Does testosterone impair mens' cognitive empathy? Evidence from two large-scale randomized controlled trials Supplementary material, bioRxiv, 2019-01-13
The capacity to infer the mental states of others (known as cognitive empathy) is essential for social interactions, and a well-known theory proposes that it is negatively affected by intrauterine testosterone exposure. Furthermore, previous studies reported that testosterone administration impaired cognitive empathy in healthy adults, and that a biomarker of prenatal testosterone exposure (finger digit ratios) moderated the effect. However, empirical support for the relationship has relied on small-sample studies with mixed evidence. We investigate the reliability and generalizability of the relationship in two large-scale double-blind placebo-controlled experiments in young men (N=243 and N=400), using two different testosterone administration protocols. We find no evidence that cognitive empathy is impaired by testosterone administration or associated with digit ratios. With an unprecedented combined sample size, these results counter current theories and previous high-profile reports, and demonstrate that previous investigations of this topic have been statistically underpowered.
biorxiv neuroscience 200-500-users 2019Does testosterone impair men’s cognitive empathy? Evidence from two large-scale randomized controlled trials, bioRxiv, 2019-01-13
AbstractThe capacity to infer others’ mental states (known as “mind reading” and “cognitive empathy”) is essential for social interactions across species, and its impairment characterizes psychopathological conditions such as autism spectrum disorder and schizophrenia. Previous studies reported that testosterone administration impaired cognitive empathy in healthy humans, and that a putative biomarker of prenatal testosterone exposure (finger digit ratios) moderated the effect. However, empirical support for the relationship has relied on small-sample studies with mixed evidence. We investigate the reliability and generalizability of the relationship in two large-scale double-blind placebo-controlled experiments in young men (N=243 and N=400), using two different testosterone administration protocols. We find no evidence that cognitive empathy is impaired by testosterone administration or associated with digit ratios. With an unprecedented combined sample size, these results counter current theories and previous high-profile reports, and demonstrate that previous investigations of this topic have been statistically underpowered.
biorxiv neuroscience 200-500-users 2019Highly-accurate long-read sequencing improves variant detection and assembly of a human genome, bioRxiv, 2019-01-13
AbstractThe major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.
biorxiv genomics 200-500-users 2019Tracking the popularity and outcomes of all bioRxiv preprints, bioRxiv, 2019-01-13
AbstractResearchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage. Here, we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find preprints are being downloaded more than ever before (1.1 million tallied in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of 2,100 per month. We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between journal impact factor and preprint downloads. Lastly, we developed Rxivist.org, a web application providing multiple ways of interacting with preprint metadata.
biorxiv scientific-communication-and-education 500+-users 2019Deep neural networks for interpreting RNA binding protein target preferences, bioRxiv, 2019-01-12
Deep learning has become a powerful paradigm to analyze the binding sites of regulatory factors including RNA-binding proteins (RBPs), owing to its strength to learn complex features from possibly multiple sources of raw data. However, the interpretability of these models, which is crucial to improve our understanding of RBP binding preferences and functions, has not yet been investigated in significant detail. We have designed a multitask and multimodal deep neural network for characterizing in vivo RBP binding preferences. The model incorporates not only the sequence but also the region type of the binding sites as input, which helps the model to boost the prediction performance. To interpret the model, we quantified the contribution of the input features to the predictive score of each RBP. Learning across multiple RBPs at once, we are able to avoid experimental biases and to identify the RNA sequence motifs and transcript context patterns that are the most important for the predictions of each individual RBP. Our findings are consistent with known motifs and binding behaviors of RBPs and can provide new insights about the regulatory functions of RBPs.
biorxiv bioinformatics 0-100-users 2019Hunter-gatherer genomes reveal diverse demographic trajectories following the rise of farming in East Africa, bioRxiv, 2019-01-12
A major outstanding question in human prehistory is the fate of hunting and gathering populations following the rise of agriculture and pastoralism. Genomic analysis of ancient and contemporary Europeans suggests that autochthonous groups were either absorbed into or replaced by expanding farmer populations. Many of the hunter-gatherer populations persisting today live in Africa, perhaps because agropastoral transitions occurred later on the continent. Here, we present the first genomic data from the Chabu, a relatively isolated and marginalized hunting-and-gathering group from the Southwestern Ethiopian highlands. The Chabu are a distinct genetic population that carry the highest levels of Southwestern Ethiopian ancestry of any extant population studied thus far. This ancestry has been in situ for at least 4,500 years. We show that the Chabu are undergoing a severe population bottleneck which began around 40 generations ago. We also study other Eastern African populations and demonstrate divergent patterns of historical population size change over the past 60 generations between even closely related groups. We argue that these patterns demonstrate that, unlike in Europe, Africans hunter-gatherers responded to agropastoralism with diverse strategies.
biorxiv genetics 0-100-users 2019