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The New England Collaborative Data Management Curriculum Pilot at the University of Manitoba: A Canadian Experience

Mon, 01/12/2015 - 9:16am

Canada’s federal funding agencies are following the directions of funding agencies in the United States and United Kingdom, and will soon require a data management plan in grant applications. The University of Manitoba Libraries in Canada has started planning and implementing research data services, and education is seen as a key component. In June 2014, the New England Collaborative Data Management Curriculum (NECDMC) (Lamar Soutter Library, University of Massachusetts Medical School 2014) was piloted and used to provide data management training for a group of subject librarians at the University of Manitoba Libraries, in combination with information about data-related policies of the Canadian funding agencies and the University of Manitoba. The seven NECDMC modules were delivered in a seminar style, with emphasis on group discussions and Canadian content. The benefits of NECDMC – adaptability and flexible framework – should be weighed against the challenges experienced in the pilot, mainly the significant amount of time needed to create local content and complement the existing curriculum. Overall, the pilot showed that NECDMC is a good, thorough introduction to data management, and that it is possible to adapt NECDMC to the local and Canadian settings in an effective way.

Gaining Traction in Research Data Management Support: A Case Study

Mon, 01/12/2015 - 9:16am

With the implementation of an institutional repository, librarians at the University of Vermont (UVM) began receiving inquiries about data management. In an effort to explore research data management roles for librarians at UVM the author led workshops based on Module One of the New England Collaborative Data Management Curriculum (NECDMC) with two audiences. In addition, the author consulted with faculty and staff from around the university to ascertain their support of research data management and integrate that information into the workshops. The first workshop was directed at UVM librarians and resulted in an understanding of their willingness to engage with research data management patron services. The second workshop was conducted for students and faculty. It built upon the first workshop and, in addition, experimented with a sixty-minute version of the NECDMC module. This second workshop will be added to an existing series of Dana Library workshops for graduate students and early-career researchers in fall 2014.

Lessons Learned From a Research Data Management Pilot Course at an Academic Library

Mon, 01/12/2015 - 9:15am

Setting and Objective:

From January-March 2014, three librarians from the University of Washington (UW) taught a course in research data management as a pilot for the New England Collaborative Data Management Curriculum (NECDMC). The goals of the workshops were to a) pilot the NECDMC curriculum to see how effective it was as an out-of-the box solution for teaching research data management (RDM), and b) to gauge interest in an RDM class among certain UW student populations, and c) to teach UW’s first RDM workshop offered to non-librarians.

Design and Methods:

The NECDMC consists of 7 modules that can be taught independently or as a series. UW decided to teach all seven modules consecutively, as one-hour long weekly workshops. Each module included a lecture and activity or discussion. We taught at one location on upper campus, and live-streamed the lecture to another location in the Health Sciences Library. Each module was assessed at the end of the class.


Interest in a research data management class is high; however, retention for a non-credit, 7-week class is low. Individual assessments show that students thought the content was important and well-delivered.


Based on registration, graduate students at UW in many disciplines are interested in learning research data management skills. A non-credit, 7-week class had low retention; another type of class structure might increase retention. The NECDMC curriculum is an excellent framework, but modification to individual modules are necessary to provide a thorough and localized curriculum specific to one institution.

Building the New England Collaborative Data Management Curriculum

Mon, 01/12/2015 - 9:15am

The need for a curriculum designed for librarians to use for teaching STEM research data management skills to their constituents from diverse STEM disciplines has been widely identified. (Qin and D’Ignazio 2010). From 2012-2014, a collaborative group of New England librarians, led by a project team from the University of Massachusetts Medical School, developed lecture notes, presentation slides, assignments, readings, and case studies for teaching research data management. The New England Collaborative Data Management Curriculum (NECDMC) is unique in its flexibility; providing subject agnostic instructional materials in a modular format for teaching common data management best practices along with a suite of teaching cases illustrating data management in disciplinary contexts. This article is a follow-up to the “Teaching Research Data Management: An Undergraduate/Graduate Curriculum (Piorun et al. 2012) that was published in the Journal of eScience Librarianship.

What is Data Literacy?

Mon, 01/12/2015 - 9:15am

JESLIB Editor Elaine R. Martin introduces the articles in Volume 3, Issue 1 by discussing data literacy and the various forms of library services designed to support it. Martin highlights that librarians are already taking advantage of the opportunity to provide data support services and that the articles in this issue can serve as a point of reference for developing further data services and strategies for service development.

Building Data Services From the Ground Up: Strategies and Resources

Mon, 01/12/2015 - 9:15am

There is a scarcity of practical guidance for developing data services in an academic library. Data services, like many areas of research, require the expertise and resources of teams spanning many disciplines. While library professionals are embedded into the teaching activities of our institutions, fewer of us are embedded in research activities occurring across the full life cycle. The significant challenges of managing, preserving, and sharing data for reuse demand that we take a more active role. Providing support for funder data management plans is just one option in the data services landscape. Awareness of the institutional and library culture in which we operate places an emphasis on the importance of relationships. Understanding the various cultures in which our researchers operate is crucial for delivering data services that are relevant and utilized. The goal of this article is to guide data specialists through this landscape by providing key resources and strategies for developing locally relevant services and by pointing to active communities of librarians and researchers tackling the challenges associated with digital research data.

Focused Outreach Final Report: Vermont (May 1, 2013 - April 30, 2014)

Fri, 01/09/2015 - 4:10pm

The National Network of Libraries of Medicine, New England Region (NN/LM NER) seeks to further the mission of the NN/LM, while increasing use of National Library of Medicine ( resources and services; and expanding collaboration with libraries through a Focused Health Information Outreach model. The mission of the National Network of Libraries of Medicine (NN/LM) is to advance the progress of medicine and improve the public health by providing all U.S. health professionals equal access to biomedical information and by improving the public's access to information to enable them to make informed decisions about their health.

The Focused Outreach Project connected underserved communities in Vermont with the resources and services of the National Library of Medicine. NER partnered with local libraries, public health agencies, school nurses, the state library, health education students, and community television. This year, the project transitioned to a train-the-trainer model. Project partners were identified following the Key Informant Interviews. NER staff worked with project partners to guide them through the project planning, proposal writing process, and initial NLM education. Project partners included:

  • Vermont State Library
  • Dana Medical Library
  • Middlebury Community TV
  • Vermont Agency of Education
  • Castleton State College Heath Education Department
  • Northeastern Vermont Regional Hospital Medical Library
  • Vermont School Nurse Health Information Access Project

Pre and post-evaluations showed that as a result of this project:

  • 92 consumers learned about MedlinePlus
  • 220 health information providers learned about MedlinePlus
  • 325 visitors at exhibits/health fairs learned more about the National Library of Medicine

Consumer post-evaluations showed that 79% reported that the trainings improved their ability to find information they could trust on the internetl: 64%were likely to use MedlinePlus in the future. Provider post-evaluations showed that 97% said the class improved their ability to find information they could trust on the internet; 100% were likely to use MedlinePlus in the future; and 62% were very likely to tell others about the NLM resources they learned.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

Fri, 01/09/2015 - 2:36pm

Comment on:

  • Getting "function" right. [Proc Natl Acad Sci U S A. 2014]
  • Defining functional DNA elements in the human genome. [Proc Natl Acad Sci U S A. 2014]

The Hitchhiker's guide to Hi-C analysis: Practical guidelines

Fri, 01/09/2015 - 2:36pm

Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches, have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this paper is to provide guidelines for analyzing and interpreting data obtained with genome-wide 3C methods such as Hi-C and 3C-seq that rely on deep sequencing to detect and quantify pairwise chromatin interactions.

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

Fri, 01/09/2015 - 2:36pm

Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions. How local chromatin interactions govern higher-order folding of chromatin fibres and the function of cohesin in this process remain poorly understood. Here we perform genome-wide chromatin conformation capture (Hi-C) analysis to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes. Our analyses of wild-type and mutant strains reveal key elements of chromosome architecture and genome organization. On chromosome arms, small regions of chromatin locally interact to form 'globules'. This feature requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories. By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains, is dispensable for globule formation but nevertheless affects genome organization. We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization. Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions. Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions.

The tripartite motif (TRIM) of nuclear factor 7 is required for its association with transcription units

Fri, 01/09/2015 - 11:48am

In amphibian oocytes, the maternal nuclear factor NF7 associates with the elongating pre-mRNAs present on the numerous lateral loops of the lampbrush chromosomes. Here, we have purified NF7 from an oocyte extract by using a combination of ion-exchange chromatography and gel filtration chromatography and demonstrated for the first time that nucleoplasmic NF7 exists primarily as free homotrimers. We confirmed the in vivo homotrimerization of NF7 by using a glutaraldehyde cross-linking assay, and we further showed that it only requires the coiled-coil domain of the NF7 tripartite motif/RBCC motif. Interestingly, we also obtained evidence that NF7 is recruited to the nucleus as a homotrimer, and expression of several mutated forms of NF7 in oocytes demonstrated that both the coiled coil and B box of NF7 are required for its chromosomal association. Together, these data strongly suggest that the interaction of NF7 with the active transcriptional units of RNA polymerase II is mediated by a trimeric B box. Finally, and in agreement with a role for NF7 in pre-mRNA maturation, we obtained evidence supporting the idea that NF7 associates with Cajal bodies.

PTSD/SUD in Individuals with Physical Disabilities: Identifying Problems and Promising Interventions

Thu, 01/08/2015 - 3:56pm

Co-occurring posttraumatic stress disorder (PTSD) and substance use disorder (SUD) is common, affects multiple domains of functioning, and presents complex challenges to recovery. Initial research indicates that individuals with physical disabilities experience higher rates of lifetime trauma and PTSD, and exhibit more severe SUD compared to non-disabled individuals. To expand upon these initial findings, we conducted a series of two studies on PTSD and SUD among individuals with physical disabilities.

[Venous thromboembolism prophylaxis in Colombian surgical and medical patients: results for Colombia of the ENDORSE study]

Wed, 01/07/2015 - 10:15am

INTRODUCTION: More information is needed on the risk of venous thromboembolism in the hospital setting, and on patterns of use of thromboprophylaxis, as advocated in consensus guidelines.ENDORSE was an international study aimed at evaluating hospital venous thromboembolism prevention practices in medical and surgical patients.

OBJECTIVES: The risk of venous thromboembolism was evaluated along with the use of thromboprophylaxis in hospitalized medical and surgical subjects; these data were compared with the international sample from the ENDORSE study.

MATERIALS AND METHODS: Participating institutions in Colombia were selected arbitrarily. The medical charts for medical and surgical patients were evaluated randomly. The 2004 American College of Chest Physician guidelines were used to evaluate risk of venous thromboembolism and adherence to recommended thromboprophylaxis regimens.

RESULTS: The study included 761 subjects (218 surgical, 543 medical) located in five acute care hospitals; 49% of these subjects were considered at risk of venous thromboembolism (40% medical, 72% surgical), compared with 52% in the international sample. Prophylaxis use was higher in medical patients at risk (63.7%, n = 137) than in surgical patients (48.4%, n = 76; p = 0.01). Compared with the international sample, the use of prophylaxis in Colombia was greater in medical patients (63.7% vs. 39.5%, p = 0.003), but lower in surgical patients (48.4% vs. 58.5%, p = 0.02).

CONCLUSIONS: Participating Colombian centers treat patients at risk of venous thromboembolism similarly to other participant countries, but appropriate prophylaxis was prescribed more frequently to medical patients. Greater efforts are needed, both in Colombia and around the world, to improve rates of appropriate venous thromboembolism prophylaxis in at-risk subjects.

Venous thromboembolism risk factors and practices of prophylaxis: ENDORSE study results in Portugal

Wed, 01/07/2015 - 10:15am

BACKGROUND: Venous thromboembolism (VTE) risk assessment is a cornerstone for the achievement of best practices and outcomes. Epidemiologic data and practices related to venous thromboprophylaxis as considered by the global ENDORSE study, (Epidemiologic International Day for the Evaluation of Patients at Risk for Venous Thromboembolism in the Acute Hospital Care Setting), enrolled 68,183 patients from 32 countries, in which Portugal. Within ENDORSE, data from all participant countries analyzed to determine their risk of VTE and to evaluate the suitability of prophylaxis.

METHODS: European patients were enrolled from randomly selected hospitals in Portugal (European Hospital Register), according to ENDORSE study inclusion/exclusion criteria. The Seventh ACCP evidence-based consensus guidelines were employed to evaluate VTE risk and prophylaxis use.

RESULTS: From a total of 3,145 beds assessed, 2,183 were considered eligible and 1,632 met all criteria. Of these, 860 (52.7%; 95% CI 50.3-55.1) were at risk of VTE: 525 surgical patients (68.9%; 95% CI 65.5-72.1) and 335 medical patients (38.5%; 95% CI 35.3-41.2). The rate of prophylaxis according to ACCP guidelines in overall patients at risk was 58.5% (503 patients). The prophylaxis rate for VTE was 59% (310 patients) in surgical patients and 57.6% (n = 193) in medical patients. 39.7% of surgical patients and 39.4 % of medical patients who did not meet the criteria for prophylaxis were also on prophylaxis with an anticoagulant, which was considered to be inappropriate.

CONCLUSIONS: More than a half of these hospitalized patients in Portugal were deemed at risk of VTE and less than two-thirds of them received appropriate prophylaxis. New strategies are required for implementation of venous thromboprophylaxis in Portuguese hospitals.

Venous thromboembolism risk and prophylaxis in the acute hospital care setting-results of the Endorse study in Tunisia

Wed, 01/07/2015 - 10:15am

BACKGROUND: There are not information about the risk of venous thromboembolism (VTE) and its prophylaxis in Tunisia. AIM: To report the Tunisian results of a multinational crosssectional study, designed to assess the prevalence of VTE risk in the acute hospital care setting and to determine the proportion of at risk patients who receive effective prophylaxis.

METHODS: All hospital inpatients aged 40 years or over admitted to a medical ward or these aged 18 years or over admitted to surgical ward, in 5 Tunisian hospitals were assessed for risk of VTE on the basis of hospital chart review. The 2004 American College of chest physicians (ACCP) evidence based consensus guidelines were used to assess VTE risk and to determine whether patients were received recommended prophylaxis.

RESULTS: 885 were enrolled, 212 (24%) were surgical and 673 (76%) were medical. 408 (44, 9%) judged to be at risk, 95 (44, 8%) are surgical and 313 (46, 5%) are medical. LWMH are the most used. Mechanical prophylaxis was never used.

CONCLUSION: The percentage of at risk patient in Tunisia is comparable to these of other countries. The majority of at risk patient are medical. The prophylaxis was under used. Hospital strategies to assess patient VTE risk and implementation of prophylaxis protocols are needed.

Assessment of venous thromboembolism risk and adequacy of prophylaxis in selected acute care medical centres in Arabian Gulf States: results from the ENDORSE study

Wed, 01/07/2015 - 10:15am

OBJECTIVES: To assess the prevalence of venous thromboembolism (VTE) risk in acutely ill surgical and medical patients in selected acute care centres in the Arabian Gulf States, and to determine the proportion of at-risk patients who received effective prophylaxis in accordance with 2004 American College of Chest Physicians (ACCP) guidelines.

MATERIALS AND METHODS: Eight hospitals from 3 countries (Kuwait, Kingdom of Saudi Arabia, and United Arab Emirates) contributed to the global ENDORSE (Epidemiological International Day for the Evaluation of Patients at Risk for Venous Thromboembolism in the Acute Hospital Care Setting) study. Medical records were reviewed for all the in-patients aged > / = 40 years admitted to medical wards, and in patients aged > / = 18 admitted to surgical wards. The VTE risk and recommended prophylaxis were assessed according to the 2004 ACCP guidelines.

RESULTS: Of 1,291 evaluable patients, 801 were considered at risk of VTE; 391 (48.8%) surgical patients and 410 (51.2%) medical patients. Of the 801 patients, 322 (40.2%) received ACCP-recommended VTE prophylaxis; 159 (40.7%) of surgical patients and 163 (39.8%) of medical patients.

CONCLUSIONS: The data showed that VTE prophylaxis was underutilized in high-risk hospitalized patients. We recommend that active measures should be implemented in acute care centres in these Arabian Gulf countries to ensure identification of patients at risk of VTE and institute the appropriate prophylaxis.

Venous thromboembolism risk and prophylaxis in the acute hospital care setting: the Irish results of the ENDORSE study

Wed, 01/07/2015 - 10:15am

ENDORSE (Epidemiologic International Day for the Evaluation of Patients at Risk for Venous Thromboembolism in the Acute Hospital Care Setting), is a multinational, cross-sectional survey of venous thromboembolism (VTE) risk prevalence and effective prophylaxis in the acute hospital care setting. Three Irish hospitals enrolled in the study. The American College of Chest Physicians (ACCP) guidelines were employed to evaluate VTE risk and prophylaxis. Of 552 patients, 297 (53.8%) and 255 (46.2%) were categorised as surgical or medical, respectively, with 175 (59%) surgical and 109 (43%) medical patients deemed to be at risk for VTE. Of these, only 112 (64%) and 51 (47%) received recommended VTE prophylaxis, respectively. The results are consistent with those observed in other countries and demonstrate a high prevalence of risk for VTE and a low rate of prophylaxis use, particularly in medical patients. Awareness of VTE guidelines should be an integral component of health policy.

Venous thromboembolism risk and prophylaxis in the acute hospital care setting: report from the ENDORSE study in Egypt

Wed, 01/07/2015 - 10:15am

BACKGROUND: Venous thromboembolism (VTE) is a leading cause of hospital-related deaths worldwide. However, the proportion of patients at risk of VTE who receive appropriate prophylaxis in Egypt is unknown. The ENDORSE study in Egypt is part of a global initiative to uncover the incidence of high-risk surgical and medical patients and determine what proportion of these patients receive appropriate VTE prophylaxis.

METHODS: Ten Egyptian hospitals participated in this observational study, enrolling all surgical and medical patients that met the study criteria. This resulted in a cohort of 1,008 patients in acute care facilities who underwent a retrospective chart review. Each patient's VTE risk status and the presence or absence of appropriate prophylactic care was assessed according to the American College of Chest Physicians (ACCP) guidelines 2004.

RESULTS: Of the 1,008 patients enrolled, 395 (39.2%) were found to be at high-risk for VTE. Overall, 227 surgical patients were at high-risk, although only 80 (35.2%) received ACCP-recommended prophylaxis. Similarly, 55/268 (32.75%) of high-risk medical patients received appropriate VTE prophylaxis. Low molecular weight heparin was the most commonly used anticoagulant, while mechanical prophylactic use was quite low (1.5%) in high-risk patients.

CONCLUSIONS: In Egypt, more than one-third of all patients hospitalized for surgery or acute medical conditions are at high risk for developing VTE. However, only a small fraction of these patients receive appropriate VTE prophylaxis. Corrective measures are necessary for preventing VTE morbidity and mortality in these high risk patients.

Venous thromboembolism risk and prophylaxis in the acute hospital care setting (ENDORSE), a multinational cross-sectional study: results from the Indian subset data

Wed, 01/07/2015 - 10:15am

BACKGROUND and OBJECTIVES: Venous thromboembolism (VTE) is a major health problem with substantial morbidity and mortality. It is often underdiagnosed due to lack of information on VTE risk and prophylaxis. The ENDORSE (Epidemiologic International Day for the Evaluation of Patients at Risk for Venous Thromboembolism in the Acute Hospital Care Setting) study aimed to assess the prevalence of VTE risk in acute hospital care setting and proportion of at-risk patients receiving effective prophylaxis. We present here the risk factor profile and prophylaxis pattern of hospitalized patients who participated in ENDORSE study in India.

METHODS: In this cross-sectional study in India, all patients (surgical >18 yr, medical >40 yr) from 10 hospitals were retrospectively studied. Demographics, VTE risk factors and prophylaxis patterns were assessed according to the 2004 American College of Chest Physicians (ACCP) evidence-based consensus guidelines.

RESULTS: We recruited 2058 patients (1110 surgical, 948 medical) from 10 randomly selected hospitals in India between August 2006 and January 2007. According to the ACCP criteria, 1104 (53.6%) patients [surgical 680 (61.3%), medical 424 (44.7%)] were at-risk for VTE. Chronic pulmonary disease/heart failure and complete immobilization were the most common risk factors before and during hospitalization, respectively. In India, 16.3 per cent surgical and 19.1 per cent medical at-risk patients received ACCP-recommended thromboprophylaxis.

INTERPRETATION and CONCLUSIONS: Despite a similar proportion of at-risk hospitalized patients in India and other participating countries, there was major underutilization of prophylaxis in India. It necessitates increasing awareness about VTE risk and ensuring appropriate thromboprophylaxis.