Data Management Plans in the genomics research revolution of Africa: Challenges and Recommendations

Drafting and writing a data management plan (DMP) is increasingly seen as a key part of the academic research process. A DMP is a document that describes how a researcher will collect, document, describe, share, and preserve the data that will be generated as part of a research project. The DMP illustrates the importance of utilizing best practices through all stages of working with data while ensuring accessibility, quality, and longevity of the data. The benefits of writing a DMP include compliance with funder and institutional mandates; making research more transparent (for reproduction and validation purposes); and FAIR (findable, accessible, interoperable, reusable); protecting data subjects and compliance with the General Data Protection Regulation (GDPR) and/or local data protection policies. In this review, we highlight the importance of a DMP in modern biomedical research, explaining both the rationale and current best practices associated with DMPs. In addition, we outline various funders’ requirements concerning DMPs and discuss open-source tools that facilitate the development and implementation of a DMP. Finally, we discuss DMPs in the context of African research, and the considerations that need to be made in this regard

What is the future for therapies derived from the microbiome (pharmabiotics)?

The personal gut microbiota is characterized by species composition, enterotype, and bacterial gene counts. Gut microbiota can be viewed as a complex microecosystem. Regulation of the diversity and stability of the gut microbiota is therefore critical for the development of future therapies. The areas with high potential for personalized management of gut microbiota are obesity and the metabolic syndrome, prevention and control of (recurrent) infections, immune-mediated disorders, and the gut-brain axis. A true and deeper understanding of the interaction between the microbiota and the host, as well as a better matching of probiotic and prebiotic mechanisms with clinical indications will be required for successful future implementation of these therapies

Spin diffusion with 13C selection and detection for the characterization of morphology in labeled polymer blends with MAS NMR

Bio-organic Synthesi

Cross-linking induced phase separation in SAN/SMA semi-interpenetrating polymer networks observed by solid state NMR and site specific isotope enrichment

Bio-organic Synthesi

Magnetic Phase Diagram of GdNi2B2C: Two-ion Magnetoelasticity and Anisotropic Exchange Couplings

Extensive magnetization and magnetostriction measurements were carried out on a single crystal of GdNi2B2C along the main tetragonal axes. Within the paramagnetic phase, the magnetic and strain susceptibilities revealed a weak anisotropy in the exchange couplings and two-ion tetragonal-preserving alpha-strain modes. Within the ordered phase, magnetization and magnetostriction revealed a relatively strong orthorhombic distortion mode and rich field-temperature phase diagrams. For H//(100) phase diagram, three field-induced transformations were observed, namely, at: Hd(T), related to the domain alignment; Hr(T), associated with reorientation of the moment towards the c-axis; and Hs(T), defining the saturation process wherein the exchange field is completely counterbalanced. On the other hand, For H//(001) phase diagram, only two field-induced transformations were observed, namely at: Hr(T) and Hs(T). For both phase diagrams, Hs(T) follows the relation Hs[1-(T/Tn)^2]^(1/2)kOe with Hs(T-->0)=128.5(5) kOe and Tn(H=0)=19.5 K. In contrast, the thermal evolution of Hr(T) along the c-axis (much simpler than along the a-axis) follows the relation Hr[1-T/Tr]^(1/3) kOe where Hr(T-->0)=33.5(5) kOe and Tr(H=0)=13.5 K. It is emphasized that the magnetoelastic interaction and the anisotropic exchange coupling are important perturbations and therefore should be explicitly considered if a complete analysis of the magnetic properties of the borocarbides is desired

Liposomal prednisolone promotes macrophage lipotoxicity in experimental atherosclerosis

Atherosclerosis is a lipid-driven inflammatory disease, for which nanomedicinal interventions are under evaluation. Previously, we showed that liposomal nanoparticles loaded with prednisolone (LN-PLP) accumulated in plaque macrophages, however, induced proatherogenic effects in patients. Here, we confirmed in low-density lipoprotein receptor knockout (LDLr−/−) mice that LN-PLP accumulates in plaque macrophages. Next, we found that LN-PLP infusions at 10 mg/kg for 2 weeks enhanced monocyte recruitment to plaques. In follow up, after 6 weeks of LN-PLP exposure we observed (i) increased macrophage content, (ii) more advanced plaque stages, and (iii) larger necrotic core sizes. Finally, in vitro studies showed that macrophages become lipotoxic after LN-PLP exposure, exemplified by enhanced lipid loading, ER stress and apoptosis. These findings indicate that liposomal prednisolone may paradoxically accelerate atherosclerosis by promoting macrophage lipotoxicity. Hence, future (nanomedicinal) drug development studies are challenged by the multifactorial nature of atherosclerotic inflammation

Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling

Objective: Our previous coeliac disease genome-wide association study (GWAS) implicated risk variants in the human leucocyte antigen (HLA) region and eight novel risk regions. To identify more coeliac disease loci, we selected 458 single nucleotide polymorphisms (SNPs) that showed more modest association in the GWAS for genotyping and analysis in four independent cohorts. Design: 458 SNPs were assayed in 1682 cases and 3258 controls from three populations (UK, Irish and Dutch). We combined the results with the original GWAS cohort (767 UK cases and 1422 controls); six SNPs showed association with p Results: We identified two novel coeliac disease risk regions: 6q23.3 (OLIG3-TNFAIP3) and 2p16.1 (REL), both of which reached genome-wide significance in the combined analysis of all 2987 cases and 5273 controls (rs2327832 p= 1.3x10(-08), and rs842647 p= 5.26x10(-07)). We investigated the expression of these genes in the RNA isolated from biopsies and from whole blood RNA. We did not observe any changes in gene expression, nor in the correlation of genotype with gene expression. Conclusions: Both TNFAIP3 (A20, at the protein level) and REL are key mediators in the nuclear factor kappa B (NF-kappa B) inflammatory signalling pathway. For the first time, a role for primary heritable variation in this important biological pathway predisposing to coeliac disease has been identified. Currently, the HLA risk factors and the 10 established non-HLA risk factors explain similar to 40% of the heritability of coeliac disease

In Situ Study of Hydrogen Permeable Electrodes for Electrolytic Ammonia Synthesis Using Near Ambient Pressure XPS

Hydrogen permeable electrodes can be utilized for electrolytic ammonia synthesis from dinitrogen, water, and renewable electricity under ambient conditions, providing a promising route toward sustainable ammonia. The understanding of the interactions of adsorbing N and permeating H at the catalytic interface is a critical step toward the optimization of this NH3 synthesis process. In this study, we conducted a unique in situ near ambient pressure X ray photoelectron spectroscopy experiment to investigate the solid gas interface of a Ni hydrogen permeable electrode under conditions relevant for ammonia synthesis. Here, we show that the formation of a Ni oxide surface layer blocks the chemisorption of gaseous dinitrogen. However, the Ni 2p and O 1s XPS spectra reveal that electrochemically driven permeating atomic hydrogen effectively reduces the Ni surface at ambient temperature, while H2 does not. Nitrogen gas chemisorbs on the generated metallic sites, followed by hydrogenation via permeating H, as adsorbed N and NH3 are found on the Ni surface. Our findings suggest that the first hydrogenation step to NH and the NH3 desorption might be limiting under the operating conditions. The study was then extended to Fe and Ru surfaces. The formation of surface oxide and nitride species on iron blocks the H permeation and prevents the reaction to advance; while on ruthenium, the stronger Ru N bond might favor the recombination of permeating hydrogen to H2 over the hydrogenation of adsorbed nitrogen. This work provides insightful results to aid the rational design of efficient electrolytic NH3 synthesis processes based on but not limited to hydrogen permeable electrode

Apercal-The Apertif calibration pipeline

Apertif (APERture Tile In Focus) is one of the Square Kilometre Array (SKA) pathfinder facilities. The Apertif project is an upgrade to the 50-year-old Westerbork Synthesis Radio Telescope (WSRT) using phased-array feed technology. The new receivers create 40 individual beams on the sky, achieving an instantaneous sky coverage of 6.5 square degrees. The primary goal of the Apertif Imaging Survey is to perform a wide survey of 3500 square degrees (AWES) and a medium deep survey of 350 square degrees (AMES) of neutral atomic hydrogen (up to a redshift of 0.26), radio continuum emission and polarisation. Each survey pointing yields 4.6 TB of correlated data. The goal of Apercal is to process this data and fully automatically generate science ready data products for the astronomical community while keeping up with the survey observations. We make use of common astronomical software packages in combination with Python based routines and parallelisation. We use an object oriented module-based approach to ensure easy adaptation of the pipeline. A Jupyter notebook based framework allows user interaction and execution of individual modules as well as a full automatic processing of a complete survey observation. If nothing interrupts processing, we are able to reduce a single pointing survey observation on our five node cluster with 24 physical cores and 256 GB of memory each within 24 h keeping up with the speed of the surveys. The quality of the generated images is sufficient for scientific usage for 44% of the recorded data products with single images reaching dynamic ranges of several thousands. Future improvements will increase this percentage to over 80%. Our design allowed development of the pipeline in parallel to the commissioning of the Apertif system

Predicting binding affinities for GPCR ligands using free-energy perturbation

Medicinal ChemistryDrug Delivery Technolog