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Identifying jets originating from heavy quarks plays a fundamental role in hadronic collider experiments. In this work, the ATLAS Collaboration describes and tests a transformer-based neural network architecture for jet flavour tagging based on low-level input and physics-inspired constraints.

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

The ALICE Collaboration provides details on the microscopic mechanism that ends up creating antideuteron in high-energy proton–proton collisions at the Large Hadron Collider.

Deterministically generated single photons are useful for quantum communications, but the processes that create such light are often non-deterministic. Here, the authors enhance the single-photon output probability by multiplexing photons from four temporal modes using fibre-integrated optics.

In this Perspective, members of the Aging Biomarker Consortium outline the X-Age Project, an Aging Biomarker Consortium plan for building standardized aging clocks in China. The authors discuss the project roadmap and its aims of decoding aging heterogeneity, detecting accelerated aging early and evaluating geroprotective interventions.

A new artificial intelligence model, DeepSeek-R1, is introduced, demonstrating that the reasoning abilities of large language models can be incentivized through pure reinforcement learning, removing the need for human-annotated demonstrations.

Comparative genomics of Shiga toxin-producing E. coli from healthy carriers and patients uncovers key virulence differences and supports risk-based management strategies.

mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.

Anisotropic hybridization between conduction and unpaired f electrons is rarely observed. Now, a lanthanide-based two-dimensional compound exhibits nodal hybridization, giving rise to heavy-fermion behaviour.

The Einstein Probe has discovered a fast X-ray transient, EP240414a, associated with a broad-lined type Ic supernova. Its unusually soft spectrum and weak jet add to the diversity of stellar deaths and suggest a previously unknown Wolf–Rayet star explosion mechanism.

A magnetic-spectrometer-free method for electron–proton scattering data reveals a proton charge radius 2.7 standard deviations smaller than the currently accepted value from electron–proton scattering, yet consistent with other recent experiments.

Composites of carbon nanotubes and superconductors provide technologically important new, or improved, functionalities. Here, with a chemical solution approach, well-aligned carbon nanotube forests embedded in a superconducting NbC matrix are shown to effectively enhance the superconducting properties of NbC.

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.

The results of the Fifth RNA-Puzzles contest highlights advances in RNA three-dimensional structure prediction and uncovers new insights into RNA folding and structure.

Flores et al. show that brain-penetrant eIF2B agonists suppress ISR activation in cellular and mouse models of ALS and reduce ISR biomarkers in humans, enabling further clinical studies of ISR inhibition in individuals with neurological diseases

Heterogeneous photocatalysts are easily separable and recyclable, but homogeneous ones are precisely tunable. Here, the authors merge the benefits of these two catalyst types by incorporating diverse dyes into solution-processable, porous polymers.

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.

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.

The authors use time-resolved scanning near-field optical microscopy to probe the ultrafast excitonic processes and their impact on waveguide operation in transition metal dichalcogenide crystals. They observe significant modulation of the complex index by monitoring waveguide modes on the fs time scale, and identify both coherent and incoherent manipulations of WSe₂ excitonic resonances.

The fabrication of perovskite heterojunctions is challenging. Mali et al. develop a heterojunction with two different crystalline phases of CsPbI₃, achieving 21.5% and 18.4% efficiencies on small-area solar cells and 18 cm² solar modules, respectively.

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.

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.

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.

The death of massive stars has traditionally been discovered by explosive events in the gamma-ray band. Liu et al. show that the sensitive wide-field monitor on board Einstein Probe can reveal a weak soft-X-ray signal much earlier than gamma rays.

Traditional photonic crystals consist of periodic media with a pre-defined optical response. Here, the authors combine nanostructured back-gate insulators with a continuous layer of graphene to demonstrate an electrically tunable two-dimensional photonic crystal suitable for controlling the propagation of surface plasmon polaritons.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

Kagome lattices host a plethora of topological phenomena. Here, the authors identify nearly flat spin-wave bands in part of the Brillouin zone and large orbital moments in the metallic kagome ferromagnet Fe₃Sn₂.

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.

Direct infrared nano-imaging of plasmonic waves in graphene carrying high current density reveals the Fizeau drag of plasmon polaritons by fast-moving quasi-relativistic electrons.

Here, the authors report the observation of two solid-state analogues of well-known high-energy physics effects in graphene samples irradiated by infrared photons under non-equilibrium conditions. Depending on the carrier density of graphene, they observed asymmetric plasmon damping, and anomalous photocurrents associated with the condensed matter versions of the Cherenkov and Schwinger effects.

This manuscript evaluates forecasts of laboratory-confirmed influenza hospital admissions, a new target for influenza forecasting in the United States. Across two influenza seasons, the FluSight ensemble is robust compared to submitted models.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

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.

A type II supernova (SN 2023ixf) was observed in the galaxy M101 at a distance of 6.85  ±  0.15 Mpc, at about 1.0  h after the explosion.

The growing need for realism in addressing complex public health questions calls for accurate models of the human contact patterns that govern disease transmission. Here, the authors generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

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.

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.

Presence of peritoneal metastasis is associated with a decreased survival in patients with colorectal cancer. Here, the authors show that peritoneal-resident macrophages promote the formation of an immunosuppressive environment that facilitate peritoneal metastasis in colorectal cancer.

Sensors of the NLR family generally activate innate immunity. Ting et al., however, demonstrate that the little-known NLRC3 negatively regulates Toll-like receptor signaling by altering ubiquitination of the signaling adaptor TRAF6.

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.

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.