The Venus score for the assessment of the quality and trustworthiness of biomedical datasets.

Biomedical datasets are the mainstays of computational biology and health informatics projects, and can be found on multiple data platforms online or obtained from wet-lab biologists and physicians. The quality and the trustworthiness of these datasets, however, can sometimes be poor, producing bad results in turn, which can harm patients and data subjects. To address this problem, policy-makers, researchers, and consortia have proposed diverse regulations, guidelines, and scores to assess the quality and increase the reliability of datasets.

Endothelial tip-cell position, filopodia formation and biomechanics require BMPR2 expression and signaling.

Blood vessel formation relies on biochemical and mechanical signals, particularly during sprouting angiogenesis when endothelial tip cells (TCs) guide sprouting through filopodia formation. The contribution of BMP receptors in defining tip-cell characteristics is poorly understood. Our study combines genetic, biochemical, and molecular methods together with 3D traction force microscopy, which reveals an essential role of BMPR2 for actin-driven filopodia formation and mechanical properties of endothelial cells (ECs).

Phosphorylation of endothelial histone H3.3 serine 31 by PKN1 links flow-induced signaling to proatherogenic gene expression.

Atherosclerotic lesions develop preferentially in arterial regions exposed to disturbed blood flow, where endothelial cells acquire an inflammatory phenotype. How disturbed flow induces endothelial cell inflammation is incompletely understood. Here we show that histone H3.

Facial signals shape predictions about the nature of upcoming conversational responses.

Increasing evidence suggests that interlocutors use visual communicative signals to form predictions about unfolding utterances, but there is little data on the predictive potential of facial signals in conversation. In an online experiment with virtual agents, we examine whether facial signals produced by an addressee may allow speakers to anticipate the response to a question before it is given. Participants (n = 80) viewed videos of short conversation fragments between two virtual humans.

Nymphal feeding suppresses oviposition-induced indirect plant defense in rice.

Feeding and oviposition by phytophagous insects are both known to trigger defenses in plants. Whether these two defenses functionally interact remains poorly studied, although these interactions are likely important for pests with overlapping generations. Here we investigated the differences and interaction between feeding- and oviposition-induced plant defenses triggered by the brown planthopper (BPH, Nilaparvata lugens), which gregariously feeds and oviposits on rice.

Modulation of Mitochondria-Endoplasmic Reticulum Contacts (MERCs) by Small Molecules as a New Strategy for Restoring Lipid Metabolism in an Amyotrophic Lateral Sclerosis Model.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease without effective treatment. The progressive motoneuron death in ALS is associated with alterations in lipid metabolism. As its regulation occurs in mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs), modulation of mitochondria-ER contacts (MERCs) is emerging as a crucial factor in MAM formation and lipid metabolism control.

Isolation of anti-inflammatory and cytotoxic secondary metabolites from Valeriana phu and evaluation of their mechanisms of action.

As a result of anti-inflammatory activity-guided fractionation, 16 secondary metabolites from the underground parts of Valeriana phu L. were obtained, including five new ones belonging to iridoid (1, 2, and 5), phenylpropanoid (6) and neolignan (7) chemical classes. Their structures were elucidated by 1D and 2D NMR analyses as well as HRESIMS.

Effective Hamiltonians from Spin-Adapted Configuration Interaction.

A generalized extraction procedure for magnetic interactions using effective Hamiltonians is presented that is applicable to systems with more than two sites featuring local spins ≥ 1. To this end, closed, nonrecursive expressions pertaining to chains of arbitrary equal spins are derived with the graphical method of angular momentum. The method is illustrated by extracting magnetic couplings from ab initio calculations on a [CaMnO] cubane.

A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.

Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp.

Experientially-grounded and distributional semantic vectors uncover dissociable representations of conceptual categories.

Neuronal populations code similar concepts by similar activity patterns across the human brain's semantic networks. However, it is unclear to what extent such meaning-to-symbol mapping reflects distributional statistics, or experiential information grounded in sensorimotor and emotional knowledge. We asked whether integrating distributional and experiential data better distinguished conceptual categories than each method taken separately.

Interactions between leaf phenological type and functional traits drive variation in isoprene emissions in central Amazon forest trees.

The Amazon forest is the largest source of isoprene emissions, and the seasonal pattern of leaf-out phenology in this forest has been indicated as an important driver of seasonal variation in emissions. Still, it is unclear how emissions vary between different leaf phenological types in this forest. To evaluate the influence of leaf phenological type over isoprene emissions, we measured leaf-level isoprene emission capacity and leaf functional traits for 175 trees from 124 species of angiosperms distributed among brevideciduous and evergreen trees in a central Amazon forest.

Genetic Analysis of Retinal Cell Types in Neuropsychiatric Disorders.

Importance: As an accessible part of the central nervous system, the retina provides a unique window to study pathophysiological mechanisms of brain disorders in humans. Imaging and electrophysiological studies have revealed retinal alterations across several neuropsychiatric and neurological disorders, but it remains largely unclear which specific cell types and biological mechanisms are involved.

Objective: To determine whether specific retinal cell types are affected by genomic risk for neuropsychiatric and neurological disorders and to explore the mechanisms through which genomic risk converges in these cell types.

Conserved features of recombination control in vertebrates.

A recent study in PLOS Biology on the epigenetic recombination regulator PRDM9 in salmonid fish reveals that its function has been preserved across vertebrates for hundreds of millions of years, with rapidly evolving DNA-binding domains being a defining attribute.

Two types of motifs enhance human recall and generalization of long sequences.

Whether it is listening to a piece of music, learning a new language, or solving a mathematical equation, people often acquire abstract notions in the sense of motifs and variables-manifested in musical themes, grammatical categories, or mathematical symbols. How do we create abstract representations of sequences? Are these abstract representations useful for memory recall? In addition to learning transition probabilities, chunking, and tracking ordinal positions, we propose that humans also use abstractions to arrive at efficient representations of sequences. We propose and study two abstraction categories: projectional motifs and variable motifs.

Embracing plant plasticity or robustness as a means of ensuring food security.

The dual challenges of global population explosion and environmental deterioration represent major hurdles for 21 Century agriculture culminating in an unprecedented demand for food security. In this Review, we revisit historical concepts of plasticity and canalization before integrating them with contemporary studies of genotype-environment interactions (G×E) that are currently being carried out at the genome-wide level. In doing so we address both fundamental questions regarding G×E and potential strategies to best secure yields in both current and future climate scenarios.

Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations.

The mutational landscape of TP53, a tumor suppressor mutated in about half of all cancers, includes over 2,000 known missense mutations. To fully leverage TP53 mutation status for personalized medicine, a thorough understanding of the functional diversity of these mutations is essential. We conducted a deep mutational scan using saturation genome editing with CRISPR-mediated homology-directed repair to engineer 9,225 TP53 variants in cancer cells.

Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy.

Autophagy is a key cellular quality control mechanism. Nutrient stress triggers bulk autophagy, which nonselectively degrades cytoplasmic material upon formation and liquid-liquid phase separation of the autophagy-related gene 1 (Atg1) complex. In contrast, selective autophagy eliminates protein aggregates, damaged organelles and other cargoes that are targeted by an autophagy receptor.

Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus).

Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species.

Metabolic engineering of Yarrowia lipolytica for the production and secretion of the saffron ingredient crocetin.

Background: Crocetin is a multifunctional apocarotenoid natural product derived from saffron, holding significant promises for protection against various diseases and other nutritional applications. Historically, crocetin has been extracted from saffron stigmas, but this method is hindered by the limited availability of high-quality raw materials and complex extraction processes. To overcome these challenges, metabolic engineering and synthetic biology can be applied to the sustainable production of crocetin.

Tracing the paths of modular evolution by quantifying rearrangement events of protein domains.

Background: Protein evolution is central to molecular adaptation and largely characterized by modular rearrangements of domains, the evolutionary and structural building blocks of proteins. Genetic events underlying protein rearrangements are relatively rare compared to changes of amino-acids. Therefore, these events can be used to characterize and reconstruct major events of molecular adaptation by comparing large data sets of proteomes.

Large-scale sampling of potential breeding sites in male ruffs.

The traditional narrative of the life cycle of migratory birds is that individuals perform long-distance movements between a breeding and a wintering site, but are largely resident at those sites. Although this pattern may apply to socially monogamous species with biparental care, in polygamous systems, the sex that only provides gametes may benefit from continuing to move and sample several potential breeding sites during a single breeding season. Such behaviour would blur the distinction between migration and breeding.

Gene expression comparisons between captive and wild shrew brains reveal captivity effects.

Compared with their free-ranging counterparts, wild animals in captivity experience different conditions with lasting physiological and behavioural effects. Although shifts in gene expression are expected to occur upstream of these phenotypes, we found no previous gene expression comparisons of captive versus free-ranging mammals. We assessed gene expression profiles of three brain regions (cortex, olfactory bulb and hippocampus) of wild shrews () compared with shrews kept in captivity for two months and undertook sample dropout to examine robustness given limited sample sizes.

Insight into the Origin of Second Harmonic Generation and Rational Design in the Metal Halide Borates.

Metal halide borates are promising candidates for high-performance nonlinear optical (NLO) applications, yet the origins of their second harmonic generation (SHG) properties remain unclear. Using atom response theory combined with density functional theory calculations, this study investigates why halogen substitution leads to distinctly different SHG responses in halide monoborates (PbBOX) versus halide pentaborates (PbBOX). We find that the SHG origins vary between these two families due to differences in the strength of the Pb-X interactions.

Spike frequency adaptation in primate lateral prefrontal cortex neurons results from interplay between intrinsic properties and circuit dynamics.

Cortical neurons in brain slices display intrinsic spike frequency adaptation (I-SFA) to constant current inputs, while extracellular recordings show extrinsic SFA (E-SFA) during sustained visual stimulation. Inferring how I-SFA contributes to E-SFA during behavior is challenging due to the isolated nature of slice recordings. To address this, we recorded macaque lateral prefrontal cortex (LPFC) neurons in vivo during a visually guided saccade task and in vitro in brain slices.