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Data-independent acquisition (DIA)-based proteomics often relies on mass spectrum libraries from data-dependent acquisition experiments. Here, the authors present a method to generate DIA-based chromatogram libraries, enabling DIA-only workflows and detecting more peptides than with spectrum libraries alone.

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.

Although Huntington’s disease (HD) is a well-studied genetic disorder, less is known about the epigenetic changes underlying it. Here, the authors characterize DNA methylation levels in tissues from patients, a mouse huntingtin (Htt) gene knock-in model, and a transgenic HTT sheep model, and provide evidence that HD is accompanied by DNA methylation changes in these three species.

This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

A transformer-based representation-learning model that processes multimodal input in a unified manner outperformed non-unified multimodal models in two clinical diagnostic tasks.

A comparison of two complete sets of human centromeres reveals that the centromeres show at least a 4.1-fold increase in single-nucleotide variation compared with their unique flanks, and up to 3-fold variation in size, resulting from an accelerated mutation rate.

Xie et al. present UnitedMet, a tool that leverages RNA–metabolite covariation to impute metabolite levels from transcriptomic data, and find oxidative phosphorylation associated with both BAP1 status and metastasis or therapy outcome in kidney cancer.

The red fluorescent protein mScarlet3-H is bright, photostable and very robust to high temperature, chaotropic conditions and oxidative environments. mScarlet3-H works well in correlative light and electron microscopy, tissue clearing and time-lapse super-resolution microscopy.

The existence and properties of tetraquark states with two heavy quarks and two light antiquarks have been widely debated. Here, the authors use a unitarized model to study the properties of an exotic narrow state compatible with a doubly charmed tetraquark.

A nanofluidic intracellular delivery (NanoFLUID) patch provides a versatile, biocompatible and efficient method for the targeted delivery of payloads to internal organs for therapeutic purposes and for biomolecular investigations.

The semileptonic decay channels of the Λc baryon can give important insights into weak interaction, but decay into a neutron, positron and electron neutrino has not been reported so far, due to difficulties in the final products’ identification. Here, the BESIII Collaboration reports its observation in e+e- collision data, exploiting machine-learning-based identification techniques.

SEAM is a platform for the analysis of high-resolution secondary ion mass spectrometry imaging that allows spatially resolved nuclear metabolomic profiling at the single-cell level.

A new compatibilization strategy installs dynamic crosslinkers into several classes of binary, ternary and postconsumer immiscible polymer mixtures in situ, with the resulting compatibilized dynamic thermosets exhibiting intrinsic reprocessability and enhanced tensile strength and creep resistance.

Gold with FCC phase is very ductile, while the yield strength is well below the theoretical limit. Here, the authors report on the mechanical properties of single-crystalline gold nanoflakes with HCP phase that illustrate the benefits of phase engineering.

CuP2 has a puzzling thermal transport behavior, with low thermal conductivity but quite large mean sound speeds. Here, the authors conduct a systematical study of the atomic structure and lattice dynamics of CuP2 to reveal the origin, finding a dimer rattling behavior.

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.

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.

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.

Intensive research efforts are underway to enable applications of layered lithium transition metal oxides in batteries. Here the authors report an oxidative chemical vapour deposition technique to conformally coat both the primary and the secondary particles of these oxides to unleash potential applications.

Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probiotic therapy could be beneficial.

Here the authors identify ZIC2 and ZIC3 as key regulators of human primed pluripotency which recruit BRG1 to open primed hESC-specific enhancers.

The integration of oxide nanoelectronics with silicon platforms is a necessary step for the fabrication of ultrahigh-density devices. Here, the authors grow a LaAlO₃/SrTiO₃interface directly on silicon, and show the reversible creation of a two-dimensional electron gas confined within nanowires located on the surface.

Analysis of copy number alterations in 1,451 patient-derived xenografts (PDXs) and matched patient tumor samples shows strong conservation from patient tumors through late-passage PDXs and a lack of systematic copy number evolution driven by the mouse host.

A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci may have helped crop plants to adapt to agricultural ecosystems.

It is unclear how often genetic mosaicism of chromosome X arises. Here, the authors examine women with cancer and cancer-free controls and show that X chromosome mosaicism occurs more frequently than on autosomes, especially on the inactive X chromosome, but is not linked to non-haematologic cancer risk

Heterogeneous populations of basal cells in the prostate epithelium contain stem cells. Here the authors show that Zeb1 marks a pool of prostate epithelial stem cells that self-renew, generate prostate glandular structures with all 3 epithelial cell types and are required for prostate basal cell 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.

Results from the first experimental campaign of the Wendelstein 7-X stellarator demonstrate that its magnetic-field design grants good control of parasitic plasma currents, leading to long energy confinement times.

Stabilizing lithium anodes has been a crucial yet challenging task in developing high-energy batteries. Here the authors design two simple steps of spontaneous reactions to achieve a porous lithium electrode with a composite protective layer, enabling high-loading Li-S batteries with excellent cyclability.

MRI data from more than 100 studies have been aggregated to yield new insights about brain development and ageing, and create an interactive open resource for comparison of brain structures throughout the human lifespan, including those associated with neurological and psychiatric disorders.

The role Tibetan Plateau uplift played in Asian inland aridification remains unclear due to a paucity of accurately dated records. Here, the authors present a continuous aeolian sequence for the period >51–39 Ma, analysis of which indicates that aridification was driven by global climatic forcing rather than uplift.

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.

Zinc batteries are receiving growing attention due to their sustainability merits not shared by lithium-ion technologies. Here the aqueous electrolyte design features unique solvation structures that render Zn–air pouch cell excellent cycling stability in a wide temperature range from −60 to 80 °C.

The Large Hadron Collider beauty collaboration reports a test of lepton flavour universality in decays of bottom mesons into strange mesons and a charged lepton pair, finding evidence of a violation of this principle postulated in the standard model.

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.

Exotic quantum states can be advantageous for sensing, but are very fragile, so that some form of quantum error correction is needed. Here, the authors show how approximate QEC helps overcoming decoherence due to noise when measuring the excitation population of a receiver mode in a superconducting circuit.

Analysis of a set of 1,863 bursts from the repeating source FRB 20201124A provides evidence of a complicated magnetized site within about an astronomical unit from the source in a barred galaxy.

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.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

Cancer-associated fibroblasts (CAFs) are the main component of the stroma in pancreatic cancer, but their tissue of origin remains to be defined. Here the authors perform lineage tracing and single cell RNA sequencing in mice and suggest the splanchnic mesenchyme as the tissue of origin for CAFs.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

With ultra-deep RNA sequencing, Zhang et al. report increased usage of alternative promoters driven by AR, FOXA1 and MYC during prostate cancer progression and suggest altered DNA methylation as a potential underlying mechanism.

Puissant and colleagues identify a myeloid-restricted PIK3CG/p110γ–PIK3R5/p101 axis as a therapeutic vulnerability in acute myeloid leukemia and develop a proteolysis-targeting chimera to potently degrade PIK3CG and suppress AML progression.

Hervera et al. show that extracellular vesicles containing NOX2 complexes are released from macrophages and incorporated into injured axons, leading to axonal regeneration through PI3K–p-Akt signalling.

A strategy that combines freeze-casting and salting-out treatments produces strong, tough, stretchable and fatigue-resistant poly(vinyl alcohol) hydrogels.

Understanding magnetic materials at the nanoscale is important for the development of novel applications, but has been hampered by a lack of suitable experimental techniques. Here, the use of transmitted electrons permits the determination of atomic site-specific magnetic information.

SNIP1 methylation initiates its oncogenic functions. Here, the authors show that SNIP1 is methylated by KMT5A and this leads to downstream signalling that activates the YAP pathway, resulting in tumorigenesis and metastasis.

Assembly of the hexaploid oat genome and its diploid and tetraploid relatives clarifies the evolutionary history of oat and allows mapping of genes for agronomic traits.