Seek and you may (not) find: A multi-institutional analysis of where research data are shared

Research data sharing has become an expected component of scientific research and scholarly publishing practice over the last few decades, due in part to requirements for federally funded research. As part of a larger effort to better understand the workflows and costs of public access to research data, this project conducted a high-level analysis of where academic research data is most frequently shared. To do this, we leveraged the DataCite and Crossref application programming interfaces (APIs) in search of Publisher field elements demonstrating which data repositories were utilized by researchers from six academic research institutions between 2012-2022. In addition, we also ran a preliminary analysis of the quality of the metadata associated with these published datasets, comparing the extent to which information was missing from metadata fields deemed important for public access to research data. Results show that the top 10 publishers accounted for 89.0% to 99.8% of the datasets connected with the institutions in our study. Known data repositories, including institutional data repositories hosted by those institutions, were initially lacking from our sample due to varying metadata standards and practices. We conclude that the metadata quality landscape for published research datasets is uneven; key information, such as author affiliation, is often incomplete or missing from source data repositories and aggregators. To enhance the findability, interoperability, accessibility, and reusability (FAIRness) of research data, we provide a set of concrete recommendations that repositories and data authors can take to improve scholarly metadata associated with shared datasets.

Data Curation Network: A Cross-Institutional Staffing Model for Curating Research Data

Funders increasingly require that data sets arising from sponsored research must be preserved and shared, and many publishers either require or encourage that data sets accompanying articles are made available through a publicly accessible repository. Additionally, many researchers wish to make their data available regardless of funder requirements both to enhance their impact and also to propel the concept of open science. However, the data curation activities that support these preservation and sharing activities are costly, requiring advanced curation practices, training, specific technical competencies, and relevant subject expertise. Few colleges or universities will be able to hire and sustain all of the data curation expertise locally that its researchers will require, and even those with the means to do more will benefit from a collective approach that will allow them to supplement at peak times, access specialized capacity when infrequently-curated types arise, and stabilize service levels to account for local staff transition, such as during turn-over periods. The Data Curation Network (DCN) provides a solution for partners of all sizes to develop or to supplement local curation expertise with the expertise of a resilient, distributed network, and creates a funding stream to both sustain central services and support expansion of distributed expertise over time. This paper presents our next steps for piloting the DCN, scheduled to launch in the spring of 2018 across nine partner institutions. Our implementation plan is based on planning phase research performed from 2016-2017 that monitored the types, disciplines, frequency, and curation needs of data sets passing through the curation services at the six planning phase institutions. Our DCN implementation plan includes a well-coordinated and tiered staffing model, a technology-agnostic submission workflow, standardized curation procedures, and a sustainability approach that will allow the DCN to prevail beyond the grant-supported implementation phase as a curation-as-service model.

Giving datasets context: a comparison study of institutional repositories that apply varying degrees of curation

This research study compared four academic libraries’ approaches to curating the metadata of dataset submissions in their institutional repositories and classified them in one of four categories: no curation, pre-ingest curation, selective curation, and post-ingest curation. The goal is to understand the impact that curation may have on the quality of user-submitted metadata. The findings were 1) the metadata elements varied greatly between institutions, 2) repositories with more options for authors to contribute metadata did not result in more metadata contributed, 3) pre- or post-ingest curation process could have a measurable impact on the metadata but are difficult to separate from other factors, and 4) datasets submitted to a repository with pre- or post-ingest curation more often included documentation.

How are we Measuring Up? Evaluating Research Data Services in Academic Libraries

INTRODUCTION In the years since the emergence of federal funding agency data management and sharing requirements (http://datasharing.sparcopen.org/data), research data services (RDS) have expanded to dozens of academic libraries in the United States. As these services have matured, service providers have begun to assess them. Given a lack of practical guidance in the literature, we seek to begin the discussion with several case studies and an exploration of four approaches suitable to assessing these emerging services. DESCRIPTION OF PROGRAM This article examines five case studies that vary by staffing, drivers, and institutional context in order to begin a practice-oriented conversation about how to evaluate and assess research data services in academic libraries. The case studies highlight some commonly discussed challenges, including insufficient training and resources, competing demands for evaluation efforts, and the tension between evidence that can be easily gathered and that which addresses our most important questions. We explore reflective practice, formative evaluation, developmental evaluation, and evidence-based library and information practice for ideas to advance practice. NEXT STEPS Data specialists engaged in providing research data services need strategies and tools with which to make decisions about their services. These range from identifying stakeholder needs to refining existing services to determining when to extend and discontinue declining services. While the landscape of research data services is broad and diverse, there are common needs that we can address as a community. To that end, we have created a community-owned space to facilitate the exchange of knowledge and existing resources.

How Important is Data Curation? Gaps and Opportunities for Academic Libraries

INTRODUCTION Data curation may be an emerging service for academic libraries, but researchers actively “curate” their data in a number of ways—even if terminology may not always align. Building on past userneeds assessments performed via survey and focus groups, the authors sought direct input from researchers on the importance and utilization of specific data curation activities. METHODS Between October 21, 2016, and November 18, 2016, the study team held focus groups with 91 participants at six different academic institutions to determine which data curation activities were most important to researchers, which activities were currently underway for their data, and how satisfied they were with the results. RESULTS Researchers are actively engaged in a variety of data curation activities, and while they considered most data curation activities to be highly important, a majority of the sample reported dissatisfaction with the current state of data curation at their institution. DISCUSSION Our findings demonstrate specific gaps and opportunities for academic libraries to focus their data curation services to more effectively meet researcher needs. CONCLUSION Research libraries stand to benefit their users by emphasizing, investing in, and/or heavily promoting the highly valued services that may not currently be in use by many researchers.

Self-Expanding Stents for Malignant Dysphagia

Self-expanding metallic stents have been employed successfully for vascular, urethral, and biliary strictures. In a prospective study we examined the efficacy of the 16 mm Wallstent for palliation of malignant dysphagia.

Eight patients with severe dysphagia due to advanced primary (four) or secondary (four) oesophageal malignant disease were recruited and nine Wallstents were inserted (one patient required two). Dysphagia was reduced in all but one patient, who died after oesophageal perforation; a second patient had a self-limiting bout of haematemesis. Two patients required subsequent treatment for tumour ingrowth but five had no further palliative therapy from stent insertion to time of death.

With careful patient selection and skilful application, a 16 mm self-expanding metal endoprosthesis affords effective palliation in malignant oesophageal obstruction.

Cruciate Retaining compared with Posterior Stabilised Nexgen total knee arthroplasty: results at 10 years in a matched cohort

INTRODUCTION Debate has persisted for many years about whether to sacrifice or replace the posterior cruciate ligament when performing total knee arthroplasty. A paucity of long-term follow-up studies comparing outcomes between cruciate-retaining and posterior-stabilised knees exist. We aimed to compare results at ten-year follow-up. METHODS A matched paired study comparing a cohort of 107 Zimmer Nexgen® Cruciate Retaining (CR) patients with a cohort of 107 Nexgen Posterior-Stabilised (PS) knees matched for age, sex, body mass index and preoperative American Knee Society score was undertaken. All patients underwent independent clinical assessment and knee society scoring preoperatively and at 1, 3, 5, 7 and 10 years postoperatively. RESULTS Fifty-three patients (49.5%) in the CR group and 44 patients (41.1%) in the PS group were alive at 10-year follow-up. There were no significant differences between the CR and PS groups with regards to functional assessment (P = 0.95), overall range of movement (P = 0.46) or patient satisfaction (P = 1.0) at 10 years. However, there was a significantly better score improvement in range of movement in PS knees compared with CR knees (P = 0.027). There were six revisions (5.6%) in the PS group and 1 (0.93%) in the CR group (P = 0.12). Both CR and PS knees showed excellent survivorship with no significant difference at 10 years (P = 0.068). CONCLUSIONS There were no significant differences in functional score, overall range of motion or patient satisfaction between the Nexgen cruciate retaining and posterior stabilised total knee arthroplasty at 10-year follow-up. However, PS knees had a greater score improvement in range of motion compared with CR knees.

Prevalence and significance of CYP2C19*2 and CYP2C19*17 alleles in a New Zealand acute coronary syndrome population

BACKGROUND

High on-treatment platelet reactivity has been associated with poor outcomes following acute coronary syndromes (ACS). Both the loss of function CYP2C19*2 allele and the gain of function CYP2C19*17 allele along with a range of clinical characteristics have been associated with variation in the response to clopidogrel.

AIM

The study aims to examine the frequency of CYP2C19 variants and understand the factors associated with on-treatment platelet reactivity in a New Zealand ACS population.

METHODS

We prospectively enrolled 312 ACS patients. We collected clinical characteristics and measured on-treatment platelet reactivity using two validated point-of-care assays, VerifyNow and Multiplate. DNA was extracted and CYP2C19*2 and *17 alleles were identified using real-time polymerase chain reaction.

RESULTS

CYP2C19*2 or CYP2C19*17 alleles were observed in 101 (32%) and 106 (34%) of patients, respectively, with significant differences in distribution by ethnicity. In Maori and Pacific Island patients, 47% (confidence interval (CI) 31-63%) had CYP2C19*2 and 11% (CI 4-19%) CYP2C19*17 compared with 26% (CI 19-32%) and 41% (CI 32-49%) in white people. Carriage of CYP2C19*2 alleles was associated with higher levels of platelet reactivity measured by either assay, but we observed no relationship between platelet reactivity and CYP2C19*17. In multivariate analysis diabetes, clopidogrel dose and CYP2C19*2 status were all significant independent predictors of platelet reactivity.

CONCLUSIONS

Both CYP2C19*2 and *17 were common in a New Zealand ACS population, with CYP2C19*2 observed in almost half the Maori and Pacific Island patients. CYP2C19*2, diabetes and clopidogrel dose were independent contributors to on-treatment platelet reactivity.

Prasugrel inhibits platelet-enhanced pro-inflammatory CD4+ T cell responses in humans

While platelets have well characterized effects on monocytes, the effect of platelet activation on CD4+ T-cell differentiation and cytokine production is not clear. To examine the effects of platelet T-cell interactions on T-cell phenotype, and whether these interactions were altered by prasugrel, we conducted a randomized, double-blind, placebo-controlled crossover study in healthy subjects. At baseline the addition of platelets to CD4+ T-cells resulted in an increase in the release of pro-inflammatory cytokine IFN-γ (192% increase in IFN-γ levels, p = 0.01) and pro-inflammatory CD4+ phenotypes, (38% and 58% increase in Th1 and Th17 phenotypic markers respectively, p = 0.01) but no change in Tregs. Prasugrel abolished the effects of platelets on CD4+ T-cells with similar levels of pro-inflammatory cytokines and cell numbers to T-cells stimulated. Antiplatelet therapy may provide therapeutic benefit both from direct platelet inhibition and also through indirect effects on immune response development.

Methodological considerations for the assessment of ADP induced platelet aggregation using the Multiplate® analyser

Factors affecting the Multiplate® assay's analytical precision have not been well defined. We investigated the effect of methodological factors on the measurement of ADP-induced platelet aggregation using the Multiplate® assay. ADP-induced platelet aggregation was analysed in whole blood using the Multiplate® assay. We tested the reproducibility of measurement, the effect of different anticoagulants (hirudin, citrate and heparin) and the effect of time delay (15, 30, 45, 60, 120 and 180 minutes) between sampling and analysis in patients. The use of a manual calibrated pipette with the Multiplate® analyser was also tested. The mean coefficient of variation (CV) using the manufacturers recommended methods was 10.8 ± 8.7% (n = 30). When compared to hirudin (359.5 ± 309 AU*min) the use of heparin (521.0 ± 316 AU*min, p = 0.0015) increased platelet aggregation, while the use of sodium citrate (245.0 ± 209 AU*min, p = 0.003) decreased the platelet aggregation (n = 20). The addition of CaCl2 to the citrate-anticoagulated blood resulted in platelet aggregation levels similar to hirudin. Platelet aggregation varied with time delay (n = 20). When compared to platelet aggregation at 30 minutes (391.1 ± 283 AU*min), platelet aggregation was reduced at 60 minutes (335.2 ± 251.6 AU*min, p < 0.05), 120 minutes (198.8 ± 122.9 AU*min, p < 0.001) and 180 minutes (160.7 ± 92 AU*min, p < 0.001). The use of a manual calibrated pipette did not significantly reduce the mean CV in the assay (n = 20). Methodological factors such as the anticoagulant used and the time delay should be standardised where possible to reduce variability, and allow thresholds derived from one study to be comparable across multiple studies.

Developing E-science and Research Services and Support at the University of Minnesota Health Sciences Libraries

This paper describes the development and implementation of e-science and research support services in the Health Sciences Libraries (HSL) within the Academic Health Center (AHC) at the University of Minnesota (UMN). A review of the broader e-science initiatives within the UMN demonstrates the needs and opportunities that the University Libraries face while building knowledge, skills, and capacity to support e-research. These experiences are being used by the University Libraries administration and HSL to apply support for the growing needs of researchers in the health sciences. Several research areas that would benefit from enhanced e-science support are described. Plans to address the growing e-research needs of health sciences researchers are also discussed.

Investigations on the percutaneous absorption of the antidepressant rolipram in vitro and in vivo

In vitro experiments using full-thickness human skin showed that it was feasible to deliver therapeutic amounts of the new antidepressant drug rolipram. Simple transdermal devices were constructed, and the presence of isopropyl myristate (IPM) in a silicone adhesive (Dow Corning X7-2920) enhanced the flux across excised human skin. The steady-state fluxes from adhesive mixtures containing 0, 5, and 10% IPM were 3, 5.2, and 6 micrograms/cm2/hr, respectively. The in vitro experiments were confirmed in a clinical study involving six healthy male volunteers. The formulations tested were an alcoholic solution and adhesive patches containing 5 and 10% IPM. The dose of drug administered was 0.5 mg/cm2 and the device size 25 cm2. Blood samples were withdrawn over a 24-hr period and analyzed using radioimmunoassay. The topical applications were well tolerated, with only mild or no side effects. A lag time of approximately 2 hr was found for the detection of rolipram in the plasma (detection limit, 50 pg/ml). Interindividual variations both for the peak drug levels and throughout the delivery were quite high but this magnitude of variation has been observed in many other transdermal studies. Plasma levels between 1 and 2 ng/ml were found for all formulations and the AUC0-30 hr was significantly higher for the patch containing 5% IPM.

The effects of ions and hypothalamic factors on the in vitro activity of rainbow trout prolactin cells

The influence of various ions and of dopamine and somatostatin on the in vitro activity of rainbow trout prolactin (PRL) cells was investigated. There was a positive correlation between medium Ca2+ concentration and both PRL synthesis and release up to 1.8 mM Ca2+, above which no further increase occurred. Even with no Ca2+ in the medium, there was still PRL secretion during the incubation. Replacement of Ca2+ with Ba2+ in the medium did not elevate either total PRL levels or PRL release above that in Ca2 +)-free medium. Neither elevated Mg2+ nor increased medium K+ had any effect on PRL synthesis or release. Dopamine inhibited PRL release but not synthesis, as did the D2 receptor agonist, apomorphine. However, the D2 receptor antagonist, (+)-butaclamol was unable to prevent the action of dopamine on PRL release. Somatostatin inhibited both PRL synthesis and release in normal Ca2+ medium, but release only in reduced Ca2+ medium. Thus, Ca2+, dopamine, and somatostatin may all have roles in regulating prolactin secretion in this fish. In addition, oPRL reduced trout PRL release, indicating a possible negative feedback mechanism for trout PRL secretion.

The intracellular regulation of prolactin cell function in the rainbow trout, Salmo gairdneri

The mechanisms for regulation of prolactin (PRL) secretion in the rainbow trout were investigated. The inhibitory action of dopamine on PRL release in vitro was enhanced by GTP and dopamine also reduced pituitary cAMP content. Forskolin increased both PRL release and cAMP content in vitro, but this effect was prevented by dopamine and did not occur in Ca2+-free medium. The cAMP analogue, dbcAMP increased PRL synthesis in low Ca2+ medium, though release was not significantly affected. The calcium ionophore, A23187, increased PRL release, but this effect was not seen with flunarizine, a voltage-dependent Ca2+-channel blocker. The calmodulin blocker, pimozide, increased PRL synthesis and pituitary PRL content in vivo and a second calmodulin blocker, trifluoperazine, also increased PRL synthesis, though not percentage release, in vitro. Both drugs elevated pituitary cAMP levels. These results indicate an involvement of agonist-dependent Gi proteins, Ca2+, calmodulin, and cAMP in the control of PRL cells in this teleost.