Adventures in data citation: sorghum genome data exemplifies the new gold standard

Scientific progress is driven by the availability of information, which makes it essential that data be broadly, easily and rapidly accessible to researchers in every field. In addition to being good scientific practice, provision of supporting data in a convenient way increases experimental transparency and improves research efficiency by reducing unnecessary duplication of experiments. There are, however, serious constraints that limit extensive data dissemination. One such constraint is that, despite providing a major foundation of data to the advantage of entire community, data producers rarely receive the credit they deserve for the substantial amount of time and effort they spend creating these resources. In this regard, a formal system that provides recognition for data producers would serve to incentivize them to share more of their data. The process of data citation, in which the data themselves are cited and referenced in journal articles as persistently identifiable bibliographic entities, is a potential way to properly acknowledge data output. The recent publication of several sorghum genomes in Genome Biology is a notable first example of good data citation practice in the field of genomics and demonstrates the practicalities and formatting required for doing so. It also illustrates how effective use of persistent identifiers can augment the submission of data to the current standard scientific repositories

Prospectus, November 28, 1979

STARCASTLE\u27 FEATURED IN FIRST PRESENTING SHOW; Week in Review: Across the globe, In the nation, Around the state; Salt of the Earth : controversial film at PC; Iranians air grievances against Shah; Briefs: Board summary listed, Women Forum meets Sat.; Letters to the Editor: Letter reasons vs. Nolen\u27s logic, Voter writes to reveal real Kennedy opinion; Campus Question: How would you handle Irainian situation?; Classifieds; NFL playoffs make blurry pic; Sports shorts; Cobras split games, play at home Fri.; Winter survival tips can keep you alive; Reviews: After big talk, \u27Tusk\u27 gets low grade, \u27Keep the Fire\u27 keeps Loggins\u27 formula; Transfer students need financial aids transcripthttps://spark.parkland.edu/prospectus_1979/1002/thumbnail.jp

The PLOS ONE collection on machine learning in health and biomedicine: Towards open code and open data

Recent years have seen a surge of studies in machine learning in health and biomedicine, driven by digitalization of healthcare environments and increasingly accessible computer systems for conducting analyses. Many of us believe that these developments will lead to significant improvements in patient care. Like many academic disciplines, however, progress is hampered by lack of code and data sharing. In bringing together this PLOS ONE collection on machine learning in health and biomedicine, we sought to focus on the importance of reproducibility, making it a requirement, as far as possible, for authors to share data and code alongside their papers

Promoting physical activity in a multi-ethnic population at high risk of diabetes: the 48-month PROPELS randomised controlled trial.

BackgroundPhysical activity is associated with a reduced risk of type 2 diabetes and cardiovascular disease but limited evidence exists for the sustained promotion of increased physical activity within diabetes prevention trials. The aim of the study was to investigate the long-term effectiveness of the Walking Away programme, an established group-based behavioural physical activity intervention with pedometer use, when delivered alone or with a supporting mHealth intervention.MethodsThose at risk of diabetes (nondiabetic hyperglycaemia) were recruited from primary care, 2013-2015, and randomised to (1) Control (information leaflet); (2) Walking Away (WA), a structured group education session followed by annual group-based support; or (3) Walking Away Plus (WAP), comprising WA annual group-based support and an mHealth intervention delivering tailored text messages supported by telephone calls. Follow-up was conducted at 12 and 48 months. The primary outcome was accelerometer measured ambulatory activity (steps/day). Change in primary outcome was analysed using analysis of covariance with adjustment for baseline, randomisation and stratification variables.ResultsOne thousand three hundred sixty-six individuals were randomised (median age = 61 years, ambulatory activity = 6638 steps/day, women = 49%, ethnic minorities = 28%). Accelerometer data were available for 1017 (74%) individuals at 12 months and 993 (73%) at 48 months. At 12 months, WAP increased their ambulatory activity by 547 (97.5% CI 211, 882) steps/day compared to control and were 1.61 (97.5% CI 1.05, 2.45) times more likely to achieve 150 min/week of moderate-to-vigorous physical activity. Differences were not maintained at 48 months. WA was no different to control at 12 or 48 months. Secondary anthropometric and health outcomes were largely unaltered in both intervention groups apart from small reductions in body weight in WA (~ 1 kg) at 12- and 48-month follow-up.ConclusionsCombining a pragmatic group-based intervention with text messaging and telephone support resulted in modest changes to physical activity at 12 months, but changes were not maintained at 48 months.Trial registrationISRCTN 83465245 (registered on 14 June 2012)

Ten Simple Rules for Taking Advantage of Git and GitHub.

Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available [1,2]. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others [3,4]. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular web-based platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use.Biotechnology and Biological Sciences Research CouncilThis is the final version of the article. It first appeared from Public Library of Science via https://doi.org/10.1371/journal.pcbi.1004947

Arthroscopic hip surgery compared with physiotherapy and activity modification for the treatment of symptomatic femoroacetabular impingement: multicentre randomised controlled trial.

OBJECTIVE: To compare arthroscopic hip surgery with physiotherapy and activity modification for improving patient reported outcome measures in patients with symptomatic femoroacetabular impingement (FAI). DESIGN: Two group parallel, assessor blinded, pragmatic randomised controlled trial. SETTING: Secondary and tertiary care centres across seven NHS England sites. PARTICIPANTS: 222 participants aged 18 to 60 years with symptomatic FAI confirmed clinically and with imaging (radiography or magnetic resonance imaging) were randomised (1:1) to receive arthroscopic hip surgery (n=112) or a programme of physiotherapy and activity modification (n=110). Exclusion criteria included previous surgery, completion of a physiotherapy programme targeting FAI within the preceding 12 months, established osteoarthritis (Kellgren-Lawrence grade ≥2), and hip dysplasia (centre-edge angle <20 degrees). INTERVENTIONS: Participants in the physiotherapy group received a goal based programme tailored to individual patient needs, with emphasis on improving core stability and movement control. A maximum of eight physiotherapy sessions were delivered over five months. Participants in the arthroscopic surgery group received surgery to excise the bone that impinged during hip movements, followed by routine postoperative care. MAIN OUTCOME MEASURES: The primary outcome measure was the hip outcome score activities of daily living subscale (HOS ADL) at eight months post-randomisation, with a minimum clinically important difference between groups of 9 points. Secondary outcome measures included additional patient reported outcome measures and clinical assessment. RESULTS: At eight months post-randomisation, data were available for 100 patients in the arthroscopic hip surgery group (89%) and 88 patients in the physiotherapy programme group (80%). Mean HOS ADL was 78.4 (95% confidence interval 74.4 to 82.3) for patients randomised to arthroscopic hip surgery and 69.2 (65.2 to 73.3) for patients randomised to the physiotherapy programme. After adjusting for baseline HOS ADL, age, sex, and study site, the mean HOS ADL was 10.0 points higher (6.4 to 13.6) in the arthroscopic hip surgery group compared with the physiotherapy programme group (P<0.001)). No serious adverse events were reported in either group. CONCLUSIONS: Patients with symptomatic FAI referred to secondary or tertiary care achieve superior outcomes with arthroscopic hip surgery than with physiotherapy and activity modification. TRIAL REGISTRATION: ClinicalTrials.gov NCT01893034.NIHR BRC oxfor