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Defining the spatial organization of tissues and organs like the brain from large datasets is a major challenge. Here, authors introduce CellTransformer, an AI tool that defines spatial domains in the mouse brain based on spatial transcriptomics, a technology that measures which genes are active in different parts of tissue.

Reframing of arousal as a latent dynamical system can reconstruct multidimensional measurements of large-scale spatiotemporal brain dynamics on the timescale of seconds in mice.

In vitro propagation of the pathogenic bacterium Coxiella burnetii, the causative agent of Q fever, leads to attenuated virulence and lipopolysaccharide (LPS) truncation. Here, Long et al. show that a strain considered to be avirulent (NMII) can be recovered from infected animals, and these isolates display increased virulence and an elongated LPS due to reversion of a 3-bp mutation in a gene.

Mutual paracrine regulation of the cytokines GREM1 and SPP1 mediate mesenchymal and epithelial cell fate in pancreatic cancer.

The International Brain Laboratory presents a brain-wide electrophysiological map obtained from pooling data from 12 laboratories that performed the same standardized perceptual decision-making task in mice.

Activity in a set of parabranchial neurons in the mouse brain is increased during chronic pain, predicts coping behaviour, and can be modulated by circuits activated by survival threats.

Brain-wide recordings in mice reveal that prior expectations are distributed through recurrent loops across all levels of cortical and subcortical processing.

To address the phase instability issue of perovskites, ammonium propionic acid is introduced to enhance the phase stability of both perovskite layers in perovskite/perovskite/silicon triple-junction solar cells, resulting in improved efficiency and reproducibility.

This study maps the connections of layer 5 pyramidal neurons in the mouse cortex, revealing distinct local and intercortical wiring patterns, and provides an open framework for exploring the connectivity of cell types.

Enhanced polyamine depletion in neuroblastoma models decreases translation of mRNA codons with adenosine in the third position, reprogramming the tumour proteome away from cell cycle progression and towards differentiation.

Reliable measuring the voltage dynamics of individual neurons in the intact brain is significantly challenging. Here authors developed an all-optical method combining two-photon voltage imaging and optogenetics to measure and induce synaptic plasticity in vivo, revealing LTP of inhibition in cerebellar circuits and providing a blueprint to link synaptic changes to learning.

Federated learning (FL) algorithms have emerged as a promising solution to train models for healthcare imaging across institutions while preserving privacy. Here, the authors describe the Federated Tumor Segmentation (FeTS) challenge for the decentralised benchmarking of FL algorithms and evaluation of Healthcare AI algorithm generalizability in real-world cancer imaging datasets.

Multiancestry fine-mapping of brain protein quantitative trait loci coupled with Mendelian randomization analyses identifies protein–trait pairs consistent with causal effects across neurological and psychiatric conditions.

Artis and colleagues show that enteric neurons produce CGRP-related ADM2 to promote intestinal tissue-protective functions in ILC2s.

Chronic care manages long-term, progressive conditions, while acute care handles short-term ones. Here, authors show chronic conditions account for most of the global health burden, with 68% of DALYs and 93% of YLDs attributed to chronic care needs.

Dense calcium imaging combined with co-registered high-resolution electron microscopy reconstruction of the brain of the same mouse provide a functional connectomics map of tens of thousands of neurons of a region of the primary cortex and higher visual areas.

A comprehensive cell atlas of the whole mouse brain with high molecular and spatial resolution is generated.

In this study, the authors develop a comprehensive taxonomy of brain-wide SPNs, identifying several novel subsets via their transcriptional signatures.

3D brain atlases enable spatial data integration across studies. Here, the authors present the Developmental Mouse Brain Common Coordinate Framework, a 3D multimodal atlas from embryonic to adult ages for cell type mapping through brain development.

The collapse of tropical forests during the Permian–Triassic Mass Extinction weakened carbon sequestration, sustaining high CO2 and extreme global warmth for millions of years: an example of a runaway feedback in Earth’s climate-carbon system.

Here they show that ATF7IP/SETDB1-mediated epigenetic programming governs T lymphoid progenitor trafficking and differentiation, providing important insights into the pathogenesis of human T lymphoid diseases.

 A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarkable cell type diversity across the brain and unique cell type characteristics of different brain regions. 

A study reports whole-genome sequences for 490,640 participants from the UK Biobank and combines these data with phenotypic data to provide new insights into the relationship between human variation and sequence variation.

Using well-calibrated statistical methods the authors jointly analyze Undiagnosed Diseases Network genomes, identifying known and novel disease genes. Software is publicly available to support future cross-cohort rare disease discovery efforts.

The subcommissural organ (SCO) is a gland in the brain, and relatively little is known about its function. Zhang et al. genetically ablated SCO cells and observed severe hydrocephalus and neuronal defects. The reintroduction of SCO-derived peptides into SCO-ablated brain substantially rescued developmental defects.

Together with a companion paper, the generation of a transcriptomic atlas for the mouse lemur and analyses of example cell types establish this animal as a molecularly tractable primate model organism.

CRISPR-Cas9 has potential as an efficient tool for information retrieval in DNA data storage. Here the authors present a Cas9-based random access and similarity search approach and test on DNA databases, progressing toward simpler, isothermal protocols.

A high-bandwidth neuromotor interface offers performant out-of-the-box generalization across people.

Zhao et al. present RAPiDock, an all-atom diffusion model that predicts peptide–protein binding patterns across 92 amino acid types, enabling high-throughput virtual screening for advancing therapeutic peptide design.

A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis pipelines. Evaluation of popular data-dependent acquisition tools indicates that these generally seem to control the FDR, but data-independent acquisition tools exhibit inconsistent control of the FDR at both the peptide and protein levels.

Multi-modal analysis is used to generate a 3D atlas of the upper limb area of the mouse primary motor cortex, providing a framework for future studies of motor control circuitry.

Together with an accompanying paper presenting a transcriptomic atlas of the mouse lemur, interrogation of the atlas provides a rich body of data to support the use of the organism as a model for primate biology and health.

A single-cell sequencing study using more than 30,000 tumour genomes from human ovarian cancers shows that whole-genome doubling is an ongoing mutational process that drives tumour evolution and disrupts immunity.

Genomic studies often lack representation from diverse populations, limiting equitable insights. Here, the authors show that the BIG Initiative captures extensive genetic diversity and reveals ancestry-linked health disparities in a community-based Mid-South cohort.

In this work the authors present Token-Mol, a token-only 3D drug design model, which deploys the Gaussian cross-entropy (GCE) loss function for regression tasks. It exhibits superior performance in molecular conformation generation, property prediction, and pocket-based generation, thus opening up new avenues for drug design.

Systematic studies are needed to discover molecular determinants of blood brain barrier dysfunction in Alzheimer’s disease. This study identifies perturbed pericytic SMAD3-astrocytic VEGFA interactions as a potential driver of this dysfunction.

As part of the BICCN consortium, the authors used a single-cell transcriptomic imaging method to produce a highly defined atlas of cell types across the mouse primary motor cortex.

Sinonasal squamous cell carcinoma (SNSCC) is an uncommon tumor, which has been associated with the human papillomavirus (HPV). Here the authors perform comprehensive genome-wide characterization of HPV-associated and HPV-independent SNSCC patient samples to reveal molecular patterns of tumorigenesis and identify HPV-driven mutational profiles.

Reducing critical materials such as indium and silver is of high importance for photovoltaics. Yu et al. demonstrate a certified 25.94% efficiency silicon heterojunction solar cell replacing part of indium-based electrodes with undoped tin oxide and using copper for contacts.

BARseq interrogates the expression of 104 cell-type marker genes in 10.3 million cells over nine mouse forebrain hemispheres to reveal the role of peripheral inputs on cortical area development.

ONIX is a data acquisition system for recording freely behaving mice. It can accommodate a variety of recording technologies, while maintaining minimal impact on animal behavior.

mBrainAligner is a cross-modal registration platform for whole mouse brains imaged with different modalities. In addition, a fluorescence micro-optical sectioning tomography-based mouse brain atlas has been generated.

The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

Collaborative augmented reconstruction (CAR) is a platform for large-scale reconstruction of neurons and other cells from multi-dimensional imaging datasets. It can be accessed from a variety of devices simultaneously for efficient and accurate reconstruction.

The expression of each of the roughly 22,000 genes of the mouse genome has been mapped, at cellular resolution, across all major structures of the mouse brain, revealing that 80% of all genes appear to be expressed in the brain.

Here the authors analyzed 3.7 petavoxels of 3D imaging data from 204 mouse brains, aiming to comprehensively characterize diverse morphological and modular patterns conserved across six spatial scales of mouse brain anatomy, ranging from the whole-brain scale to synaptic levels.

Gene selection for spatial transcriptomics is currently not optimal. Here the authors report PERSIST, a flexible deep learning framework that uses existing scRNA-seq data to identify gene targets for spatial transcriptomics; they show this allows you to capture more information with fewer genes.