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Artificial neural networks face challenges of robustness and efficiency as they scale. Here, the authors show that incoherent network motifs provide greater stability and resilience to noise than coherent network motifs, offering new structural insights for designing stronger neural networks.

While the photoreceptor outer segments in the bird outer retina have access to oxygen, the inner retina operates under chronic anoxia, supported by anaerobic glycolysis in the retinal neurons.

Clinical trials testing efficacy of novel HIV treatments rely on analytical treatment interruption (ATI). Using data from 24 prospective studies, the authors here show that the virus becomes detectable after around 16 days of ATI and that only 4% of individuals have sustained control of HIV, providing information for future clinical trial design.

In people with HIV-1 undergoing antiretroviral treatment interruption, lefitolimod combined with broadly neutralizing antibodies (bNAbs) did not delay viral rebound beyond that achieved with bNAbs alone, raising the question of how to optimize combination immunotherapy to control HIV-1.

Pl@ntBERT is a language-based AI model that learned the ‘syntax’ of plant assemblages, predicting likely species and inferring habitats by modelling biotic relationships.

The use of III-V semiconductor nanowires can overcome the need for lattice matching in multi-junction solar cells, which restricts the choice of materials and their bandgaps. This work demonstrates efficient solar cells with GaAsP single nanowires with tunable bandgap and grown on low-cost Si substrates.

Andreev bound states in semiconductor–superconductor hybrid structures are studied using microwave spectroscopy — a tool that could be also used for investigating Majorana modes.

Analysis of soundscape data from 139 globally distributed sites reveals that sounds of biological origin exhibit predictable rhythms depending on location and season, whereas sounds of anthropogenic origin are less predictable. Comparisons between paired urban–rural sites show that urban green spaces are noisier and dominated by sounds of technological origin.

An analysis involving the shotgun sequencing of more than 300 ancient genomes from Eurasia reveals a deep east–west genetic divide from the Black Sea to the Baltic, and provides insight into the distinct effects of the Neolithic transition on either side of this boundary.

Integrated data, including 100 human genomes from the Mesolithic, Neolithic and Early Bronze Age periods show that two major population turnovers occurred over just 1,000 years in Neolithic Denmark, resulting in dramatic changes in the genes, diet and physical appearance of the local people, as well as the landscape in which they lived.

Using intricately sculpted light fields to control tiny objects is a well-understood and important technique. Now, the concept of sculpting the object rather than the light field promises to propel light–matter research in an exciting new direction.

A new mass spectrometry strategy combines the advantages of data-dependent and data-independent acquisition.

Observations of SN 2021yfj reveal that its progenitor is a massive star stripped down to its O/Si/S core, which remarkably continued to expel vast quantities of silicon-, sulfur-, and argon-rich material before the explosion, informing us that current theories for how stars evolve are too narrow.

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.

N-terminal acetylation is a common modification with unclear function. Here, using multidimensional proteomics, the authors found that NatA-deficient yeast show increased ribosomal protein degradation and decreased ribosome thermostability, suggesting that N-terminal acetylation enhances proteome stability.

Protein activity regulated by phosphorylation can result in subcellular relocation. Here, the authors present a high throughput spatial phosphoproteomics approach to profile six subcellular compartments, providing insights into EGFR and stress signalling dynamics.

Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens coincide with the widespread domestication of livestock.

Traditional proteomics methods are complex and resource-intensive. Here, the authors develop One-Tip, a highly simplified approach that enables efficient, sensitive, and comprehensive analysis across various sample types, from blood plasma to single cells.

Whether paired corticospinal-motoneuronal stimulation (PCMS)-protocols can promote motor learning and how PCMS protocols interact with mechanisms of experience-dependent plasticity is not fully understood. Here authors show that non-invasively induced plasticity targeting corticomotoneuronal synapses promotes motor learning by interacting positively with experience-dependent plasticity.

During starvation, muscle strength and endurance, are still critical for survival. Seven days of complete fasting did not reduce maximal strength in leg muscles, but maximal endurance capacity was decreased because carbohydrate oxidation was restrained.

Many drug targets remain unknown for small molecules. Here, the authors develop a label-free Proteome Integral Solubility Alteration (PISA) workflow to automate target identification and analysis. Applied to rat organs, the authors identify previously unknown drug targets for common medication.

Mineralized plaque, or dental calculus, is a valuable reservoir of the ancient oral microbiome. Here, the authors use quantitative metaproteomics to analyze the dental calculus of 21 individuals from a medieval cemetery, identifying human and microbial proteins that shed light on their oral health status.

The possibility to trap biomolecules is important for analysing them by optical methods. Here we show how nanoscale chambers with macromolecular gates can be used to trap hundreds of proteins in a volume of one attoliter at physiological conditions without exposing them to any direct forces.

Methicillin-resistant strains of Staphylococcus aureus appeared in European hedgehogs in the pre-antibiotic era as a co-evolutionary adaptation to antibiotic-producing dermatophytes and have spread within the local hedgehog populations and between hedgehogs and secondary hosts.

Localizing phosphorylation sites by data-independent acquisition (DIA)-based proteomics is still challenging. Here, the authors develop algorithms for phosphosite localization and stoichiometry determination, and incorporate them into single-shot DIA-phosphoproteomics workflows.

A genome-wide-association meta-analysis of 18,381 austim spectrum disorder (ASD) cases and 27,969 controls identifies five risk loci. The authors find quantitative and qualitative polygenic heterogeneity across ASD subtypes.

Successful skeletal muscle regeneration involves a complex and finely tuned inter-cellular response. Here, by using spatial transcriptomics, the authors identify an intercellular communication axis between fibro-adipogenic progenitors and macrophages to enhance macrophage-mediated tissue repair.

Most machine learning approaches extract statistical features from data, rather than the underlying causal mechanisms. A different approach analyses information in a general way by extracting recursive patterns from data using generative models under the paradigm of computability and algorithmic information theory.

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.

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.

The authors demonstrate a holographic light engine enabling volumetric 3D printing with high precision and flexibility. Enhanced light projection efficiency and speckle noise mitigation enable rapid fabrication of millimetric objects, including soft cell-laden hydrogels, with 31 µm resolution.

Sex differences in fasting glucose and insulin have been identified, but the genetic loci underlying these differences have not. Here, the authors perform a meta-analysis of genome-wide association studies to detect sex-specific and sex-dimorphic loci associated with fasting glucose and insulin.

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.

Here, Parzych et al describe the development of a DNA-delivered SARS-CoV-2 mAb cocktail displaying synergistic RBD binding that confers broad neutralizing activity against variants of concern and prophylactic efficacy in multiple small animal models.

Prophages are quiescent bacterial viruses that, when activated, produce viral particles and kill their host cells. Here, Haaber et al. show that these viral particles can mediate the transfer of antibiotic resistance genes from neighbouring cells back to the remaining prophage-containing cells.

Functional diversity and phylogenetic diversity are expected to be positively correlated. Here the authors show that the covariation between these metrics in vascular plant communities around the world is often either inconsistent or negative.

Available methods to identify species from fragmented archaeological bone and remains suffer a trade-off between cost and resolution. Here, the authors present a workflow that uses automated sample preparation, 10 to 20 times faster data acquisition, and computerized data interpretation to make the technology applicable to large-scale studies.

Valence tautomerism in lanthanide-based materials is rare. Now a one-dimensional samarium–pyrazine polymer has been shown to exhibit a temperature-induced hysteretic Sm(III)-to-Sm(II) reversible switch. The transition temperature is modulated in a 150 K window by alloying with Yb(II), presenting a strategy for developing new materials with chemically tunable magnetic switchability.

Obesity is associated with an increased risk of the intimately related esophageal disorders GERD, Barrett esophagus and esophageal adenocarcinoma. In this Review, Jesper Lagergren evaluates the effect of BMI and body fat distribution on the risk of these esophageal conditions and discusses the potential underlying mechanisms.

After infection with SARS-CoV-2, individuals show a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and a greater reduction in global brain size.

Genome-wide analyses yield insights into the polygenic effects contributing to clinical heterogeneity in attention deficit hyperactivity disorder, advancing understanding of its genetic etiology and serving as a model for future studies in other complex disorders.

The authors identify a DNA-protein crosslink (DPC) repair pathway orchestrated by poly-ADP-ribosylation. In this process, PARP1 PARylates the DPC, marking it for removal by proteolysis. Consequently, PARP1 facilitates the repair of DPCs located next to DNA breaks, such as topoisomerase 1-DPCs.

Integration of single-cell RNA sequencing with genome-wide association data implicates specific brain cell types in schizophrenia. Gene sets previously associated with schizophrenia implicate the same cell types, which include pyramidal cells and medium spiny neurons.

Quantitative trait loci mapping of a cross between red junglefowl and domestic chickens provides evidence for the role of methylation in regulating gene expression in the domestication process.

The function of proteins is often regulated by their phosphorylation at specific amino-acid residues. The authors of this article have catalogued phosphoproteins and their phosphorylation sites in 14 rat organs and tissues, and provide these data as a resource for researchers.