Towards computational reproducibility: researcher perspectives on the use and sharing of software

Research software, which includes both source code and executables used as part of the research process, presents a significant challenge for efforts aimed at ensuring reproducibility. In order to inform such efforts, we conducted a survey to better understand the characteristics of research software as well as how it is created, used, and shared by researchers. Based on the responses of 215 participants, representing a range of research disciplines, we found that researchers create, use, and share software in a wide variety of forms for a wide variety of purposes, including data collection, data analysis, data visualization, data cleaning and organization, and automation. More participants indicated that they use open source software than commercial software. While a relatively small number of programming languages (e.g., Python, R, JavaScript, C++, MATLAB) are used by a large number, there is a long tail of languages used by relatively few. Between-group comparisons revealed that significantly more participants from computer science write source code and create executables than participants from other disciplines. Differences between researchers from computer science and other disciplines related to the knowledge of best practices of software creation and sharing were not statistically significant. While many participants indicated that they draw a distinction between the sharing and preservation of software, related practices and perceptions were often not aligned with those of the broader scholarly communications community

Face masks to prevent transmission of respiratory infections : Systematic review and meta-analysis of randomized controlled trials on face mask use

Funding Information: The Strategic Research Council, Academy of Finland, 340551, LL. The Strategic Research Council, Academy of Finland, 340539, HMO. Publisher Copyright: Copyright: © 2022 Ollila et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Objectives To examine the use of face mask intervention in mitigating the risk of spreading respiratory infections and whether the effect of face mask intervention differs in different exposure settings and age groups. Design Systematic review and meta-analysis. We evaluated the risk of bias using the Cochrane Risk of Bias 2 tool (ROB2). Data sources We searched PubMed, Embase, Cochrane Central Register of Controlled Trials, and Web of Science were searched for randomized controlled trials investigating the effect of face masks on respiratory infections published between 1981 and February 9, 2022. We followed the PRISMA 2020 guidelines. Eligibility criteria for selecting studies We included randomized controlled trials investigating the use of face mask intervention in mitigating the risk of spreading respiratory infections across different exposure settings. Results We identified 2,400 articles for screening. 18 articles passed the inclusion criteria for both evidence synthesis and meta-analysis. There were N = 189,145 individuals in the face mask intervention arm and N = 173,536 in the control arm, and the follow-up times ranged from 4 days to 19 months. Our results showed between-study heterogeneity (p < 0.0001). While there was no statistically significant association over all studies when the covariate unadjusted intervention effect estimates were used (RR = 0.977 [0.858–1.113], p = 0.728), our subgroup analyses revealed that a face mask intervention reduced respiratory infections in the adult subgroup (RR = 0.8795 [0.7861–0.9839], p = 0.0249) and in a community setting (RR = 0.890 [0.812–0.975], p = 0.0125). Furthermore, our leave-one-out analysis found that one study biased the results towards a null effect. Consequently, when using covariate adjusted odds ratio estimates to have a more precise effect estimates of the intervention effect to account for differences at the baseline, the results showed that a face mask intervention did reduce respiratory infections when the biasing study was excluded from the analysis (OR = 0.8892 [0.8061–0.9810], p = 0.0192). Conclusion Our findings support the use of face masks particularly in a community setting and for adults. We also observed substantial between-study heterogeneity and varying adherence to protocol. Notably, many studies were subject to contamination bias thus affecting the efficacy of the intervention, that is when also some controls used masks or when the intervention group did not comply with mask use leading to a downward biased effect of treatment receipt and efficacy.Peer reviewe

Exercise training in group 2 pulmonary hypertension: which intensity and what modality

Pulmonary hypertension (PH) due to left-sided heart disease (LSHD) is a common and disconcerting occurrence. For example, both heart failure (HF) with preserved and reduced ejection fraction (HFpEF and HFrEF) often lead to PH as a consequence of a chronic elevation in left atrial filling pressure. A wealth of literature demonstrates the value of exercise training (ET) in patients with LSHD, which is particularly robust in patients with HFrEF and growing in patients with HFpEF. While the effects of ET have not been specifically explored in the LSHD–PH phenotype (i.e., composite pathophysiologic characteristics of patients in this advanced disease state), the overall body of evidence supports clinical application in this subgroup. Moderate intensity aerobic ET significantly improves peak oxygen consumption, quality of life and prognosis in patients with HF. Resistance ET significantly improves muscle strength and endurance in patients with HF, which further enhance functional capacity. When warranted, inspiratory muscle training and neuromuscular electrical stimulation are becoming recognized as important components of a comprehensive rehabilitation program. This review will provide a detailed account of ET programing considerations in patients with LSHD with a particular focus on those concomitantly diagnosed with PH

Aliskiren, enalapril, or aliskiren and enalapril in heart failure

BACKGROUND Among patients with chronic heart failure, angiotensin-converting–enzyme (ACE) inhibitors reduce mortality and hospitalization, but the role of a renin inhibitor in such patients is unknown. We compared the ACE inhibitor enalapril with the renin inhibitor aliskiren (to test superiority or at least noninferiority) and with the combination of the two treatments (to test superiority) in patients with heart failure and a reduced ejection fraction. METHODS After a single-blind run-in period, we assigned patients, in a double-blind fashion, to one of three groups: 2336 patients were assigned to receive enalapril at a dose of 5 or 10 mg twice daily, 2340 to receive aliskiren at a dose of 300 mg once daily, and 2340 to receive both treatments (combination therapy). The primary composite outcome was death from cardiovascular causes or hospitalization for heart failure. RESULTS After a median follow-up of 36.6 months, the primary outcome occurred in 770 patients (32.9%) in the combination-therapy group and in 808 (34.6%) in the enalapril group (hazard ratio, 0.93; 95% confidence interval [CI], 0.85 to 1.03). The primary outcome occurred in 791 patients (33.8%) in the aliskiren group (hazard ratio vs. enalapril, 0.99; 95% CI, 0.90 to 1.10); the prespecified test for noninferiority was not met. There was a higher risk of hypotensive symptoms in the combination-therapy group than in the enalapril group (13.8% vs. 11.0%, P=0.005), as well as higher risks of an elevated serum creatinine level (4.1% vs. 2.7%, P=0.009) and an elevated potassium level (17.1% vs. 12.5%, P&lt;0.001). CONCLUSIONS In patients with chronic heart failure, the addition of aliskiren to enalapril led to more adverse events without an increase in benefit. Noninferiority was not shown for aliskiren as compared with enalapri

Evaluation of Data Sharing After Implementation of the International Committee of Medical Journal Editors Data Sharing Statement Requirement.

Importance The benefits of responsible sharing of individual-participant data (IPD) from clinical studies are well recognized, but stakeholders often disagree on how to align those benefits with privacy risks, costs, and incentives for clinical trialists and sponsors. The International Committee of Medical Journal Editors (ICMJE) required a data sharing statement (DSS) from submissions reporting clinical trials effective July 1, 2018. The required DSSs provide a window into current data sharing rates, practices, and norms among trialists and sponsors. Objective To evaluate the implementation of the ICMJE DSS requirement in 3 leading medical journals: JAMA, Lancet, and New England Journal of Medicine (NEJM).Design, setting, and participantsThis is a cross-sectional study of clinical trial reports published as articles in JAMA, Lancet, and NEJM between July 1, 2018, and April 4, 2020. Articles not eligible for DSS, including observational studies and letters or correspondence, were excluded. A MEDLINE/PubMed search identified 487 eligible clinical trials in JAMA (112 trials), Lancet (147 trials), and NEJM (228 trials). Two reviewers evaluated each of the 487 articles independently. Exposure Publication of clinical trial reports in an ICMJE medical journal requiring a DSS. Main outcomes and measures The primary outcomes of the study were declared data availability and actual data availability in repositories. Other captured outcomes were data type, access, and conditions and reasons for data availability or unavailability. Associations with funding sources were examined. Results A total of 334 of 487 articles (68.6%; 95% CI, 64%-73%) declared data sharing, with nonindustry NIH-funded trials exhibiting the highest rates of declared data sharing (89%; 95% CI, 80%-98%) and industry-funded trials the lowest (61%; 95% CI, 54%-68%). However, only 2 IPD sets (0.6%; 95% CI, 0.0%-1.5%) were actually deidentified and publicly available as of April 10, 2020. The remaining were supposedly accessible via request to authors (143 of 334 articles [42.8%]), repository (89 of 334 articles [26.6%]), and company (78 of 334 articles [23.4%]). Among the 89 articles declaring that IPD would be stored in repositories, only 17 (19.1%) deposited data, mostly because of embargo and regulatory approval. Embargo was set in 47.3% of data-sharing articles (158 of 334), and in half of them the period exceeded 1 year or was unspecified. Conclusions and relevance Most trials published in JAMA, Lancet, and NEJM after the implementation of the ICMJE policy declared their intent to make clinical data available. However, a wide gap between declared and actual data sharing exists. To improve transparency and data reuse, journals should promote the use of unique pointers to data set location and standardized choices for embargo periods and access requirements

Case-Finding tool for COPD in LMIC (COLA) - translation and cross-cultural adaptation into Brazilian Portuguese language

OBJECTIVE: To translate and cross-culturally adapt the COPD in Low- and middle-income countries (LMICs) Assessment (COLA) questionnaire into Brazilian Portuguese, a case-finding instrument for chronic obstructive pulmonary disease (COPD). METHODS: Translation and cross-cultural adaptation were completed in six steps: the original version was translated into Brazilian Portuguese by two native speakers of the target language; the translated versions were synthesized; back-translation was performed by two native speakers of the original language; the back-translation and the Brazilian Portuguese version of the COLA were reviewed and harmonized by an expert committee of specialists; and, then, the pre-final version was tested by 30 health professionals who were asked if the items were clear to understand. The acceptability, clarity, and understandability of the translated version were evaluated. A final review of the questionnaire was produced by the authors and approved by the author of the original questionnaire. RESULTS: Some idiomatic, semantic, and experiential inconsistencies were identified and properly adjusted. Item 3 was considered the most unclear item (23,3%). Items 7, 8, and 9 presented clarity above 80% (93%, 90%, and 90%, respectively). Suggestions were discussed and incorporated into the tool and COLA was found to be clear and easy to understand. CONCLUSIONS: The Brazilian version of the COLA was easily understood by healthcare professionals and adapted to Brazilian culture. Translation and cultural adaptation of the COLA instrument into Brazilian Portuguese can be an important case-finding instrument for chronic obstructive pulmonary disease in Brazil

Improving Newborn Survival in Southern Tanzania (INSIST) trial; community-based maternal and newborn care economic analysis.

Despite health systems improvements in Tanzania, gaps in the continuum of care for maternal, newborn and child health persist. Recent improvements have largely benefited those over one month of age, leading to a greater proportion of under-five mortality in newborns. Community health workers providing home-based counselling have been championed as uniquely qualified to reach the poorest. We provide financial and economic costs of a volunteer home-based counselling programme in southern Tanzania. Financial costs of the programme were extracted from project accounts. Ministry of Health and Social Welfare costs associated with programme implementation were collected based on staff and project monthly activity plans. Household costs associated with facility-based delivery were also estimated based on exit interviews with post-natal women. Time spent on the programme by implementers was assessed by interviews conducted with volunteers and health staff. The programme involved substantial design and set-up costs. The main drivers of set-up costs were activities related to volunteer training. Total annualized costs (design, set-up and implementation) amounted to nearly US$300 000 for financial costs and just over US$400 000 for economic costs. Volunteers (n = 842) spent just under 14 hours per month on programme-related activities. When volunteer time was valued under economic costs, this input amounted to just under half of the costs of implementation. The economic consequences of increased service use to households were estimated at US$36 985. The intervention cost per mother-newborn pair visited was between US$12.60 and US$19.50, and the incremental cost per additional facility-based delivery ranged from US$85.50 to US$137.20 for financial and economic costs (with household costs). Three scale-up scenarios were considered, with the financial cost per home visit respectively varying from$1.44 to $3.21 across scenarios. Cost-effectiveness compares well with supply-side initiatives to increase coverage of facility-based deliveries, and the intervention would benefit from substantial economies of scale