Search

Chronic inflammation hinders the repair of muscle injury, and macrophages are known to play roles in reparative processes. Here the authors show in an nlrc3l-mutant zebrafish model, chronic inflammation drives repression of a mannose-receptor-dependent reparative pathway in macrophages and results in the loss of discrete macrophage states.

Stratospheric solar geoengineering using calcium carbonate particles might have little impact on ozone, according to simulations with an atmospheric chemistry model using experimental reaction rates.

Glutamatergic and GABAergic (γ-aminobutyric acid-producing) cortical neuronal activity drives proliferation of small lung cell cancer via paracrine interactions and through synapses formed with tumour cells.

Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynamics.

A compact source of 60-fs pulses is demonstrated, based on a semiconductor laser that is mode-locked using a saturable absorber mirror in an external cavity.

DNA2 suppresses recombination-restarted replication and checkpoint activation at stalled forks, and its loss triggers recombination-dependent synthesis, checkpoint signalling and cell-cycle exit, highlighting its essential role in proliferation and growth failure in primordial dwarfism.

Electrostatic effects of separators under internal electric field is crucial for Li metal batteries. Here, authors develop a high dielectric constant fiber separator that shows substantial polarization under electric field to facilitate a robust and low-resistance solid-electrolyte interphase.

The International Union for Conservation of Nature’s Global Ecosystem Typology has been developed to provide a systematic framework for data on all of Earth’s ecosystems in a unified theoretical context to support biodiversity conservation and ecosystem services.

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.

Citizens in middle-income countries (Brazil, India, Indonesia) support aligning local sustainability rules with new laws originating in OECD nations. People favor stricter regulations, driven by optimistic expectations of the benefits outweighing potential costs.

Simple analytic estimates and detailed numerical calculations show that the solar dynamo begins near the surface, rather than at the much-deeper tachocline.

Here, the authors reveal variability in chromosome 21 gene overexpression among individuals with Down syndrome, identifying three distinct molecular subtypes. Each subtype exhibits unique biosignatures and immune profiles, offering new insights into the complex biology of Down syndrome.

Single-cell RNAseq can struggle to capture cellular heterogeneity due to the relatively low expression of biologically meaningful transcripts. Here the authors present an approach called scCLEAN, which uses CRISPR/Cas9 to target and remove certain ubiquitous transcripts, thereby enhancing the detection of low-abundance transcripts.

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.

Photoluminescence blinking is a ubiquitous phenomenon that detrimentally reduces emission stability and quantum yield. Now, an all-optical method, which employs ultrafast mid-infrared pulses, can effectively suppress the blinking of single CdSe/CdS core–shell quantum dots.

To facilitate more accurate long-term projections of primary production and export over oceanic low latitudes (LLs), we identified the first-order importance of the temperature dependence of remineralization of the LL nutrient reservoir, with this serving to enhance LL mesopelagic retention under warming.

An electric dipole spin resonance protocol making use of hyperfine interaction enacts high-fidelity initialization of a four-qubit nuclear spin register in silicon. This protocol allows for high-fidelity qubit control and a path towards a register-based quantum computer using the exceptional coherence properties of donors in silicon.

Whole-genome sequencing and phenotype data sharing are introduced in a national health system to streamline diagnosis and to discover coding and non-coding variants that cause rare diseases.

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.

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.

Sharma et al. identify an early metabolic checkpoint dependent upon lactate dehydrogenase for newly activated B cells to enter germinal centers.

New variants of SARS-CoV-2 virus can evolve such that antibodies that recognised previous versions are not able to recognise newer versions. Here the authors characterise antibody binding to the XBB.1.5 variant and how antibodies and T cells from persons infected with earlier versions of SARS-CoV-2 are able to recognise and/or bind to the XBB.1.5 spike protein.

BilR is identified as a bilirubin reductase encoded by gut bacteria, which reduces bilirubin to urobilinogen.

Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

In a warming world, future rapid permafrost thawing can cause significant soil drying, surface warming, and atmospheric drying in the Arctic-Subarctic region, leading to an intensification of peat and forest fires in western Siberia and Canada.

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.

PLX4032 is a selective inhibitor of the B-RAF protein that has shown promising results in an early clinical trial in melanoma patients with an activating mutation in B-RAF. Now the structure and function of this inhibitor are described. Translational data from a phase I trial show that clinical efficacy requires a substantial degree of inhibition of the ERK pathway downstream of B-RAF. The data also show that BRAF-mutant melanomas are highly dependent on B-RAF activity.

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.

Inspired by human analogical reasoning in cognitive science, the authors propose an approach combining deep learning systems with an analogical reasoning mechanism, to detect abstract similarity in real-world images without intensive training in reasoning tasks.

Analysis of age of onset and disease duration in a large, international cohort of people with SOD1-ALS shows that there is a distinct phenotype and that onset and progression are decoupled.

Investigation of variation in three cohorts has identified multiple genetic signals associated with the pregnancy-specific liver disorder, intrahepatic cholestasis of pregnancy, giving insight into the disease which can cause preterm birth and stillbirth.

The gut microbiota in mice can modulate social behaviour by influencing activity in stress-related brain areas.

A choice experiment shows that perceived benefits of vehicle ownership, including non-use values such as schedule flexibility and status in addition to the transport value, are on average larger than their private costs.

Land surface models often use a spatially uniform air temperature threshold when partitioning rain and snow. Here Jennings et al. show that the threshold varies significantly across the Northern Hemisphere and that threshold selection is a large source of uncertainty in snowfall simulations.

Inducing coherent interactions between distinct magnon modes—collective excitations of magnetic order—has been challenging. A canted antiferromagnet has demonstrated coherent magnon upconversion induced by terahertz laser pulses.

The efficacy of cancer drugs is profiled by measuring changes in the mass of single tumor cells.

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.

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.

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.

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.