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Lead concentrations in the South China Sea have reduced ~60% post-2000, according to a reconstructed record of lead concentration and isotopic composition from a coral reef.

Wang et al. clarify the regional heterogeneity of intestinal AMPs and identify that chromatin accessibility determines the potential of BATFs to regulate AMPs at the pre-transcriptional level, thus shaping the regional heterogeneity of AMPs.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

Globally, as a major public health problem, low back pain has been the leading cause of disability worldwide for the past 30 years. Here, the authors propose a segmentation network and a quantitative method lumbar intervertebral disc degeneration assessment.

Genome assemblies for the SunUp transgenic papaya and its progenitor Sunset identify three transgene-insertions in SunUp. Resequencing of 86 papaya genomes highlights the impacts of breeding and geographic origin.

Developing biointerfaces that combine the advantages of both monolithic and focal elements remains challenging. Now, a hydrogel that releases surface-modified granules and shows biointerface transition capability has been developed. This granule-releasing hydrogel manages colitis, accelerates wound healing, and facilitates cardiac tissue regeneration and mapping of cardiac activity with bioelectronic devices.

Natal downs adapted for heat conservation transition to juvenile feathers that support simple flight during bird development. Here the authors characterize gene expression networks and epigenetic changes and use functional perturbations to characterize evolutionarily conserved regulatory switches that control this transition in birds.

Neoadjuvant treatment represents a therapeutic option for locally advanced gastric cancer (LAGC). Here the authors report the results of a randomized phase 2 trial of camrelizumab (anti-PD1) and apatinib (anti-VEGFR2) combined with nab-paclitaxel plus S-1 versus chemotherapy alone as neoadjuvant treatment for LAGC.

Some materials host multiple charge density wave states, however, their dynamics and the nature of phase transitions are often unclear. Here, using temperature and orientation resolved ultrafast spectroscopy, the authors reveal charge density waves of different dimensionality in CuTe and elucidate their mechanism.

A spatial multi-omics method with high decoding capacity and reduced sequencing and imaging costs enhances the high-throughput detection of gene mutations, allele-specific expression and RNA modifications in tissue samples.

Lung fibrosis development involves alveolar macrophages, with mechanisms that are incompletely understood. Here, the authors show that alveolar macrophages mediate the disassembly of pleuro-alveolar junctions, driving fibrosis via connective tissue transfer, and demonstrate that targeting this process can reverse chronic fibrosis in mice.

The precise rule of replication origin selection and activation in metazoans remains unclear. Here, the authors identify NFIB as a genome organizer and replication pioneer by facilitating nucleosome remodeling and chromatin assembly of the pre-RC.

SARS- CoV-2 hijacks ACE2 for cell entry. Here, the authors report that dynamic SUMOylation modulates the TOLLIP-directed selective autophagic degradation of ACE2 and suggest SUMOylation inhibition as a potential intervention against SARS-CoV-2 infection.

Spatially selective actuation and large output force enables versatile task performance in soft robotics. Here, the authors report a method for actuating untethered soft robots using focused ultrasound waves to perform liquid cargo delivery and biopsy.

It can be difficult to find rare transcripts when sequencing a transcriptome. Here the authors show adaptive sampling on direct RNA runs to increase the likelihood of finding less frequent ones while selectively ejecting the higher-abundance transcripts.

Achieving direct solar-to-hydrogen conversion from pure water using solely organic heterogeneous catalysts is still challenging. Here the authors report an all-organic semiconductor catalyst system for overall water splitting under visible to near-infrared light via triplet-triplet annihilation up conversion based on spin coupling.

Verticillum wilt is an important cotton disease caused by fungal pathogen Verticillium dahiae. Here, the authors assemble the genomes of defoliating and non-defoliating isolates of the pathogen, identify virulence gene SP3, and develop a disease control strategy using polyethyleneimine-coated MXene quantum dots.

Chemo-activation of mitochondrial ClpP exhibits promising anticancer properties. Here, the authors develop a potent activator ZK53 that is highly selective on human ClpP but inactive toward bacterial ClpP proteins, and show that ZK53 causes cell cycle arrest via ClpP on lung squamous cell carcinoma cells and exhibits therapeutic effects in animal models.

Understanding and controlling morphogenesis is vital for biology and organoid technology. Here, the authors report an efficient biomechanical system to generate gut spheroids, and reveal instability-driven morphogenetic transitions with computational models.

For packaging enzymes into metal–organic frameworks (MOFs), crystalline MOFs are usually used. Here, the authors encapsulated enzymes in amorphous MOFs a via one-pot co-precipitation process under ambient condition, which led to higher enzymatic activity than in a corresponding crystalline MOF composite.

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.

Primary biliary cholangitis is a chronic autoimmune disease critically linked to immunological dysregulation but the local immune-pathogenesis is poorly understood. Here the authors present single cell transcriptomic characterisation of primary biliary cholangitis and implicates Th1 like cells in a murine model.

Cell fate decisions remain poorly understood at the molecular level. Here Ming et al. show that BMP4 as the signal diverting cell fate away from epiblast/pluripotency to hypoblast/primitive endoderm fate during JGES reprogramming by promoting the dissociation of SALL4 from NuRD.

How aging induces aortic aneurysm and dissection (AAD) remains unclear. Here, the authors show that aging induces miR-1204 to inhibit MYLK, promoting vascular smooth muscle cells to acquire senescence-associated secretory phenotype, resulting in vascular inflammation, and the aggravation of AAD formation.

Machine learning can be used to identify subtypes of psychiatric disease. Here the authors identified two neurostructural subgroups in schizophrenia, each showing reproducibility and generalizability across different collection locations and illness stages, using the SuStain algorithm.

Spatiotemporal regulation of wound healing in mice and humans occurs via retinoic acid and hypoxia signalling, which regulate the differentiation of CD201⁺ fibroblast progenitors into proinflammatory and myofibroblast states.

A small-molecule aldolase inhibitor, aldolazin is reported and shown to selectively activate the lysosomal pool of AMPK, which has glucose-lowering effects in rodents.

Establishing protein gradients for asymmetric cell division is fundamental across all kingdoms of life. Here the authors construct asymmetric cell division in E. coli by localizing the expression of RNA polymerase using an orthogonal unipolar scaffold, and restricting diffusion of its products.

A foundation model for the motion correction, resolution enhancement, denoising and harmonization of magnetic resonance images improves the performance of machine-learning models across a wide range of tasks.

Gasdermin E (GSDME) is a pyroptotic cell death effector and a promising target for pyroptotic tissue injury. Here, the authors show that methylcobalamin in base-off conformation coordinates to Cys180 in GSDME to prevent caspase-3/GzmB-GSDME interactions and thereby GSDME-mediated liver failure.