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Integrated multi-omic analyses using samples from the TRACERx study highlight cross-talk between DNA hypermethylation and genomic lesions in non-small cell lung cancer.

In freely moving rodents, eye movements serve to keep the visual fields of the two eyes continuously overlapping overhead at the expense of continuous alignment, a strategy that may have evolved to maintain constant overhead surveillance of predators.

Passive isolators that offer unitary transmission, infinite isolation and large non-reciprocal intensity range can be created by combining Fano and Lorentzian nonlinear resonators, separated by suitably designed delay lines.

By exploiting stochastic resonance — in which nonlinear coupling allows signals to grow at the expense of noise — scientists show that they can recover noise-hidden images propagating in a self-focusing medium. The findings pave the way for a variety of nonlinear instability-driven imaging techniques.

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.

Neuronal organoids derived from human induced pluripotent stem cells can be transplanted and integrated into the rodent cortex for the study of brain development and function. Here the authors demonstrate use of transparent graphene microelectrodes and two photon imaging for longitudinal, multimodal monitoring of functional connectivity between human iPSC derived neuronal organoids and the mouse cortex.

T cell large granular lymphocytic leukemia (T-LGLL) is a lymphoproliferative disorder involving clonally expanded T cell clones and is not fully understood. Here the authors show that the rest of the immune repertoire is interconnected with the T-LGLL clonotype(s) and is more mature, cytotoxic and clonally restricted than in other cancers and autoimmune disorders.

Pose estimation in combination with an anatomically constrained model allows inferring skeletal kinematics in rodents.

Bosonic qubits can be engineered to feature intrinsic protection against certain kinds of errors, which makes quantum error correction across many bosonic qubits possible with less overhead.

Using electrostatic doping, the real and imaginary parts of the refractive index along the extraordinary axis of semiconducting, highly aligned, single-walled carbon nanotubes over 4″ wafers can be tuned by up to 5.9% and 14.3% in the infrared at 2,200 nm and 1,660 nm, respectively.

Circulating tumour DNA profiling in early-stage non-small-cell lung cancer can be used to track single-nucleotide variants in plasma to predict lung cancer relapse and identify tumour subclones involved in the metastatic process.

A lightweight three-photon miniature microscope allows imaging neuronal activity throughout the cortex in freely moving mice.

Imaging through a nonlinear medium can be difficult because signals distort as they propagate through it owing to intensity-dependent phase changes. Here, digital reconstruction of optical spatial beams propagating in a nonlinear medium is presented, which could help the understanding of coupled-wave dynamics and suggest new image-processing techniques.

Nonlinear optics can overcome the diffraction limit through the presence and interaction of many photons. Abbe's diffraction theory is now generalized to include spatial nonlinearity, and wave mixing is treated as a self-induced structured illumination, thereby allowing a standard imaging system to be nonlinearly enhanced beyond its conventional limits.

Here, the authors demonstrate a chip-scale device that realizes a comprehensive set of resonant second order nonlinear processes including optical parametric oscillation with a threshold power of 70 microwatts.

A manufacturable platform for quantum computing with photons is introduced and a set of monolithically integrated silicon-photonics-based modules is benchmarked, demonstrating dual-rail photonic qubits with performance close to thresholds required for operation.

This study assessed COVID-19 social science preprints’ replicability using structured groups. Both beginners and more-experienced participants used a elicitation protocol to make better-than-chance predictions about the reliability of research claims under high uncertainty.

Exciton dynamics can be strongly affected by lattice vibrations through electron-phonon (e-ph) coupling. Here, the authors show the presence of strong e-ph coupling in bilayer CrI₃ and observe a Raman feature with periodic broad modes up to the 8th order, attributed to the polaronic character of excitons.

Combination of epidemiology, preclinical models and ultradeep DNA profiling of clinical cohorts unpicks the inflammatory mechanism by which air pollution promotes lung cancer

The energy extrema of an electronic band are referred to as valleys. In 2D materials, two distinguishable valleys can be used to encode information and explore other valleytronic applications.

A topological transition in a nonlinear photonic lattice results in new vortex dynamics and a change from photonic fluid behaviour to that of a plasma-like gas.

Mixed responses to targeted therapy within a patient are a clinical challenge. Here the authors show that TP53 loss-of-function cooperates with whole genome doubling which increases chromosomal instability. This leads to greater cellular diversity and multiple routes of resistance, which in turn promotes mixed responses to treatment.

A head-mounted three-photon microscope based on a custom-designed optical fiber and dispersion compensation enables imaging of activity from neuronal populations deep in the cortex of freely moving rats.

The visual callosal pathway reciprocally connects mammalian visual cortices and is proposed to facilitate activation of binocular neurons. Here, the authors show that this pathway facilitates responses in both monocular and binocular neurons but these responses are gated by the ipsilateral lateral geniculate nucleus.

Analyses of multiregional tumour samples from 421 patients with non-small cell lung cancer prospectively enrolled to the TRACERx study reveal determinants of tumour evolution and relationships between intratumour heterogeneity and clinical outcome.

Most genomics research cohorts are made up of participants of European ancestry, which limits the reach of precision medicine. Here, the authors describe the genetic diversity in the All of Us research program, which is enriched in underrepresented ancestries.

Swanton and colleagues present a clonal expression signature, ORACLE, which, in combination with clinicopathological and molecular risk factors, can predict survival of patients with lung adenocarcinoma, and they prospectively validate its prognostic value.

Immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS) infers B cell and T cell fractions from whole-genome sequencing data. Applied to the 100,000 Genomes Project datasets, circulating T cell fraction provides sex-dependent and prognostic insights in patients.

A longitudinal evolutionary analysis of 126 lung cancer patients with metastatic disease reveals the timing of metastatic divergence, modes of dissemination and the genomic events subject to selection during the metastatic transition.

Greenberg and colleagues directly compare the activity of cortical neurons in awake and subsequently anesthetized rats, finding that anesthesia modulates the relationship between firing rate and correlation, and suggesting that brain activity during wakefulness cannot be inferred from data gathered under anesthesia.

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

CD4⁺ T cells are known to be important in Plasmodium infection. Here the authors use mouse models to track antigen-experienced TCR transgenic and polyclonal CD4⁺ T cells during Plasmodium re-infection, and show different T cell phenotypes and varied responses in different areas of the spleen.

In the TRACERx cohort of 171 patients with lung cancer, the ultrasensitive detection of ctDNA improves preoperative patient stratification, also in early-stage disease.

Advances in cellular imaging have been crucial for improving our understanding of many aspects of neuroscience. Kerr and Denk describe how sophisticated optical imaging techniques allow us to image activity in single neurons or neuron populations in living animals.

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.

Results of the TRACERx study shed new light into the association between body composition and body weight with survival in individuals with non-small cell lung cancer, and delineate potential biological processes and mediators contributing to the development of cancer-associated cachexia.

Patient-derived xenografts are important tools for cancer drug development. Here, the authors develop models from 22 non-small cell lung cancer patients. They show genomic differences between models created from different spatial regions of tumours and a bottleneck on model establishment.

Openshaw and colleagues find myeloid inflammation and complement activation signatures in patients with long COVID who were previously hospitalized.

Globally, urban areas experienced increases in ozone concentrations from 2005 to 2019, whereas fine particulate matter, nitrogen dioxide, and fossil-fuel carbon dioxide emissions showed non-significant variations, according to analysis of large geospatial air pollution datasets.

In lung adenocarcinoma, antibodies against endogenous retroviruses promote anti-tumour activity, and expression of endogenous retroviruses can predict outcomes of immunotherapy.

Major histocompatibility complex (MHC) loss of heterozygosity, allele-specific mutation and measurement of expression and repression (MHC Hammer) detects disruption to human leukocyte antigens due to mutations, loss of heterogeneity, altered gene expression or alternative splicing. Applied to lung and breast cancer datasets, the tool shows that these aberrations are common across cancer and can have clinical implications.

Measurements of subclonal expansion of ctDNA in the plasma before surgery may enable the prediction of future metastatic subclones, offering the possibility for early intervention in patients with non-small-cell lung cancer.

Optical microscopy allows neural cells to be studied in the intact brain, but imaging deep neural tissue presents substantial challenges. Prevedel and colleagues outline the principles of three-photon microscopy, highlighting its advantages for deep tissue imaging and its applications in neuroscience.

Computational and machine-learning approaches that integrate genomic and transcriptomic variation from paired primary and metastatic non-small cell lung cancer samples from the TRACERx cohort reveal the role of transcriptional events in tumour evolution.