoba, Canada, suggests that the transport of nutrients can be divided in five phases of dominant transport mechanisms due to the available nutrient sources progressively changing from the snowpack to the thawing frozen soil during melt. The vertical distribution of nutrient in the snowpack also varies due to ion exclusion processes at the snow crystal-air interface. Such findings are an important step towards more accurate and

  10. A new HDV mouse model identifies mitochondrial antiviral signaling protein (MAVS) as a key player in IFN-β induction.

    PubMed

    Suárez-Amarán, Lester; Usai, Carla; Di Scala, Marianna; Godoy, Cristina; Ni, Yi; Hommel, Mirja; Palomo, Laura; Segura, Víctor; Olagüe, Cristina; Vales, Africa; Ruiz-Ripa, Alicia; Buti, Maria; Salido, Eduardo; Prieto, Jesús; Urban, Stephan; Rodríguez-Frias, Francisco; Aldabe, Rafael; González-Aseguinolaza, Gloria

    2017-10-01

    Studying hepatitis delta virus (HDV) and developing new treatments is hampered by the limited availability of small animal models. Herein, a description of a robust mouse model of HDV infection that mimics several important characteristics of the human disease is presented. HDV and hepatitis B virus (HBV) replication competent genomes were delivered to the mouse liver using adeno-associated viruses (AAV; AAV-HDV and AAV-HBV). Viral load, antigen expression and genomes were quantified at different time points after AAV injection. Furthermore, liver pathology, genome editing, and the activation of the innate immune response were evaluated. AAV-HDV infection initiated HDV replication in mouse hepatocytes. Genome editing was confirmed by the presence of small and large HDV antigens and sequencing. Viral replication was detected for 45days, even after the AAV-HDV vector had almost disappeared. In the presence of HBV, HDV infectious particles were detected in serum. Furthermore, as observed in patients, co-infection was associated with the reduction of HBV antigen expression and the onset of liver damage that included the alteration of genes involved in the development of liver pathologies. HDV replication induced a sustained type I interferon response, which was significantly reduced in immunodeficient mice and almost absent in mitochondrial antiviral signaling protein (MAVS)-deficient mice. The animal model described here reproduces important characteristics of human HDV infection and provides a valuable tool for characterizing the viral infection and for developing new treatments. Furthermore, MAVS was identified as a main player in HDV detection and adaptive immunity was found to be involved in the amplification of the innate immune response. Lay summary: Co-infection with hepatitis B and D virus (HBV and HDV, respectively) often causes a more severe disease condition than HBV alone. Gaining more insight into HDV and developing new treatments is hampered by limited

  11. Key informants and community members in community-based participatory research: one is not like the other.

    PubMed

    McKenna, Stacey A; Iwasaki, Patricia G; Stewart, Tracey; Main, Deborah S

    2011-01-01

    As community-based participatory research (CBPR) gains national prominence, it is increasingly important to examine critically the meaning of community participation and the roles of research participants. Many CBPR projects rely heavily on key informants, but because of their social position, economic status, or professional role, they may not represent the views of community members. This paper compares key informant and community member perspectives about neighborhood health to explore the types of knowledge produced by each group. The data used for this study are part of a larger CBPR project, Taking Neighborhood Health to Heart (TNH2H). We conducted five focus groups with community members and 16 interviews with key informants. Reported knowledge and beliefs about the community generally came from three perspectives: Primary key informant (key informant reports about neighborhoods and community members), secondary key informant (key informant assessments of community member beliefs and motivations for their behaviors), and community members. A number of differences emerged between key informants and community members in the types of knowledge they shared, revealing important assumptions held by key informants about community members. As more funders call for health researchers to engage community members to improve the reach, impact, and translation of their research to improve population health, they must clarify what is meant by community engagement and recognize the roles that people's relative status and positions in society play in their knowledge about a given place.

  12. Enhanced Recovery after Urological Surgery: A Contemporary Systematic Review of Outcomes, Key Elements, and Research Needs.

    PubMed

    Azhar, Raed A; Bochner, Bernard; Catto, James; Goh, Alvin C; Kelly, John; Patel, Hiten D; Pruthi, Raj S; Thalmann, George N; Desai, Mihir

    2016-07-01

    Enhanced Recovery after Surgery (ERAS) programs are multimodal care pathways that aim to decrease intra-operative blood loss, decrease postoperative complications, and reduce recovery times. To overview the use and key elements of ERAS pathways, and define needs for future clinical trials. A comprehensive systematic MEDLINE search was performed for English language reports published before May 2015 using the terms "postoperative period," "postoperative care," "enhanced recovery after surgery," "enhanced recovery," "accelerated recovery," "fast track recovery," "recovery program," "recovery pathway", "ERAS," and "urology" or "cystectomy" or "urologic surgery." We identified 18 eligible articles. Patient counseling, physical conditioning, avoiding excessive alcohol and smoking, and good nutrition appeared to protect against postoperative complications. Fasting from solid food for only 6h and perioperative liquid-carbohydrate loading up to 2h prior to surgery appeared to be safe and reduced recovery times. Restricted, balanced, and goal-directed fluid replacement is effective when individualized, depending on patient morbidity and surgical procedure. Decreased intraoperative blood loss may be achieved by several measures. Deep vein thrombosis prophylaxis, antibiotic prophylaxis, and thermoregulation were found to help reduce postsurgical complications, as was a multimodal approach to postoperative nausea, vomiting, and analgesia. Chewing gum, prokinetic agents, oral laxatives, and an early resumption to normal diet appear to aid faster return to normal bowel function. Further studies should compare anesthetic protocols, refine analgesia, and evaluate the importance of robot-assisted surgery and the need/timing for drains and catheters. ERAS regimens are multidisciplinary, multimodal pathways that optimize postoperative recovery. This review provides an overview of the use and key elements of Enhanced Recovery after Surgery programs, which are multimodal

  13. Key research issues in the pulsed fast-neutron analysis technique for cargo inspection

    SciTech Connect

    Micklich, B.J.; Fink, C.L.; Yule, T.J.

    1994-07-01

    Non-invasive inspection systems based on the use of fast neutrons are being studied for the inspection of large cargo containers. A key advantage of fast neutrons is their sensitivity to low-Z elements such as carbon, nitrogen, and oxygen, which are the primary constituents of explosives and narcotics. The high energy allows penetration of relatively large containers. The pulsed fast-neutron analysis (PFNA) technique is currently the baseline system. A workshop on the PFNA technique involving industrial, government, and university participants was held at Argonne National Lab. in January 1994. The purpose of this workshop was to review the status of research on the key technical issues involved in PFNA, and to develop a list of those areas where additional modeling and/or experimentation were needed. The workshop also focused on development of a near-term experimental assessment program using existing prototypes and on development of a long-term test program at the Tacoma Testbed, where a PFNA prototype will be installed in 1995. A summary of conclusions reached at this workshop is presented. Results from analytic and Monte Carlo modeling of simplified PFNA systems are also presented.

  14. Key research issues in the pulsed fast-neutron analysis technique for cargo inspection

    NASA Astrophysics Data System (ADS)

    Micklich, Bradley J.; Fink, Charles L.; Yule, Thomas J.

    1994-10-01

    Non-invasive inspection systems based on the use of fast neutrons are being studied for the inspection of large cargo containers. A key advantage of fast neutrons is their sensitivity to low-Z elements such as carbon, nitrogen, and oxygen, which are the primary constituents of explosives and narcotics. The high energy allows penetration of relatively large containers. The pulsed fast-neutron analysis (PFNA) technique is currently the baseline system. A workshop on the PFNA technique involving industrial, government, and university participants was held at Argonne National Laboratory in January 1994. The purpose of this workshop was to review the status of research on the key technical issues involved in PFNA, and to develop a list of those areas where additional modeling and/or experimentation were needed. The workshop also focused on development of a near-term experimental assessment program using existing prototypes and on development of a long-term test program at the Tacoma Testbed, where a PFNA prototype will be installed in 1995. A summary of conclusions reached at this workshop is presented. Results from analytic and Monte Carlo modeling of simplified PFNA systems are also presented.

  15. Identification of miRNA Signatures Associated with Epithelial Ovarian Cancer Chemoresistance with Further Biological and Functional Validation of Identified Key miRNAs

    DTIC Science & Technology

    2012-08-01

    physiological conditions, including pregnancy [2], diabetes [3], radiation sickness [4], and numerous forms of cancer [5]. In cancer , circulating miRNAs will...undetectable by RT-PCR (Ct > 40, data not shown). Figure 6. ARIA tests on ovarian cancer cell lines. (A) Relative fold change comparing...Epithelial Ovarian Cancer Chemoresistance with Further Biological and Functional Validation of Identified Key miRNAs PRINCIPAL INVESTIGATOR: Analisa

  16. Research and validation of key measurement technologies of large aperture optical elements

    NASA Astrophysics Data System (ADS)

    Guo, Renhui; Chen, Lei; Jiang, Chao; Cao, Hui; Zhang, Huiqin; Zhou, Binbin; Song, Le

    2015-07-01

    A lot of optical components with large aperture are employed in high-power solid-state laser driver. These optical components are with high requirement on the surface shape, optical homogeneity and stress distribution. In order to test these parameters, different types of interferometers, surface profilers and stress meters from different manufacturers are needed. But the problem is the products from different manufacturers may provide different test results. To solve the problem, the research and verification of the key measurement technologies of large aperture optical components are carried out in this paper. The absolute flatness and optical homogeneity measurement methods are analyzed. And the test results of different interferometric software are compared. The test results from different surface profilers and stress meters are also compared. The consistency and reliability of different test software are obtained with the comparing results, which will guide users to select a suitable product.

  17. Positioning Arabidopsis in plant biology. A key step toward unification of plant research.

    PubMed

    Bevan, Michael; Walsh, Sean

    2004-06-01

    One of the major challenges in biological investigation involves developing a robust predictive framework in which biological outputs can be predicted from input data and knowledge of the state of the system. Currently, genomics-based strategies provide a strong framework for integrating biological knowledge within a species and linking knowledge between diverse organisms, as DNA sequence is a durable, accurate, and complete record of biological information. As such, it provides the best source of information upon which predictive rules can start to be built, tested, and generalized. Generalization is a key component of predictive biology because it defines the extent to which we can accurately predict from one instance to another. In plant science, several important research themes are concerned with generalization, and progress in these areas is reviewed here. The importance of developing a framework for predictive biology that includes a much wider variety of plant species is also emphasized.

  18. Small is useful in endocrine disrupter assessment--four key recommendations for aquatic invertebrate research.

    PubMed

    Hutchinson, Thomas H

    2007-02-01

    As we enter the 21st "biocentury", with issues such as biodiversity and biotechnology growing in public profile, it is important to reflect on the immense ecological, medical and economic importance of invertebrates. Efforts to understand the diverse biology of invertebrates come from many directions, including Nobel Prize winning developmental biology, research to control insects that threaten human health and food supplies, aquaculture opportunities and also within ecotoxicology. In the latter context, this special journal volume highlights the importance of addressing endocrine disruption in aquatic invertebrates, from molecular and cellular biomarkers to population-relevant adverse effects. The contributors to this special volume have provided an excellent assessment of both the fundamental endocrinology and applied ecotoxicology of many aquatic invertebrate groups. On the premise that reproductive success is ultimately the vital population parameter, this chapter gives a personal view of key gaps in knowledge in invertebrate reproductive and developmental endocrinology and ecotoxicology. Based on current knowledge, there are four key issues that need to be prioritised within aquatic ecotoxicology: (1) a wider assessment of the reproductive status of invertebrates in both freshwater and coastal ecosystems; (2) prioritisation of laboratory studies in OECD and other regulatory test organisms, including basic endocrinology and ADME (absorption, distribution, metabolism and excretion) research; (3) development and validation of mechanistic biomarkers that can be used as "signposts" to help prioritise species and chronic test endpoint selection, and help link data from laboratory and field studies; and (4) develop a comparative invertebrate toxicology database utilising the prioritised reference chemicals from the EDIETA workshop, encompassing the diverse modes-of-action pertinent to endocrine disrupter testing in both aquatic arthropod and non

  19. Key challenges and ways forward in researching the “good death”: qualitative in-depth interview and focus group study

    PubMed Central

    Harris, Fiona; Boyd, Kirsty; Sheikh, Aziz; Murray, Scott A; Brown, Duncan; Mallinson, Ian; Kearney, Nora; Worth, Allison

    2007-01-01

    Objective To understand key challenges in researching end of life issues and identify ways of overcoming these. Design Qualitative study involving in-depth interviews with researchers and focus groups with people affected by cancer. Participants An international sample of 32 researchers; seven patients with experience of cancer; and four carers in south east Scotland. Results Researchers highlighted the difficulty of defining the end of life, overprotective gatekeeping by ethics committees and clinical staff, the need to factor in high attrition rates associated with deterioration or death, and managing the emotions of participants and research staff. People affected by cancer and researchers suggested that many people nearing the end of life do want to be offered the chance to participate in research, provided it is conducted sensitively. Although such research can be demanding, most researchers believed it to be no more problematic than many other areas of research and that the challenges identified can be overcome. Conclusions The continuing taboos around death and dying act as barriers to the commissioning and conduct of end of life research. Some people facing death, however, may want to participate in research and should be allowed to do so. Ethics committees and clinical staff must balance understandable concern about non-maleficence with the right of people with advanced illness to participate in research. Despite the inherent difficulties, end of life research can be conducted with ethical and methodological rigour. Adequate psychological support must be provided for participants, researchers, and transcribers. PMID:17329313

  20. Using Community-Based Participatory Research to Prevent HIV Disparities: Assumptions and Opportunities Identified by The Latino Partnership

    PubMed Central

    Rhodes, Scott D.; Duck, Stacy; Alonzo, Jorge; Daniel-Ulloa, Jason; Aronson, Robert E.

    2013-01-01

    Background HIV disproportionately affects vulnerable populations in the United States (US), including recently arrived immigrant Latinos. However, the current arsenal of effective approaches to increase adherence to risk-reduction strategies and treatment within Latino populations remains insufficient. Methods Our community-based participatory research (CBPR) partnership blends multiple perspectives of community members, organizational representatives, local business leaders, and academic researchers to explore and intervene on HIV risk within Latino populations. We used CBPR to develop, implement, and evaluate two interventions that were found to be efficacious. Results We identified seven assumptions of CBPR as an approach to research, including more authentic study designs, stronger measurement, and improved quality of knowledge gained; increased community capacity to tackle other health disparities; the need to focus on community priorities; increased participation and retention rates; more successful interventions; reduced generalizability; and increased sustainability. Conclusions Despite the advancement of CBPR as an approach to research, key assumptions remain. Further research is needed to compare CBPR to other more traditional approaches to research. Such research would move us from assuming the value of CBPR to identifying its actual value in health disparity reduction. After all, communities carrying disproportionate burden of HIV, including immigrant Latino communities, deserve the best science possible. PMID:23673883

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

    PubMed

    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. Citizen science participation in research in the environmental sciences: key factors related to projects' success and longevity.

    PubMed

    Cunha, Davi G F; Marques, Jonatas F; Resende, Juliana C DE; Falco, Patrícia B DE; Souza, Chrislaine M DE; Loiselle, Steven A

    2017-06-29

    The potential impacts of citizen science initiatives are increasing across the globe, albeit in an imbalanced manner. In general, there is a strong element of trial and error in most projects, and the comparison of best practices and project structure between different initiatives remains difficult. In Brazil, the participation of volunteers in environmental research is limited. Identifying the factors related to citizen science projects' success and longevity within a global perspective can contribute for consolidating such practices in the country. In this study, we explore past and present projects, including a case study in Brazil, to identify the spatial and temporal trends of citizen science programs as well as their best practices and challenges. We performed a bibliographic search using Google Scholar and considered results from 2005-2014. Although these results are subjective due to the Google Scholar's algorithm and ranking criteria, we highlighted factors to compare projects across geographical and disciplinary areas and identified key matches between project proponents and participants, project goals and local priorities, participant profiles and engagement, scientific methods and funding. This approach is a useful starting point for future citizen science projects, allowing for a systematic analysis of potential inconsistencies and shortcomings in this emerging field.

  3. Key health outcomes for children and young people with neurodisability: qualitative research with young people and parents

    PubMed Central

    Allard, Amanda; Fellowes, Andrew; Shilling, Valerie; Janssens, Astrid; Beresford, Bryony; Morris, Christopher

    2014-01-01

    Objectives To identify key health outcomes, beyond morbidity and mortality, regarded as important in children and young people with neurodisability, and their parents. Design Qualitative research incorporating a thematic analysis of the data supported by the Framework Approach; the International Classification of Functioning, Disability and Health (ICF) provided a theoretical foundation. Setting The study was conducted in community settings. Participants Participants were 54 children and young people with neurodisability: 50 participated in focus groups, and 4 in interviews; 53 parents participated: 47 in focus groups and 6 in interviews. Children/young people and parents were recruited through different networks, and were not related. Results Children/young people and parents viewed health outcomes as inter-related. Achievement in some outcomes appeared valued to the extent that it enabled or supported more valued domains of health. Health outcomes prioritised by both young people and parents were: communication, mobility, pain, self-care, temperament, interpersonal relationships and interactions, community and social life, emotional well-being and gaining independence/future aspirations. Parents also highlighted their child's sleep, behaviour and/or safety. Conclusions Those responsible for health services for children/young people with neurodisability should take account of the aspects of health identified by families. The aspects of health identified in this study provide a basis for selecting appropriate health indicators and outcome measures. PMID:24747792

  4. Stem Cells of Dental Origin: Current Research Trends and Key Milestones towards Clinical Application

    PubMed Central

    About, Imad

    2016-01-01

    Dental Mesenchymal Stem Cells (MSCs), including Dental Pulp Stem Cells (DPSCs), Stem Cells from Human Exfoliated Deciduous teeth (SHED), and Stem Cells From Apical Papilla (SCAP), have been extensively studied using highly sophisticated in vitro and in vivo systems, yielding substantially improved understanding of their intriguing biological properties. Their capacity to reconstitute various dental and nondental tissues and the inherent angiogenic, neurogenic, and immunomodulatory properties of their secretome have been a subject of meticulous and costly research by various groups over the past decade. Key milestone achievements have exemplified their clinical utility in Regenerative Dentistry, as surrogate therapeutic modules for conventional biomaterial-based approaches, offering regeneration of damaged oral tissues instead of simply “filling the gaps.” Thus, the essential next step to validate these immense advances is the implementation of well-designed clinical trials paving the way for exploiting these fascinating research achievements for patient well-being: the ultimate aim of this ground breaking technology. This review paper presents a concise overview of the major biological properties of the human dental MSCs, critical for the translational pathway “from bench to clinic.” PMID:27818690

  5. Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling.

    PubMed

    Grad, Yonatan H; Goldstein, Edward; Lipsitch, Marc; White, Peter J

    2016-03-15

    The rise in gonococcal antibiotic resistance and the threat of untreatable infection are focusing attention on strategies to limit the spread of drug-resistant gonorrhea. Mathematical models provide a framework to link the natural history of infection and patient behavior to epidemiological outcomes and can be used to guide research and enhance the public health impact of interventions. While limited knowledge of key disease parameters and networks of spread has impeded development of operational models of gonococcal transmission, new tools in gonococcal surveillance may provide useful data to aid tracking and modeling. Here, we highlight critical questions in the management of gonorrhea that can be addressed by mathematical models and identify key data needs. Our overarching aim is to articulate a shared agenda across gonococcus-related fields from microbiology to epidemiology that will catalyze a comprehensive evidence-based clinical and public health strategy for management of gonococcal infections and antimicrobial resistance. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  6. Florida Keys

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Florida Keys are a chain of islands, islets and reefs extending from Virginia Key to the Dry Tortugas for about 309 kilometers (192 miles). The keys are chiefly limestone and coral formations. The larger islands of the group are Key West (with its airport), Key Largo, Sugarloaf Key, and Boca Chica Key. A causeway extends from the mainland to Key West.

    This image was acquired on October 28, 2001, by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long- term research effort to understand and protect our home planet. Through the study of Earth, NASA will help to provide sound science to policy and economic

  7. Florida Keys

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Florida Keys are a chain of islands, islets and reefs extending from Virginia Key to the Dry Tortugas for about 309 kilometers (192 miles). The keys are chiefly limestone and coral formations. The larger islands of the group are Key West (with its airport), Key Largo, Sugarloaf Key, and Boca Chica Key. A causeway extends from the mainland to Key West.

    This image was acquired on October 28, 2001, by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long- term research effort to understand and protect our home planet. Through the study of Earth, NASA will help to provide sound science to policy and economic

  8. Novel target for high-risk neuroblastoma identified in pre-clinical research | Center for Cancer Research

    Cancer.gov

    Pre-clinical research by investigators at the Center for Cancer Research and their colleagues have identified a number of novel epigenetic targets for high-risk neuroblastoma and validated a promising new targeted inhibitor in pre-clinical models.  Read more...

  9. Enhanced Recovery after Urological Surgery: A Contemporary Systematic Review of Outcomes, Key Elements, and Research Needs

    PubMed Central

    Azhar, Raed A.; Bochner, Bernard; Catto, James; Goh, Alvin C.; Kelly, John; Patel, Hiten D.; Pruthi, Raj S.; Thalmann, George N.; Desai, Mihir

    2017-01-01

    Context Enhanced Recovery after Surgery (ERAS) programs are multimodal care pathways that aim to decrease intra-operative blood loss, decrease postoperative complications, and reduce recovery times. Objective To overview the use and key elements of ERAS pathways, and define needs for future clinical trials. Evidence acquisition A comprehensive systematic MEDLINE search was performed for English language reports published before May 2015 using the terms “postoperative period,” “postoperative care,” “enhanced recovery after surgery,” “enhanced recovery,” “accelerated recovery,” “fast track recovery,” “recovery program,” “recovery pathway”,“ERAS ” , and “urology” or “cystectomy” or “urologic surgery.” Evidence synthesis We identified 18 eligible articles. Patient counseling, physical conditioning, avoiding excessive alcohol and smoking, and good nutrition appeared to protect against postoperative complications. Fasting from solid food for only 6 h and perioperative liquid – carbohydrate loading up to 2 h prior to surgery appeared to be safe and reduced recovery times. Restricted, balanced, and goal-directed fluid replacement is effective when individualized, depending on patient morbidity and surgical procedure. Decreased intraoperative blood loss may be achieved by several measures. Deep vein thrombosis prophylaxis, antibiotic prophylaxis, and thermoregulation were found to help reduce postsurgical complications, as was a multimodal approach to postoperative nausea, vomiting, and analgesia. Chewing gum, prokinetic agents, oral laxatives, and an early resumption to normal diet appear to aid faster return to normal bowel function. Further studies should compare anesthetic protocols, refine analgesia, and evaluate the importance of robot-assisted surgery and the need/timing for drains and catheters. Conclusions ERAS regimens are multidisciplinary, multimodal pathways that optimize postoperative recovery. Patient summary

  10. Identifying emerging issues in forestry as a tool for research planning.

    Treesearch

    Hans M. Gregersen; Allen L. Lundgren; Pamela J. Jakes; David N. Bengston

    1989-01-01

    A Delphi exercise is used to identify emerging issues in National Forest management and use, the relative importance of the issues, and barriers to resolving issues. USDA Forest Service managers agree on the importance of the 11 issues identified; however, researchers and National Forest managers do not always agree on the importance of issues or barriers.

  11. Low risk research using routinely collected identifiable health information without informed consent: encounters with the Patient Information Advisory Group.

    PubMed

    Metcalfe, C; Martin, R M; Noble, S; Lane, J A; Hamdy, F C; Neal, D E; Donovan, J L

    2008-01-01

    Current UK legislation is impacting upon the feasibility and cost-effectiveness of medical record-based research aimed at benefiting the NHS and the public heath. Whereas previous commentators have focused on the Data Protection Act 1998, the Health and Social Care Act 2001 is the key legislation for public health researchers wishing to access medical records without written consent. The Act requires researchers to apply to the Patient Information Advisory Group (PIAG) for permission to access medical records without written permission. We present a case study of the work required to obtain the necessary permissions from PIAG in order to conduct a large scale public health research project. In our experience it took eight months to receive permission to access basic identifying information on individuals registered at general practices, and a decision on whether we could access clinical information in medical records without consent took 18 months. Such delays pose near insurmountable difficulties to grant funded research, and in our case 560,000pound of public and charitable money was spent on research staff while a large part of their work was prohibited until the third year of a three year grant. We conclude by arguing that many of the current problems could be avoided by returning PIAG's responsibilities to research ethics committees, and by allowing "opt-out" consent for many public health research projects.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  14. Identifying Research Priorities: Themes and Directions for the TESOL International Research Foundation.

    ERIC Educational Resources Information Center

    Tucker, G. Richard; Lightbown, Patsy M.; Snow, Catherine; Christian, Donna; de Bot, Kees; Lynch, Brian K.; Nunan, David; Duff, Patricia A.; Freeman, Donald; Bailey, Kathleen M.

    2001-01-01

    Highlights research priorities for the Teaching English to Speakers of Other Languages (TESOL) field, including the following: age of beginning instruction, learning to read in a second language, dual-language education for English language learners, language assessment and program evaluation, English as a global language, learning English for…

  15. Person/Situation Selection Research: The Problem of Identifying Salient Situational Dimensions. Research Report No. 13.

    ERIC Educational Resources Information Center

    Schneider, Benjamin

    The study was concerned with the persistent problem in conducting person/situation research--the identification of relevant dimensions or features of the situation. Since the usual strategy for discovering relevant perceptual dimension of organizational life is to ask organizational employees to respond to a set of predetermined questions, this…

  16. Identifying national health research priorities in Timor-Leste through a scoping review of existing health data

    PubMed Central

    2013-01-01

    Health research is crucial to understand a country’s needs and to improve health outcomes. We conducted a scoping review and analysis of existing health data in Timor-Leste to identify the health research priorities of the country. Published and unpublished health research in Timor-Leste from 2001 to 2011 that reported objectives, methods and results were identified. Key findings were triangulated with data from national surveys and the Health Management Information System; 114 eligible articles were included in the analysis, the leading topics of which were communicable (malaria, tuberculosis, HIV and sexually transmitted diseases and dengue) and non-communicable (eye and mental health) diseases. There were 28 papers (25%) on safe motherhood, child health and nutrition, of which 20 (71%) were unpublished. The review of national indicators showed high infant, under-five and maternal mortality rates. Burden of disease is greatest in young children, with respiratory infections, febrile illnesses and diarrheal disease predominating. There is poor access to and utilization of health care. Childhood malnutrition is an important unresolved national health issue. There are several obstacles leading to under-utilization of health services. The following topics for future health research are suggested from the review: nutrition, safe motherhood, childhood illness (in particular identifying the causes and cause-specific burden of severe respiratory, febrile and diarrheal diseases) and access to and use of health services. PMID:23452321

  17. Systematically Identifying Relevant Research: Case Study on Child Protection Social Workers' Resilience

    ERIC Educational Resources Information Center

    McFadden, Paula; Taylor, Brian J.; Campbell, Anne; McQuilkin, Janice

    2012-01-01

    Context: The development of a consolidated knowledge base for social work requires rigorous approaches to identifying relevant research. Method: The quality of 10 databases and a web search engine were appraised by systematically searching for research articles on resilience and burnout in child protection social workers. Results: Applied Social…

  18. Removing the College Involvement "Research Asterisk": Identifying and Rethinking Predictors of American Indian College Student Involvement

    ERIC Educational Resources Information Center

    Garland, John L.

    2010-01-01

    The purpose of this study was to identify campus environmental predictors of American Indian college student involvement. The American Indian research asterisk, or not including American Indian data, has prevailed over student development research for decades. As a result, student affairs professionals have been limited in their ability to develop…

  19. Removing the College Involvement "Research Asterisk": Identifying and Rethinking Predictors of American Indian College Student Involvement

    ERIC Educational Resources Information Center

    Garland, John L.

    2010-01-01

    The purpose of this study was to identify campus environmental predictors of American Indian college student involvement. The American Indian research asterisk, or not including American Indian data, has prevailed over student development research for decades. As a result, student affairs professionals have been limited in their ability to develop…

  20. Systematically Identifying Relevant Research: Case Study on Child Protection Social Workers' Resilience

    ERIC Educational Resources Information Center

    McFadden, Paula; Taylor, Brian J.; Campbell, Anne; McQuilkin, Janice

    2012-01-01

    Context: The development of a consolidated knowledge base for social work requires rigorous approaches to identifying relevant research. Method: The quality of 10 databases and a web search engine were appraised by systematically searching for research articles on resilience and burnout in child protection social workers. Results: Applied Social…

  1. Researchers Use a Kinome Screen to Identify New Therapeutic Targets | Office of Cancer Genomics

    Cancer.gov

    The tumor suppressor p53 is mutated in over 50% of head and neck squamous cell carcinomas (HNSCC), yet there are currently no available therapies to target it. CTD2 researchers at the Fred Hutchison Cancer Research Center hypothesized that HNSCC cancer cells with p53 mutations are dependent on particular kinases for survival. In a study published in Clinical Cancer Research, they sought to identify these kinases using RNAi against known kinase genes in mouse and human cell lines.

  2. A modified Delphi consensus study to identify UK osteopathic profession research priorities.

    PubMed

    Rushton, A B; Fawkes, C A; Carnes, D; Moore, A P

    2014-10-01

    There is an increasing emphasis to take an evidence-based approach to healthcare. To obtain evidence relevant to the osteopathic profession a clear research direction is required based on the views of stakeholders in the osteopathic profession. A modified Delphi consensus approach was conducted to explore the views of osteopaths and patients regarding research priorities for osteopathy. Osteopaths and patients were invited to complete an online questionnaire survey (n = 145). Round 1 requested up to 10 research priority areas and the rationale for their selection. All of the themes from Round 1 were fed back verbatim, and in Round 2 participants were asked to rank the importance of the research priorities on a 5-point Likert scale. Finally, in Round 3 participants were asked to rank the importance of a refined list of research topics which had reached consensus. Descriptive analysis and use of Kendall's coefficient of concordance enabled interpretation of consensus. The response rate for Round 1 was 87.9% and identified 610 research priority areas. Round 2 identified 69 research themes as important, and Round 3 identified 20 research priority topic areas covering four themes: effectiveness of osteopathic treatment (7 areas prioritised), role of osteopathy: the management of four conditions were prioritised, risks with osteopathic treatment (two areas prioritised) and outcomes of osteopathic treatment (two areas prioritised). The findings will be taken forward to develop the research strategy for osteopathy.

  3. Using Liberating Structures to Increase Engagement in Identifying Priorities for the APNA Research Council.

    PubMed

    Mahoney, Jane S; Lewin, Linda; Beeber, Linda; Willis, Danny G

    2016-11-01

    In 2015, the Co-Chairs and Steering Committee of the Research Council members recognized the need to reevaluate the council's priorities. To determine the top priorities for the Research Council. Use of liberating structures: Impromptu Speed Networking, 1-2-4-all, and Crowd Sourcing. Identified Research Council priorities included the following: efforts to increase psychiatric mental health (PMH) research funding; serve as a connector to bring researchers together; foster research through state chapters; increase collaboration between PhDs and DNPs; and develop models for organizational support for PMH staff nurse involvement in research. The liberating structures used are valuable strategies for engaging groups of people to identify what matters most to the group. Through the use of these novel techniques, the American Psychiatric Nurses Association Research Council has identified priorities for the work of the council. This has led to actions planned for the coming future with the intent to move PMH nursing research forward. © The Author(s) 2016.

  4. DIII-D research towards resolving key issues for ITER and steady-state tokamaks

    NASA Astrophysics Data System (ADS)

    Hill, D. N.; the DIII-D Team

    2013-10-01

    The DIII-D research program is addressing key ITER research needs and developing the physics basis for future steady-state tokamaks. Pellet pacing edge-localized mode (ELM) control in the ITER configuration reduces ELM energy loss in proportion to 1/fpellet by inducing ELMs at up to 12× the natural ELM rate. Complete suppression of ELMs with resonant magnetic perturbations has been extended to the q95 expected for ITER baseline scenario discharges, and long-duration ELM-free QH-mode discharges have been produced with ITER-relevant co-current neutral-beam injection (NBI) using external n = 3 coils to generate sufficient counter-Ip torque. ITER baseline discharges at βN ˜ 2 and scaled NBI torque have been maintained in stationary conditions for more than four resistive times using electron cyclotron current drive (ECCD) for tearing mode suppression and disruption avoidance; active tracking with steerable launchers and feedback control catch these modes at small amplitude, reducing the ECCD power required to suppress them. Massive high-Z gas injection into disruption-induced 300-600 kA 20 MeV runaway electron (RE) beams yield dissipation rates ˜10× faster than expected from e-e collisions and demonstrate the possibility of benign dissipation of such REs should they occur in ITER. Other ITER-related experiments show measured intrinsic plasma torque in good agreement with a physics-based model over a wide range of conditions, while first-time main-ion rotation measurements show it to be lower than expected from neoclassical theory. Core turbulence measurements show increased temperature fluctuations correlated with sharply enhanced electron transport when \

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

    PubMed Central

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

    2016-01-01

    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. PMID:27222291

  6. Research on measurement-device-independent quantum key distribution based on an air-water channel

    NASA Astrophysics Data System (ADS)

    Zhou, Yuan-yuan; Zhou, Xue-jun; Xu, Hua-bin; Cheng, Kang

    2016-11-01

    A measurement-device-independent quantum key distribution (MDI-QKD) method with an air-water channel is researched. In this method, the underwater vehicle and satellite are the legitimate parties, and the third party is at the airwater interface in order to simplify the unilateral quantum channel to water or air. Considering the condition that both unilateral transmission distance and transmission loss coefficient are unequal, a perfect model of the asymmetric channel is built. The influence of asymmetric channel on system loss tolerance and secure transmission distance is analyzed. The simulation results show that with the increase of the channel's asymmetric degree, the system loss tolerance will descend, one transmission distance will be reduced while the other will be increased. When the asymmetric coefficient of channel is between 0.068 and 0.171, MDI-QKD can satisfy the demand of QKD with an air-water channel, namely the underwater transmission distance and atmospheric transmission distance are not less than 60 m and 12 km, respectively.

  7. Research progress in the key device and technology for fiber optic sensor network

    NASA Astrophysics Data System (ADS)

    Liu, Deming; Sun, Qizhen; Lu, Ping; Xia, Li; Sima, Chaotan

    2016-03-01

    The recent research progress in the key device and technology of the fiber optic sensor network (FOSN) is introduced in this paper. An architecture of the sensor optical passive network (SPON), by employing hybrid wavelength division multiplexing/time division multiplexing (WDM/TDM) techniques similar to the fiber communication passive optical network (PON), is proposed. The network topology scheme of a hybrid TDM/WDM/FDM (frequency division multiplexing) three-dimension fiber optic sensing system for achieving ultra-large capacity, long distance, and high resolution sensing performance is performed and analyzed. As the most important device of the FOSN, several kinds of light source are developed, including the wideband multi-wavelength fiber laser operating at C band, switchable and tunable 2 μm multi-wavelength fiber lasers, ultra-fast mode-locked fiber laser, as well as the optical wideband chaos source, which have very good application prospects in the FOSN. Meanwhile, intelligent management techniques for the FOSN including wideband spectrum demodulation of the sensing signals and real-time fault monitoring of fiber links are presented. Moreover, several typical applications of the FOSN are also discussed, such as the fiber optic gas sensing network, fiber optic acoustic sensing network, and strain/dynamic strain sensing network.

  8. Key Topics for High-Lift Research: A Joint Wind Tunnel/Flight Test Approach

    NASA Technical Reports Server (NTRS)

    Fisher, David; Thomas, Flint O.; Nelson, Robert C.

    1996-01-01

    Future high-lift systems must achieve improved aerodynamic performance with simpler designs that involve fewer elements and reduced maintenance costs. To expeditiously achieve this, reliable CFD design tools are required. The development of useful CFD-based design tools for high lift systems requires increased attention to unresolved flow physics issues. The complex flow field over any multi-element airfoil may be broken down into certain generic component flows which are termed high-lift building block flows. In this report a broad spectrum of key flow field physics issues relevant to the design of improved high lift systems are considered. It is demonstrated that in-flight experiments utilizing the NASA Dryden Flight Test Fixture (which is essentially an instrumented ventral fin) carried on an F-15B support aircraft can provide a novel and cost effective method by which both Reynolds and Mach number effects associated with specific high lift building block flows can be investigated. These in-flight high lift building block flow experiments are most effective when performed in conjunction with coordinated ground based wind tunnel experiments in low speed facilities. For illustrative purposes three specific examples of in-flight high lift building block flow experiments capable of yielding a high payoff are described. The report concludes with a description of a joint wind tunnel/flight test approach to high lift aerodynamics research.

  9. Description of male, pupa and larva of Simulium (Asiosimulium) wanchaii (Diptera: Simuliidae) from Thailand, with keys to identify four species of the subgenus Asiosimulium.

    PubMed

    Srisuka, W; Takaoka, H; Saeung, A

    2015-09-01

    The male, pupa and mature larva of Simulium (Asiosimulium) wanchaii Takaoka & Choochote, one of the four species of the small Oriental black fly subgenus Asiosimulium, are described for the first time based on samples collected from Thailand. The male S. (A.) wanchaii is characterized based on the enlarged hind basitarsus and the ventral plate which is much wider than long. The pupa and larva are characterized by the gill with 19 filaments and the deep postgenal cleft, respectively. Keys are provided to identify all the four species of the subgenus Asiosimulium for females, males, pupae and mature larvae.

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

    SciTech Connect

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

    2007-07-01

    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)

  11. Research review: the shared environment as a key source of variability in child and adolescent psychopathology.

    PubMed

    Burt, S Alexandra

    2014-04-01

    Behavioral genetic research has historically concluded that the more important environmental influences were nonshared or result in differences between siblings, whereas environmental influences that create similarities between siblings (referred to as shared environmental influences) were indistinguishable from zero. Recent theoretical and meta-analytic work {Burt. Psychological Bulletin [135 (2009) 608]} has challenged this conclusion as it relates to child and adolescent psychopathology, however, arguing that the shared environment is a moderate, persistent, and identifiable source of individual differences in such outcomes prior to adulthood. The current review seeks to bolster research on the shared environment by highlighting both the logistic advantages inherent in studies of the shared environment, as well as the use of nontraditional but still genetically informed research designs to study shared environmental influences. Although often moderate in magnitude prior to adulthood and free of unsystematic measurement error, shared environmental influences are nevertheless likely to have been underestimated in prior research. Moreover, the shared environment is likely to include proximal effects of the family, as well as the effects of more distal environmental contexts such as neighborhood and school. These risk and protective factors could influence the child either as main effects or as moderators of genetic influence (i.e. gene-environment interactions). Finally, because the absence of genetic relatedness in an otherwise nonindependent dataset also qualifies as 'genetically informed', studies of the shared environment are amenable to the use of novel and non-traditional designs (with appropriate controls for selection). The shared environment makes important contributions to most forms of child and adolescent psychopathology. Empirical examinations of the shared environment would thus be of real and critical value for understanding the development and

  12. Assessing the Key Processes of Youth-Led Participatory Research: Psychometric Analysis and Application of an Observational Rating Scale

    ERIC Educational Resources Information Center

    Ozer, Emily J.; Douglas, Laura

    2015-01-01

    Youth-led Participatory Action Research (YPAR)--in which young people conduct research aimed at improving problems in their schools and communities--is increasing in public health, youth development, and education. We report on the development and psychometric testing of the YPAR Process Template (YPT)--to assess the quality of key YPAR processes…

  13. EPRRI's Research Activities into the Impact of Key NCLBA Requirements. EPRRI Policy Updates. Issue Three, Fall 2004.

    ERIC Educational Resources Information Center

    Educational Policy Reform Research Institute, 2004

    2004-01-01

    The Educational Policy Reform Research Institute (EPRRI), with funding from the U.S. Department of Education's Office of Special Education Programs, investigates the impact of educational accountability reforms on students with disabilities and on special education. EPRRI addresses the research needs of policymakers and other key stakeholders by…

  14. Twenty-six key research questions in urban stream ecology: an assessment of the state of the science

    EPA Science Inventory

    Although urban streams have been the focus of much research activity in recent years, there remain many unanswered questions about the mechanisms driving the “urban stream syndrome.” Identification of these key research questions is an important step toward effective, efficient ...

  15. Research and Teaching: An Investigation of the Evolution of High School and Undergraduate Student Researchers' Understanding of Key Science Ethics Concepts

    ERIC Educational Resources Information Center

    Mabrouk, Patricia Ann

    2013-01-01

    High school and undergraduate research students were surveyed over the 10-week period of their summer research programs to investigate their understanding of key concepts in science ethics and whether their understanding changed over the course of their summer research experiences. Most of the students appeared to understand the issues relevant to…

  16. Research and Teaching: An Investigation of the Evolution of High School and Undergraduate Student Researchers' Understanding of Key Science Ethics Concepts

    ERIC Educational Resources Information Center

    Mabrouk, Patricia Ann

    2013-01-01

    High school and undergraduate research students were surveyed over the 10-week period of their summer research programs to investigate their understanding of key concepts in science ethics and whether their understanding changed over the course of their summer research experiences. Most of the students appeared to understand the issues relevant to…

  17. Molecular locks and keys: the role of small molecules in phytohormone research.

    PubMed

    Fonseca, Sandra; Rosado, Abel; Vaughan-Hirsch, John; Bishopp, Anthony; Chini, Andrea

    2014-01-01

    Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds.

  18. The building blocks of a 'Liveable Neighbourhood': Identifying the key performance indicators for walking of an operational planning policy in Perth, Western Australia.

    PubMed

    Hooper, Paula; Knuiman, Matthew; Foster, Sarah; Giles-Corti, Billie

    2015-11-01

    Planning policy makers are requesting clearer guidance on the key design features required to build neighbourhoods that promote active living. Using a backwards stepwise elimination procedure (logistic regression with generalised estimating equations adjusting for demographic characteristics, self-selection factors, stage of construction and scale of development) this study identified specific design features (n=16) from an operational planning policy ("Liveable Neighbourhoods") that showed the strongest associations with walking behaviours (measured using the Neighbourhood Physical Activity Questionnaire). The interacting effects of design features on walking behaviours were also investigated. The urban design features identified were grouped into the "building blocks of a Liveable Neighbourhood", reflecting the scale, importance and sequencing of the design and implementation phases required to create walkable, pedestrian friendly developments. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Felker's Five Keys to Self-Concept Enhancement: Secondary Classroom Research.

    ERIC Educational Resources Information Center

    Bernhoft, Franklin O.

    A study incorporated Donald Felker's 5 Keys to Self-Concept Enhancement in 20 minutes of timed writing weekly or bi-weekly for three months using the Coopersmith Adult Form as pre-post measure. Felker's 5 Keys are: (1) adults, praise yourselves; (2) help children evaluate realistically; (3) teach children to set realistic goals; (4) teach children…

  20. Lessons Learned from Research about Informal Reading Inventories: Keys to Data-Driven Instructional Recommendations

    ERIC Educational Resources Information Center

    L'Allier, Susan K.

    2013-01-01

    This study examined how effectively candidates in an MSEd in literacy education with a focus on reading program used the results from the Basic Reading Inventory to develop key instructional recommendations. The results indicated that, overall, candidates made about two thirds of the key recommendations suggested by an expert in the area of…

  1. Mont Terri Underground Rock Laboratory, Switzerland-Research Program And Key Results

    NASA Astrophysics Data System (ADS)

    Nussbaum, C. O.; Bossart, P. J.

    2012-12-01

    Argillaceous formations generally act as aquitards because of their low hydraulic conductivities. This property, together with the large retention capacity of clays for cationic contaminants and the potential for self-sealing, has brought clay formations into focus as potential host rocks for the geological disposal of radioactive waste. Excavated in the Opalinus Clay formation, the Mont Terri underground rock laboratory in the Jura Mountains of NW Switzerland is an important international test site for researching clay formations. Research is carried out in the underground facility, which is located adjacent to the security gallery of the Mont Terri motorway tunnel. Fifteen partners from European countries, USA, Canada and Japan participate in the project. The objectives of the research program are to analyze the hydrogeological, geochemical and rock mechanical properties of the Opalinus Clay, to determine the changes induced by the excavation of galleries and by heating of the rock formation, to test sealing and container emplacement techniques and to evaluate and improve suitable investigation techniques. For the safety of deep geological disposal, it is of key importance to understand the processes occurring in the undisturbed argillaceous environment, as well as the processes in a disturbed system, during the operation of the repository. The objectives are related to: 1. Understanding processes and mechanisms in undisturbed clays and 2. Experiments related to repository-induced perturbations. Experiments of the first group are dedicated to: i) Improvement of drilling and excavation technologies and sampling methods; ii) Estimation of hydrogeological, rock mechanical and geochemical parameters of the undisturbed Opalinus Clay. Upscaling of parameters from laboratory to in situ scale; iii) Geochemistry of porewater and natural gases; evolution of porewater over time scales; iv) Assessment of long-term hydraulic transients associated with erosion and thermal

  2. Community Participatory Research With Deaf Sign Language Users to Identify Health Inequities

    PubMed Central

    Barnett, Steven; Klein, Jonathan D.; Pollard, Robert Q.; Samar, Vincent; Schlehofer, Deirdre; Starr, Matthew; Sutter, Erika; Yang, Hongmei

    2011-01-01

    Deaf people who use American Sign Language (ASL) are medically underserved and often excluded from health research and surveillance. We used a community participatory approach to develop and administer an ASL-accessible health survey. We identified deaf community strengths (e.g., a low prevalence of current smokers) and 3 glaring health inequities: obesity, partner violence, and suicide. This collaborative work represents the first time a deaf community has used its own data to identify health priorities. PMID:22021296

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

    PubMed

    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

    2013-07-30

    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.

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26652084

  8. Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells

    PubMed Central

    Kulbe, Hagen; Iorio, Francesco; Chakravarty, Probir; Milagre, Carla S.; Moore, Robert; Thompson, Richard G.; Everitt, Gemma; Canosa, Monica; Montoya, Alexander; Drygin, Denis; Braicu, Ioana; Sehouli, Jalid; Saez-Rodriguez, Julio; Cutillas, Pedro R.; Balkwill, Frances R.

    2016-01-01

    We previously showed how key pathways in cancer-related inflammation and Notch signaling are part of an autocrine malignant cell network in ovarian cancer. This network, which we named the “TNF network”, has paracrine actions within the tumor microenvironment, influencing angiogenesis and the immune cell infiltrate. The aim of this study was to identify critical regulators in the signaling pathways of the TNF network in ovarian cancer cells that might be therapeutic targets. To achieve our aim, we used a systems biology approach, combining data from phospho-proteomic mass spectrometry and gene expression array analysis. Among the potential therapeutic kinase targets identified was the protein kinase Casein kinase II (CK2). Knockdown of CK2 expression in malignant cells by siRNA or treatment with the specific CK2 inhibitor CX-4945 significantly decreased Notch signaling and reduced constitutive cytokine release in ovarian cancer cell lines that expressed the TNF network as well as malignant cells isolated from high grade serous ovarian cancer ascites. The expression of the same cytokines was also inhibited after treatment with CX-4945 in a 3D organotypic model. CK2 inhibition was associated with concomitant inhibition of proliferative activity, reduced angiogenesis and experimental peritoneal ovarian tumor growth. In conclusion, we have identified kinases, particularly CK2, associated with the TNF network that may play a central role in sustaining the cytokine network and/or mediating its effects in ovarian cancer. PMID:26871292

  9. A critical assessment of research needs identified by the dietary guidelines committees from 1980 to 2010.

    PubMed

    Myers, Esther F; Khoo, Chor-San; Murphy, William; Steiber, Alison; Agarwal, Sanjiv

    2013-07-01

    The Dietary Goals for the United States were introduced in 1977 and have been followed by the Dietary Guidelines for Americans (DGA) every 5 years from 1980 to 2010. The DGA provide science-based advice to promote health and reduce risk for major chronic diseases through diet and physical activity. The Dietary Guidelines Advisory Committees are charged to provide updates of the DGA topics using the best available science. The Dietary Guidelines Advisory Committees' reports also identified 169 research gaps. To date, these gaps have not been compiled and assessed. We evaluated trends in number, topics, and specificity of research gaps by year by placing them in the following topic categories: general, chronic diseases/conditions, diet/diet pattern, food/ingredient, and nutrient-specific research gaps. Some research topics (eg, sodium and hypertension and appropriate uses of DGA) have been identified consistently across the years, some emerged in later years (eg, increasingly specific research gaps between dietary fatty acids and cardiovascular disease), and others appeared intermittently (eg, relationships between dietary components and cancer). These results are a call to action for all DGA stakeholders to have an immediate dialogue about how the research enterprise can best address critical research needs in a timely way to support public policy. Copyright © 2013 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

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

    Treesearch

    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...

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  14. Philosophy of science: how to identify the potential research for the day after tomorrow?

    PubMed

    Ventegodt, Søren; Merrick, Joav

    2004-06-25

    We were asked to participate in a workshop to assist the European Commission on how to choose financial support for high-potential, basic research projects that can give new scientific breakthroughs and thus contribute significantly to the positive development of society, industry, and economy for the day after tomorrow. At this workshop, we analyzed the problem in some detail using experience from our own research on the global quality of life. We would suggest that the most promising projects have the following characteristics: (1) they are led by a brilliant researcher who considers his/her research to be "sweet science", who wants to explain the anomalies of his/her field of science, and who lives in a nonmainstream scientific paradigm; (2) they are deeply engaged in the philosophical problems of their research field, they are searching eagerly for a new understanding and a new theory, giving new tools for measurement and creating change, and results are taken as feedback on all levels from tool to theory and philosophy; (3) they are focused on the key point(s), which is an essential feature of the universe that creates global change if intervened upon. At the NEST Pathfinder 2005 Topic Identification Workshop, Brussels 28 May 2004 entitled "Measuring the Impossible", we advised the European Commission Research Directorate to allocate funds for projects focusing on the state of consciousness--how to understand it, how to map it, and how to develop it.

  15. A Workplace Incivility Roadmap: Identifying Theoretical Speedbumps and Alternative Routes for Future Research.

    PubMed

    Miner, Kathi N; Diaz, Ismael; Wooderson, R Linden; McDonald, Jennifer N; Smittick, Amber L; Lomeli, Laura C

    2017-07-27

    Andersson and Pearson's (1999) seminal article on workplace incivility has paved the way for nearly two decades of research focusing on rude and discourteous behavior at work. We now have a better understanding of the dynamics associated with uncivil workplace interactions including the characteristics of those who instigate and are targeted with workplace incivility, the negative consequences of incivility, the mechanisms that link incivility and negative outcomes, and the boundary conditions that affect these relationships. The present article provides a "roadmap" for workplace incivility researchers by identifying five assumptions that we propose are acting as "speedbumps" in current workplace incivility research by limiting advancements about what workplace incivility is and how it functions. We then introduce five "alternative routes" for future workplace incivility research based on these identifications. Our goal is to guide and accelerate research toward a more nuanced understanding of workplace incivility as behavior that occurs within an organizational system. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  16. Stathmin, a new target of PRL-3 identified by proteomic methods, plays a key role in progression and metastasis of colorectal cancer.

    PubMed

    Zheng, Ping; Liu, Yong-Xia; Chen, Lin; Liu, Xun-Hua; Xiao, Zheng-Quan; Zhao, Liang; Li, Guang-Qiu; Zhou, Jun; Ding, Yan-Qing; Li, Jian-Ming

    2010-10-01

    To better understand the role of PRL-3 in progression and metastasis of colorectal cancer (CRC), we searched for PRL-3 associated proteins using proteomic methods. We identified 39 PRL-3 associated proteins based on proteomic strategy. Stathmin, a key oncoprotein, was proved to be a new PRL-3 associated protein. Notably, co-immunoprecipitation assays in both endogenous CRC cell lines and CRC tissues indicated that PRL-3 could interact with stathmin. And, both stathmin and PRL-3 contributed to microtubule (MT) destabilization of CRC cells. Moreover, gain-of-function and loss-of-function analyses revealed that stathmin promoted proliferation, cell adhesion, and migration of human CRC cells. Immunohistochemical analysis of 149 colorectal tumor samples showed that overexpression of stathmin was strongly correlated with tumor differentiation (P = 0.035), tumor invasion (P = 0.024), lymph node status (P < 0.001), Dukes classification (P < 0.001), and TNM staging (P < 0.001) of CRC patients. Univariate and multivariate survival analyses further supported that overexpression of stathmin protein was a potential independent poor prognostic factor for CRC. Our results reveal many PRL-3 associated proteins for the first time. The oncoprotein stathmin plays a key role in CRC as a new target of PRL-3. Interaction between PRL-3 and stathmin leads to MT destabilization of CRC cells, which contributes to progression and metastasis of CRC.

  17. The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize.

    PubMed

    Amiour, Nardjis; Imbaud, Sandrine; Clément, Gilles; Agier, Nicolas; Zivy, Michel; Valot, Benoît; Balliau, Thierry; Armengaud, Patrick; Quilleré, Isabelle; Cañas, Rafael; Tercet-Laforgue, Thérèse; Hirel, Bertrand

    2012-09-01

    Linking plant phenotype to gene and protein expression and also to metabolite synthesis and accumulation is one of the main challenges for improving agricultural production worldwide. Such a challenge is particularly relevant to crop nitrogen use efficiency (NUE). Here, the differences in leaf gene transcript, protein, and metabolite accumulation in maize subjected to long-term nitrogen (N)-deficient growth conditions at two important stages of plant development have been studied. The impact of N deficiency was examined at the transcriptomic, proteomic, and metabolomic levels. It was found that a number of key plant biological functions were either up- or down-regulated when N was limiting, including major alterations to photosynthesis, carbon (C) metabolism, and, to a lesser extent, downstream metabolic pathways. It was also found that the impact of the N deficiency stress resembled the response of plants to a number of other biotic and abiotic stresses, in terms of transcript, protein, and metabolite accumulation. The genetic and metabolic alterations were different during the N assimilation and the grain-filling period, indicating that plant development is an important component for identifying the key elements involved in the control of plant NUE. It was also found that integration of the three 'omics' studies is not straightforward, since different levels of regulation seem to occur in a stepwise manner from gene expression to metabolite accumulation. The potential use of these 'omics' studies is discussed with a view to improve our understanding of whole plant nitrogen economics, which should have applications in breeding and agronomy.

  18. Using the Theory of Planned Behavior to identify key beliefs underlying chlamydia testing intentions in a sample of young people living in deprived areas.

    PubMed

    Booth, Amy R; Norman, Paul; Harris, Peter R; Goyder, Elizabeth

    2015-09-01

    The Theory of Planned Behavior was used to identify the key behavioural, normative and control beliefs underlying intentions to test regularly for chlamydia among young people living in socially and economically deprived areas - a high-risk group for infection. Participants (N = 278, 53% male; mean age 17 years) were recruited from a vocational college situated in an area in the most deprived national quintile (England). Participants completed measures of behavioural, normative and control beliefs, plus intention to test regularly for chlamydia. The behavioural, normative and control beliefs most strongly correlated with intentions to test regularly for chlamydia were beliefs about stopping the spread of infection, partners' behaviour and the availability of testing. These beliefs represent potential targets for interventions to increase chlamydia testing among young people living in deprived areas.

  19. Key Challenges for Tertiary Education Policy and Research--An Australian Perspective

    ERIC Educational Resources Information Center

    Goedegebuure, Leo; Schoen, Marian

    2014-01-01

    Australia has had a mixed history in the way in which policy research has related to higher education policy. Recognising a history of policy-related research and to some extent research-informed policy-making, Australia has followed the trend of other New Public Management-driven systems of de-emphasising policy-oriented independent research. In…

  20. Key Challenges for Tertiary Education Policy and Research--An Australian Perspective

    ERIC Educational Resources Information Center

    Goedegebuure, Leo; Schoen, Marian

    2014-01-01

    Australia has had a mixed history in the way in which policy research has related to higher education policy. Recognising a history of policy-related research and to some extent research-informed policy-making, Australia has followed the trend of other New Public Management-driven systems of de-emphasising policy-oriented independent research. In…

  1. Comparison of Analytical Mathematical Approaches for Identifying Key Nuclear Magnetic Resonance Spectroscopy Biomarkers in the Diagnosis and Assessment of Clinical Change of Diseases

    PubMed Central

    Nikas, Jason B.; Keene, C. Dirk; Low, Walter C.

    2010-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a rapidly emerging technology that can be used to assess tissue metabolic profile in the living animal. At the present time, no approach has been developed 1) to systematically identify profiles of key chemical alterations that can be used as biomarkers to diagnose diseases and to monitor disease progression; and 2) to assess mathematically the diagnostic power of potential biomarkers. To address this issue, we have evaluated mathematical approaches that employ receiver operating characteristic (ROC) curve analysis, linear discriminant analysis, and logistic regression analysis to systematically identify key biomarkers from NMR spectra that have excellent diagnostic power and can be used accurately for disease diagnosis and monitoring. To validate our mathematical approaches, we studied the striatal concentrations of 17 metabolites of 13 R6/ 2 transgenic mice with Huntington's disease, as well as those of 17 wild-type (WT) mice, which were obtained via in vivo proton NMR spectroscopy (9.4 Tesla). We developed diagnostic biomarker models and clinical change assessment models based on our three aforementioned mathematical approaches, and we tested all of them, first, with the 30 original mice and, then, with 31 unknown mice. Their prediction results were compared with genotyping—the gold standard. All models correctly diagnosed all of the 30 original mice (17 WT and 13 R6/2) and all of the 31 unknown mice (20 WT and 11 R6/2), with a positive likelihood ratio approximating infinity [1/0 (→ ∞)], and with a negative likelihood ratio equal to zero [0/1 = 0]. PMID:20878778

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

    PubMed

    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.

  3. A feasibility study of returning clinically actionable somatic genomic alterations identified in a research laboratory.

    PubMed

    Arango, Natalia Paez; Brusco, Lauren; Mills Shaw, Kenna R; Chen, Ken; Eterovic, Agda Karina; Holla, Vijaykumar; Johnson, Amber; Litzenburger, Beate; Khotskaya, Yekaterina B; Sanchez, Nora; Bailey, Ann; Zheng, Xiaofeng; Horombe, Chacha; Kopetz, Scott; Farhangfar, Carol J; Routbort, Mark; Broaddus, Russell; Bernstam, Elmer V; Mendelsohn, John; Mills, Gordon B; Meric-Bernstam, Funda

    2017-06-27

    Molecular profiling performed in the research setting usually does not benefit the patients that donate their tissues. Through a prospective protocol, we sought to determine the feasibility and utility of performing broad genomic testing in the research laboratory for discovery, and the utility of giving treating physicians access to research data, with the option of validating actionable alterations in the CLIA environment. 1200 patients with advanced cancer underwent characterization of their tumors with high depth hybrid capture sequencing of 201 genes in the research setting. Tumors were also tested in the CLIA laboratory, with a standardized hotspot mutation analysis on an 11, 46 or 50 gene platform. 527 patients (44%) had at least one likely somatic mutation detected in an actionable gene using hotspot testing. With the 201 gene panel, 945 patients (79%) had at least one alteration in a potentially actionable gene that was undetected with the more limited CLIA panel testing. Sixty-four genomic alterations identified on the research panel were subsequently tested using an orthogonal CLIA assay. Of 16 mutations tested in the CLIA environment, 12 (75%) were confirmed. Twenty-five (52%) of 48 copy number alterations were confirmed. Nine (26.5%) of 34 patients with confirmed results received genotype-matched therapy. Seven of these patients were enrolled onto genotype-matched targeted therapy trials. Expanded cancer gene sequencing identifies more actionable genomic alterations. The option of CLIA validating research results can provide alternative targets for personalized cancer therapy.

  4. Identifying research priorities for the health care of children and adolescents.

    PubMed

    Gillies, Donna

    2005-01-01

    In an effort to identify priority statements for research into the healthcare of children and adolescents a search of multiple research databases and the Internet was undertaken. There is a considerable body of literature outlining research priorities that are built around specific disorders or specialist services, which are not readily applicable to the general healthcare of children and adolescents. A few general statements of research priorities were identified, but these were mainly developed to inform research programs in the US. In addition there was little evidence that these agendas had incorporated the needs of the consumers of this healthcare namely, children and adolescents, and their families. Therefore, there is a need to address the needs of a broader community in regards to the research agenda for the healthcare of children and adolescents. The advantage of an agenda developed by multiple stakeholder groups is that it will have broader meaning to a wider community. However at this stage, there is no such statement that can readily inform a general program of reserch into the healthcare of children and adolescents.

  5. Towards cash transfer interventions for tuberculosis prevention, care and control: key operational challenges and research priorities.

    PubMed

    Boccia, Delia; Pedrazzoli, Debora; Wingfield, Tom; Jaramillo, Ernesto; Lönnroth, Knut; Lewis, James; Hargreaves, James; Evans, Carlton A

    2016-06-21

    Cash transfer interventions are forms of social protection based on the provision of cash to vulnerable households with the aim of reduce risk, vulnerability, chronic poverty and improve human capital. Such interventions are already an integral part of the response to HIV/AIDS in some settings and have recently been identified as a core element of World Health Organization's End TB Strategy. However, limited impact evaluations and operational evidence are currently available to inform this policy transition. This paper aims to assist national tuberculosis (TB) programs with this new policy direction by providing them with an overview of concepts and definitions used in the social protection sector and by reviewing some of the most critical operational aspects associated with the implementation of cash transfer interventions. These include: 1) the various implementation models that can be used depending on the context and the public health goal of the intervention; 2) the main challenges associated with the use of conditionalities and how they influence the impact of cash transfer interventions on health-related outcomes; 3) the implication of targeting diseases-affected households and or individuals versus the general population; and 4) the financial sustainability of including health-related objectives within existing cash transfer programmes. We aimed to appraise these issues in the light of TB epidemiology, care and prevention. For our appraisal we draw extensively from the literature on cash transfers and build upon the lessons learnt so far from other health outcomes and mainly HIV/AIDS. The implementation of cash transfer interventions in the context of TB is still hampered by important knowledge gaps. Initial directions can be certainly derived from the literature on cash transfers schemes and other public health challenges such as HIV/AIDS. However, the development of a solid research agenda to address persisting unknowns on the impact of cash transfers on

  6. Research citation analysis of nursing academics in Canada: identifying success indicators.

    PubMed

    Hack, Thomas F; Crooks, Dauna; Plohman, James; Kepron, Emma

    2010-11-01

    This article is a report of a citation analysis of research publications by Canadian nursing academics. Citation analysis can yield objective criteria for assessing the value of published research and is becoming increasingly popular as an academic evaluation tool in universities around the world. Citation analysis is useful for examining the research performance of academic researchers and identifying leaders among them. The journal publication records of 737 nursing academics at 33 Canadian universities and schools of nursing were subject to citation analysis using the Scopus database. Three primary types of analysis were performed for each individual: number of citations for each journal publication, summative citation count of all published papers and the Scopus h-index. Preliminary citation analysis was conducted from June to July 2009, with the final analysis performed on 2 October 2009 following e-mail verification of publication lists. The top 20 nursing academics for each of five citation categories are presented: the number of career citations for all publications, number of career citations for first-authored publications, most highly cited first-authored publications, the Scopus h-index for all publications and the Scopus h-index for first-authored publications. Citation analysis metrics are useful for evaluating the research performance of academic researchers in nursing. Institutions are encouraged to protect the research time of successful and promising nursing academics, and to dedicate funds to enhance the research programmes of underperforming academic nursing groups. © 2010 The Authors. Journal of Advanced Nursing © 2010 Blackwell Publishing Ltd.

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

    PubMed

    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.

  8. Are there pollination syndromes in the Australian epacrids (Ericaceae: Styphelioideae)? A novel statistical method to identify key floral traits per syndrome

    PubMed Central

    Johnson, Karen A.

    2013-01-01

    Background and Aims Convergent floral traits hypothesized as attracting particular pollinators are known as pollination syndromes. Floral diversity suggests that the Australian epacrid flora may be adapted to pollinator type. Currently there are empirical data on the pollination systems for 87 species (approx. 15 % of Australian epacrids). This provides an opportunity to test for pollination syndromes and their important morphological traits in an iconic element of the Australian flora. Methods Data on epacrid–pollinator relationships were obtained from published literature and field observation. A multivariate approach was used to test whether epacrid floral attributes related to pollinator profiles. Statistical classification was then used to rank floral attributes according to their predictive value. Data sets excluding mixed pollination systems were used to test the predictive power of statistical classification to identify pollination models. Key Results Floral attributes are correlated with bird, fly and bee pollination. Using floral attributes identified as correlating with pollinator type, bird pollination is classified with 86 % accuracy, red flowers being the most important predictor. Fly and bee pollination are classified with 78 and 69 % accuracy, but have a lack of individually important floral predictors. Excluding mixed pollination systems improved the accuracy of the prediction of both bee and fly pollination systems. Conclusions Although most epacrids have generalized pollination systems, a correlation between bird pollination and red, long-tubed epacrids is found. Statistical classification highlights the relative importance of each floral attribute in relation to pollinator type and proves useful in classifying epacrids to bird, fly and bee pollination systems. PMID:23681546

  9. Midwifery-led antenatal care models: mapping a systematic review to an evidence-based quality framework to identify key components and characteristics of care.

    PubMed

    Symon, Andrew; Pringle, Jan; Cheyne, Helen; Downe, Soo; Hundley, Vanora; Lee, Elaine; Lynn, Fiona; McFadden, Alison; McNeill, Jenny; Renfrew, Mary J; Ross-Davie, Mary; van Teijlingen, Edwin; Whitford, Heather; Alderdice, Fiona

    2016-07-19

    Implementing effective antenatal care models is a key global policy goal. However, the mechanisms of action of these multi-faceted models that would allow widespread implementation are seldom examined and poorly understood. In existing care model analyses there is little distinction between what is done, how it is done, and who does it. A new evidence-informed quality maternal and newborn care (QMNC) framework identifies key characteristics of quality care. This offers the opportunity to identify systematically the characteristics of care delivery that may be generalizable across contexts, thereby enhancing implementation. Our objective was to map the characteristics of antenatal care models tested in Randomised Controlled Trials (RCTs) to a new evidence-based framework for quality maternal and newborn care; thus facilitating the identification of characteristics of effective care. A systematic review of RCTs of midwifery-led antenatal care models. Mapping and evaluation of these models' characteristics to the QMNC framework using data extraction and scoring forms derived from the five framework components. Paired team members independently extracted data and conducted quality assessment using the QMNC framework and standard RCT criteria. From 13,050 citations initially retrieved we identified 17 RCTs of midwifery-led antenatal care models from Australia (7), the UK (4), China (2), and Sweden, Ireland, Mexico and Canada (1 each). QMNC framework scores ranged from 9 to 25 (possible range 0-32), with most models reporting fewer than half the characteristics associated with quality maternity care. Description of care model characteristics was lacking in many studies, but was better reported for the intervention arms. Organisation of care was the best-described component. Underlying values and philosophy of care were poorly reported. The QMNC framework facilitates assessment of the characteristics of antenatal care models. It is vital to understand all the

  10. Integrated research in natural resources: the key role of problem framing.

    Treesearch

    Roger N. Clark; George H. Stankey

    2006-01-01

    Integrated research is about achieving holistic understanding of complex biophysical and social issues and problems. It is driven by the need to improve understanding about such systems and to improve resource management by using the results of integrated research processes.Traditional research tends to fragment complex problems, focusing more on the pieces...

  11. Online Tutoring Procedure for Research Project Supervision: Management, Organization and Key Elements

    ERIC Educational Resources Information Center

    Darder Mesquida, Antònia; Pérez Garcias, Adolfina

    2015-01-01

    Research project tutoring appears as a crucial element for teaching; it is a planned action based on the relationship between a tutor and a student. This paper presents the findings of a design and development research which has as its main aim to create an organization system for the tutoring of online research projects. That system seeks to…

  12. Key Elements and challenges of USEPA’s developing ecological services research program

    EPA Science Inventory

    Over the past year, EPA’s Office of Research and Development (ORD) has redirected research within the Ecological Services Research Program (ESRP) to focus on ecosystem services and their associated benefits to human well-being. By 2009, all of EPA/ORD’s Ecological Services Resear...

  13. Conducting Research in Experience-Based Training and Development Programs: Pass Keys to Locked Doors.

    ERIC Educational Resources Information Center

    Priest, Simon; And Others

    1993-01-01

    Calls for further research evaluating corporate adventure training (CAT) programs. Reviews activities and benefits associated with CAT, summarizes studies conducted on the efficacy of CAT programs, describes appropriate research designs for investigating how and why CAT programs work, and addresses barriers to producing meaningful research. (LP)

  14. Key Elements and challenges of USEPA’s developing ecological services research program

    EPA Science Inventory

    Over the past year, EPA’s Office of Research and Development (ORD) has redirected research within the Ecological Services Research Program (ESRP) to focus on ecosystem services and their associated benefits to human well-being. By 2009, all of EPA/ORD’s Ecological Services Resear...

  15. [Testing method research for key performance indicator of imaging acousto-optic tunable filter (AOTF)].

    PubMed

    Hu, Shan-Zhou; Chen, Fen-Fei; Zeng, Li-Bo; Wu, Qiong-Shui

    2013-01-01

    Imaging AOTF is an important optical filter component for new spectral imaging instruments developed in recent years. The principle of imaging AOTF component was demonstrated, and a set of testing methods for some key performances were studied, such as diffraction efficiency, wavelength shift with temperature, homogeneity in space for diffraction efficiency, imaging shift, etc.

  16. Building persistent identifier systems for geoscience research - Technical solutions and community governance

    NASA Astrophysics Data System (ADS)

    Klump, J. F.; Lehnert, K. A.; Huber, R.

    2015-12-01

    The emergence of the Internet gave rise to the expectation that the internet would lead to greater accessibility, transparency and reproducibility of research results. New communication technologies enabled far easier and faster collaboration in larger, geographically more distributed networks. However, the distributed and disorganised nature of the internet not only allowed new technologies to emerge, it also made it difficult to maintain a persistent record of science. Persistent identifiers were invented to allow unambiguous identification of resources on the net. At first, these resources referred to scholarly literature and related resources. The concept of using persistent identifiers has since been expanded to other, non-textual resources, like datasets and geological specimens, and more recently to authors and contributors of scholarly works, and to software and instruments.Setting up identifier systems is technically trivial. The real challenge lies in creating a governance system for the respective identifiers. While Digital Object Identifiers (DOI) were originally invented by the publishing industry, they quickly became an established way for the identification of research resources. Other identifier systems, some of them using DOI as an example, were developed as grass-roots efforts by the scientific community.Together with semantic technologies and linked data, unambiguous identification allows us to harness information at large scales beyond human comprehension. The technical possibilities offered by technology challenge some of the norms of scholarly cooperation, such as using and sharing resources beyond the emulation of paper-based publications.This presentation will discuss the development of persistent identification of research resources as a community effort, using the technical and governance patterns developed for DOI and for IGSN for data as an example.

  17. Patient Participation in Research in the Managed Care Environment: Key Perceptions of Members in an HMO

    PubMed Central

    Purdy, Sarah; Finkelstein, Jonathan A; Fletcher, Robert; Christiansen, Cindy; Inui, Thomas S

    2000-01-01

    This study's objective was to elicit the views of research among enrollees in an HMO. A questionnaire was mailed to 207 adult enrollees, 55% had been exposed to research and 45% had not. Ninety-four percent of respondents supported research within the HMO, and 87% thought using information from medical records for research was acceptable. Sixty-three percent thought participation in research increased patient understanding of health care. Significantly more prior research participants thought that participation in research improves care. More patients would participate if written information were provided (67%), if feedback of results was provided (72%), and if their clinician invited them (67%). Only a modest percentage (20%) of patients would participate in a randomized trial. PMID:10940136

  18. Multi-Task Project to Provide Research Support for Human Research and Engineering Goals Identified by the Army

    DTIC Science & Technology

    2009-06-01

    Jefferson City, MO Phone:573-681-5126 E-mail: rooneyi(a>lincolnu.edu Principle Investigators for contract’s 5 Task Areas: Task I : James Rooney...identified Tasks all structured within a single contract. This contract contained Five Task areas: Task I was an administrative task; Task II-V were...Manager’s Overview of the Report (Task I ) 3. Summary Final Budget Invoice and Budget unspent balance 4. Technical Reports of the Research Tasks (II - V

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

    PubMed Central

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

    2015-01-01

    Background 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. Objective 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. Methods 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 f 1, f 2, ..., f k. The input for each function f i has 3 components: a random number r, an integer n, and input data m. The result, f i(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 f 1(r 1, n 1, m 1), f 2(r 2, n 2, m 2), ..., f k(r k, n k, m k). In the second phase, the intermediate string generated in Phase 1 is encrypted

  20. Using Research: A Key to Elementary School Mathematics. Planning for Research in School. Final Bulletin, Set A.

    ERIC Educational Resources Information Center

    Suydam, Marilyn N.; Weaver, J. Fred

    This bulletin serves as a guide to those persons interested in conducting or implementing educational research. Research is described as being "controlled inquiry", either in the form of an experiment or a survey. Descriptions are given of the procedures and complications associated with planning and initiating experimental research. A suggested…

  1. InFlo: a novel systems biology framework identifies cAMP-CREB1 axis as a key modulator of platinum resistance in ovarian cancer.

    PubMed

    Dimitrova, N; Nagaraj, A B; Razi, A; Singh, S; Kamalakaran, S; Banerjee, N; Joseph, P; Mankovich, A; Mittal, P; DiFeo, A; Varadan, V

    2017-04-27

    Characterizing the complex interplay of cellular processes in cancer would enable the discovery of key mechanisms underlying its development and progression. Published approaches to decipher driver mechanisms do not explicitly model tissue-specific changes in pathway networks and the regulatory disruptions related to genomic aberrations in cancers. We therefore developed InFlo, a novel systems biology approach for characterizing complex biological processes using a unique multidimensional framework integrating transcriptomic, genomic and/or epigenomic profiles for any given cancer sample. We show that InFlo robustly characterizes tissue-specific differences in activities of signalling networks on a genome scale using unique probabilistic models of molecular interactions on a per-sample basis. Using large-scale multi-omics cancer datasets, we show that InFlo exhibits higher sensitivity and specificity in detecting pathway networks associated with specific disease states when compared to published pathway network modelling approaches. Furthermore, InFlo's ability to infer the activity of unmeasured signalling network components was also validated using orthogonal gene expression signatures. We then evaluated multi-omics profiles of primary high-grade serous ovarian cancer tumours (N=357) to delineate mechanisms underlying resistance to frontline platinum-based chemotherapy. InFlo was the only algorithm to identify hyperactivation of the cAMP-CREB1 axis as a key mechanism associated with resistance to platinum-based therapy, a finding that we subsequently experimentally validated. We confirmed that inhibition of CREB1 phosphorylation potently sensitized resistant cells to platinum therapy and was effective in killing ovarian cancer stem cells that contribute to both platinum-resistance and tumour recurrence. Thus, we propose InFlo to be a scalable and widely applicable and robust integrative network modelling framework for the discovery of evidence-based biomarkers

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

    PubMed

    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.

  3. A nursing informatics research agenda for 2008-18: contextual influences and key components.

    PubMed

    Bakken, Suzanne; Stone, Patricia W; Larson, Elaine L

    2008-01-01

    The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on 3 specific aspects of context--genomic health care, shifting research paradigms, and social (Web 2.0) technologies--that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008-18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context.

  4. A Nursing Informatics Research Agenda for 2008–18: Contextual Influences and Key Components

    PubMed Central

    Bakken, Suzanne; Stone, Patricia W.; Larson, Elaine L.

    2008-01-01

    The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on three specific aspects of context - genomic health care, shifting research paradigms, and social (Web 2.0) technologies - that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008–18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context. PMID:18922269

  5. A Plan for the Next Generation of HIV Prevention Research: Seven Key Policy Investigative Challenges

    ERIC Educational Resources Information Center

    Coates, Thomas J.; Szekeres,Gregory

    2004-01-01

    Although HIV prevention research has accomplished much over the last 2 decades, significant challenges remain. The accomplishments have included rapid progression through various stages of research--from descriptive to clinical trials--and the fielding of several Phase 3 trials with biological endpoints. The challenges include developing…

  6. A Plan for the Next Generation of HIV Prevention Research: Seven Key Policy Investigative Challenges

    ERIC Educational Resources Information Center

    Coates, Thomas J.; Szekeres,Gregory

    2004-01-01

    Although HIV prevention research has accomplished much over the last 2 decades, significant challenges remain. The accomplishments have included rapid progression through various stages of research--from descriptive to clinical trials--and the fielding of several Phase 3 trials with biological endpoints. The challenges include developing…

  7. Ethics in Community-University-Artist Partnered Research: Tensions, Contradictions and Gaps Identified in an 'Arts for Social Change' Project.

    PubMed

    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.

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

    PubMed Central

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

    2014-01-01

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

  9. Key statistical and analytical issues for evaluating treatment effects in periodontal research.

    PubMed

    Tu, Yu-Kang; Gilthorpe, Mark S

    2012-06-01

    Statistics is an indispensible tool for evaluating treatment effects in clinical research. Due to the complexities of periodontal disease progression and data collection, statistical analyses for periodontal research have been a great challenge for both clinicians and statisticians. The aim of this article is to provide an overview of several basic, but important, statistical issues related to the evaluation of treatment effects and to clarify some common statistical misconceptions. Some of these issues are general, concerning many disciplines, and some are unique to periodontal research. We first discuss several statistical concepts that have sometimes been overlooked or misunderstood by periodontal researchers. For instance, decisions about whether to use the t-test or analysis of covariance, or whether to use parametric tests such as the t-test or its non-parametric counterpart, the Mann-Whitney U-test, have perplexed many periodontal researchers. We also describe more advanced methodological issues that have sometimes been overlooked by researchers. For instance, the phenomenon of regression to the mean is a fundamental issue to be considered when evaluating treatment effects, and collinearity amongst covariates is a conundrum that must be resolved when explaining and predicting treatment effects. Quick and easy solutions to these methodological and analytical issues are not always available in the literature, and careful statistical thinking is paramount when conducting useful and meaningful research. © 2012 John Wiley & Sons A/S.

  10. Constancy and Change: Key Issues in Housing and Health Research, 1987–2017

    PubMed Central

    2017-01-01

    The low impact of scientific research on the relations between housing and health during the last 30 years can be attributed to a number of reasons. First, statistical analyses have meant to improve understanding of the relations between what are interpreted and measured as causal factors. However, any single statistical approach fails to account for the dynamic non-linear relations between multiple factors and therefore cannot analyze systemic complexity. Second, there has been too little accumulation and validation of knowledge from scientific research owing to the dominance of cross-sectional studies, and the lack of coordinated research agendas using these approaches in order to confirm empirical findings. Hence, there is little evidence indicating that public policies in both the housing and the public health sectors in specific localities have benefited from the accumulated evidence of empirical research. Third, the findings from empirical studies have been published in academic journals and monographs but rarely disseminated to actors and institutions in the public and private sectors. Hence housing and health research and policy formulation have not been consolidated during the last three decades. The author of this communication argues for a radical shift from conventional disciplinary and multi-disciplinary contributions to transdisciplinary research programmes and projects that formulate and apply innovative approaches founded on conceptual frameworks that apply systems thinking for the integration of knowledge and know-how of researchers, policy makers, and professional practitioners in precise localities. PMID:28704943

  11. Constancy and Change: Key Issues in Housing and Health Research, 1987-2017.

    PubMed

    Lawrence, Roderick J

    2017-07-12

    The low impact of scientific research on the relations between housing and health during the last 30 years can be attributed to a number of reasons. First, statistical analyses have meant to improve understanding of the relations between what are interpreted and measured as causal factors. However, any single statistical approach fails to account for the dynamic non-linear relations between multiple factors and therefore cannot analyze systemic complexity. Second, there has been too little accumulation and validation of knowledge from scientific research owing to the dominance of cross-sectional studies, and the lack of coordinated research agendas using these approaches in order to confirm empirical findings. Hence, there is little evidence indicating that public policies in both the housing and the public health sectors in specific localities have benefited from the accumulated evidence of empirical research. Third, the findings from empirical studies have been published in academic journals and monographs but rarely disseminated to actors and institutions in the public and private sectors. Hence housing and health research and policy formulation have not been consolidated during the last three decades. The author of this communication argues for a radical shift from conventional disciplinary and multi-disciplinary contributions to transdisciplinary research programmes and projects that formulate and apply innovative approaches founded on conceptual frameworks that apply systems thinking for the integration of knowledge and know-how of researchers, policy makers, and professional practitioners in precise localities.

  12. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

    PubMed

    Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

    2016-10-01

    Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Combined integrin phosphoproteomic analyses and small interfering RNA--based functional screening identify key regulators for cancer cell adhesion and migration.

    PubMed

    Chen, Yanling; Lu, Bingwen; Yang, Qingkai; Fearns, Colleen; Yates, John R; Lee, Jiing-Dwan

    2009-04-15

    Integrins interact with extracellular matrix (ECM) and deliver intracellular signaling for cell proliferation, survival, and motility. During tumor metastasis, integrin-mediated cell adhesion to and migration on the ECM proteins are required for cancer cell survival and adaptation to the new microenvironment. Using stable isotope labeling by amino acids in cell culture-mass spectrometry, we profiled the phosphoproteomic changes induced by the interactions of cell integrins with type I collagen, the most common ECM substratum. Integrin-ECM interactions modulate phosphorylation of 517 serine, threonine, or tyrosine residues in 513 peptides, corresponding to 357 proteins. Among these proteins, 33 key signaling mediators with kinase or phosphatase activity were subjected to small interfering RNA-based functional screening. Three integrin-regulated kinases, DBF4, PAK2, and GRK6, were identified for their critical role in cell adhesion and migration possibly through their regulation of actin cytoskeleton arrangement. Altogether, we not only depict an integrin-modulated phosphorylation network during cell-ECM protein interactions but also reveal novel regulators for cell adhesion and migration.

  14. Research on key techniques of nanometer scale macro-micro dual-drive precision positioning

    NASA Astrophysics Data System (ADS)

    Xie, Xiaohui; Du, Ruxu

    2007-12-01

    With the development of science and technology, high precision of positioning platform is needed in many areas, for example, cell fusing in biology and precision surgery in medical area. In such areas, both high efficiency and high precision are needed in some cases, for example, semiconductor processing equipment, super precision lathe etc. In a word, precision positioning platform becomes an important tool in exploring microscope world. Precision positioning platform is a key element in microscope operation. Macro/micro dual-drive precision positioning is a key technique in high-efficiency high-precision area. By such techniques, large distance and high precision can get. In order to realize nanometer scale macro/micro dual-drive precision positioning there are some key problems. First, system structure of macro/micro combination precision positioning platform is worthy to work on. Another key work is realization method of micrometer scale macroscope motion and nanometer scale microscope motion. The third is mechanics, drive, detection and control techniques in nanometer scale positioning of piezoelectric ceramics drive, in which realization of nanometer scale microscope positioning and micro drive is important by solving hysteresis, creep deformation and non-linearity in piezoelectric ceramics driving. To solve hysteresis problem, instead of traditional Preisach algorithm, a new type hysteresis model with simple computation and identification is needed. The inverse model is also easily to get. So we can present new control method to solve hysteresis and creep deformation problem based on this inverse model. Another way, hysteresis and creep deformation problem exist in traditional voltage-feedback power source for piezoelectric ceramics. To solve this problem, a new type current feedback power source for piezoelectric ceramics is presented. In the end, a macro-micro dual-drive super precision positioning mechanism is presented. Combining macro with micro

  15. Research on the Key Technology of Large Scale Mapping from Low Altitude Photogrammetry

    NASA Astrophysics Data System (ADS)

    Bo-Yi, Wu; Ning, Zhang; Guo-Zhong, Su

    2016-06-01

    Based on the theoretic analysis of the accuracy in large scale photogrammetric mapping, some defects in traditional procedure were discussed. A set of key technologies dedicate to accuracy improvement in low altitude photogrammetry were analyzed in detail, namely the utilization of wide angle camera and low altitude flight, enhancement in image matching, predesigned layout of Ground Control Points (GCPs) in field survey, optimization of adjustment model and improvement in map processing. Besides, a low altitude aerial unmanned airship system was established. Finally, successful implementation in 1:500 topographic mapping project in built-up areas of 30 counties in Shanxi Province proves the practicability and effectiveness of the proposed approaches.

  16. Clinically relevant variants identified in thoracic aortic aneurysm patients by research exome sequencing.

    PubMed

    Schubert, Jeffrey A; Landis, Benjamin J; Shikany, Amy R; Hinton, Robert B; Ware, Stephanie M

    2016-05-01

    Thoracic aortic aneurysm (TAA) is a genetically heterogeneous disease involving subclinical and progressive dilation of the thoracic aorta, which can lead to life-threatening complications such as dissection or rupture. Genetic testing is important for risk stratification and identification of at risk family members, and clinically available genetic testing panels have been expanding rapidly. However, when past testing results are normal, there is little evidence to guide decision-making about the indications and timing to pursue additional clinical genetic testing. Results from research based genetic testing can help inform this process. Here we present 10 TAA patients who have a family history of disease and who enrolled in research-based exome testing. Nine of these ten patients had previous clinical genetic testing that did not identify the cause of disease. We sought to determine the number of rare variants in 23 known TAA associated genes identified by research-based exome testing. In total, we found 10 rare variants in six patients. Likely pathogenic variants included a TGFB2 variant in one patient and a SMAD3 variant in another. These variants have been reported previously in individuals with similar phenotypes. Variants of uncertain significance of particular interest included novel variants in MYLK and MFAP5, which were identified in a third patient. In total, clinically reportable rare variants were found in 6/10 (60%) patients, with at least 2/10 (20%) patients having likely pathogenic variants identified. These data indicate that consideration of re-testing is important in TAA patients with previous negative or inconclusive results. © 2016 Wiley Periodicals, Inc.

  17. Clinically Relevant Variants Identified in Thoracic Aortic Aneurysm Patients by Research Exome Sequencing

    PubMed Central

    Schubert, Jeffrey A.; Landis, Benjamin J.; Shikany, Amy R.; Hinton, Robert B.; Ware, Stephanie M.

    2016-01-01

    Thoracic aortic aneurysm (TAA) is a genetically heterogeneous disease involving subclinical and progressive dilation of the thoracic aorta, which can lead to life-threatening complications such as dissection or rupture. Genetic te