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Helping a Department of Energy Laboratory respond to Public Access requirements

Wed, 04/06/2016 - 3:30pm

Objective: The Princeton Plasma Physics Laboratory (PPPL) is a Department of Energy (DOE) Laboratory operated by Princeton University. The DOE released a Public Access plan in October of 2014 in response to the White House Office of Science and Technology Policy (OSTP) memo from February of 2013 titled “Increasing Access to the Results of Federally Funded Scientific Research”. To determine how the Princeton University Library and Office of Information Technology can help PPPL comply with the DOE Public Access Plan.

Methods: Several meetings were held between the PPPL committee charged with Public Access Plan compliance, the E-science and Scholarly Communications Librarians, and Princeton’s Dspace repository architect and programmer. These meetings served to help librarians provide PPPL with information about OSTP and DOE requirements and to determine how the Library and OIT could help PPPL with compliance.

Results: Librarians helped align the PPPL Data Management Plan with DOE requirements. Librarians also helped PPPL’s communications and technology licensing understanding of Open Access to published research and consult on publisher copyright policies. The E-Science Librarian, DSpace repository architect, and DSpace programmer worked with PPPL to set up a DSpace community, associated metadata, and guidelines for documentation to make the data underlying publications publicly accessible.

Conclusion: Many U. S. funding agencies have released the Public Access plans in response the OSTP Memo from February 2013 with requirements for open access to articles, data management plans, and making data underlying publications publicly available. Librarians can play a role in helping their institutions respond to these requirements.

Compliance: Data Management Plans and Public Access to Data

Wed, 04/06/2016 - 1:30pm

Three years ago, the Office of Science and Technology Policy released the memo “Increasing Public Access to the Results of Federally Funded Research.” So far, 16 agencies have released plans. These new requirements relate to information access so librarians are well placed to help researchers and grants administrators comply. Many librarians have previous experience with NIH Public Access Policy and/or NSF data management plan requirements, so the transition to the new mandates should be easy. This breakout session will help you focus your efforts on the most important aspects of public access and data management plans when helping researchers with compliance.

Margaret Henderson is Director of Research Data Services and Hillary Miller is Scholarly Communications Outreach Librarian, Virginia Commonwealth University Libraries.

Informationist: Informationist Breakout Session

Wed, 04/06/2016 - 1:30pm

In this session Leah will discuss her experiences working on an NIH Supplement for Informationist Services grant, what was accomplished, and what she learned along the way. Within the psychiatric neuroimaging research community, data and resource sharing have become accepted as standard, but issues related to attribution and citing data in novel research are still hindering meaningful reuse. This project aimed to illustrate a system of data identification that would not only allow for proper citation of whole datasets, but maintain the chain of attribution in derived and remixed datasets, allowing for a more complete picture of research impact and author contribution.

Leah Honor is Library Fellow and Informationist Liaison to the Child and Adolescent Neurodevelopment Initiative, University of Massachusetts Medical School.

Data Information Literacy: Developing Data Information Literacy Programs

Wed, 04/06/2016 - 1:30pm

Researchers are under increasing pressure to manage, organize, describe and document their data in ways that enable others to discover, understand and reuse their work. However, the knowledge and skills needed to be successful in these tasks are not often a part of a student's education in college or graduate school. Librarians have an opportunity to address this gap in student's education through developing data literacy programming, but developing effective data literacy programs can seem daunting.

This session will introduce students to a model for creating data literacy programming developed as a part of the Data Information Literacy project. We will begin by reviewing the findings from interviews conducted with faculty and students at four universities. We will then walk through the DIL model step by step. Finally, participants will work through case studies to explore potential opportunities and generate possible approaches to offering data literacy programs.

Jake Carlson is Research Data Services Manager, University of Michigan.

Data Repositories: The Answer that Actually Came with a Question

Wed, 04/06/2016 - 1:30pm

Data repositories: the answer that actually came with a question. Funders, journal publishers, and disciplinary societies recognize the benefits of long-term access to valuable data that could validate results, increase scholarly democracy, or possibly lead to future discoveries. With this in mind, a majority of research now being done in academia is subject to data sharing requirements that the underlying data be publicly accessible, citable, and persevered. As many subject-based data repositories help make this happen, particularly for computing-intensive disciplines with shared infrastructure, such as high-energy physics or real-time climate monitoring, who will manage the "long-tail" of smaller or multi-disciplinary research data?

Our institutional repositories (IR) could be the answer. With a few key policy decisions, and robust review and curation procedures, libraries are well-positioned to help researchers comply with mandates to share and archive their data. Whether you use Hydra, DSpace, Fedora, E-prints, or Digital Commons, this talk will outline important issues to consider as you build new capacity with existing IR infrastructure or a custom data repository, including staffing, curation procedures, and metadata and documentation requirements. Finally it will explore the results and faculty response to launching the Data Repository for the University of Minnesota in 2015, which is based on the Libraries’ existing IR service. Our data submission process, curation procedures, faculty usage, and lessons learned will be placed in context of our broader data management and curation program.

Lisa Johnston is Research Data Management/Curation Lead and Co-Director of the University Digital Conservancy, University of Minnesota.

Breakout Session Descriptions: 2016 University of Massachusetts and New England Area Librarian e-Science Symposium

Wed, 04/06/2016 - 1:00pm

Descriptions of the Breakout Sessions held at the 8th annual University of Massachusetts and New England Area Librarian e-Science Symposium, held Wednesday, April 6, 2016 at the University of Massachusetts Medical School, Worcester, MA. Sessions include Data Information Literacy, Compliance, Data Repositories, and Informationist.

Keynote Presentation: Data Work: Research Data Services in Canada & the U.S.

Wed, 04/06/2016 - 12:15pm

Kendall Roark, PhD, is Assistant Professor and Research Data Specialist at Purdue University. In her keynote presentation, she provides a broad perspective on the research data management services that U.S. and Canadian libraries are implementing.

Event Brochure: 2016 University of Massachusetts and New England Area Librarian e-Science Symposium

Wed, 04/06/2016 - 11:30am

Event brochure for the 8th annual University of Massachusetts and New England Area Librarian e-Science Symposium, held Wednesday, April 6, 2016, at the University of Massachusetts Medical School, Worcester, MA. The brochure includes the symposium event schedule, speaker biographies, and additional resources.

Symposium Agenda: 2016 University of Massachusetts and New England Area Librarian e-Science Symposium

Wed, 04/06/2016 - 11:30am

Agenda for the 8th annual University of Massachusetts and New England Area Librarian e-Science Symposium, held Wednesday, April 6, 2016 at the University of Massachusetts Medical School, Worcester, MA.

Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut

Fri, 04/01/2016 - 2:22pm

Given mounting evidence of the importance of gut-microbiota/immune-cell interactions in immune homeostasis and responsiveness, surprisingly little is known about leukocyte movements to, and especially from, the gut. We address this topic in a minimally perturbant manner using Kaede transgenic mice, which universally express a photoconvertible fluorescent reporter. Transcutaneous exposure of the cervical lymph nodes to violet light permitted punctual tagging of immune cells specifically therein, and subsequent monitoring of their immigration to the intestine; endoscopic flashing of the descending colon allowed specific labeling of intestinal leukocytes and tracking of their emigration. Our data reveal an unexpectedly broad movement of leukocyte subsets to and from the gut at steady state, encompassing all lymphoid and myeloid populations examined. Nonetheless, different subsets showed different trafficking proclivities (e.g., regulatory T cells were more restrained than conventional T cells in their exodus from the cervical lymph nodes). The novel endoscopic approach enabled us to evidence gut-derived Th17 cells in the spleens of K/BxN mice at the onset of their genetically determined arthritis, thereby furnishing a critical mechanistic link between the intestinal microbiota, namely segmented filamentous bacteria, and an extraintestinal autoinflammatory disease.

Chronic kidney disease prevalence in Rivas, Nicaragua: use of a field device for creatinine measurement

Fri, 04/01/2016 - 2:20pm

OBJECTIVE: An epidemic of chronic kidney disease (CKD) has been identified in Pacific coastal regions of Central America, and screening in the field in these low income countries remains logistically problematic. We tested the performance characteristics of a point of care creatinine analyzer compared to standardized serum creatinine measurements.

METHODS: Measurements were conducted in 100 persons from a local health center (n=34) and hospital (n=66) in Rivas, Nicaragua using both a point-of-care analyzer (StatSensor Xpress, Nova Biomedical) and serum creatinine by Jaffe kinetic method with a Roche Cobas Integra 400 analyzer. Percent coefficient of variation, sensitivity and specificity of the StatSensor Xpress were determined.

RESULTS: The average coefficient of variation (CV) was 1.28% for the serum creatinine and CV for the StatSensor Xpress analyzer was 6.8%. The median intra-individual creatinine results obtained with the StatSensor Xpress device were 0.32 mg/dL higher than those by serum creatinine by Jaffe kinetic method. The sensitivity and specificity of the StatSensor Xpress device for identifying subjects with abnormal creatinine (defined as > 1.2 mg/dL) was 100% and 79%, respectively.

CONCLUSIONS: Point of care testing for creatinine demonstrated acceptable repeatability, excellent sensitivity (100%) and modest specificity (79%). Using the point of care testing will allow for generalized screening in the field in low income countries; however, confirmation for elevated levels > 1.2 mg/dL will require a second laboratory test confirmation.

Adjuvant chemotherapy for invasive bladder cancer: a 2013 updated systematic review and meta-analysis of randomized trials

Fri, 04/01/2016 - 2:20pm

CONTEXT: The role of adjuvant chemotherapy remains poorly defined for the management of muscle-invasive bladder cancer (MIBC). The last meta-analysis evaluating adjuvant chemotherapy, conducted in 2005, had limited power to fully support its use.

OBJECTIVE: To update the current evidence of the benefit of postoperative adjuvant cisplatin-based chemotherapy compared with control (ie, surgery alone) in patients with MIBC.

EVIDENCE ACQUISITION: A comprehensive literature review was performed to identify all randomized controlled trials (RCTs) comparing adjuvant cisplatin-based chemotherapy with control for patients with MIBC. The search included the Medline, Embase, Cochrane Central Register of Controlled Trials databases, and abstracts from the American Society of Clinical Oncology meetings up to May 2013. An updated systematic review and meta-analysis was performed.

EVIDENCE SYNTHESIS: A total of 945 patients included in nine RCTs (five previously analyzed, one updated, and three new) were examined. For overall survival, the pooled hazard ratio (HR) across all nine trials was 0.77 (95% confidence interval [CI], 0.59-0.99; p=0.049). For disease-free survival, the pooled HR across seven trials reporting this outcome was 0.66 (95% CI, 0.45-0.91; p=0.014). This disease-free survival benefit was more apparent among those with positive nodal involvement (p=0.010).

CONCLUSIONS: This updated and improved meta-analysis of randomized trials provides further evidence of an overall survival and disease-free survival benefit in patients with MIBC receiving adjuvant cisplatin-based chemotherapy after radical cystectomy.

A systematic review and meta-analysis of adjuvant and neoadjuvant chemotherapy for upper tract urothelial carcinoma

Fri, 04/01/2016 - 2:20pm

CONTEXT: The role of adjuvant chemotherapy (AC) or neoadjuvant chemotherapy (NC) remains poorly defined for the management of upper tract urothelial carcinoma (UTUC), although some studies suggest a benefit.

OBJECTIVE: To update the current evidence on the role of NC and AC for UTUC patients.

EVIDENCE ACQUISITION: We searched for all studies investigating NC or AC for UTUC in Medline, Embase, the Cochrane Central Register of Controlled Trials, and abstracts from the American Society of Clinical Oncology meetings prior to February 2014. A systematic review and meta-analysis were performed.

EVIDENCE SYNTHESIS: No randomized trials investigated the role of AC for UTUC. There was one prospective study (n=36) investigating adjuvant carboplatin-paclitaxel and nine retrospective studies, with a total of 482 patients receiving cisplatin-based or non-cisplatin-based AC after nephroureterectomy (NU) and 1300 patients receiving NU alone. Across three cisplatin-based studies, the pooled hazard ratio (HR) for overall survival (OS) was 0.43 (95% confidence interval [CI], 0.21-0.89; p=0.023) compared with those who received surgery alone. For disease-free survival (DFS), the pooled HR across two studies was 0.49 (95% CI, 0.24-0.99; p=0.048). Benefit was not seen for non-cisplatin-based regimens. For NC, two phase 2 trials demonstrated favorable pathologic downstaging rates, with 3-yr OS and disease-specific survival (DSS) < /= 93%. Across two retrospective studies investigating NC, there was a DSS benefit, with a pooled HR of 0.41 (95% CI, 0.22-0.76; p=0.005).

CONCLUSIONS: There appears to be an OS and DFS benefit for cisplatin-based AC in UTUC. This evidence is limited by the retrospective nature of studies and their relatively small sample size. NC appears to be promising, but more trials are needed to confirm its utility.

PATIENT SUMMARY: After a comprehensive search of studies examining the role of chemotherapy for upper tract urothelial cancer, the pooled evidence shows that cisplatin-based adjuvant chemotherapy was beneficial for prolonging survival.

Unveiling the surgical risk associated with neoadjuvant chemotherapy in bladder cancer

Fri, 04/01/2016 - 2:20pm

William Martin-Doyle participated in this study as a medical student as part of the Senior Scholars research program at the University of Massachusetts Medical School.

Reexamining treatment of high-grade T1 bladder cancer according to depth of lamina propria invasion: a prospective trial of 200 patients

Fri, 04/01/2016 - 2:19pm

BACKGROUND: Management of high-grade T1 (HGT1) bladder cancer represents a major challenge. We studied a treatment strategy according to substaging by depth of lamina propria invasion.

METHODS: In this prospective observational cohort study, patients received initial transurethral resection (TUR), mitomycin-C, and BCG. Subjects with shallower lamina propria invasion (HGT1a) were followed without further surgery, whereas subjects with HGT1b received a second TUR. Association of clinical and histological features with outcomes (primary: progression; secondary: recurrence and cancer-specific survival) was assessed using Cox regression.

RESULTS: Median age was 71 years; 89.5% were males, with 89 (44.5%) cases T1a and 111 (55.5%) T1b. At median follow-up of 71 months, disease progression was observed in 31 (15.5%) and in univariate analysis, substaging, carcinoma in situ, tumour size, and tumour pattern predicted progression. On multivariate analysis only substaging, associated carcinoma in situ, and tumour size remained significant for progression.

CONCLUSIONS: In HGT1 bladder cancer, the strategy of performing a second TUR only in T1b cases results in a global low progression rate of 15.5%. Tumours deeply invading the lamina propria (HGT1b) showed a three-fold increase in risk of progression. Substaging should be routinely evaluated, with HGT1b cases being thoroughly evaluated for cystectomy. Inclusion in the TNM system should also be carefully considered.

Factors influencing the development of antibiotic associated diarrhea in ED patients discharged home: risk of administering IV antibiotics

Fri, 04/01/2016 - 2:19pm

OBJECTIVE: Antibiotic-associated diarrhea (AAD) and Clostridium difficile infection (CDI) are well-known outcomes from antibiotic administration. Because emergency department (ED) visits frequently result in antibiotic use, we evaluated the frequency of AAD/CDI in adults treated and discharged home with new prescriptions for antibiotics to identify risk factors for acquiring AAD/CDI.

METHODS: This prospective multicenter cohort study enrolled adult patients who received antibiotics in the ED and were discharged with a new prescription for antibiotics. Antibiotic-associated diarrhea was defined as 3 or more loose stools for 2 days or more within 30 days of starting the antibiotic. C difficile infection was defined by the detection of toxin A or B within this same period. We used multivariate logistic regression to assess predictors of developing AAD.

RESULTS: We enrolled and followed 247 patients; 45 (18%) developed AAD, and 2 (1%) developed CDI. Patients who received intravenous (IV) antibiotics in the ED were more likely to develop AAD/CDI than patients who did not: 25.7% (95% confidence interval [CI], 17.4-34.0) vs 12.3% (95% CI, 6.8-17.9). Intravenous antibiotics had adjusted odds ratio of 2.73 (95% CI, 1.38-5.43), and Hispanic ethnicity had adjusted odds ratio of 3.04 (95% CI, 1.40-6.58). Both patients with CDI had received IV doses of broad-spectrum antibiotics.

CONCLUSION: Intravenous antibiotic therapy administered to ED patients before discharge was associated with higher rates of AAD and with 2 cases of CDI. Care should be taken when deciding to use broad-spectrum IV antibiotics to treat ED patients before discharge home.

Prostate-specific antigen level, stage or Gleason score: which is best for predicting outcomes after radical prostatectomy, and does it vary by the outcome being measured? Results from Shared Equal Access Regional Cancer Hospital database

Fri, 04/01/2016 - 2:19pm

OBJECTIVES: To assess the ability of preoperative prostate-specific antigen level, Gleason score and stage to predict prostate cancer outcomes beyond biochemical recurrence, specifically castration-resistant prostate cancer, metastases and prostate cancer-specific mortality in radical prostatectomy patients.

METHODS: We carried out a retrospective study of 2735 men in the Shared Equal Access Regional Cancer Hospital database treated by radical prostatectomy from 1988 to 2011 with data available on pathological stage, grade and preoperative prostate-specific antigen. We used Cox hazards analyses to examine the predictive accuracy (c-index) of the preoperative prostate-specific antigen (log-transformed), path Gleason score ( < /= 7, 3 + 4, 4 + 3 and 8-10) and path stage grouping (pT2 negative margins; pT2 positive margins; pT3a negative margins; pT3a positive margins; pT3b; vs positive nodes) to predict biochemical recurrence, castration-resistant prostate cancer, metastases and prostate cancer-specific mortality.

RESULTS: Median follow up was 8.7 years, during which, 937 (34%) had biochemical recurrence, 108 (4%) castration-resistant prostate cancer, 127 (5%) metastases and 68 (2%) prostate cancer-specific mortality. For the outcomes of biochemical recurrence, castration-resistant prostate cancer, metastases and prostate cancer-specific mortality, the c-indices were, respectively: prostate-specific antigen 0.65, 0.66, 0.64 and 0.69; Gleason score 0.66, 0.83, 0.76 and 0.85; and pathological stage group 0.69, 0.76, 0.72 and 0.80.

CONCLUSIONS: Gleason score can predict with very high accuracy prostate cancer-specific mortality in patients undergoing radical prostatectomy. Thus, Gleason score should be given more weight in nomograms to predict prostate cancer-specific mortality. Furthermore, men with a high Gleason score should be given special consideration for adjuvant treatment or referral to clinical trials because of a higher risk of prostate cancer-specific mortality.

PTEN loss in biopsy tissue predicts poor clinical outcomes in prostate cancer

Fri, 04/01/2016 - 2:19pm

OBJECTIVES: To determine whether PTEN status in prostate biopsy represents a predictor of intermediate and long-term oncological outcomes after radical prostatectomy, and whether PTEN status predicts response to androgen deprivation therapy.

METHODS: In a retrospective analysis of 77 men treated by radical prostatectomy who underwent diagnostic biopsy between 1992-2006, biopsy samples were stained for PTEN expression by the PREZEON assay with > 10% staining reported as positive. Cox proportional hazards and log-rank models were used to assess the correlation between PTEN loss and clinical outcomes.

RESULTS: During a median follow-up period after radical prostatectomy of 8.8 years, 39 men (51%) developed biochemical recurrence, four (5%) had castration-resistant prostate cancer, two (3%) had metastasis and two (3%) died from prostate cancer. PTEN loss was not significantly associated with biochemical recurrence (hazard ratio 2.1, 95% confidence interval 0.9-5.1, P = 0.10), but significantly predicted increased risk of castration-resistant prostate cancer, metastasis and prostate cancer-specific mortality (all log-rank, P < 0.0001), and time from androgen deprivation therapy to castration-resistant prostate cancer (log-rank, P = 0.003). No patient without PTEN loss developed metastases or died from prostate cancer.

CONCLUSIONS: PTEN loss at the time of biopsy seems to predict time to development of metastasis, prostate cancer-specific mortality and, for the first time, castration-resistant prostate cancer and response to androgen deprivation therapy after radical prostatectomy. If confirmed by larger studies, this would support the use of PTEN loss as an early marker of aggressive prostate cancer.

Inspiring careers in STEM and healthcare fields through medical simulation embedded in high school science education

Fri, 04/01/2016 - 2:18pm

The most effective ways to promote learning and inspire careers related to science, technology, engineering, and mathematics (STEM) remain elusive. To address this gap, we reviewed the literature and designed and implemented a high-fidelity, medical simulation-based Harvard Medical School MEDscience course, which was integrated into high school science classes through collaboration between medical school and K-12 faculty. The design was based largely on the literature on concepts and mechanisms of self-efficacy. A structured telephone survey was conducted with 30 program alumni from the inaugural school who were no longer in high school. Near-term effects, enduring effects, contextual considerations, and diffusion and dissemination were queried. Students reported high incoming attitudes toward STEM education and careers, and these attitudes showed before versus after gains (P < .05). Students in this modest sample overwhelmingly attributed elevated and enduring levels of impact on their interest and confidence in pursuing a science or healthcare-related career to the program. Additionally, 63% subsequently took additional science or health courses, 73% participated in a job or educational experience that was science related during high school, and 97% went on to college. Four of every five program graduates cited a health-related college major, and 83% offered their strongest recommendation of the program to others. Further study and evaluation of simulation-based experiences that capitalize on informal, naturalistic learning and promote self-efficacy are warranted.

Office-based anesthesia: safety and outcomes

Fri, 04/01/2016 - 2:18pm

The increasing volume of office-based medical and surgical procedures has fostered the emergence of office-based anesthesia (OBA), a subspecialty within ambulatory anesthesia. The growth of OBA has been facilitated by numerous trends, including innovations in medical and surgical procedures and anesthetic drugs, as well as improved provider reimbursement and greater convenience for patients. There is a lack of randomized controlled trials to determine how office-based procedures and anesthesia affect patient morbidity and mortality. As a result, studies on this topic are retrospective in nature. Some of the early literature broaches concerns about the safety of office-based procedures and anesthesia. However, more recent data have shown that care in ambulatory settings is comparable to hospitals and ambulatory surgery centers, especially when offices are accredited and their proceduralists are board-certified. Office-based suites can continue to enhance the quality of care that they deliver to patients by engaging in proper procedure and patient selection, provider credentialing, facility accreditation, and incorporating patient safety checklists and professional society guidelines into practice. These strategies aiming at patient morbidity and mortality in the office setting will be increasingly important as more states, and possibly the federal government, exercise regulatory authority over the ambulatory setting. We explore these trends, their implications for patient safety, strategies for minimizing patient complications and mortality in OBA, and future developments that could impact the field.