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

Diamond, a statistically rigorous method, is capable of finding meaningful feature interactions within machine learning models, making black-box models more interpretable for science and medicine.

The authors integrate single-cell transcriptomic data with prior gene graphs to produce a biologically meaningful cell state manifold that can predict driver genes for genetic perturbations and differentiation events across diverse cell types.

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.

Cross-modality mapping extends to 3D with image-varifold based technologies for partial matching, spatial resampling, and feature selection to efficiently represent and integrate high-dimensional spatial-omics data with tissue-scale imaging.

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.

High-throughput mapping of neural projections at the single-cell level remains challenging. Here, the authors have developed axonal BARseq, a new technique that allows for mapping projections from thousands of neurons within a single brain.

Neural networks fundamentally dictate function. Here, the authors show thirteen uniquely connected neuron populations within the anterior thalamic nuclei, suggesting multiple parallel subnetworks support its emotional and cognitive functions.

 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. 

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.

Chen et al. show that in mice, extracellular matrix remodeling drives early migration of the anterior signaling center, establishing the body axis sooner than expected—a mechanism potentially conserved in humans.

The NeuroXiv platform enables AI-powered open mining of a database of reconstructions of more than 175,000 mouse neurons, registered to the Common Coordinate Framework. The platform supports queries about connectivity, projection patterns and other morphological features.

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.

We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference.

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.

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.

Molecular glue degraders eliminate cellular proteins by promoting their interaction with E3 ubiquitin ligases. Here, the authors identify molecular glue degraders targeting the E3 ligase TRIM21 and synthesize a heterobifunctional degrader that recruits TRIM21 to degrade an engineered protein aggregate.

Omics data’s diversity and high-dimensionality challenge integration across technologies and with imaging. Here, authors introduce mapping method xIV-LDDMM that estimates geometric and feature transformations to integrate tissue-scale atlases with molecular and cellular-scale data.

A pangenome of the Cannabis genus including 193 genomes demonstrates high variability in most of the genome but low diversity in cannabinoid synthesis genes and provides a resource for future genetic studies and crop optimization.

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.

A dataset of 3D images from more than 200,000 human induced pluripotent stem cells is used to develop a framework to analyse cell shape and the location and organization of major intracellular structures.

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.

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.

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.

Meta-analysis of genome-wide association studies on Alzheimer’s disease and related dementias identifies new loci and enables generation of a new genetic risk score associated with the risk of future Alzheimer’s disease and dementia.

This Resource presents a method to define connectivity types of neurons based on a spatially registered large database containing more than 20,000 neuronal reconstructions. A brain connectivity map is also generated using such connectivity features.

Entanglement was observed in top–antitop quark events by the ATLAS experiment produced at the Large Hadron Collider at CERN using a proton–proton collision dataset with a centre-of-mass energy of √s  = 13 TeV and an integrated luminosity of 140 fb⁻¹.

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

This study uses epi-retro-seq to link single-cell epigenomes and cell types to long-distance projections for neurons dissected from different regions projecting to different targets across the whole mouse brain.

A genome-wide association meta-analysis study of blood lipid levels in roughly 1.6 million individuals demonstrates the gain of power attained when diverse ancestries are included to improve fine-mapping and polygenic score generation, with gains in locus discovery related to sample size.

Sparse labelling and whole-brain imaging are used to reconstruct and classify brain-wide complete morphologies of 1,741 individual neurons in the mouse brain, revealing a dependence on both brain region and transcriptomic profile.

Skilled reaching movements are critical for survival. Here, the authors show in mice that the parafascicular (Pf) and ventroanterior/ventrolaber (VAL) nuclei of the thalamus govern distinct circuits related to reaching direction and speed, respectively.

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.

Methylome-based clustering and cross-modality integration with companion datasets from the BRAIN Initiative Cell Census Network enabled the construction of a 3D multi-omic genome atlas of the adult mouse brain featuring thousands of cell-type-specific profiles.

Behavioural and electrophysiological studies in simultaneously thirsty and hungry mice reveal a neural basis for resolving conflicts between needs, in which choices are guided by a persistent and distributed neural goal state that undergoes spontaneous transitions between goals.

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 growing complexity of quantum computing devices makes presents challenges for benchmarking their performance as previous, exhaustive approaches become infeasible. Here the authors characterise the quality of their 11-qubit device by successfully computing two quantum algorithms.

Tracking raw materials is critical for securing global supply chains, but traditional tags lack in traceability and anticounterfeiting. The authors present a DNATag-based system for secure traceability, featuring error tolerance, mobile phone readability, and robust forgery protection.

Mutations reducing the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder, yet it remains unclear which cell types are most impacted by MYT1L loss. Here authors use single-nuclei RNA sequencing to profile the forebrains of MYT1L-deficient mice at three developmental stages and reveal MYT1L deficiency disrupts cortical neuron proportions and gene expression, primarily affecting excitatory neuron maturation programs.

Therapeutic T cells engineered to recognize tumour antigens are frequently short-lived and acquire unfavourable phenotypes in tumours. Here authors show that a tandem approach using autologous T cells targeted against the tumour antigen NY-ESO-1, followed by transfer of hematopoietic stem cells with the same specificity in the clinical trial NCT03240861, provides a safe and promising therapeutic option.

A genome-wide association study meta-analysis combined with multiomics data of osteoarthritis identifies 700 effector genes as well as biological processes with a convergent involvement of multiple effector genes; 10% of these genes express the target of approved drugs.