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Recovery of damaged ecosystems can vary in time and extent. Here, Moreno-Mateos and colleagues perform a meta-analysis to describe and quantify what they call recovery debt, an interim reduction in biodiversity, populations, and biogeochemical function of ecosystems during the recovery process.

A study reports single-cell RNA-sequencing profiles for more than 1.6 million cell nuclei from 101 whole mouse embryos including 22 mutant and 4 wild-type genotypes, from one experiment.

The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

CREBBP and KMT2D mutations frequently co-occur in B cell lymphomas with unclear significance. Here the authors show that they cooperate to skew B cell fate decisions and induce a CD8-depleted immune-evasive microenvironment to facilitate lymphomagenesis.

New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.

Individual dietary specialization is impacted by development, social learning, genetics, and environment. Here, the authors document European brown bear diet in a multigenerational female sample, finding that social learning during rearing was the most important contributor to dietary specialization.

In the phase 2 RENOBATE trial, the combination of regorafenib and nivolumab as first-line treatment for unresectable hepatocellular carcinoma exhibited a safe profile and met the primary endpoint with a 31% overall response rate.

Mouse models of lung and colorectal cancer with sporadic DNA mismatch repair deficiency clarify that the intratumor heterogeneity and clonal architecture rather than tumor mutational burden are powerful determinants of immunotherapy response.

Combinations of transcription factors (TFs) bind DNA to fine-tune gene expression. Here, the authors map cooperative and antagonistic DNA binding across hundreds of TF-pairs. TF-TF relationships vary depending on DNA targets and TF isoforms.

Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here, the authors present the largest FL study to-date to generate an automatic tumor boundary detector for glioblastoma.

Nitrogen vacancy centres can be used for nanoscale nuclear magnetic resonance detection but this typically involves strong microwave control pulses, making practical realizations difficult. Here the authors demonstrate a microwave-free spectroscopic protocol that can detect spins in external samples.

Plasma turbulence is the main driver to deteriorate the performance of fusion power plants. This work presents an unprecedented comparison of plasma turbulence between experiment and simulation, proving that the gyrokinetic model GENE reached a high level of maturity to predict core turbulence.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.

Tumor-antigen-specific CD8⁺ T cells are generally thought to help fight against cancer, but here the authors identify a subpopulation of CD8⁺ T cells that are associated with a poor clinical outcome in melanoma. Although these cells can recognize tumor antigens, they suppress cancer immunity.

As anyone who has ever spent any time in California can attest, much public attention is being focused on the great earthquake-prediction debate. Unfortunately, this attention focuses on deterministic predictions on the day-to-week timescale. But as some of the participants in this debate have pointed out^1,2 current efforts to identify reliable short-term precursors to large earthquakes have been largely unsuccessful, suggesting that earthquakes are such a complicated process that reliable (and observable) precursors might not exist. That is not to say that earthquakes do not have some 'preparatory phase', but rather that this phase might be not be consistently observable by geophysicists on the surface. But does this mean that all efforts to determine the size, timing and locations of future earthquakes are fruitless? Or are we being misled by human scales of time and distance?

Contrary to expectations from studies of birds, ecological radiation in crown bats is associated with strong trait integration both within and between forelimb and hindlimb.

Analyses of the TRACERx study unveil the relationship between tissue morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk of lung adenocarcinomas.

Nearly 90% of global variation in species richness of birds, mammals, amphibians and reptiles is shown to be explained by the joint effects of climate and the geographic structure (area and isolation) of climate.

Discovery cohorts from three continents, plus experiments in mouse models, are used to identify microbial species and mechanisms involved in post-antibiotic gut community recovery.

Metagenomic analyses of European pig and poultry farms show differing resistome profiles and an association with country-level antibiotic use.

How, when and from where did Madagascar's unique mammalian fauna originate? The idea that the ancestors of that fauna rafted from Africa finds support in innovative simulations of ancient ocean currents.

Using metagenomics and proteomics on Mediterranean grassland soil samples resulted in the recovery of 793 metagenome-assembled genomes and provided insights into microbial activity in this environment, and how this changes with soil depth and exposure to extended rainfall.

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

A video-based deep learning algorithm—EchoNet-Dynamic—accurately identifies subtle changes in ejection fraction and classifies heart failure with reduced ejection fraction using information from multiple cardiac cycles.

Multi-omics datasets are integrated to generate a unified and clinically informed molecular classification of meningiomas.

David Bertioli and colleagues report the genomes of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut, Arachis hypogaea. Their analyses are a first step in understanding the evolution of the peanut's tetraploid genome.

This paper proposes an open-source, impact-based forecast for tropical cyclone population displacement using both cyclone forecasts and population settlements and vulnerabilities. This is applied to Tropical Cyclone Yasa, striking Fiji in 2020.

Dietary protein influences metabolic health and ageing. Here Solon-Biet et al. show that, rather than having a direct toxic effect, dietary branched-chain amino acids (BCAAs) appear to induce hyperphagia, owing to an imbalance between BCAAs and other amino acids, which reduces lifespan as a consequence of obesity.

This study introduces AdipoExpress, an eQTL meta-analysis of 2,344 subcutaneous adipose tissue samples, which triples the size of previous studies and expands the discovery of eQTLs colocalized with GWAS signals for cardiometabolic traits.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

Here, the authors used electronic healthcare records to analyse the genetic basis of variation in 42 routinely-acquired quantitative blood tests among up to 40,000 British South Asian volunteers from the Genes and Health study. By combining their results with genetic findings from UK Biobank, they explore similarities and differences between ancestries in the genetic basis of these traits.

Efficient, large-scale genomic analysis is facilitated on the cloud by a computational tool with error-diagnosing and self-healing capabilities.

In the phase 2 HUDSON study, patients with advanced non-small-cell lung cancer received anti-PD-L1 combined with biomarker-guided therapy targeting ATR kinase, PARP, STAT3 or CD73, leading to encouraging clinical benefit in response to combination of the ATR kinase inhibitor ceralasertib with durvalumab.

Post-infectious myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) is a disabling disorder, yet the clinical phenotype is poorly defined and the pathophysiology unknown. Here, the authors conduct deep phenotyping of a cohort of PI-ME/CFS patients.

The expansion and intensification of agriculture has led to a loss of soil carbon. Here the authors show that increasing plant diversity within an agricultural soil increases positive associations within the soil microbial community, which increases carbon use efficiency.

Analysis of gut microbiomes from Gambian infants reveals bacterial trophic networks based around Prevotella species, which are typically enriched in non-industrialized populations.

Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.