A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.

Background: In recent decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.

Genetic and environmental contributions to epigenetic aging across adolescence and young adulthood.

Background: Epigenetic aging estimators commonly track chronological and biological aging, quantifying its accumulation (i.e., epigenetic age acceleration) or speed (i.

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes.

OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes.

Trace Elements in Medicinal Metallomics.

This analytical mini-review focuses on the effects of trace elements, which includes Cu, Mn, Zn, and Se, as well as some rarer microelements, on the regulation of oxidative stress in the body and of certain diseases associated with it. Synergism and competition between certain microelements have been considered a hot topic in the applied molecular pharmacology of these specific bio-effects. Some ideas for further possible directions of research are expressed.

Asymmetric Catalytic Hydroboration of Enol Carbamates Enables an Enantioselective Matteson Homologation.

Rh-catalyzed asymmetric hydroboration of enol carbamates yields α-boryl carbamates in good enantioselectivity. The enol carbamate starting materials can be prepared with moderate selectivity using a modified Juila olefination and used as an mixture, taking advantage of the faster reactivity of the major isomer in the directed hydroboration. Optically active α-boryl carbamates participate in a Matteson-type homologation with Grignard reagents in which the O-carbamate is substituted with high conservation of optical activity to provide enantioenriched secondary boronic esters.

Estimating risk of consequences following hypoglycaemia exposure using the Hypo-RESOLVE cohort: a secondary analysis of pooled data from insulin clinical trials.

Aims/hypothesis: Whether hypoglycaemia increases the risk of other adverse outcomes in diabetes remains controversial, especially for hypoglycaemia episodes not requiring assistance from another person. An objective of the Hypoglycaemia REdefining SOLutions for better liVEs (Hypo-RESOLVE) project was to create and use a dataset of pooled clinical trials in people with type 1 or type 2 diabetes to examine the association of exposure to all hypoglycaemia episodes across the range of severity with incident event outcomes: death, CVD, neuropathy, kidney disease, retinal disorders and depression. We also examined the change in continuous outcomes that occurred following a hypoglycaemia episode: change in eGFR, HbA, blood glucose, blood glucose variability and weight.

Risk factors and prediction of hypoglycaemia using the Hypo-RESOLVE cohort: a secondary analysis of pooled data from insulin clinical trials.

Aims/hypothesis: The objective of the Hypoglycaemia REdefining SOLutions for better liVES (Hypo-RESOLVE) project is to use a dataset of pooled clinical trials across pharmaceutical and device companies in people with type 1 or type 2 diabetes to examine factors associated with incident hypoglycaemia events and to quantify the prediction of these events.

Methods: Data from 90 trials with 46,254 participants were pooled. Analyses were done for type 1 and type 2 diabetes separately.

Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study.

Introduction: Type 2 diabetes (T2D) onset, progression and outcomes differ substantially between individuals. Multi-omics analyses may allow a deeper understanding of these differences and ultimately facilitate personalised treatments. Here, in an unsupervised "bottom-up" approach, we attempt to group T2D patients based solely on -omics data generated from plasma.

An omics-based machine learning approach to predict diabetes progression: a RHAPSODY study.

Aims/hypothesis: People with type 2 diabetes are heterogeneous in their disease trajectory, with some progressing more quickly to insulin initiation than others. Although classical biomarkers such as age, HbA and diabetes duration are associated with glycaemic progression, it is unclear how well such variables predict insulin initiation or requirement and whether newly identified markers have added predictive value.

Methods: In two prospective cohort studies as part of IMI-RHAPSODY, we investigated whether clinical variables and three types of molecular markers (metabolites, lipids, proteins) can predict time to insulin requirement using different machine learning approaches (lasso, ridge, GRridge, random forest).

Longitudinal support for the correlative triad among aging, dopamine D2-like receptor loss, and memory decline.

Dopamine decline is suggested to underlie aging-related cognitive decline, but longitudinal examinations of this link are currently missing. We analyzed 5-year longitudinal data for a sample of healthy, older adults (baseline: n = 181, age: 64-68 years; 5-year follow-up: n = 129) who underwent positron emission tomography with C-raclopride to assess dopamine D2-like receptor (DRD2) availability, magnetic resonance imaging to evaluate structural brain measures, and cognitive tests. Health, lifestyle, and genetic data were also collected.

Sensitivity analysis and parameters estimation for the transmission of lymphatic filariasis.

Lymphatic filariasis is a neglected tropical disease which poses public health concern and socio-economic challenges in developing and low-income countries. In this paper, we formulate a deterministic mathematical model for transmission dynamics of lymphatic filariasis to generate data by white noise and use least square method to estimate parameter values. The validity of estimated parameter values is tested by Gaussian distribution method.

Towards a Systemic Concept of the Brain Ishemia Stroke: Monte Carlo Driven Model.

Background: The work proposes a new mathematical model of dynamic processes of a typical spatially heterogeneous biological system, and sets and solves a mathematical problem of modeling the dynamics of the system of neurovascular units of the brain in conditions of ischemic stroke. There is a description of only a small number of mathematical models of stroke in the literature. This model is being studied and a numerical and software implementation of the corresponding mathematical problem is proposed.

Triggering gel-sol transition by weak magnetic field.

The self-assembly of small and always chiral molecules into fiber-like structures is a mysterious process, as the physics underlying such self-assembly is unclear. The energy necessary for this process exceeds the one provided by common dispersion interactions and hydrogen bonding. The recent results obtained by the scientific group of Prof.

Maximizing the value of twin studies in health and behaviour.

In the classical twin design, researchers compare trait resemblance in cohorts of identical and non-identical twins to understand how genetic and environmental factors correlate with resemblance in behaviour and other phenotypes. The twin design is also a valuable tool for studying causality, intergenerational transmission, and gene-environment correlation and interaction. Here we review recent developments in twin studies, recent results from twin studies of new phenotypes and recent insights into twinning.

Identification of biomarkers for glycaemic deterioration in type 2 diabetes.

We identify biomarkers for disease progression in three type 2 diabetes cohorts encompassing 2,973 individuals across three molecular classes, metabolites, lipids and proteins. Homocitrulline, isoleucine and 2-aminoadipic acid, eight triacylglycerol species, and lowered sphingomyelin 42:2;2 levels are predictive of faster progression towards insulin requirement. Of ~1,300 proteins examined in two cohorts, levels of GDF15/MIC-1, IL-18Ra, CRELD1, NogoR, FAS, and ENPP7 are associated with faster progression, whilst SMAC/DIABLO, SPOCK1 and HEMK2 predict lower progression rates.

Modeling cryptosporidiosis in humans and cattle: Deterministic and stochastic approaches.

Cryptosporidiosis is a zoonotic disease caused by . The disease poses a public and veterinary health problem worldwide. A deterministic model and its corresponding continuous time Markov chain (CTMC) stochastic model are developed and analyzed to investigate cryptosporidiosis transmission dynamics in humans and cattle.

Anti-cancer activity of ultra-short single-stranded polydeoxyribonucleotides.

One of the features that differentiate cancer cells is their increased proliferation rate, which creates an opportunity for general anti-tumor therapy directed against the elevated activity of replicative apparatus in tumor cells. Besides DNA synthesis, successful genome replication requires the reparation of the newly synthesized DNA. Malfunctions in reparation can cause fatal injuries in the genome and cell death.

Magnetic field and nuclear spin influence on the DNA synthesis rate.

The rate of a chemical reaction can be sensitive to the isotope composition of the reactants, which provides also for the sensitivity of such "spin-sensitive" reactions to the external magnetic field. Here we demonstrate the effect of the external magnetic field on the enzymatic DNA synthesis together with the effect of the spin-bearing magnesium ions ([Formula: see text]Mg). The rate of DNA synthesis monotonously decreased with the external magnetic field induction increasing in presence of zero-spin magnesium ions ([Formula: see text]Mg).

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity.

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity.

Dynamics for a non-autonomous fall armyworm-maize interaction model with a saturation functional response.

In this study, we present a non-autonomous model with a Holling type II functional response, to study the complex dynamics for fall armyworm-maize biomass interacting in a periodic environment. Understanding how seasonal variations affect fall armyworm-maize dynamics is critical since maize is one of the most important cereals globally. Firstly, we study the dynamical behaviours of the basic model; that is, we investigate positive invariance, boundedness, permanence, global stability and non-persistence.

Distinct Molecular Signatures of Clinical Clusters in People With Type 2 Diabetes: An IMI-RHAPSODY Study.

Type 2 diabetes is a multifactorial disease with multiple underlying aetiologies. To address this heterogeneity, investigators of a previous study clustered people with diabetes according to five diabetes subtypes. The aim of the current study is to investigate the etiology of these clusters by comparing their molecular signatures.

Advanced Large-Scale Nanofabrication Route for Ultrasensitive SERS Platforms Based on Precisely Shaped Gold Nanostructures.

One of the key issues for SERS-based trace applications is engineering structurally uniform substrates with ultrasensitivity, stability, and good reproducibility. A label-free, cost-effective, and reproducible fabrication strategy of ultrasensitive SERS sensors was reported in this work. Herein, we present recent progress in self-assembly-based synthesis to elaborate precisely shaped and abundant gold nanoparticles in a large area.