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The NetID algorithm annotates untargeted LC-MS metabolomics data by combining known biochemical and metabolomic principles with a global network optimization strategy.

Murcy et al. show that increasing the plasma glutamine-to-glutamate ratio in atherosclerosis can distally reprogram transcriptional and post-transcriptional remodeling of the aorta by GLS2-dependent hepatic glutaminolysis.

The authors determine the synaptic wiring diagram of a vertebrate circuit and reveal behaviorally associated modules. A model based on this connectome predicts neural coding and dynamics that are verified with calcium imaging data.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

By extracting non-Gaussian cosmological information on galaxy clustering at nonlinear scales, a framework for cosmic inference (SimBIG) provides more precise constraints for testing cosmological models.

Primed adaptation in the CRISPR-Cas system helps recognition of previously encountered sequence elements and promotes the formation of new memories. Here the authors characterized spacer precursors of type I-E and type I-F CRISPR-Cas system using in vivo models.

This study examines the history of North Atlantic deep-water masses, as recorded in marine sediments. Major lithological changes and increased rate of deposition reveal that stronger deep-ocean circulation initiated 3.6 million years ago.

The orbital structure of charge density waves on a square lattice has attracted renewed interest. Here, the authors use scanning tunneling microscopy to visualize and interpret the charge density wave in CeSbTe using p-orbital bond density waves.

In this study, the authors report that post-vaccination neutralizing and binding antibody levels in the ENSEMBLE trial associate with Ad26.COV2.S vaccine efficacy (VE) against severe-critical COVID-19, with substantial VE even at unquantifiable neutralizing antibody titer.

Nuclear quantum effects affect chemical processes and material properties. Here the authors use path-integral molecular dynamics simulation to analyze their effects on themophysical properties of 92 organic liquids across the chemical space.

New tuberculosis therapies, targeting respiratory chain components of Mycobacterium tuberculosis, are under development. Here the authors show that, contrary to common belief, some of these components are not essential for pathogen viability and/or virulence in animal models of infection.

Fossil fuel companies need to align their activities with the climate goals and reduce their production rapidly. This research based on an updated methodology shows that these companies would produce more than their cumulative production budgets by 2050 if the recent trend continues.

An ex vivo 3D culture model of mycobacterial granulomas recapitulates the in vivo physiology of these structures and enables longitudinal imaging studies. The platform allows genetic and pharmacological manipulation of this key structure.

A 43-year dataset of rodents in the Hu region of China reveals how urbanization-induced changes to land-use configuration affect rodent community composition, including benefitting striped field mice, the primary local hosts of the zoonotic pathogen Hantaan virus.

Utilizing short-term dietary interventions for surgical preconditioning stands as an emerging approach to enhance surgical outcomes. Here, the authors show the potential of short-term preoperative methionine restriction as a simple intervention to ameliorate postinterventional vascular remodelling.

In this Stage 2 Registered Report, Buchanan et al. show evidence confirming the phenomenon of semantic priming across speakers of 19 diverse languages.

Climate change-induced sea-level rise and coastal extremes pose serious threats to Small Island Developing States (SIDS). This study provides a coastal flood risk assessment for SIDS globally and reveals the need for timely adaptation.

Not much is known about how intrinsic timescales, which characterize the dynamics of endogenous fluctuations in neural activity, change during cognitive tasks. Here, the authors show that intrinsic timescales of neural activity in the primate visual cortex change during spatial attention. Experimental data were best explained by a network model in which timescales arise from spatially arranged connectivity.

The advantage of living in cities compared with rural areas with respect to height and BMI in children and adolescents has generally become smaller globally from 1990 to 2020, except in sub-Saharan Africa.

Lee et al. show that DMXL1, a regulator of V-ATPase assembly, is recruited to lysosomes upon TRPML1 activation in a manner dependent on conjugation of ATG8 proteins on lysosomal membranes (CASM) and promotes lysosomal function.

The authors present the largest genome-wide association study to date for a rare Parkinsonian disorder, progressive supranuclear palsy (PSP). They include follow-up investigations of the identified susceptibility loci, functional consequences, and cell-specific pathologies, providing insights into genetic and molecular mechanisms underlying PSP.

Systematic analysis from the Global Burden of Disease study reported that, despite global improvements from 1990 to 2021, dietary iron deficiency-associated disease burden remains high in women, children and residents in low socio-demographic index countries.

Trees come in all shapes and size, but what drives this incredible variation in tree form remains poorly understood. Using a global dataset, the authors show that a combination of climate, competition, disturbance and evolutionary history shape the crown architecture of the world’s trees and thereby constrain the 3D structure of woody ecosystems.

Helical motifs in dense inorganic solids have remained exceedingly scarce. Now a type of 1D van der Waals helical crystal, GaSeI, is presented that manifests the rare quasi-periodic Boerdijk–Coxeter helix motif.

The functional relationship between subchondral bone and articular cartilage is unclear. Here, the authors show that transforming growth factor-beta propagates the mechanical impact of subchondral bone on articular cartilage through αV integrin–talin mechanical transduction system in chondrocytes.

Parks provide deep value to urban residents, but the distribution of those services is unclear. This study finds that US urban residents have unequal access to the crucial environmental, social and health amenities of urban parks.

Complex systems can undergo abrupt transitions leading to dramatic changes in the structural properties of the system by crossing the critical point. The authors study the origin of such critical transitions in spatially embedded networks and discover processes when external intervention on microscopic level leads to macroscopic transition of the system.

SEUDO is a tool for detecting and correcting errors introduced by automated processing of calcium imaging data.

Here, the authors use a massively parallel reporter assay RNA polymerase II massively systematic transcript end readout, to quantify factors that influence transcriptional start site selection in the genome of Saccharomyces cerevisiae to reveal patterns of dependence on DNA sequence, RNA polymerase II activity and nucleoside triphosphate abundance.

Making rewarding choices can require either generalization or individuation. Here, the authors show that across contexts, people adapt the specificity with which they represent and, increasingly across development, remember their experiences.

Plasmonic effects in organic light-emitting devices, which are normally considered a source of energy loss, are harnessed to enhance the stability of these devices while maintaining operational efficiency.

Zhou, Novak and colleagues identify that the Caenorhabditis elegans hypodermis, a peripheral liver-like metabolic tissue, regulates memory via insulin/IGF-1 and Notch signaling, and show that activating this pathway rescues CREB-dependent memory in aged worms.

Here the authors address how embryos control the timing of specific gene activation in early frog development. They find transcription factors for early gene activation are maternally loaded and remain at constant levels, and rather that order of activation is based on their sequential entry into the nucleus based largely on their respective affinity to importins.

Clinical and genetic evaluation of individuals with childhood-onset amyotrophic lateral sclerosis identifies a new monogenic cause for early-onset ALS and proposes a specific metabolic mechanism leading to motor neuron disease via sphingolipid excess.

Climate change is likely to impact the circulation of many infectious diseases. Here, the authors characterize the impact of climatic and demographic factors on enterovirus disease transmission and project how changes in climate may impact future transmission.

How conflicting contingencies between stimulus and outcome can be resolved by attention are not fully understood. Here authors, combining computational model and experimental approaches, show that mouse anterior cingulate cortex (ACC) effectively operates on low-dimensional neuronal subspaces to combine stimulus-related information with internal cues to drive actions under conflict.

Authors show that the MKP5 phosphatase domain – required for catalysis – contains an allosteric site maintained by key hydrophobic residues, and this allosteric pocket binds MAPK which induces conformational changes that promote MAPK dephosphorylation.

The archaeological site Shinfa-Metema 1 in the lowlands of northwest Ethiopia provides early evidence of intensive riverine-based foraging aided by the likely adoption of the bow and arrow.

A single component built from sputtered niobium dioxide, a Mott insulator–metal transition material, can simultaneously exhibit both visible light emission and electrical threshold switching with neuron-like oscillations.

This study presents the first sub-THz retrodirective wideband backscatter. Instead of phased arrays, it uses key properties of leaky waveguides, i.e., frequency-angle dependency and reciprocity for wideband retro directivity with ultra-low power.

A new biosynthetic core-forming enzyme, arginine cyclodipeptide synthase (RCDPS), was found to produce cyclo-arginine-Xaa dipeptides via a tRNA-dependent mechanism, and further genome mining using RCDPS as a beacon uncovered new natural products.

How animals generate perceptual decisions remains poorly understood. Here, the authors show that during a discrimination task, the mouse visual cortex does not encode the orientations of the cues but a categorical probability predicting the animal’s choice.

The experimental realization of lattice-born flat bands with nontrivial topology has been elusive. Here, the authors observe topological flat bands near the Fermi level in a kagome metal CoSn, with flat bands as well as Dirac bands originating from 3d orbitals in a frustrated kagome geometry.