hadge: a comprehensive pipeline for donor deconvolution in single-cell studies.

Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution.

RAB32 Ser71Arg in autosomal dominant Parkinson's disease: linkage, association, and functional analyses.

Background: Parkinson's disease is a progressive neurodegenerative disorder with multifactorial causes, among which genetic risk factors play a part. The RAB GTPases are regulators and substrates of LRRK2, and variants in the LRRK2 gene are important risk factors for Parkinson's disease. We aimed to explore genetic variability in RAB GTPases within cases of familial Parkinson's disease.

A pathogenic variant in RAB32 causes autosomal dominant Parkinson's disease and activates LRRK2 kinase.

Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder. Mendelian forms have revealed multiple genes, with a notable emphasis on membrane trafficking; RAB GTPases play an important role in PD as a subset are both regulators and substrates of LRRK2 protein kinase. To explore the role of RAB GTPases in PD, we undertook a comprehensive examination of their genetic variability in familial PD.

escheR: unified multi-dimensional visualizations with Gestalt principles.

Summary: The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables.

aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3.

Amazon Simple Storage Service (Amazon S3) is a widely used platform for storing large biomedical datasets. Unintended data alterations can occur during data writing and transmission, altering the original content and generating unexpected results. However, no open-source and easy-to-use tool exists to verify end-to-end data integrity.

Age-related telomere attrition in the human putamen.

Age is a major risk factor for neurodegenerative diseases. Shortening of leucocyte telomeres with advancing age, arguably a measure of "biological" age, is a known phenomenon and epidemiologically correlated with age-related disease. The main mechanism of telomere shortening is cell division, rendering telomere length in post-mitotic cells presumably stable.

Splicing accuracy varies across human introns, tissues and age.

Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation.

escheR: Unified multi-dimensional visualizations with Gestalt principles.

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex.

Generation of a molecular neuroanatomical map of the human prefrontal cortex reveals novel spatial domains and cell-cell interactions relevant for psychiatric disease. The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture.

No strong HLA association with MOG antibody disease in the UK population.

Improvements in assays for detecting serum antibodies against myelin oligodendrocyte glycoprotein (MOG) have led to the appreciation of MOG-antibody-associated disease (MOGAD) as a novel disorder. However, much remains unknown about its etiology. We performed human leukocyte antigen (HLA) analysis in 82 MOGAD patients of European ancestry in the UK population.

Interwoven four-compartment capillary membrane technology for three-dimensional perfusion with decentralized mass exchange to scale up embryonic stem cell culture.

We describe hollow fiber-based three-dimensional (3D) dynamic perfusion bioreactor technology for embryonic stem cells (ESC) which is scalable for laboratory and potentially clinical translation applications. We added 2 more compartments to the typical 2-compartment devices, namely an additional media capillary compartment for countercurrent 'arteriovenous' flow and an oxygenation capillary compartment. Each capillary membrane compartment can be perfused independently.

Hepatic maturation of human fetal hepatocytes in four-compartment three-dimensional perfusion culture.

Bio-artificial liver support systems have been utilized as bridging devices to support acute and chronic liver injury. However, prolonged function of adult hepatocytes has not been achieved due to compromised proliferation and long-term survival of adult cells in vitro. As an alternative cell source, we investigated the potential of human fetal hepatocytes (hFH) in a four-compartment hollow fiber-based three-dimensional (3D) perfusion culture system.

Cardiac actinomycosis: an unusual cause of an intracardiac mass.

Actinomycosis is a chronic disease characterized by abscess formation, tissue fibrosis, and draining sinuses that may involve the cervicofacial area, thorax, abdominopelvic region, or central nervous system. We describe a patient with cardiac actinomycosis presenting with pericardial disease and an intracardiac mass. The diagnosis failed to be obtained by pericardiocentesis, but was obtained after echocardiographically guided biopsy of the intracardiac mass.

Cardiorespiratory adjustments of homing pigeons to steady wind tunnel flight.

We made detailed cardiorespiratory measurements from homing pigeons during quiet rest and steady wind tunnel flight. Our pigeons satisfied their 17.4-fold increase in oxygen consumption during flight with a 7.

Administration of adenosine receptor agonists or antagonists after controlled cortical impact in mice: effects on function and histopathology.

Adenosine is an endogenous neuroprotectant via anti-excitotoxic effects at A(1) receptors, and blood flow promoting and anti-inflammatory effects at A(2a) receptors. Previous studies showed improved motor function after fluid percussion injury (FPI) in rats treated with the broad-spectrum adenosine receptor agonist 2-chloroadenosine (2-CA). We studied the effects of 2-CA, a specific A(1) agonist (2-chloro-N(6)-cyclopentyladenosine, CCPA), and a specific A(1) antagonist (8-cyclopentyl-1,3-dipropylxanthine, DPCPX) on motor task and Morris water maze (MWM) performance, and histopathology (contusion volume, hippocampal cell counts) after controlled cortical impact (CCI) in mice.