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While population transfer between electronic states occurs instantly in two-state model systems, here the authors show that real-world systems with coupling to additional states can exhibit measurable delays for transfer on a single femtosecond timescale.

Preservation strategy.

Dual-comb spectroscopy has become a valuable tool for broadband high-resolution measurements. Here Bergevin et al. apply this technique to a laser-induced plasma detecting different species in a solid sample with a spectral resolution sufficient to resolve hyperfine splitting of the Rb D₂ line.

Proliferation of adult tissue stem cells is tightly regulated to balance maintenance of the tissue against stem cell exhaustion or cancerous expansion. Here they show that zebrafish lateral line progenitors are differentially regulated by two cyclinD genes, which control developmental and adult progenitor proliferation as well as hair cell polarization.

Multimode interference devices could allow the implementation of multiport circuits for quantum technologies. Here, quantum interference is demonstrated in 2×2 and 4×4 multimode interference devices, and a technique is reported to characterize such devices.

Two-dimensional arrays of trapped ion qubits are attractive platforms for quantum information processing, but rapid reloading remains a challenge. Here the authors use a continuous flux of pre-cooled neutral atoms to achieve fast loading of single ions without affecting the coherence of adjacent qubits.

The hyperfine states of ultracold polar molecules are a strong candidate for storing quantum information. Identifying and eliminating all detectable causes of decoherence has extended the qubit coherence time beyond 5.6 s in RbCs molecules.

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.

Structures associated with the final steps of non-homologous end joining (NHEJ) and gap filling present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.

Tracking immobilized molecular complexes under in situ conditions is vital for the development of next-generation catalysts, although the poor surface sensitivity of many techniques makes this challenging. Now, the role of the anchoring group in a nickel bis(terpyridine) complex has been elucidated by in situ gap-plasmon-assisted SERS coupled with DFT calculations.

Immune gene expression analysis can help differentiate between inflammatory skin diseases. Here the authors compare expression profiles between different human inflammatory skin diseases and identify gene modules such as cytokines or inflammatory mediators and a molecular map to assist in diagnosis and treatment.

Synthetic hydrogels and immune organs-on-chip mimicking human immune tissue developed from blood samples allow effective modelling of immune responses and B cell disorders, with implications for the development of improved immunotherapies and vaccines.

Hydroxide exchange membrane fuel cells are promising devices for energy conversion. Now, a porous nitrogen-doped carbon-supported PtRu catalyst for the hydrogen oxidation reaction is presented, consisting of Pt single atoms and PtRu nanoparticles that work synergistically. The catalyst enables a fuel cell that exceeds the US Department of Energy 2022 performance target.

Here, the authors describe biallelic loss-of-function variants in human SHARPIN in individuals with autoinflammation and immunodeficiency, termed sharpenia. They also successfully treat one of these individuals with TNF inhibitors.

The haplotype-resolved genome in Amborella trichopoda addresses outstanding questions on the structure and gene content of the recently evolved ZW sex chromosomes.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Synthetic Notch (SynNotch) receptors can be used to endow cells with custom sense-and-respond capabilities. Here, the authors introduce a fluorescein-binding SynNotch as a versatile tool for controlling gene expression responses to diverse stimuli via ligands based on fluorescein-conjugates.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

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.

Researchers report rewritable nanoscale photodetectors that exploit 2–3 nm nanowire junctions. Large electromagnetic fields in the gap region aid the detector response, which is electric-field-tunable and spans the visible to near-infrared regime.

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.

Stratified medicine promises to tailor treatment for individual patients, however it remains a major challenge to leverage genetic risk data to aid patient stratification. Here the authors introduce an approach to stratify individuals based on the aggregated impact of their genetic risk factor profiles on tissue-specific gene expression levels, and highlight its ability to identify biologically meaningful and clinically actionable patient subgroups, supporting the notion of different patient ‘biotypes’ characterized by partially distinct disease mechanisms.

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.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

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.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Quantum reservoir computing might in principle give advantages in solving signal classification tasks, but current implementations usually incur in the digitalization bottleneck. Here, the authors demonstrate an implementation dealing directly with the analogue MW signals.

Ultracold polar molecules are an excellent platform for quantum science but experiments so far see fast trap losses that are poorly understood. Here the authors investigate collisional losses of nonreactive RbCs, and show they are consistent with the sticky collision hypothesis, but are slower than the universal rate.

Abiraterone acetate (AA) is indicated for the treatment of patients with metastatic castrate-resistant prostate cancer. Here, the authors show that, in prostate cancer patients, orally administered AA remodels the gut microbiome and promotes the enrichment of the commensal bacterium Akkermansia muciniphila at the expense of androgen-utilizing Corynebacterium species.

Single-cell imaging, metabolomics and modelling quantify metabolic exchanges between cyanobacteria and heterotrophic bacteria, showing transient nutritional exchanges facilitated by chemotaxis of the heterotroph.

Here, the authors report the observation of an interlayer plasmon polaron in heterostructures composed of graphene and monolayer WS₂. This is manifested in the ARPES spectra as a strong quasiparticle peak accompanied by several carrier density-dependent shake-off replicas around the WS₂ conduction band minimum.

The potential power of the saturated carbocycle bicyclo[3.1.1]heptane as a beneficial motif for improving the pharmacokinetic and physicochemical properties of drug candidates is demonstrated.

The immunological parameters that define severe influenza disease are not clear within human real time infections. Here the authors compare a severe influenza infection cohort with an influenza vaccinated cohort to understand correlates of severe influenza disease.

Extreme confinement of light in plasmonic nanocavities strongly enhances the optomechanical coupling of light with molecular vibrations. Here, the authors use a giant optical spring effect to reversibly weaken molecular bonds.

New analytical tools are needed to identify chemical degradation and failure mechanisms in Li-ion batteries. Here, the authors report an operando Raman spectroscopy method, based on hollow-core optical fibres, that enables monitoring the chemistry of liquid electrolytes during battery cycling.