Fair Data, Bayesian Statistics and Human Cohort Studies: Current Trends in Metabolomic Research.

This Special Issue was published to celebrate 10+ years of research and services at the UC Davis West Coast Metabolomics Center (WCMC) [...

Associations of Left Atrial Volume Index to Left Ventricular Ejection Fraction Ratio with Clinical Outcomes in Transthyretin Cardiac Amyloidosis.

Background: Transthyretin amyloid cardiomyopathy (ATTR-CM) affects all cardiac chambers to cause left ventricular (LV) deformation as well as left atrial (LA) remodeling and functional impairment. We investigated the associations of the LA volume index (LAVI):LV ejection fraction (LVEF) ratio with the increased risk of death, heart transplant, or LV assist device implantation (LVAD) in patients with ATTR-CM.

Methods: This was a retrospective cohort study involving 69 heart failure (HF) patients with ATTR-CM at an academic medical center between 1 November 2008 and 31 March 2024.

Large herbivores link plant phenology and abundance in Arctic tundra.

Plant phenological dynamics have been well studied in relation to abiotic conditions and climate change, but comparatively poorly studied in relation to herbivory. In contrast, plant abundance dynamics have been well studied in relation to abiotic conditions and herbivory, but poorly studied in relation to phenology. Consequently, the contribution of herbivory to plant phenological dynamics and therefrom to plant abundance dynamics remains obscure.

Nebulized vasopressin penetrates CSF and improves social cognition without inducing aggression in a rhesus monkey model of autism.

Low cerebrospinal (CSF) arginine vasopressin (AVP) concentration is a biomarker of social impairment in low-social monkeys and children with autism, suggesting that AVP administration may improve primate social functioning. However, AVP administration also increases aggression, at least in "neurotypical" animals with intact AVP signaling. Here, we tested the effects of a voluntary drug administration method in low-social male rhesus monkeys with high autistic-like trait burden.

Epigenetic Landscape of DNA Methylation in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, characterized by its aggressive progression and dismal prognosis. Advances in epigenetic profiling, specifically DNA methylation analysis, have significantly deepened our understanding of PDAC pathogenesis. This review synthesizes findings from recent genome-wide DNA methylation studies, which have delineated a complex DNA methylation landscape differentiating between normal and cancerous pancreatic tissues, as well as across various stages and molecular subtypes of PDAC.

Leveraging Walnut Somatic Embryos as a Biomanufacturing Platform for Recombinant Proteins and Metabolites.

Biomanufacturing enables novel sources of compounds with constant demand, such as food coloring and preservatives, as well as new compounds with peak demand, such as diagnostics and vaccines. The COVID-19 pandemic has highlighted the need for alternative sources of research materials, thrusting research on diversification of biomanufacturing platforms. Here, we show initial results exploring the walnut somatic embryogenic system expressing the recombinant receptor binding domain (RBD) and ectodomain of the spike protein (Spike) from the SARS-CoV-2 virus.

Evolution of sulfonated tannins in red wines with ageing: A targeted metabolomic approach.

During wine ageing, tannins could react with sulfur dioxide to form sulfonated flavanols which are anticipated to alter tannin binding to proteins contributing to the reduction of astringency during ageing. Previous studies have identified or quantified monomeric and dimeric sulfonated flavanols in aged wines, but the evolution of sulfonated tannins has been lacking. Here, we quantified sulfonated tannins in three Washington state vineyards over a 20-year period, employing targeted LC-QToF analysis.

Epigenetic modifications control CYP1A1 Inducibility in human and rat keratinocytes.

Serially passaged rat keratinocytes exhibit dramatically attenuated induction of Cyp1a1 by aryl hydrocarbon receptor ligands such as TCDD. However, the sensitivity to induction can be restored by protein synthesis inhibition. Previous work revealed that the functionality of the receptor was not affected by passaging.

Identifying rice varieties for mitigating methane and nitrous oxide emissions under intermittent irrigation.

Context Or Problem: Most of the research evaluating rice varieties, a major global staple food, for greenhouse gas (GHG) mitigation has been conducted under continuous flooding. However, intermittent irrigation practices are expanding across the globe to address water shortages, which could alter emissions of methane (CH) compared to nitrous oxide (NO) for reducing overall global warming potential (GWP). To develop climate-smart rice production systems, it is critical to identify rice varieties that simultaneously reduce CH and NO emissions while maintaining crop productivity under intermittent irrigation.

Many-body physics of ultracold alkaline-earth atoms with SU()-symmetric interactions.

Symmetries play a crucial role in understanding phases of matter and the transitions between them. Theoretical investigations of quantum models with SU() symmetry have provided important insights into many-body phenomena. However, these models have generally remained a theoretical idealization, since it is very difficult to exactly realize the SU() symmetry in conventional quantum materials for large.

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years.

Tomato roots exhibit distinct, development-specific responses to bacterial-derived peptides.

Plants possess cell-surface recognition receptors that detect molecular patterns from microbial invaders and initiate an immune response. Understanding the conservation of pattern-triggered immunity within different plant organs and across species is crucial to its sustainable and effective use in plant disease management but is currently unclear.We examined the activation and immune response patterns of three pattern recognition receptors (PRRs: FLS2, FLS3, and CORE) in different developmental regions of roots and in leaves of multiple accessions of domesticated and wild tomato ( and ) using biochemical and genetic assays.

A double knockout for zinc transporter 8 and somatostatin in mice reveals their distinct roles in regulation of insulin secretion and obesity.

Background: Both zinc transporter 8 (ZnT8) and somatostatin (Sst) play crucial roles in the regulation of insulin and glucagon secretion. However, the interaction between them in controlling glucose metabolism was not well understood. The aim of this study was to explore the interactive effects of a double knockout of Znt8 and Sst on insulin and glucose metabolism in mice.

Effects of Different Loading Programs on Finger Strength in Rock Climbers.

Background: Climbing places high loads through the hands and fingers, and climbers may benefit from specific finger strength training (hangboarding) protocols. The purpose of this study was to evaluate the effect of a 10-minute low intensity hangboard finger strengthening protocol ("Abrahangs"), compared with the generally accepted Max Hangs protocol for training maximal grip strength.

Methods: We retrospectively evaluated the change in grip strength and Strength: Weight following Max Hangs, Abrahangs, or the two protocols performed concurrently in rock climbers who used the Crimpd app to log their training.

A global assessment of plant-mite mutualism and its ecological drivers.

Mutualisms are mediated by adaptive traits of interacting organisms and play a central role in the ecology and evolution of species. Thousands of plant species possess tiny structures called "domatia" that house mites which protect plants from pests, yet these traits remain woefully understudied. Here, we release a worldwide database of species with mite domatia and provide an evaluation of the phylogenetic and geographic distribution of this mutualistic trait.

Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data.

The Plant Metabolic Network (PMN) is a free online database of plant metabolism available at https://plantcyc.org. The latest release, PMN 16, provides metabolic databases representing >1200 metabolic pathways, 1.

Comparative RNA profiling identifies stage-specific phasiRNAs and coexpressed Argonaute genes in Bambusoideae and Pooideae species.

Phased, small interfering RNAs (PhasiRNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa)-and subsequently many other plant species-identified premeiotic 21-nucleotide (nt) and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs was discovered in the anthers of 2 Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum).

Genetic and linguistic comparisons reveal complex sex-biased transmission of language features.

The history of people's movements and interactions shapes both genetic and linguistic variation. Genes and languages are transmitted separately and their distributions reflect different aspects of human history, but some demographic processes can cause them to be similarly distributed. In particular, forms of societal organization, including movements in and out of a community, may have shaped the transmission of both genes and languages.

Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors.

Genome-wide association studies (GWAS) and polygenic score (PGS) development are typically constrained by the data available in biobank repositories in which European cohorts are vastly overrepresented. Here, we increase the utility of non-European participant data within the UK Biobank (UKB) by characterizing the genetic affinities of UKB participants who self-identify as Bangladeshi, Indian, Pakistani, "White and Asian" (WA), and "Any Other Asian" (AOA), towards creating a more robust South Asian sample size for future genetic analyses. We assess the relationships between genetic structure and self-selected ethnic identities resulting in consistent patterns of clustering used to train a support vector machine (SVM).

Optimizing spatial distribution of wastewater-based epidemiology to advance health equity.

In 2022, the US Centers for Disease Control and Prevention commissioned the National Academies of Sciences, Engineering, and Medicine to assess the role of community-level wastewater-based epidemiology (WBE) beyond COVID-19. WBE is recognized as a promising mechanism for promptly identifying infectious diseases, including COVID-19 and other novel pathogens. An important conclusion from this initiative is the critical importance of maintaining equity and expanding access to fully realize the benefits of wastewater surveillance for marginalized communities.

Feasibility of PET-enabled dual-energy CT imaging: First physical phantom and initial patient study results.

Purpose: Dual-energy (DE) CT enables material decomposition by using two different x-ray energies and may be combined with PET for improved multimodality imaging. However, this increases radiation dose and may require a hardware upgrade due to the added second x-ray CT scan. The recently proposed PET-enabled DECT method allows dual-energy imaging using a conventional PET/CT scanner without the need to change scanner hardware or increase radiation exposure.