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

(E)-5-(2-Thienylmethyl­eneamino)quinolin-8-ol

Two mol­ecules of the title compound, C14H10N2OS, are hydrogen bonded about a center of inversion. In the mol­ecule, the two aromatic rings are twisted by 37.27 (5)° with respect to one another. The azomethine bond is in the E configuration

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

Partial characterization of Agrobacterium vitis strains

Seventeen strains of Agrobacterium vitis (formerly classified A. tumefaciens biovar 3) were characterized using part of the T-DNA and virA regions of the Ti plasmid as probes. All strains except one were of the wide host range (WHR) strains and were classified into two groups depending on their ability to utilize octopine or nopaline. These WHR type oncogenic strains had homology with the limited host range type (LHR) virA gen of A. vitis but not with the WHR virA gene of A. tumefaciens. The frequency of T-DNA excision in some Agrobacterium strains was estimated with the plasmid pTMA which mimics T-DNA excision from Ti plasmid DNA. In an A. vitis strain isolated from grapevine, T-DNA excision occurred after co-cultivation with grapevine tissues, but not with acetosyringone. In contrast, in A. tumefaciens, T-DNA excision occurred after co-cultivation with acetosyringone, but not with grapevine tissue

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

Single-nucleus RNA sequencing (snRNA-seq) is used as an alternative to single-cell RNA-seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-seq is able to detect cellular state in human tissue. Indeed, snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's disease. Our comparison of microglia from single cells and single nuclei of four human subjects reveals that, although most genes show similar relative abundances in cells and nuclei, a small population of genes (∼1%) is depleted in nuclei compared to whole cells. This population is enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously identified microglial-disease-associated genes. Given the low sensitivity of snRNA-seq to detect many activation genes, we conclude that snRNA-seq is not suited for detecting cellular activation in microglia in human disease

A Peer to Peer Protocol for Online Dispute Resolution over Storage Consumption

In bilateral accounting of resource consumption both the consumer and provider independently measure the amount of resources consumed by the consumer. The problem here is that potential disparities between the provider's and consumer's accountings, might lead to conflicts between the two parties that need to be resolved. We argue that with the proper mechanisms available, most of these conflicts can be solved online, as opposite to in court resolution; the design of such mechanisms is still a research topic; to help cover the gap, in this paper we propose a peer--to--peer protocol for online dispute resolution over storage consumption. The protocol is peer--to--peer and takes into consideration the possible causes (e.g, transmission delays, unsynchronized metric collectors, etc.) of the disparity between the provider's and consumer's accountings to make, if possible, the two results converge.Comment: 12 pages, 7 figure

Structural Basis for the Autoinhibition and STI-571 Inhibition of c-Kit Tyrosine Kinase

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Uptake and transport of novel amphiphilic polyelectrolyte-insulin nanocomplexes by caco-2 cells - towards oral insulin

“The original publication is available at www.springerlink.com”. Copyright SpringerPurpose: The influence of polymer architecture on cellular uptake and transport across Caco-2 cells of novel amphiphilic polyelectrolyte-insulin nanocomplexes was investigated. Method: Polyallylamine (PAA) (15 kDa) was grafted with palmitoyl chains (Pa) and subsequently modified with quaternary ammonium moieties (QPa). These two amphiphilic polyelectrolytes (APs) were tagged with rhodamine and their uptake by Caco-2 cells or their polyelectrolyte complexes (PECs) with fluorescein isothiocyanate-insulin (FITC-insulin) uptake were investigated using fluorescence microscopy. The integrity of the monolayer was determined by measurement of transepithelial electrical resistance (TEER). Insulin transport through Caco-2 monolayers was determined during TEER experiments. Result: Pa and insulin were co-localised in the cell membranes while QPa complexes were found within the cytoplasm. QPa complex uptake was not affected by calcium, cytochalasin D or nocodazole. Uptake was reduced by co-incubation with sodium azide, an active transport inhibitor. Both polymers opened tight junctions reversibly where the TEER values fell by up to 35 % within 30 minutes incubation with Caco-2 cells. Insulin transport through monolayers increased when QPa was used (0.27 ngmL-1 of insulin in basal compartment) compared to Pa (0.14 ngmL-1 of insulin in basal compartment) after 2 hours. Conclusion: These APs have been shown to be taken up by Caco-2 cells and reversibly open tight cell junctions. Further work is required to optimise these formulations with a view to maximising their potential to facilitate oral delivery of insulin.Peer reviewe

Estimating trace deposition time with circadian biomarkers: a prospective and versatile tool for crime scene reconstruction

Linking biological samples found at a crime scene with the actual crime event represents the most important aspect of forensic investigation, together with the identification of the sample donor. While DNA profiling is well established for donor identification, no reliable methods exist for timing forensic samples. Here, we provide for the first time a biochemical approach for determining deposition time of human traces. Using commercial enzyme-linked immunosorbent assays we showed that the characteristic 24-h profiles of two circadian hormones, melatonin (concentration peak at late night) and cortisol (peak in the morning) can be reproduced from small samples of whole blood and saliva. We further demonstrated by analyzing small stains dried and stored up to 4 weeks the in vitro stability of melatonin, whereas for cortisol a statistically significant decay with storage time was observed, although the hormone was still reliably detectable in 4-week-old samples. Finally, we showed that the total protein concentration, also assessed using a commercial assay, can be used for normalization of hormone signals in blood, but less so in saliva. Our data thus demonstrate that estimating normalized concentrations of melatonin and cortisol represents a prospective approach for determining deposition time of biological trace samples, at least from blood, with promising expectations for forensic applications. In the broader context, our study opens up a new field of circadian biomarkers for deposition timing of forensic traces; future studies using other circadian biomarkers may reveal if the time range offered by the two hormones studied here can be specified more exactly