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This large comparative phylogenetic study across angiosperms shows that species that are herbaceous or have small conduits evolved these traits before colonizing environments with freezing conditions, whereas deciduous species changed their climate niche before becoming deciduous.

In this Stage 2 Registered Report, Buchanan et al. show evidence confirming the phenomenon of semantic priming across speakers of 19 diverse languages.

Although historically common chemicals were frequently used as secret inks, the ease of readout could not prevent unauthorized reading. Here, the authors report a multi-analyte sensor that can conceal and encrypt messages by responding to simple chemicals, demonstrating a chemical means to secure communication.

CRISPR-Cas9 has potential as an efficient tool for information retrieval in DNA data storage. Here the authors present a Cas9-based random access and similarity search approach and test on DNA databases, progressing toward simpler, isothermal protocols.

This pilot trial showed that perioperative treatment with the isocitrate dehydrogenase (IDH) inhibitor safusidenib of patients with low-grade IDH-mutant glioma, with craniotomy and lumbar puncture before and after treatment, is feasible and safe and enabled in-depth translational investigation of safusidenib treatment-induced changes in the tumor, including electrophysiological effects.

Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.

A technique for the de novo design of switchable protein systems controlled by induced conformational change is demonstrated for three functional motifs, in vitro and in yeast and mammalian cells.

Magic state distillation is achieved with logical qubits on a neutral-atom quantum computer using a dynamically reconfigurable architecture for parallel quantum operations.

The identification of the positions and patterns of amino acids that form the selectivity determinants for the entire human G-protein and G-protein-coupled receptor signalling system.

Current machine learning techniques for graph-structured data rely on message passing between nodes. Here, the authors introduce an approach based purely on efficient and exact attention that shifts the focus from nodes to edges.

Here, the authors show that reactivating motor memories during sleep at moments of high (vs. low) neuronal excitability (up vs. down phases of slow oscillations) enhances their consolidation. Up-reactivation strengthens sleep markers of plasticity and the neural responses supporting memory consolidation.

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarking.

Integral equations are used in science and engineering to model complex systems with non-local dependencies; however, existing traditional and machine-learning-based methods cannot yield accurate or efficient solutions in several complex cases. Zappala and colleagues introduce a neural-network-based method that can learn an integral operator and its dynamics from data, demonstrating higher accuracy or scalability compared with several state-of-the-art methods.

As the 'war on terrorism' unfolds, some politicians are calling for controls on the availability of encryption software. But many computer scientists claim such moves would play into the terrorists' hands. David Adam reports.

The use of time-bin entangled qudits is hindered by the phase instability, timing inaccuracy and low scalability of current interferometric schemes. Here, the authors show a fiber-pigtailed photonic chip for generating and processing picosecond-spaced time-bin entangled qudits and utilize the system to implement a quantum key distribution protocol.

Genome assembly approaches are limited by factors including cost, power and incomplete resolution. Here, the authors present Aquila, a method that uses a reference sequence and linked read data to generate high quality diploid genome assemblies from which genetic variation can be detected and phased.

Following spinal cord injury, gamified physical therapy that incorporates closed-loop vagus nerve stimulation can aid restoration of arm and hand function.

Polyamines are essential metabolites linked to aging, cancer, and Parkinson’s disease. Here, authors develop a live-cell polyamine reporter and use a genome-wide CRISPR screen to uncover a link between mitochondrial respiration and polyamine import.

Trained on large and multicenter datasets with different imaging modalities, a foundation model is shown to have strong performance on the full spectrum of clinically relevant tasks and to increase user accuracy in diagnostic tasks.

Wells et al. profile RNA and surface protein expression to describe dominant tissue-specific effects on immune cell composition and function across lineages in the human tissues across age.

Strain in Si nanostructures is used to achieve higher carrier mobility, making these devices candidates for the next generation of transistors. Minamisawaet al. fabricate silicon nanowires subject to elastic tensile strain up to 4.5%, exceeding the limit achievable with the use of SiGe virtual substrates.

Individual decisions drive the dynamics of collective systems. Here, the authors use an immersive-reality experiment to show that group incentives reduce social information use and improve performance in naturalistic collectives.

An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.

Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.

Cancer genomes are rife with genetic variants, and one key outcome of this variation is widespread gain-of-cysteine mutations. Here, the authors pair cysteine chemoproteomics with genomics to investigate the landscape of cysteine genetic variation.

AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.

The authors show PTEN mutations, which can cause both congenital hydrocephalus and autism spectrum disorder, disrupt CSF homeostasis and brain connectivity in mice. Reducing mTORC1 activation ameliorates ventricular enlargement and neuronal deficits.

By using a new deep learning architecture, Enformer leverages long-range information to improve prediction of gene expression on the basis of DNA sequence.

A single-cell transcriptomic analysis of endometriosis, endometriomas, eutopic endometrial samples and uninvolved ovary tissues highlights cell populations characteristic of these tissue types. Transcriptional and cellular heterogeneity across tissues suggests novel therapeutic targets and biomarkers for this disease.

Quantum digital signatures exploit quantum mechanics to provide verification of messages at the limits of information theory. Clarkeet al.demonstrate a photonic system that provides quantum digital signatures for messages sent to two receivers and is secure against forgery and repudiation.

A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mouse brain.

Multiple omics platforms and deep single-cell profiling in the I4 astronauts reveal both conserved and distinct immune system disruptions across missions, provide a single-cell immune reference for future missions.

Multiple myeloma is frequently characterised by translocation of genes next to the immunoglobulin heavy chain locus. In this study, the authors sequence a large cohort of high risk myeloma samples and find translocations of cMyc to the immunoglobulin heavy chain locus and this is associated with poor prognosis.

A benchmarking competition improves tools that predict how regulatory regions control gene expression.

Sustainable chemistry can benefit from biocatalysis, but a high diversity of enzymes is needed. Here, the authors screen billions of protein sequences to provide an overview of the native amine dehydrogenase family for amine synthesis.

SF-GWAS is a workflow for secure, federated genome-wide association studies, implementing accurate, privacy-preserving principal-component analysis, linear/logistic regression and linear mixed model methods for biobank-scale multisite analyses.

A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions, with generalizability to unseen cell types.