Mandated data archiving greatly improves access to research data

The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with about 8 days delay and some disagreement with authors. Given the long term benefits of data accessibility to the academic community, we believe that journal based mandatory data archiving policies and mandatory data availability statements should be more widely adopted

Mortality in adult children of parents with alcohol use disorder: a nationwide register study

Research suggests that adult children of parents with harmful alcohol use are at increased risk for premature death. This national cohort study investigated mortality in adult children of parents with alcohol use disorder (AUD), adjusting for sociodemographic variables. The study used 1973 to 2018 data from Swedish national registers to compare mortality risk in children who had >= 1 parent with AUD (ICD-10 code F10 and its ICD-8 and ICD-9 equivalents) (n = 122,947) and those who did not (n = 2,298,532). A Cox regression model adjusted for year of birth, sex, parental education, and childhood loss of a parent was used. Before the age of 18 years, about 5% of children born in Sweden lived with >= 1 parent who had a clinical diagnosis of AUD. Overall mortality was higher in adult children of parents with AUD: hazard ratio (HR) 1.76, 95% confidence interval (CI) 1.71-1.82. Mortality remained elevated after adjustments for sociodemographic factors (HR 1.45, 95% CI 1.40-1.50). Children of parents with AUD had increased mortality from all investigated causes. The highest excess risk was for death from drug-related causes (excluding accidental poisonings) (HR 3.08, 95% CI 2.74-3.46). For most causes, mortality was higher if the mother had AUD than if the father had AUD. Patterns of mortality were similar in both sexes. This study provides evidence that parental AUD raises the risk of offspring mortality from preventable causes such as drug use, suicide (HR 2.16, 95% CI 1.98-2.36), accident (HR 2.00, 95% CI 1.87-2.13), and assault (HR 1.76, 95% CI 1.38-2.24).</p

The Demographics of Terrestrial Planets in the Venus Zone

Understanding the physical characteristics of Venus, including its atmosphere, interior, and its evolutionary pathway with respect to Earth, remains a vital component for terrestrial planet evolution models and the emergence and/or decline of planetary habitability. A statistical strategy for evaluating the evolutionary pathways of terrestrial planets lies in the atmospheric characterization of exoplanets, where the sample size provides sufficient means for determining required runaway greenhouse conditions. Observations of potential exoVenuses can help confirm hypotheses about Venus' past, as well as the occurrence rate of Venus-like planets in other systems. Additionally, the data from future Venus missions, such as DAVINCI, EnVision, and VERITAS, will provide valuable information regarding Venus, and the study of exoVenuses will be complimentary to these missions. To facilitate studies of exoVenus candidates, we provide a catalog of all confirmed terrestrial planets in the Venus Zone, including transiting and non-transiting cases, and quantify their potential for follow-up observations. We examine the demographics of the exoVenus population with relation to stellar and planetary properties, such as the planetary radius gap. We highlight specific high-priority exoVenus targets for follow-up observations including: TOI-2285 b, LTT 1445 A c, TOI-1266 c, LHS 1140 c, and L98-59 d. We also discuss follow-up observations that may yield further insight into the Venus/Earth divergence in atmospheric properties.Comment: 27 pages, 7 figures, accepted for publication in the Astronomical Journa

"We can't expect much": Childbearing women's 'horizon of expectations' of the health system in rural Vietnam.

Highlights • Responsiveness centres on understanding peoples' ‘legitimate’ expectations of their health system. • Healthcare-related expectations are shaped at the intersection of social, temporal, and spatial ‘locations’. • Expectations are also shaped by social norms, and market-driven practices and forces in the health system. • There is a need for health system actors to consider the impact of market forces on responsive care provision. • Active citizen participation and contestation is also needed to establish ‘legitimate’ expectations of care

GoMiner: a resource for biological interpretation of genomic and proteomic data

We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources

Tissue-Specific Differences in Human Transfer RNA Expression

Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms