FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis.

Motivation: We are witnessing an enormous growth in the amount of molecular profiling (-omics) data. The integration of multi-omics data is challenging. Moreover, human multi-omics data may be privacy-sensitive and can be misused to de-anonymize and (re-)identify individuals.

Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds.

In the present study 1,709 cattle, including 1,118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150 K bovine SNP panel. A genomic data set of 122,632 quality-filtered single nucleotide polymorphisms (SNPs) were used to identify selection signatures within breeds based on conserved runs of homozygosity (ROH) and heterozygosity (ROHet) estimated with the detectRUNS R package. The mean number of ROH per animal varied across breeds ranging from 36.

Tracking the uptake of labelled host-derived extracellular vesicles by the human fungal pathogen .

Extracellular vesicles (EVs) have gained attention as facilitators of intercellular as well as interkingdom communication during host-microbe interactions. Recently we showed that upon infection, host polymorphonuclear leukocytes produce antifungal EVs targeting the clinically important fungal pathogen ; however, the small size of EVs (<1 µm) complicates their functional analysis. Here, we employed a more tractable, reporter-based system to label host alveolar epithelial cell-derived EVs and enable their visualization during interaction.

The impact of myostatin variants on growth traits in South African Bonsmara beef cattle.

Double muscling occurs when the myostatin (MSTN) gene is deactivated due to a series of mutations, leading to uncontrolled muscle growth and excessive muscle fiber accumulation, as the gene can no longer effectively regulate muscle development. This study aimed to assess the impact of MSTN variants and their combinations on growth traits, namely direct birth weight (BW), direct weaning weight (WW), average daily gain (ADG) and feed conversion ratio (FCR) in the South African (SA) Bonsmara. Genomically enhanced estimated breeding value (GEBVs) for traits of interest, and MTSN genotypes for SA Bonsmara animals were available for the study.

Characteristics and Outcomes of Occult Infections in Presumed Aseptic Nonunions: A Retrospective Cohort Study.

Objectives: To determine (1) the rate of positive cultures in presumed aseptic nonunions, (2) the rate and microbial spectrum of positive cultures that represented occult infection, and (3) rates of nonunion healing.

Design: Retrospective cohort study.

Setting: Tertiary referral center.

Short-acting β-agonists (SABA) overuse in asthma and patients' perceptions for this behavior.

Background: Short-acting β-agonists (SABA) overuse is associated with poor asthma control. The Global Initiative for Asthma (GINA) 2019-updated strategy report has therefore taken a paradigm shift in reliever therapy recommendations.

Objectives: (I) To investigate the status of SABA overuse and medication dispensing patters in asthma in the Netherlands (II) validate dispensing data for SABA overuse identification and (III) understand patients' perspectives towards this SABA-taking behavior to inform future improvement strategies.

The performance of single and combination test strategies using visual inspection, cytology, high-risk HPV DNA and HPV16/18 to screen South African women with and without HIV-infection.

Background: Cervical cancer screening strategies should ideally be informed by population-specific data. Strategies recommended for secondary prevention, are often inadequately studied in populations with high cervical disease burdens. This report describes the test performance measured against CIN2 + /CIN3 + histology in HIV-positive women (HPW) and HIV-negative women (HNW) with the aim to determine the most effective strategies to identify South African women at risk.

Sociodemographics, behaviour and knowledge of first South African HPV-vaccine recipients.

Background: Infection with the human papillomavirus (HPV) is a necessary cause of cervical cancer and is one of the most prevalent sexually transmitted infections worldwide. Primary prevention strategies target reducing HPV acquisition through vaccination, limiting exposure (e.g.

European soybean to benefit people and the environment.

Europe imports large amounts of soybean that are predominantly used for livestock feed, mainly sourced from Brazil, USA and Argentina. In addition, the demand for GM-free soybean for human consumption is project to increase. Soybean has higher protein quality and digestibility than other legumes, along with high concentrations of isoflavones, phytosterols and minerals that enhance the nutritional value as a human food ingredient.

Self-management support with the Respiratory Adherence Care Enhancer instrument in asthma and chronic obstructive pulmonary disease: An implementation trial.

Aim: Suboptimal self-management with controller inhalation therapy in asthma and COPD is frequently observed with poor treatment outcomes. The developed 'Respiratory Adherence Care Enhancer' (RACE) instrument identifies and addresses individual barriers to self-management with a theoretical underpinning. This study investigates the feasibility of pharmaceutical support with this instrument.

Secretion of the fungal toxin candidalysin is dependent on conserved precursor peptide sequences.

The opportunistic fungal pathogen Candida albicans damages host cells via its peptide toxin, candidalysin. Before secretion, candidalysin is embedded in a precursor protein, Ece1, which consists of a signal peptide, the precursor of candidalysin and seven non-candidalysin Ece1 peptides (NCEPs), and is found to be conserved in clinical isolates. Here we show that the Ece1 polyprotein does not resemble the usual precursor structure of peptide toxins.

A multi-omics data analysis workflow packaged as a FAIR Digital Object.

Background: Applying good data management and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines.

Transient Autoreactive PF4 and Antiphospholipid Antibodies in COVID-19 Vaccine Recipients.

Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare autoimmune condition associated with recombinant adenovirus (rAV)-based COVID-19 vaccines. It is thought to arise from autoantibodies targeting platelet factor 4 (aPF4), triggered by vaccine-induced inflammation and the formation of neo-antigenic complexes between PF4 and the rAV vector. To investigate the specific induction of aPF4 by rAV-based vaccines, we examined sera from rAV vaccine recipients (AZD1222, AD26.

Surprise positive culture rate in the treatment of presumed aseptic long-bone nonunion: a systematic review with meta-analysis of 2397 patients.

Introduction: In pre-operatively presumed aseptic nonunions, the definitive diagnosis of infection relies on intraoperative cultures. Our primary objective was to determine (1) the rate of surprise positive intraoperative cultures in presumed aseptic long-bone nonunion (surprise positive culture nonunion), and (2) the rate of surprise positive cultures that represent infection vs. contamination.

Enhancing Cervical Cancer Prevention in South African Women: Primary HPV mRNA Screening with Different Genotype Combinations.

Background: Cervical cancer prevention in regions with limited access to screening and HPV vaccination necessitates innovative approaches. This study explored the potential of a test-and-treat strategy using mRNA HPV tests to impact cervical cancer prevention in a high-prevalence HIV population.

Methods: A cervical screening study was conducted at three South African hospitals involving 710 under-screened, non-pregnant women (25 to 65 years) without known cervical diseases.

Ten quick tips for building FAIR workflows.

Research data is accumulating rapidly and with it the challenge of fully reproducible science. As a consequence, implementation of high-quality management of scientific data has become a global priority. The FAIR (Findable, Accesible, Interoperable and Reusable) principles provide practical guidelines for maximizing the value of research data; however, processing data using workflows-systematic executions of a series of computational tools-is equally important for good data management.

Twelve tips for designing, implementing and sustaining interprofessional training units on hospital wards.

Dedicated Interprofessional Training Units (ITUs) in hospital wards are one way to prepare healthcare students for Interprofessional patient-centered care. Based on theoretical foundations, research, and our lived experiences of successes as well as failures, we propose 12 tips on how to prepare, implement, and sustain a dedicated ITU, combining the Grol & Wensing model for planning change with the Self-determination Theory of motivation. Start with a steering group, with a dedicated project leader, to translate awareness of the need for an ITU into wider awareness and motivation among stakeholders, with the ITU being a solution to authentic problems.

Changes in incidence of hospitalization for cardiovascular diseases during the COVID-19 pandemic in The Netherlands in 2020.

This population-based cohort study aimed to describe changes in incidence of cardiovascular disease (CVD) hospital diagnoses during the COVID-19 pandemic in The Netherlands compared with the pre-pandemic period. We used Dutch nationwide statistics about hospitalizations to estimate incidence rate ratios (IRR) of hospital diagnoses of CVD during the first and second COVID-19 waves in The Netherlands in 2020 versus the same periods in 2019. Compared with 2019, the incidence rate of a hospital diagnosis of ischemic stroke (IRR 0.

Levels of Fibrinogen Variants Are Altered in Severe COVID-19.

 Fibrinogen variants as a result of alternative messenger RNA splicing or protein degradation can affect fibrin(ogen) functions. The levels of these variants might be altered during coronavirus disease 2019 (COVID-19), potentially affecting disease severity or the thrombosis risk.  To investigate the levels of fibrinogen variants in plasma of patients with COVID-19.

Nonequilibrium sensing of volatile compounds using active and passive analyte delivery.

Although sensor technologies have allowed us to outperform the human senses of sight, hearing, and touch, the development of artificial noses is significantly behind their biological counterparts. This largely stems from the sophistication of natural olfaction, which relies on both fluid dynamics within the nasal anatomy and the response patterns of hundreds to thousands of unique molecular-scale receptors. We designed a sensing approach to identify volatiles inspired by the fluid dynamics of the nose, allowing us to extract information from a single sensor (here, the reflectance spectra from a mesoporous one-dimensional photonic crystal) rather than relying on a large sensor array.