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The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both single-cell RNA-seq and ATAC-seq data.

Treatments for Alzheimer’s disease (AD) remain limited. Here, the authors show that 40 hertz blue light activates a visual circuit to boost glymphatic drainage, and enhances memory, motivation, and anti-Aβ therapy efficacy in a mouse model of AD.

Proposals for the realization of Weyl semimetals, topologically non-trivial materials which host Weyl fermion quasiparticles, have faced demanding experimental requirements. Here, the authors predict such a state in stoichiometric TaAs, arising due to the breaking of inversion symmetry.

Compromised killing effects of oncolytic viruses due to attenuation of virulence remains a challenge. Here, the authors use a directed natural evolution approach to increase the oncolytic effect of the oncolytic virus M1 attributed to mutations in the E2 and nsP3 genes.

Ahmed, Nguyen et al. show that two FDA-approved antibiotics, paromomycin and neomycin, promote cardiomyocyte proliferation and improve cardiac function after myocardial infarction in mice and pigs by interfering with the cell division inhibiting function of transcription factors Meis1 and Hoxb13.

How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.

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.

Response rate to anti-CD276 based immunotherapy remains suboptimal in patients with cancer. Here, in a chemically-induced murine model of head and neck squamous cell carcinoma, the authors show that expression of ITGB6 in tumor cells promotes resistance to anti-CD276 therapy, associated with accumulation of PF4+ macrophages and T cell dysfunction.

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.

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.

Cheng et al. identify a mitochondrial complex IV (CIV) deficiency in the brains of patients with sporadic amyotrophic lateral sclerosis (ALS). They demonstrate that defects in mitochondrial CIV induce ALS-like phenotypes in rats and highlight CIV deficiency as a potential risk factor and therapeutic target for ALS.

Rab-controlled trafficking pathways have been implicated in tumourigenesis. Here the authors show that Rab37 suppresses metastasis by regulating the exocytosis of tissue inhibitor of metalloproteinase 1 to repress matrix metalloproteinase 9 and represents a novel prognostic marker for lung cancer.

Here, the authors report a Trident strategy-enhanced generative model able to produce a large volume of high-quality simulated atomic microscopy images, which can be used to automatically resolve the interlayer sliding and twist angle of few-layered van der Waals materials with improved robustness to defects and image quality.

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.

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.

This study identifies a new germline-to-soma aging signal tuned by mating in Caenorhabditis elegans. The authors find that germline piRNAs influence longevity and somatic maintenance by transcriptionally regulating germline-to-soma Hedgehog signaling.

The authors report a Yin-Yang balance between α-Synuclein and β-Synuclein via regulating phase separation in physiological states and Parkinson’s disease. AI-designed peptides mitigate the symptoms and prolong the lifespan of C. elegans PD models.

Jujube is a perennial fruit crop with significant economic and medicinal values. Here, the author report genome assemblies of four jujube accessions, construct pan-genome together with four previously published genomes, and generate resequencing data to reveal genetic basis of domestication traits.

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.

An antiferromagnetic diode effect was observed in a centrosymmetric crystal without directional charge separation. This effect could be used to create in-plane field-effect transistors and microwave-energy-harvesting devices.

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.

This study elucidates that d-galacturonic acid and d-glucuronic acid regulate apple fruit softening by repressing MdHb1 expression through the MdMYB2/MdNAC14/MdNTL9-MdHb1 regulatory module, offering new insights into postharvest fruit quality control.

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.

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.

Hypoxia induces d-serine production by Mycobacterium tuberculosis which inhibits mTORC1 and T-bet expression to restrict downstream CD8⁺ T cell immune responses and macrophage activation, and inhibit control of tuberculosis in mice.

3D covalent organic frameworks (COF) show interesting hierarchical arrangements of nanopores and open sites but their synthesis remains challenging. Here the authors report a fluorescent AIEgen-based 3D COF and demonstrate application as a coating material for white LEDs and for sensing of picric acid

Pikor et al. show that a set of conserved, bidirectional cues exchanged between fibroblastic reticular cells and immune cells sustain B cell niches, which control humoral immune responses across mouse and human lymphoid organs.

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 promise of X-ray tabletop broadband light sources by high-order harmonics generated in a gas medium has been limited by low conversion efficiencies. Here, Jin et al.show a method to enhance the high harmonic generation by optimizing the waveform of synthesized two and three colour laser fields.

Low-frequency quasiperiodic oscillations in X-ray data are thought to trace the accretion flow in X-ray binaries. Here, the detection of 200 keV oscillations probes the innermost regions of MAXI J1820+070, revealing the precession of a small-scale jet.

A deep learning algorithm shows promising performance in predicting progression to diabetic retinopathy in patients, up to 5 years in advance, potentially providing support for medical treatment decisions and indications for personalized screening frequency in a real-world cohort.

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.

Superionic materials are of interest for solid-state batteries or thermoelectrics, yet a clear understanding of the atomistic mechanisms is lacking. Here it is shown that transverse acoustic phonons persist above the superionic transition in argyrodite Ag₈SnSe₆, and that the free-Se sublattice controls fast Ag cation diffusion.

Combination immunotherapy with anti-PD-1 and anti-LAG-3 antibodies has shown anti-tumor effects across various cancers, however not all patients respond. Here the authors report that resistance to anti-LAG-3 plus anti-PD-1 therapy in head and neck cancer is mediated by the interaction of Sox9+ tumor cells with Frp1+ neutrophils, resulting in impaired anti-tumor immunity.

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.

We find that, relative to central neuropeptide Y, peripheral neuropeptide Y produced by sympathetic nerves has the opposite effect on body weight by sustaining energy expenditure independently of food intake.

Low level of pyruvate kinase M2 (PKM2) activity in cancer cells is essential for the dependence on aerobic glycolysis. Here the authors show that PKM2 sulfhydration by hydrogen sulfide destabilizes the PKM2 tetramer, leading to reduced PKM2 enzyme activity and enhanced proliferation of breast cancer cells.

Huang et al. show that ADAM9 loss upregulates PAI-1, promoting its interaction with KRAS and resulting in selective lysosomal degradation of KRAS. They also identify a small-molecule inhibitor of ADAM9 with therapeutic benefits in the context of PDAC.

Arterial vascular grafts are promising for vascular reconstruction but face risk of restenosis. Here, the authors report an electronic vascular conduit for in situ, long-term monitoring of thrombosis concurrent with postoperative vascular repair in in small animals and nonhuman primates.

Single-atomic impurities may induce novel quantum state, but they are unexplored in topological magnets. Here, the authors report spin-down polarized bound states which further interact with neighboring states to form spin-orbit split quantized orbitals in a topological magnet Co₃Sn₂S₂.

Multiple synchronous lung cancers (MSLCs) are a subtype of lung cancer. Here the authors characterise MSLCs using single cell RNA sequencing, single cell TCR sequencing and bulk whole-exome sequencing to investigate the mutations that arise in and are associated with invasive adenocarcinoma development, and immune microenvironment changes in this process.

This Review provides an overview of the theoretical foundations, recent advances and promising applications of Raman scattering microscopy.

Weyl semimetals are interesting because they are characterized by topological invariants, but specific examples discovered to date tend to have complicated band structures with many Weyl points. Here, the authors show that TaIrTe₄ has only four Weyl points, the minimal number required by time-reversal symmetry.

TDP-43 proteinopathies are characterized by TDP-43 aggregates but the relationship of these aggregates to the pathogenesis is still not well defined. Here, the authors show that the recombinant full-length human TDP-43 forms oligomers that are neurotoxic, can promote the formation of A-beta amyloid oligomers in vitroand can be detected in postmortem brain of patients.

A consensus cell type atlas for the fly brain provides both an intellectual framework and open-source toolchains for brain-scale comparative connectomics.

Soft magnetic materials are critical components in the electric transport and energy sectors, such that even minor improvements in their properties can yield vast savings in energy. Here, Cao, Zhang and coauthors demonstrate via an additive manufacturing based approach, a medium entropy alloy with superior magnetic properties.