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Cell type labelling in single-cell datasets remains a major bottleneck. Here, the authors present AnnDictionary, an open-source toolkit that enables atlas-scale analysis and provides the first benchmark of LLMs for de novo cell type annotation from marker genes, showing high accuracy at low cost.

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.

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.

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.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

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.

The authors investigate junctions made of two flakes of the cuprate superconductor Bi₂Sr_2-xLa_xCuO_6+y (Bi2201) twisted by 45 degrees. They find evidence for an isotropic pairing component, and call into question theoretical predictions of d+id superconductivity in this system.

Wafer-scale 3R-MoS₂ with high phase purity is achieved through a homoepitaxy strategy, which demonstrates ferroelectricity and holds promise for multifunctional integration.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

The LHCb experiment at CERN has observed significant asymmetries between the decay rates of the beauty baryon and its CP-conjugated antibaryon, thus demonstrating CP violation in baryon decays.

Given that the human body is composed of many microbial niches, and there have been few reports on the biogeography of the microbiome, the authors analyse the intra-individual inter-organ and intra-organ microbiome of seven surface organs of deceased individuals.

The joint analysis of datasets from NOvA and T2K, the two currently operating long-baseline neutrino oscillation experiments, provides new constraints related to neutrino masses and fundamental symmetries.

Fractional quantum Hall states in 2D electron gases arise due to strong electron-electron interactions, which makes a general theoretical understanding difficult. Fu et al. present data showing the ν = 5/3 quantum Hall state has a 3/2 plateau in the diagonal resistance that has not been captured by existing models.

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.

Investigating the inner structure of baryons is important to further our understanding of the strong interaction. Here, the BESIII Collaboration extracts the absolute value of the ratio of the electric to magnetic form factors and its relative phase for e + e − → J/ψ → ΛΣ decays, enhancing the signal thanks to the vacuum polarisation effect at the J/ψ peak.

Heteroepitaxy is used to precisely control the growth of Mn₃O₄ shells on the faces of a Co₃O₄ nanocube crystal, producing uniform grain boundary defects and highly ordered multigrain nanostructures.

The local delivery of a calcium channel blocker and a Rho-kinase inhibitor, determined by screening for small molecules that cause ureteral relaxation, significantly reduce ureteral contraction in pigs.

The authors address spin–orbit torques and magnetization switching in MnPd₃/CoFeB hetrostructures.

We find that 2D–3D perovskitoid passivation applied to perovskite solar cells impedes cation migration and decreases carrier recombination at the interface, providing enhanced operating stability at elevated temperatures and increased power conversion efficiencies.

Neural Decomposition (NEURD) is a software package that decomposes neuronal data from high-resolution electron microscopy volumes into feature-rich graph representations to facilitate analysis for neuroscience research.

CTCF, which is known to play critical role in chromatin structure, undergoes post-translational modifications (PTMs). In this research, O-GlcNAcylation was found to inhibit CTCF binding, impacting 3D chromatin structure, gene expression and cellular development.

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.

Exploring low-cost, efficient catalysts to replace platinum is crucial for electrocatalytic hydrogen generation. Here, the authors report a termination-acidity strategy that boosts the activity of molybdenum carbides, achieving a low overpotential and sustaining hydrogen generation for over 200 h.

Understanding interfacial proton transport in an excited state is crucial for catalytic and diagnostic applications of nanomaterials. Here, the authors combine ultra-low-field NMR relaxometry with a light source to study the light-induced proton dissociation of graphene quantum dots.

RNA conformational heterogeneity is important to diverse functions. Here, the authors use AFM to directly visualize individual RNA molecules that are in various conformational states under near physiological solution conditions for the first time.

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.

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.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Highly stretchable organic electrochemical transistors with stable charge transport under severe tensional strains are demonstrated using a honeycomb semiconducting polymer morphology, thereby enabling controllable signal output for diverse stretchable bioelectronic applications.

Pyrochlore iridates have been studied for their potential to explore novel phases due to the interplay of correlations, spin-orbit interaction, and more recently dimensionality. Here the authors report a chiral spin-liquid-like state in (111)-oriented Y₂Ir₂O₇ thin films which emerges at a reduced thickness.

Adding minute amounts of rhenium to Ni-based single crystal superalloys extends their high temperature performance in engines, but the reasons behind that are still unclear. Here, the authors combine high resolution imaging and modelling to show that rhenium enriches and slows down partial dislocations to improve creep performance.

Bayati et al. discovered that sequential treatment of iPSC-derived dopaminergic neurons with α-synuclein fibrils and proinflammatory cytokines leads to the formation of Lewy body–like inclusions, through the downregulation of lysosomal proteins.

Designing an efficient electrocatalyst of hydrogen oxidation reaction is highly critical for anion exchange membrane fuel cells. Here the authors report implanting oxophilic metal atoms in PtRu nanowires to significantly improve the mass activity, stability, and resistance to CO-poisoning for hydrogen oxidation.

Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.

Using a spectroscopy streaking technique at LCLS (Linac Coherent Light Source), researchers demonstrate temporal characterization of X-ray pulses with sub-femtosecond resolution.

Self-referenced attosecond streaking enables in situ measurements of Auger emission in atomic neon excited by femtosecond pulses from an X-ray free-electron laser with subfemtosecond time resolution and despite the jitter inherent to X-ray free-electron lasers.

Sensitive, biocompatible and stable contrast agents for MRI are in demand. Here, the authors combine gadolinium ions with amorphous calcium carbonate to make stable paramagnetic amorphous carbonate nanoclusters with high MRI contrast and significantly improved biocompatibility over commercial gadolinium-based agents.

A new type of fermion, corresponding to a three-fold degeneracy in the electronic band structure of crystalline molybdenum phosphide, is observed, which lies conceptually between Dirac and Weyl fermions.

This work shows that by designing appropriate alloying elements in a body-centred-cubic high-entropy alloy, local chemical order and lattice distortion can be tuned, which influences the evolution of planar-slip bands, realizing pure-metal-like tensile ductility at gigapascal yield strength.

GWAS have identified more than 500 genetic loci associated with blood lipid levels. Here, the authors report a genome-wide analysis of interactions between genetic markers and physical activity, and find that physical activity modifies the effects of four genetic loci on HDL or LDL cholesterol.

Modules of foldable crystalline silicon solar cells retain their power-conversion efficiency after being subjected to bending stress or exposure to air-flow simulations of a violent storm.

Enhancing the intrinsic activity and space time yield of Cu based heterogeneous methanol synthesis catalysts is one of the major topics in CO₂ hydrogenation. Here the authors develop a highly active inverse catalyst composed of fine ZrO₂ islands dispersed on metallic Cu nanoparticles.

The ATLAS Collaboration reports a measurement of the ratio of the decay rates of W bosons to τ leptons and muons, in agreement with universal lepton couplings as postulated in the standard model of particle physics.

SET domain–containing 2 (SETD2) is reported as an immunosuppressor in clear cell renal cell carcinoma (ccRCC). Here the authors show that SETD2 loss enhances de novo sphingomyelin biosynthesis during the transition from polycystic kidney disease to ccRCC.

A study identifies TMEFF1 as a neuron-specific restriction factor essential for prevention of replication of herpes simplex virus type 1 in the central nervous system.

Triggering and sustaining fusion reactions — with the goal of overall energy production — in a tokamak plasma requires efficient heating. Radio-frequency heating of a three-ion plasma is now experimentally shown to be a potentially viable technique.

Analysis of interactions between the wheels of the Zhurong rover and the terrain along the rover’s traverse reveals soils with high bearing strength and cohesion.

Experiments realizing the indirect-drive fast ignition scheme for inertial confinement fusion are reported. Enabled by a tightly compressed target, an increase of neutron yield is observed.

Here, the authors present a resonance theory to describe the bonding configuration of flat boron materials without quantum calculation. Like aromaticity theory in carbon, it allows to intuitively understand the stability and properties of boron-related materials