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Europe's bid for a world lead in subnuclear physics in the 1990s brings CERN's future into question, writes Robert Walgate

Near-infrared (NIR) fluorophores have attracted interest for bioimaging; yet availability, biocompatibility and application can be an issue. Here, the authors report on the development of Egyptian Blue nanosheets with high NIR fluorescence and photostability demonstrating bioimaging applications in vivo.

Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

Severe sepsis has a high mortality rate. Here, the authors provide genomic, transcriptomic, proteomic and metabolomic data across four sepsis-causing pathogens and identify a signature of global increase in fatty acid and lipid biosynthesis as well as cholesterol acquisition.

A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci may have helped crop plants to adapt to agricultural ecosystems.

Vaccination against COVID-19 has shown activation of different immune cell types. Here the authors characterise the immune response to the SARS-CoV-2 mRNA vaccine using longitudinal CyTOF single cell approaches to characterise antigen specific B and T-cell responses promoted by this vaccine.

During each replication cycle of P. falciparum in the human bloodstream, a small proportion of parasites commits to sexual development and differentiates into transmission-relevant gametocytes. Applying CRISPR-based genome editing, Boltryk et al. engineer P. falciparum lines with sexual commitment rates of 75% to promote future studies on gametocyte biology.

This analysis of a large, clinically annotated cohort of individuals with predisposition to myelodysplastic syndromes reveals insights into the genetic determinants of disease progression and their relationship with clinical manifestations and therapy outcome.

People blinded in infancy have sharper listening skills than those who lost their sight later.

Analysis of genetic variation underlying an antipredator morphological defence in Daphnia pulex shows that stabilizing selection operates on this plastic trait.

The clinical benefit from immunotherapy response in patients with mutations of genes forming the chromatin remodelling complex PBAF remains controversial. Here the authors show that PBAF complex mutations are not associated with favourable response in pan-cancer cohorts of patients treated with immune-checkpoint blockade.

Patients with cancer undergoing anti-PD-1 immune checkpoint blockade can experience immune-related adverse effects. Wherry and colleagues examined the immunity elicited upon immunization of patients with cancer and report that anti-PD-1 immunotherapy dynamically affects influenza vaccine-induced immune responses.

Injury repair is characterized by the generation of transient cell states important for tissue recovery. Here, the authors present a single cell RNA-seq map of recovery from bleomycin lung injury in mice and uncover a Krt8+ transitional stem cell state that precedes the regeneration of AT1 cells and persists in human lung fibrosis.

A subset of renal cell carcinomas have uncertain histology and are aggressive in nature. Here, the authors examine this group of unclassified renal cancers using genomics techniques and identify further subclasses of the tumours that have differing prognoses.

Kistamicin is a structurally divergent glycopeptide antibiotic (GPA) that contains a unique 15-membered A-O-B ring. Here, the authors obtained a crystal structure of the kistamicin OxyA/X-domain complex and analysed the cyclisation cascade leading to the formation of the A-O-B ring.

Tarsiers occupy a key node between strepsirrhines and anthropoids in the primate phylogeny. Here, Warren and colleagues present the genome of Tarsius syrichta, including a survey of transposable elements, an unusual mitochondrial insertion, and evidence for positive gene selection.

Analysis of advanced cancer patients treated with immune-checkpoint inhibitors shows that tumor mutational burden, as assessed by targeted next-generation sequencing, predicts survival after immunotherapy across multiple cancer types.

Cancer evolution is often depicted using a tree model and many current therapies target gene mutations mapped to the tree trunk. Here, Wei and Hsieh propose a novel paradigm—the river model—and examine how this model might describe phenotypically convergent events to better guide effective cancer control in renal cell carcinoma and overcome treatment-resistance that eventually develops in most patients.

Using functional MRI in a large multisite sample of more that 1,000 patients, four distinct neurophysiological biotypes of depression are defined. These biotypes are used to develop diagnostic classifiers that distinguish patients with depression from controls in separate multisite validation and replication cohorts, and can predict patient responsiveness to therapy.

Particulate optical backscattering is key to studying the oceanic carbon pump though it remains unclear what particles are detected. Here the authors show that complex particles larger than 1 µm help reproduce all the measured backscattering across the Atlantic Ocean and explain the majority of the signal.

The surface oxygen storage capacity is an important metric of catalytic activity, but its dependence on strain is not well characterized. Here, the authors show the surface oxygen nonstoichiometry in coherently strained CeO2-δ films increases non-monotonically with biaxial strain.

High salt intake changed the gut microbiome and increased T_H17 cell numbers in mice, and reduced intestinal survival of Lactobacillus species, increased the number of T_H17 cells and increased blood pressure in humans.

The management of advanced renal cell carcinoma (RCC) has dramatically changed over the past decade. In this Review, the authors discuss the development of novel immunotherapies to treat RCC, including inhibitors of checkpoint receptors, vaccines, T-cell agonists, and chimeric antigen receptor T cells.