Assessing the Prevalence and Archival Rate of URIs to Git Hosting Platforms in Scholarly Publications

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, Software Heritage is working to archive public source code, but there is value in archiving the surrounding ephemera that provide important context to the code while maintaining their original URIs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.64 million publications. Authors have increasingly included GHP URIs in scholarly publications and, in 2021, one in five arXiv publications included a GitHub URI. Next, we analyzed the archival coverage of scholarly GHP URIs in Web archives and Software Heritage. Overall, 79.15% of GHP URIs were archived in the Web archives while only 62.06% of GHP URIs were archived in Software Heritage. We used a machine learning classifier to identify other Open Access Data and Software (OADS) URIs outside of the four GHPs previously studied. We found almost 50,000 unique OADS hostnames and more non-GHP OADS URIs than GHP URIs. The prevalence of OADS URIs and vast number of unique hostnames points to the utility of a classifier to identify OADS URIs as opposed to manual enumeration. Lastly, we found a statistically significant relationship between the popularity of a GitHub repository as determined by engagement metrics and archival coverage indicating that less popular repositories less likely to be archived and, thus, more vulnerable to being unrecoverable. The growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera

The Impact Of Social Media On Fraternal Organizations: Ethical Concerns

This case study concerns how the personal behavior of students involved in fraternal organizations is depicted in social media, and how that behavior impacts the organization and its image. The legal and ethical implications of individuals’ behaviors in social media has become a major issue for many organizations. This case follows an example of a fraternal organization and how the governing body must handle the information members post on social media. The mission of many fraternal organizations is to champion or contribute to specific causes. Members’ social media postings may reflect poorly on the organization and may not always align with the principles of the organization. This case examines how those postings impact the organization, and what it can do to mitigate the effects. The ethical issues that can affect the actions of both the governing body and the members are probed throughout the case

It’s Not Just GitHub

Les publications papier ne sont plus la seule forme de recherche En raison des initiatives récentes par lieu de publication et du financement en institutions, les jeux de données en libre accès et les produits logiciels sont de plus en plus répandus dans les publications savantes. Toutefois, les sources trouvées sur le Web en direct ne sont pas permanentes

Scaling up depot medroxyprogesterone acetate (DMPA): a systematic literature review illustrating the AIDED model

BACKGROUND: Use of depot medroxyprogesterone acetate (DMPA), often known by the brand name Depo-Provera, has increased globally, particularly in multiple low- and middle-income countries (LMICs). As a reproductive health technology that has scaled up in diverse contexts, DMPA is an exemplar product innovation with which to illustrate the utility of the AIDED model for scaling up family health innovations. METHODS: We conducted a systematic review of the enabling factors and barriers to scaling up DMPA use in LMICs. We searched 11 electronic databases for academic literature published through January 2013 (n = 284 articles), and grey literature from major health organizations. We applied exclusion criteria to identify relevant articles from peer-reviewed (n = 10) and grey literature (n = 9), extracting data on scale up of DMPA in 13 countries. We then mapped the resulting factors to the five AIDED model components: ASSESS, INNOVATE, DEVELOP, ENGAGE, and DEVOLVE. RESULTS: The final sample of sources included studies representing variation in geographies and methodologies. We identified 15 enabling factors and 10 barriers to dissemination, diffusion, scale up, and/or sustainability of DMPA use. The greatest number of factors were mapped to the ASSESS, DEVELOP, and ENGAGE components. CONCLUSIONS: Findings offer early empirical support for the AIDED model, and provide insights into scale up of DMPA that may be relevant for other family planning product innovations

Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

A de novo paradigm for male infertility

Genetics of Male Infertility Initiative (GEMINI) consortium: Donald F. Conrad, Liina Nagirnaja, Kenneth I. Aston, Douglas T. Carrell, James M. Hotaling, Timothy G. Jenkins, Rob McLachlan, Moira K. O’Bryan, Peter N. Schlegel, Michael L. Eisenberg, Jay I. Sandlow, Emily S. Jungheim, Kenan R. Omurtag, Alexandra M. Lopes, Susana Seixas, Filipa Carvalho, Susana Fernandes, Alberto Barros, João Gonçalves, Iris Caetano, Graça Pinto, Sónia Correia, Maris Laan, Margus Punab, Ewa Rajpert-De Meyts, Niels Jørgensen, Kristian Almstrup, Csilla G. Krausz & Keith A. Jarvi.De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10−5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10−4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.This project was funded by The Netherlands Organization for Scientific Research (918-15-667) to J.A.V. as well as an Investigator Award in Science from the Wellcome Trust (209451) to J.A.V. a grant from the Catherine van Tussenbroek Foundation to M.S.O. a grant from MERCK to R.S. a UUKi Rutherford Fund Fellowship awarded to B.J.H. and the German Research Foundation Clinical Research Unit “Male Germ Cells” (DFG, CRU326) to C.F. and F.T. This project was also supported in part by funding from the Australian National Health and Medical Research Council (APP1120356) to M.K.O.B., by grants from the National Institutes of Health of the United States of America (R01HD078641 to D.F.C. and K.I.A., P50HD096723 to D.F.C.) and from the Biotechnology and Biological Sciences Research Council (BB/S008039/1) to D.J.E.info:eu-repo/semantics/publishedVersio

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Depression among diabetic women in urban centers in Mexico and the United States of America: a comparative study

OBJECTIVE: To compare the prevalence and patterns of depressive symptoms among women with type 2 diabetes in Puebla, Mexico, and Chicago, United States. METHODS: Two cross-sectional studies were conducted independently, in Puebla (September 2010-March 2011) and in Chicago (January-July 2010). Depression symptomatology was evaluated in a random sample of 241 women self-reporting type 2 diabetes in Puebla and a convenience sample of 121 women of Mexican descent seeking care for type 2 diabetes in Chicago. Depressive symptomatology was measured by the Center for Epidemiologic Studies Depression Scale administered in either English or Spanish. Women were similarly socioeconomically disadvantaged with low education levels in both locations. RESULTS: The Chicago sample of women reported higher levels of depression than the Puebla sample (38% versus 17%, P < 0.0001). Among those with comorbid depression and diabetes in both sites, minimal variations in symptoms were observed. Depressive symptoms, specifically the subjective element (feeling sad) and symptoms associated with diabetes (fatigue and sleep problems) were heightened in both groups. More frequent reporting of "feeling fearful" was statistically significant in Puebla. CONCLUSIONS: Despite a higher prevalence of depression among Mexican immigrant women with diabetes in the United States compared to Mexico, there was little variation in their depressive symptoms, regardless of residence. However, women in Mexico did report a higher incidence of fear. Screening for depression in patients with diabetes should take into account symptoms of fatigue and sleep and the bi-directional relationship of depression and diabetes