The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages

Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers (https://github.com/neurogenomics/rworkflows). rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action. Each time it is triggered by a push to a GitHub repository, it automatically creates virtual machines across multiple OS, installs all dependencies, runs code checks, builds/deploys a documentation website, and builds/deploys version-controlled containers with a built-in RStudio interface. Additional analyses demonstrate that >50% of all R packages are only available via GitHub, highlighting the need for accessible solutions. Thus, rworkflows greatly reduces the barriers to implementing robust and reproducible best practices

The Cannon Hall Muscat grape

The Canon Hall Muscat table grape grown for export in Western Australia is consistent with the early descriptions and the present appearance of the original  Cannon Hall Muscat vine, and is clearly the same variety. It has the diploid number of chromosomes and the use of its name for tetraploid sports of Muscat of Alexandria is not justified.Die Rebensorte Cannon Hall MuscatDie Tafeltraube Canon Hall Muscat, die in Westaustralien zum Export angebaut wird, gleicht der ursprünglichen Cannon-Hall-Muscat-Rebe, da die erstgenannte eindeutig den alten Beschreibungen und dem heutigen Aussehen der letzteren entspricht. Canon Hall Muscat ist diploid, und deshalb sollte dieser Name nicht für tetraploide Mutanten von Muscat of Alexandria gebraucht werden

EpiCompare: R package for the comparison and quality control of epigenomic peak files

Summary EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just one line of code and provides all results of the analysis in a single interactive HTML report. EpiCompare thus enables downstream analysis of multiple epigenomic datasets in a simple, effective and user-friendly manner. Availability and Implementation EpiCompare is available on Bioconductor (≥ v3.15): https://bioconductor.org/packages/release/bioc/html/EpiCompare.html All source code is publically available via GitHub: https://github.com/neurogenomics/EpiCompare Documentation website https://neurogenomics.github.io/EpiCompare EpiCompare DockerHub repository: https://hub.docker.com/repository/docker/neurogenomicslab/epicompare Competing Interest Statement The authors have declared no competing interest

Rational Topological Design for Fluorescence Enhancement upon Aggregation of Distyrylfuran Derivatives

A series of 2,5-distyrylfuran derivatives bearing pentafluorophenyl- and cyanovinyl units have been synthesized for aggregation-induced emission (AIE). The effect of the type and extent of the supramolecular connections on the AIE of the furan derivatives were examined and correlated with their X-ray crystal structures. It was found that the simultaneous presence of cyano and perfluorophenyl units strongly enhances the fluorescence upon aggregation. Single-crystal X-ray diffraction analysis confirmed that C — H⋅⋅⋅F, F⋅⋅⋅F, C — H⋅⋅⋅nitrile, Ar⋅⋅⋅ArF (Ar=aryl, ArF=fluoroaryl), and nitrile⋅⋅⋅ArF intra- and intermolecular interactions drive the topology of the molecule and that solid-state supramolecular contacts favor AIE of the furan derivatives

Genetic origins of social networks in rhesus macaques

This is the final version of the article. Available from the publisher via the DOI in this record.Sociality is believed to have evolved as a strategy for animals to cope with their environments. Yet the genetic basis of sociality remains unclear. Here we provide evidence that social network tendencies are heritable in a gregarious primate. The tendency for rhesus macaques, Macaca mulatta, to be tied affiliatively to others via connections mediated by their social partners - analogous to friends of friends in people - demonstrated additive genetic variance. Affiliative tendencies were predicted by genetic variation at two loci involved in serotonergic signalling, although this result did not withstand correction for multiple tests. Aggressive tendencies were also heritable and were related to reproductive output, a fitness proxy. Our findings suggest that, like humans, the skills and temperaments that shape the formation of multi-agent relationships have a genetic basis in nonhuman primates, and, as such, begin to fill the gaps in our understanding of the genetic basis of sociality.We thank Bonn Aure, Jacqueline Buhl, Monica Carlson, Matthew McConnell, Elizabeth Maldonado, David Paulsen, Cecilia Penedo & the Caribbean Primate Research Center (CPRC) for assistance, and Roger Mundry for the use of PSAM software. The authors were supported by NIMH grant R01-MH089484, an Incubator Award from the Duke Institute for Brain Sciences, and a Duke Center for Interdisciplinary Decision Sciences Fellowship to LJNB. The CPRC is supported by grant 8-P40 OD012217-25 from the National Center for Research Resources (NCRR) and the Office of Research Infrastructure Programs (ORIP) of the National Institutes of Health

Genetic influences on social attention in free-ranging rhesus macaques

An ethological approach to attention predicts that organisms orient preferentially to valuable sources of information in the environment. For many gregarious species, orienting to other individuals provides valuable social information but competes with food acquisition, water consumption and predator avoidance. Individual variation in vigilance behaviour in humans spans a continuum from inattentive to pathological levels of interest in others. To assess the comparative biology of this behavioural variation, we probed vigilance rates in free-ranging macaques during water drinking, a behaviour incompatible with the gaze and postural demands of vigilance. Males were significantly more vigilant than females. Moreover, vigilance showed a clear genetic component, with an estimated heritability of 12%. Monkeys carrying a relatively infrequent ‘long’ allele of TPH2, a regulatory gene that influences serotonin production in the brain, were significantly less vigilant compared to monkeys that did not carry the allele. These findings resonate with the hypothesis that the serotonin pathway regulates vigilance in primates and by extension provoke the idea that individual variation in vigilance and its underlying biology may be adaptive rather than pathological

Water wave transmission and energy dissipation by a floating plate in the presence of overwash

A numerical model, based on the two-phase incompressible Navier–Stokes equations, is used to study transmission of regular water waves by a thin floating plate in two dimensions. The model is shown to capture the phenomenon of waves overwashing the plate, and the generation of turbulent bores on the upper plate surface. It is validated against laboratory experimental measurements, in terms of the transmitted wave field and overwash depths, for a set of incident wave periods and steepness values. Corresponding simulations are performed for a thick plate that does not experience overwash, which are validated using experiments where an edge barrier prevents thin-plate overwash. The model accurately reproduces (i) the linear relationship between the transmitted and incident amplitudes for the thick plate, and (ii) the decrease in proportion of incident-wave transmission for the thin plate, as incident steepness increases. Model outputs are used to link the decreasing transmission to wave-energy dissipation in the overwash, particularly where bores collide, and in the surrounding water, particularly at the plate ends. It is shown that most energy dissipation occurs in the overwash for the shortest incident waves tested, and in the surrounding water for the longer incident waves. Further, evidence is given that overwash suppresses plate motions, and causes asymmetry in plate rotations.Filippo Nelli, Luke G. Bennetts, David M. Skene and Alessandro Toffol