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A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

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.

Genome-wide analyses identify 30 independent loci associated with obsessive–compulsive disorder, highlighting genetic overlap with other psychiatric disorders and implicating putative effector genes and cell types contributing to its etiology.

The number of individuals in a given space influences animal interactions and network dynamics. Here the authors identify general rules underlying density dependence in animal networks and reveal some fundamental differences between spatial and social dynamics.

An open-access resource, nano-org, enables researchers to explore and compare the nanoscale 2 organisation of proteins imaged using single-molecule localisation microscopy, advancing insights 3 into cell biology, disease, and drug response.

A purpose-built implantable system based on biomimetic epidural electrical stimulation of the spinal cord reduces the severity of hypotensive complications in people with spinal cord injury and improves quality of life.

Ricca et al discover a new family of tubular pili in Microcystis aeruginosa, a harmful algal bloom-forming cyanobacterium. These pili are crucial for buoyancy by forming cell micro-colonies, which increases drag and prevents sinking. The pili also enrich microcystin and co-localize with iron-enriched extracellular matrix components, suggesting a vital role in bloom proliferation.

Azetidine is a four-membered aza-cycle important in medicinal and organic chemistry. This study describes a mechanism of azetidine amino acid biosynthesis from l-isoleucine or l-valine by two non-haem Fe enzymes, PolF and PolE, in the polyoxin antifungal biosynthetic pathway.

Xavier Argout and colleagues report the draft genome of Theobroma cacao, the tropical crop that is the source of chocolate. The sequence assembly covers approximately 80% of the genome.

Diversity-oriented synthesis is a valuable strategy to construct complex molecules of medicinal interest. Here, the authors show a folding cascade strategy to convert linear substrates into polycyclic compounds with multiple stereocentres by combining the reductive chemistry of SmI₂ with 1,5-hydrogen atom transfer.

A comparison of alpha diversity (number of plant species) and dark diversity (species that are currently absent from a site despite being ecologically suitable) demonstrates the negative effects of regional-scale anthropogenic activity on plant diversity.

Practical implementations of quantum communication need to securely deliver information over long distances without line-of-sight. Towards this goal, Cuevas et al.use an actively stabilized interferometer to close the geometry loophole for a Bell inequality violation over 1 km of optical fibre.

In-cell NMR reveals the molecular details of NDM-1 degradation, an enzyme linked to antibiotic resistance, and sheds light on protein quality control in the periplasm of live bacteria at an atomic level.

Analysis of data from multiple instruments reveals a giant exoplanet in orbit around the 0.2-solar-mass star TOI-6894. The existence of this exoplanetary system challenges assumptions about planet formation and it is an excellent target for atmospheric characterization.

The processes of earthquakes and plastic deformation are examples of systems which respond to slow external forces by avalanche dynamics. Here, the authors show how a fundamental fingerprint of such dynamics - the average shape of the avalanches - evolves with its universality class.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate results across diverse datasets.

Profiling of 53,193 individual epithelial cells from the mouse small intestine identifies previously unknown cell subtypes and corresponding gene markers, providing insight into gut homeostasis and response to pathogens.

Using large cohorts from published clinical trials involving more than 8,000 patients with multiple sclerosis, a probabilistic machine learning model reconstructs the transition probabilities from data-derived diseases statuses, showing patterns that suggest how progression to severe stages occur and potential inversion of the process.

A neural epigenetic signature detectable via plasma analyses is prognostic in patients with glioblastoma, resembling an oligodendrocyte-progenitor- and neuronal-progenitor-cell-like state and showing increased neuro-to-glioma synapse formation.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

Here, the authors present trained models of genetically regulated enhancer RNA expression, finding that genetically regulated expression predicts chromatin contact frequency and that enhancer RNAs play a key role in complex trait heritability.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Binge drinking is a rising issue in women, yet the underlying neurobiology remains underexplored. Here authors show the Edinger-Westphal (EWcp) peptidergic neurons as a critical regulator of binge drinking in female mice via actions at the ghrelin receptor (GHSR).

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

A tryptophan metabolite was identified that acts systemically to promote defense against bacterial infection by targeting kainate receptors (KARs), revealing a novel intersection between tryptophan metabolism and KARs in immune defense.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Here, the authors identify in the 3′ untranslated region of the genome of Usutu virus, an emerging mosquito-borne flavivirus, a sequence that confers a unique capacity to resist degradation by the ISG20 exonuclease.

Mass cytometry can be used to scale up multiplexed serology testing, as shown for the simultaneous detection of antibody levels against multiple SARS-CoV-2 proteins in hundreds of serum samples.

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.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here, the authors present the largest FL study to-date to generate an automatic tumor boundary detector for glioblastoma.

Intercalation — a cornerstone of materials science with wide-ranging applications — has now been demonstrated in a superatomic crystal. A redox-active tetracyanoethylene guest was inserted into the lattice of a material consisting of alternate layers of {Co₆Te₈} clusters and C₆₀ fullerenes, leading to a single-crystal-to-single-crystal transformation that significantly modulates the material's optical and electrical transport properties.

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

Although it has been shown that engineering of conducting polymers such as poly(3,4-ethyldioxythiophene) can improve the Seebeck coefficient and the figure of merit ZT of these materials, the mechanisms underlying this improved thermoelectric behaviour are still not fully understood. It is now reported that the band structure of semicrystalline films of these bipolaronic polymers, resembling that of inorganic semi-metals used for thermoelectric applications, can explain these findings.

Phosphorylation of residues in the N-terminal tail of histone H3 signals different biological outcomes. High-resolution NMR analyses now reveal a mechanistic hierarchy of H3 phosphorylation events, whereby phosphorylation of Ser10 impedes the phosphorylation of Thr6 and Thr11 by PKC and Chk1, respectively. Because both enzymes also target Ser10, this establishes an autoinhibitory feedback loop on H3 tails.

The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of genome architecture and spatial genome regulation emerged early in animal evolution.