The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary

The sharing and documentation of cardiovascular research data are essential for efficient use and reuse of data, thereby aiding scientific transparency, accelerating the progress of cardiovascular research and healthcare, and contributing to the reproducibility of research results. However, challenges remain. This position paper, written on behalf of and approved by the German Cardiac Society and German Centre for Cardiovascular Research, summarizes our current understanding of the challenges in cardiovascular research data management (RDM). These challenges include lack of time, awareness, incentives, and funding for implementing effective RDM; lack of standardization in RDM processes; a need to better identify meaningful and actionable data among the increasing volume and complexity of data being acquired; and a lack of understanding of the legal aspects of data sharing. While several tools exist to increase the degree to which data are findable, accessible, interoperable, and reusable (FAIR), more work is needed to lower the threshold for effective RDM not just in cardiovascular research but in all biomedical research, with data sharing and reuse being factored in at every stage of the scientific process. A culture of open science with FAIR research data should be fostered through education and training of early-career and established research professionals. Ultimately, FAIR RDM requires permanent, long-term effort at all levels. If outcomes can be shown to be superior and to promote better (and better value) science, modern RDM will make a positive difference to cardiovascular science and practice. The full position paper is available in the supplementary materials.

Needs assessment towards research data management at the Medical Faculty of the University of Freiburg – Data of the BE-KONFORM study

In order to investigate employees' needs of the Medical Faculty of the University of Freiburg regarding research data management, the BE-KONFORM study was performed in a two-step approach. First, guideline-based qualitative video interviews with four researchers were performed to identify key constructs of relevance. Second, a standardized online survey was conducted from 1^st to 15^th of November 2020 based on e-mail invitation by the dean and a faculty newsletter. The questionnaire was provided bilingual (English and German) using a backward-forward translation method, no reminders and incentives were used to increase the response rate. The online survey was programmed in REDCap and was accessible via online link. The target population were members of the Medical Faculty (listed in the newsletter mailing list) regardless of the type of working contract signed. The final dataset contains 236 complete cases (90% German and 10% English). The study includes a randomised module asking for data publication (group A) or not (group B). 113 cases were randomized into group A and 99% of them consented to the publication of the collected research data in anonymized form (n=112). The dataset comprised questions about work-related characteristics (professional status, working experience, scientific field of work), data management-related items (definition of research data management, type of data used, type of storage used for saving data, use of electronic laboratory notebooks), experience and attitudes towards data publication in data repositories, as well as needs and preferences regarding research data management support. The produced data offers the possibility to connect with other data collected in this field in other contexts (faculties or universities).

Netboost: Boosting-Supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease

State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. We present Netboost, a three-step dimension reduction technique. First, a boosting-based filter is combined with the topological overlap measure to identify the essential edges of the network. Second, sparse hierarchical clustering is applied on the selected edges to identify modules and finally module information is aggregated by the first principal components. We demonstrate the application of the newly developed Netboost in combination with CoxBoost for survival prediction of DNA methylation and gene expression data from 180 acute myeloid leukemia (AML) patients and show, based on cross-validated prediction error curve estimates, its prediction superiority over variable selection on the full dataset as well as over an alternative clustering approach. The identified signature related to chromatin modifying enzymes was replicated in an independent dataset, the phase II AMLSG 12-09 study. In a second application we combine Netboost with Random Forest classification and improve the disease classification error in RNA-sequencing data of Huntington's disease mice. Netboost is a freely available Bioconductor R package for dimension reduction and hypothesis generation in high-dimensional omics applications.

Systemic Immunomodulating Therapies for Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis: A Systematic Review and Meta-analysis

Importance

Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) are rare but severe adverse reactions with high mortality. There is no evidence-based treatment, but various systemic immunomodulating therapies are used.

Objectives

To provide an overview on possible immunomodulating treatments for SJS/TEN and estimate their effects on mortality compared with supportive care.

Data Sources

A literature search was performed in December 2012 for articles published in MEDLINE, MEDLINE Daily, MEDLINE Inprocess, Web of Science, EMBASE, Scopus, and the Cochrane Library (Central) from January 1990 through December 2012, and updated in December 2015, in the English, French, Spanish, and German languages looking for treatment proposals for SJS/TEN. Other sources were screened manually.

Study Selection

Initially, 157 randomized and nonrandomized studies on therapies (systemic immunomodulating therapies or supportive care) for SJS/TEN were selected.

Data Extraction and Synthesis

Relevant data were extracted from articles. Authors were contacted for further information. Finally, 96 studies with sufficient information regarding eligibility and adequate quality scores were considered in the data synthesis. All steps were performed independently by 2 investigators. Meta-analyses on aggregated study data (random-effects model) and individual patient data (IPD) (logistic regression adjusted for confounders) were performed to assess therapeutic efficacy. In the analysis of IPD, 2 regression models, stratified and unstratified by study, were fitted.

Main Outcomes and Measures

Therapy effects on mortality were expressed in terms of odds ratios (ORs) with 95% CIs.

Results

Overall, 96 studies (3248 patients) were included. Applied therapies were supportive care or systemic immunomodulating therapies, including glucocorticosteroids, intravenous immunoglobulins, cyclosporine, plasmapheresis, thalidomide, cyclophosphamide, hemoperfusion, tumor necrosis factor inhibitors, and granulocyte colony-stimulating factors. Glucocorticosteroids were associated with a survival benefit for patients in all 3 analyses but were statistically significant in only one (aggregated data: OR, 0.5; 95%% CI, 0.3-1.01; IPD, unstratified: OR, 0.7; 95% CI, 0.5-0.97; IPD, stratified: OR, 0.8; 95% CI, 0.4-1.3). Despite the low patient size, cyclosporine was associated with a promising significant result in the only feasible analysis of IPD (unstratified model) (OR, 0.1; 95% CI, 0.0-0.4). No beneficial findings were observed for other therapies, including intravenous immunoglobulins.

Conclusions and Relevance

Although all analyses, including the unstratified model, had limitations, glucocorticosteroids and cyclosporine were the most promising systemic immunomodulating therapies for SJS/TEN. Further evaluation in prospective studies is required. However, this work provides a comprehensive overview on proposed systemic immunomodulating treatments for SJS/TEN, which is of great relevance for treating physicians.

Costs of cloud computing for a biometry department. A case study

BACKGROUND

"Cloud" computing providers, such as the Amazon Web Services (AWS), offer stable and scalable computational resources based on hardware virtualization, with short, usually hourly, billing periods. The idea of pay-as-you-use seems appealing for biometry research units which have only limited access to university or corporate data center resources or grids.

OBJECTIVES

This case study compares the costs of an existing heterogeneous on-site hardware pool in a Medical Biometry and Statistics department to a comparable AWS offer.

METHODS

The "total cost of ownership", including all direct costs, is determined for the on-site hardware, and hourly prices are derived, based on actual system utilization during the year 2011. Indirect costs, which are difficult to quantify are not included in this comparison, but nevertheless some rough guidance from our experience is given. To indicate the scale of costs for a methodological research project, a simulation study of a permutation-based statistical approach is performed using AWS and on-site hardware.

RESULTS

In the presented case, with a system utilization of 25-30 percent and 3-5-year amortization, on-site hardware can result in smaller costs, compared to hourly rental in the cloud dependent on the instance chosen. Renting cloud instances with sufficient main memory is a deciding factor in this comparison.

CONCLUSIONS

Costs for on-site hardware may vary, depending on the specific infrastructure at a research unit, but have only moderate impact on the overall comparison and subsequent decision for obtaining affordable scientific computing resources. Overall utilization has a much stronger impact as it determines the actual computing hours needed per year. Taking this into ac count, cloud computing might still be a viable option for projects with limited maturity, or as a supplement for short peaks in demand.

Application of microarray analysis on computer cluster and cloud platforms

BACKGROUND

Analysis of recent high-dimensional biological data tends to be computationally intensive as many common approaches such as resampling or permutation tests require the basic statistical analysis to be repeated many times. A crucial advantage of these methods is that they can be easily parallelized due to the computational independence of the resampling or permutation iterations, which has induced many statistics departments to establish their own computer clusters. An alternative is to rent computing resources in the cloud, e.g. at Amazon Web Services.

OBJECTIVES

In this article we analyze whether a selection of statistical projects, recently implemented at our department, can be efficiently realized on these cloud resources. Moreover, we illustrate an opportunity to combine computer cluster and cloud resources.

METHODS

In order to compare the efficiency of computer cluster and cloud implementations and their respective parallelizations we use microarray analysis procedures and compare their runtimes on the different platforms.

RESULTS

Amazon Web Services provide various instance types which meet the particular needs of the different statistical projects we analyzed in this paper. Moreover, the network capacity is sufficient and the parallelization is comparable in efficiency to standard computer cluster implementations.

CONCLUSION

Our results suggest that many statistical projects can be efficiently realized on cloud resources. It is important to mention, however, that workflows can change substantially as a result of a shift from computer cluster to cloud computing.

Die Mobilisation des linken Hemikolons von medial

INTRODUCTION

Laparoscopic surgery of the colon is becoming more and more popular. However, regarding sigmoid resection, controversy remains concerning the extent of mobilisation, particularly regarding the splenic flexure. We developed a technique for anterior resection that meets all surgical standards: the anterior approach.

MATERIALS AND METHODS

From October 1999 to March 2001, 50 patients with benign diseases of the colon underwent laparoscopically assisted sigmoid resection. A completely anterior approach for mobilisation of the left hemicolon was used in all cases. Positioning the patients in Trendelenburg position on the extreme right side enabled primary ligation of the inferior mesenteric vein and artery as well as complete mobilisation of the splenic flexure from the middle. A transanal circular stapling device was used to reanastomose the colon 10-12 cm from the anus.

RESULTS

There were conversion and complication rates of 10% each, and three patients needed to be reoperated. The median operating time was 180 min. Patients could be dismissed on the 14th postoperative day.

CONCLUSION

To establish an operative standard, this technique has so far been used only for benign colon diseases. According to our experience, we think that it meets all oncological standards. Use of this technique in the treatment of malignant diseases seems therefore justified.

The urinary bladder angiotensin system: response to infusions of angiotensin I and angiotensin-converting enzyme inhibitors

The circulating and urinary bladder tissue concentrations of angiotensin I (ANG I) and angiotensin II [ANG-(1-8)] were examined in anesthetized Sprague-Dawley male rats given an intravenous bolus infusion of either ANG I, the angiotensin-converting enzyme (ACE) inhibitors enalaprilat or ramiprilat, or saline. The mean concentrations of ANG I and ANG-(1-8) were markedly higher in the urinary bladder tissue than in whole blood. There was a significant increase in the concentration of ANG I and ANG-(1-8), both in the urinary bladder tissue and the circulation, after the ANG I infusion. Both ACE inhibitors were associated with an increase in the concentration of whole blood ANG I; however, tissue ANG I levels were significantly increased only following ACE inhibition with ramiprilat but not with enalaprilat. Both plasma and urinary bladder tissue ANG-(1-8) levels decreased significantly following ACE inhibition, but only with ramiprilat. The elevated urinary bladder tissue levels of ANG I and ANG-(1-8) at baseline, compared with circulating levels, and the maintenance of ANG-(1-8) in bladder tissue in the face of inhibition of the circulatory renin-angiotensin system with enalaprilat support the presence of an autocrine/paracrine renin-angiotensin system in the urinary bladder. Under the current experimental conditions, ramiprilat appears to have enhanced bladder activity compared with enalaprilat.

[Bisphosphonate therapy of Paget's disease of bone with pamidronate]

BACKGROUND

Paget's disease of bone is a disease with massive focal increase of bone turnover. Bisphosphonates like etidronate inhibit of osteoclastic bone resorption and are therefore established in the treatment of Paget's disease. The aminobisphosphonate pamidronate is 100 times more potent than etidronate. To assess the therapeutic potential for Paget's disease, we have investigated the long-term efficacy of two different dosages of pamidronate.

PATIENTS AND METHODS

40 consecutive patients with Paget's disease received a total dose of either 180 mg (n = 21) or 100 mg (n = 19) of pamidronate i.v. over 9 or 5 days respectively in two independent phases of a prospective trial. Efficacy and side effects were monitored for a follow up period of up to two years.

RESULTS

For both dosages a significant reduction of urinary 24-h-hydroxyprolin excretion and serum alkaline phosphatase (AP) levels as parameters of disease activity was recorded. AP levels fell to a minimum of 31 +/- 3% (180 mg) and 41 +/- 5% (100 mg) of pretreatment values, respectively. Two years after treatment, a significant reduction of disease activity could still be detected. Side effects, including transient fever, head ache or bone pain occurred in one third of the patients.

CONCLUSION

Pamidronate treatment for Paget's disease of bone leads to a sustained inhibition of elevated bone turnover.

Glomerular function and structure in the sodium-replete and sodium-deplete uninephrectomized spontaneously hypertensive rat: effect of blood pressure reduction, glomerular structure, and blood pressure reduction

To assess the effects of chronic dietary sodium restriction and blood pressure reduction on glomerular function and structure during the pathogenesis of hypertensive renal disease, experiments were conducted in uninephrectomized (UNX) spontaneously hypertensive rats (SHR) using the dihydropyridine calcium antagonist manidipine. Male SHRs underwent UNX at age 10-11 weeks and subsequently were assigned to one of four groups: sodium-replete (0.4%); sodium-replete and a predetermined antihypertensive dose of manidipine (20 mg/kg body weight); sodium-deplete (0.09%); and sodium-deplete and manidipine (20 mg/kg body weight). Twelve weeks later, renal morphologic and functional studies were performed. Sodium restriction had no significant effect on systolic blood pressure, but creatinine clearance and urinary protein excretion were decreased. Importantly, mean glomerular volume and the prevalence of mesangial expansion were lower with sodium restriction. This occurred in the presence of high concentrations of plasma and renal tissue angiotensin II. Manidipine significantly reduced systolic blood pressure in the sodium-replete and sodium-deplete UNX-SHRs. This therapy was not associated with significant changes in creatinine clearance and urinary protein excretion in the sodium-deplete or sodium-replete UNX-SHRs. The prevalence of mesangial expansion in the sodium-replete UNX-SHR was approximately 50% lower with manidipine. Plasma and renal tissue angiotensin II concentrations were not affected by the drug. In the sodium-deplete UNX-SHR, the prevalence of mesangial expansion was not reduced further by manidipine. However, plasma and renal tissue angiotensin II concentrations were increased significantly.(ABSTRACT TRUNCATED AT 250 WORDS)

Intraoperative catheter thrombolysis as an adjunct to surgical revascularisation for infrainguinal limb-threatening ischaemia

The objective of this study was to assess the benefits of intraoperative thrombolysis (IOL) on patients with acute leg ischaemia. This study was conducted in the Department of Cardiovascular Surgery, Inselspital, Berne, Switzerland. IOL was prospectively assessed in 25 patients with infrainguinal limb-threatening ischaemia due to acute thrombosis of atherosclerotic lesions and aneurysms (44%), occluded grafts (32%), arterial injuries (12%), delayed embolism (8%) and trash foot (8%). Three hundred and seventy-five thousand units of urokinase were delivered over 30 min with inflow occlusion to the profunda femoral artery in 8%, to the calf arteries via exposed trifurcation in 88% and to the pedal arch via exposed posterior tibial artery at the ankle in 8% of the patients. This was followed by graft thrombectomy in 24%, femoropopliteal bypass in 60%, intraoperative percutaneous transluminal angioplasty in 12% and vein patch angioplasty in 16%. Chief outcome measures were: postoperative morbidity; mortality; patency and limb salvage up to a maximum of 2 years. Postoperative bleeding complications occurred in two patients (8%) and consisted of two wound haematomas. Four patients died within 30 days after IOL, but no death could be attributed to IOL. All remaining patients were followed with a mean follow-up time of 10.9 months. The patency and limb salvage rate remained stable at 71 and 86% after 6 and 2 months, respectively. Conclusions were that IOL followed by surgical inflow restoration is a straightforward procedure for limb-threatening ischaemia with rewarding results regarding side effects, patency and limb salvage.