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To circumvent the limitations of electronic computers, moving to hybrid optical-electronic or all-optical devices may be useful. Here, Babaeian et al. present an all-optical implementation of the probabilistic graphical model using nonlinear optics in thin films to implement mathematical functions.

Assessing cell phenotypes in image-based assays requires solid computational methods for transforming images into quantitative data. Here, the authors present a strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation.

How groundwater recharge changes with global warming is not well constrained. Here, the authors use an empirical relationship to show that groundwater recharge is more sensitive to aridity changes than expected, implying a strong response of water resources to climate change.

A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome.

Statistically unbiased prediction utilizing spatiotemporal information in imaging data (SUPPORT) is a self-supervised deep learning approach to accurately denoise voltage and calcium imaging data while preserving true dynamic signals.

Figs and their wasp pollinators are a classic example of coevolution. By assembling and analysing genomes from across the Ficus clade, authors suggest that fig hybridization driven by pollinator host-switching in this obligate pollination system, is more common than previously thought.

Methane emissions from aquatic systems contribute approximately half of global methane emissions, according to meta-analysis of natural, impacted and human-made aquatic ecosystems and indicating potential mitigation strategies to reduce emissions.

Nsp15 is a uridine specific endoribonuclease present in all coronaviruses. Here, the authors determine the cryo-EM structures of SARS-CoV-2 Nsp15 in the apo and UTP-bound states, which together with biochemical experiments, mass spectrometry and molecular dynamics simulations provide insights into the catalytic mechanism of Nsp15 and its conformational dynamics.

Zika and dengue incidence in the Americas declined in 2017–2018, but dengue resurged in 2019 in Brazil. This study uses epidemiological, climatological and genomic data to show that the decline of dengue may be explained by protective immunity from pre-exposure to ZIKV and/or DENV in prior years.

An extinction-risk assessment of reptiles shows that at least 21.1% of species are threatened by factors such as agriculture, logging, urban development and invasive species, and that efforts to protect birds, mammals and amphibians probably also benefit many reptiles.

Social animals have sophisticated ways of classifying relationships with conspecifics. Data from 30 years of observations and playback experiments on dolphins with a multi-level alliance system show that individuals form social concepts that categorize conspecifics according to their shared cooperative history.

A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.

Cell groups in the hypothalamic suprachiasmatic clock contribute to the genesis of circadian rhythms. The authors identified two populations of vasoactive intestinal polypeptide-expressing neurons in the suprachiasmatic nucleus which regulate locomotor circadian rhythm in mice.

Changes in penguin populations on the Antarctic Peninsula in recent decades have been linked to environmental factors such as sea ice. Here, the authors show that penguin colony change on Ardley Island, NW Antarctic Peninsula during the last 8,500 years was primarily driven by volcanic activity.

In 1966, Frank Westheimer proposed that the large shift in the pK_a of a key lysine residue (Lys 115) in the active site of the enzyme acetoacetate decarboxylase was because of the neighbouring charge of another lysine reside (Lys 116); this is said to be a classic example of enzymatic 'microenvironment effects'. Here, the X-ray crystal structure of acetoacetate decarboxylase is solved, revealing that the shift in pK_a cannot be due to Lys 116 but is instead due to the presence of a long hydrophobic funnel near Lys 115.

The mechanisms underlying drought-induced tree mortality are not fully resolved. Here, the authors show that, across multiple tree species, loss of xylem conductivity above 60% is associated with mortality, while carbon starvation is not universal.

An optical-based scheme for ultrasound sensing provides very high sensitivity with excellent broadband acoustic frequency response and wide directivity.

Neural processing speed slows with age, but the relationship between this slowing and brain atrophy is unknown. Here, authors show that age-related functional brain differences in auditory and visual processing are partly due to structural differences in the distinct brain regions underlying these processes.

Lavas erupted at ocean island hotspots have complex geochemical signatures. Numerical simulations suggest that this complexity may result from the mixing of subducted oceanic crust with reservoirs of more primitive material in the deep mantle, with the resulting mixture entrained into rising mantle plumes.

The genetic basis of tinnitus and how it relates to hearing loss genetics is unknown. In a large GWAS for tinnitus, the authors discover tinnitus’ distinct genetic architecture from hearing loss and its correlation with a spectrum of psychiatric disorders.

A combination of gentle stimulated emission depletion microscopy imaging and deep-learning-based improvements in signal-to-noise ratio enables high-resolution reconstruction of neuronal architecture in living tissue.

Fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks yields a generative model for protein design that achieves outstanding performance on a wide range of protein structure and function design challenges.

Metal-halide perovskite based tandem solar cells are appealing but making a high efficiency device is not trivial. Here Chen et al. increase the carrier collection in the perovskite layer and largely enhance the efficiency in tandem cells when combined with colloidal quantum dot or silicon layers.

Microbial plant-soil feedbacks (PSF) are fundamentally important for plant diversity. The authors present a spatially explicit dynamic model that separates the effects of microbial mutualists and pathogens, thereby presenting a testable mechanistic framework to reconcile previously puzzling observations of the strength and direction of PSF with diversity maintenance.

Defective protein quality control is a key feature of neurodegeneration. Here, the authors show that mutations in Nemf/NEMF, a component of the Ribosome-associated Quality Control complex, have a neurodegenerative effect in mice and may underlie neuromuscular disease in seven unrelated families.

Cryo-electron microscopy is widely employed in structural biology and uses phase contrast imaging. Here, the authors employ electron ptychography, a quantitative phase retrieval method for high-contrast, low-dose phase imaging of cryo-state rotavirus and immature HIV-1 virus-like particles, and show that electron ptychography is more efficient for phase recovery than conventional phase contrast imaging.

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.

Enhanced drought frequency and magnitude have impacted tree mortality, leading to multiple examples of regional-scale dieback. This Review outlines the mechanisms leading to mortality, including carbon starvation and hydraulic failure.

Dopamine receptor agonists are used for the treatment of various psychiatric diseases. Here, the authors screen approximately three million compounds and identify a novel class of D1R agonists that do not have a catechol scaffold and possess promising pharmacokinetic properties.

Bile salt hydrolases encoded by the gut microbiome shape the bile acid pool, including microbial conjugated bile acids, which impact Clostridioides difficile infection in the murine gut.

This study reveals how Klotho and heparan sulfate glycosaminoglycan coreceptors enable FGF hormones to induce asymmetric 1:2 FGF–FGFR dimerization mandatory for FGFR kinase activation and hence signalling.

Crosstalk between the brain and gut is modulated and recorded with microelectronics fibers.

Climate simulations suggest that the contribution of methane to climate warming and wetting due to absorption of long-wave radiation is partially counteracted by short-wave absorption.

This study uses data assimilation to reconstruct the Southern Annular Mode over the last 2000 years. The authors find that the mode’s history reflects natural climate variability, except for the most-recent positive trend

An anti-inflammatory enzyme fused with a tissue-anchoring protein and injected into inflamed tissues ameliorates local inflammation without causing systemic immune suppression, as shown in multiple rodent models of inflammatory diseases.

A low-cost probe for otoacoustic emissions made from off-the-shelf earbuds and microphones performs similarly to a clinical-grade device, as shown via a clinical study involving 201 paediatric ears screened for hearing loss.

Transmission spectroscopy observations from the James Webb Space Telescope show the detection of carbon dioxide in the atmosphere of the gas giant exoplanet WASP-39b.

New silicon probes known as Neuropixels are shown to record from hundreds of neurons simultaneously in awake and freely moving rodents.

Assessing the conservation status of 1,020 European marine fishes reveals half of large (>1.5 m) fishes are threatened with extinction and stock status diverges geographically: almost all Mediterranean stock is overfished, most northern European stock is not.

Technical difficulties have so far limited the application of high-resolution secondary-electron microscopy in imaging surface structures. Here, the authors report a successful determination of surface reconstruction of strontium titanate, using the secondary-electron microscopy along with other techniques.

Somatic mutations have been reported in pancreatic adenocarcinomas. Here, Sausen et al. identify further mutations and find that mutations in the chromatin modifying gene, MLL, are associated with increased survival, and that the presence of circulating tumour DNA in the serum of patients is associated with poor survival.

Solution-shearing process has been recently developed as a large-area coating method of producing crystallographic organic thin films, but how this process works is still unknown. Giri et al.monitor it in real time and find the degree of polymorphism can be tailored by varying solution conditions.

Excitatory pyramidal neurons preferentially target inhibitory interneurons with the same selectivity and, in turn, inhibitory interneurons preferentially target pyramidal neurons with opposite selectivity, forming an opponent inhibition motif that supports decision-making.

Many countries have submitted updated and new emissions reduction pledges in COP26, but further ratcheting of pledges is needed to reach the 1.5 °C goal. Ratcheting near-term ambition through 2030 could bring the largest climate benefits and avoid potential long-term temperature overshoot.

A combination of three monoclonal antibodies transiently reduced viremia in people living with HIV-1 and not on antiretroviral therapy, but it did not prevent viral rebound. Further studies are needed to determine if this approach can be optimized.