Search

A high-resolution update of Antarctic bed topography using mass conservation reveals broad stabilizing ridges for glaciers flowing across the Transantarctic Mountains, and stabilizing slopes beneath Moscow University, Totten and Lambert glacier system.

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.

Heterostructures of graphene and hexagonal boron nitride have great potential for high-mobility electronics, yet little is known about the electronic interaction between these two atomically thin materials. Here, the authors perform angle-resolved reflected-electron spectroscopy to unveil their interplay.

Known genetic loci account for only a fraction of the genetic contribution to Alzheimer’s disease. Here, the authors have performed a large genome-wide meta-analysis comprising 409,435 individuals to discover 6 new loci and demonstrate the efficacy of an Alzheimer’s disease polygenic risk score.

In liquid-phase TEM, microfluidic reactors are used to monitor nanoscale (electro)chemical dynamics in liquid environments. Here, the authors develop a reactor design with accelerated mass transport, facilitating quantitative in-situ and in-operando studies.

The design, synthesis and characterization of a series of circular sandwich compounds, cyclocenes, is described, and these cyclic sandwich compounds are expected to lead to further innovations in new functional organometallic materials.

Here the authors apply machine learning approaches to Alzheimer’s genetics, confirm known associations and suggest novel risk loci. These methods demonstrate predictive power comparable to traditional approaches, while also offering potential new insights beyond standard genetic analyses.

It has recently been shown that synaptic transmission delays enhance the computational capabilities of spiking neural networks. In this manuscript, the authors introduce an exact, event-based training method for various types of delays and benchmark it on mixed-signal neuromorphic hardware.

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.

Polygenic risk scores for Alzheimer’s disease derived from individuals of European ancestry can show improved performance in multiancestry settings after incorporating genome-wide association summary statistics from diverse populations.

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.

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.

Nucleoside-processing enzymes exhibit strict regioselectivity for glycosylation of purine nucleobases at N9. Here, the authors report an exception and show that wild type nucleoside phosphorylases also furnish N7-xanthosine, a non-native ribosylation regioisomer of xanthosine.

By making use of the hydrodynamic behaviour of phonons in graphitic materials, a thermal version of a micrometre-scale Tesla valve is demonstrated, resulting in a method for thermal rectification in solids.

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.

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.

The layered structure of van der Waals materials leads to highly anisotropic thermal conductivity, due to the van der Waals gap between the layers. Here, Da̧browski et al show how this anisotropic heat transport can be harnessed for ultrafast, optically-induced control of magnetism in Cr₂Ge₂Te₆.

Systemic AL amyloidosis is caused by misfolding of immunoglobulin light chains (LCs) but how post-translational modifications (PTMs) of LCs influence amyloid formation is not well understood. Here, the authors present the cryo-EM structure of an AL amyloid fibril derived from the heart tissue of a patient that is partially pyroglutamylated, N-glycosylated and contains an intramolecular disulfide bond. Based on their structure and biochemical experiments the authors conclude that the mutational changes, disulfide bond and glycosylation determine the fibril protein fold and that glycosylation protects the fibril core from proteolytic degradation.

Symmetry-protected topological phases are special states of matter that rely on symmetries to exhibit unique, robust properties. This work explores how these properties can reappear even when the symmetry seems broken at small scales, using a model system where quantum fluctuations effectively “restore" the symmetry and revive topological behavior.

Channeling between enzymes is a uniquely nanoscale phenomenon that can improve multienzymatic reaction rates. Here, the authors demonstrate that multistep enzyme cascades can self-assemble with nanoparticles into nanoclusters that access channeling and improve the underlying catalytic flux by several fold.

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.

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.

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.

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.

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.

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 occurrence of thermodynamically metastable nanoparticles determines the particle growth in nature, but capturing them is experimentally challenging. Barke et al. identify the three-dimensional shape of metastable silver nanoparticles in gas phase, characterized by X-ray free-electron laser.

Non-coding variants can regulate transcription factor binding and gene expression at variable chromatin modules. Here, the authors show that a germline variant induces transcription factor nucleation through chromatin compaction leading to AXIN2 up-regulation and is associated to better prognosis in chronic lymphocytic leukaemia.

Fabrication of hybrid photoelectrodes on a subsecond timescale with low energy consumption remains a challenge. Here, the authors report a modular approach, laser-driven transfer synthesis, to build a library of structurally defined transition metal oxide composite films, enabling the creation of materials for diverse applications.

The high thermal conductivity of graphene is considerably reduced when the two-dimensional material is in contact with a substrate. Here, the authors show that thermal management of a micro heater is improved using graphene-based films covalently bonded by amino-silane molecules to graphene oxide.

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.

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.

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.

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.

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.

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

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.

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.

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.

MnBi2Te4, referred to as MBT, is a van der Waals material combining topological electron bands with magnetic order. Here, Lujan et al study collective spin excitations in MBT, and show that magnetic fluctuations increase as samples reduce in thickness, implying less robust magnetic order.

A machine learning approach is used to analyse multi-omics (proteomics, metabolomics and transcriptomics) data, producing genetic scores for more than 17,000 biomolecular traits in human blood, and identifying possible associations with disease.

Nanostructured plasmonic substrates are used for in situ, label-free detection, by surface-enhanced resonance Raman scattering spectroscopy, of quorum sensing in growing Pseudomonas aeruginosa biofilms.

Structural analysis and functional assays of S. aureus LtaA reveal that it functions as a proton-coupled flippase of the lipoteichoic acid precursor and that it contributes to S. aureus survival under physiological acidic conditions.

Physical computing, particularly photonic computing, offers a promising alternative by directly encoding data in physical quantities, enabling efficient probabilistic computing. This Perspective discusses the challenges and opportunities in photonic probabilistic computing and its applications in artificial intelligence.

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses.

Memristors hold promise for massively-parallel computing at low power. Aguirre et al. provide a comprehensive protocol of the materials and methods for designing memristive artificial neural networks with the detailed working principles of each building block and the tools for performance evaluation.

Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.

There is a pressing need for therapeutic agents against Zika virus (ZIKV). Here the authors present cryoEM structures of a neutralizing antibody (C10) complexed with ZIKV that show C10 preventing structural changes required for virus entry into the cell, suggesting it might be effective in treating Zika infections.