Browse Articles

Reply to Neveu and Neveu: Inference in an information-restricted environment

Neurofluid circulation changes during a focused attention style of mindfulness meditation

Neurofluids, including cerebrospinal fluid (CSF) and interstitial fluid, circulate through regulated central nervous system pathways to clear cerebral waste and support brain health, with elevated CSF flow hyperdynamicity and regurgitation through the cerebral aqueduct associating with aging and neurodegeneration. Sleep exerts state-dependent effects on neurofluid circulation, yet similar modulation during unique waking states, such as meditation, remains underexplored. Notably, mindfulness meditation shares several regulatory features with sleep, with core meditation practices representing distinct arousal states. We investigated whether the focused attention (FA) style of mindfulness meditation modulates neurofluid dynamics directionally opposite to aging and consistent with sleep. Using phase-contrast MRI, we assessed absolute CSF flow and velocity through the aqueduct, and using blood oxygenation level–dependent (BOLD) MRI, we assessed CSF fluctuations near the cervicomedullary junction together with total supratentorial gray matter fluctuations. Assessments were repeated in meditation-naïve adults during mind wandering (MW) without (n = 13; repeatability controls) and with (n = 14; breath controls) respiration rate modulation and in adept meditators (n = 23) during MW and FA meditation. No aqueduct CSF flow changes were observed in control groups. In meditators, aqueduct absolute CSF flow motion decreased from MW to FA meditation (4.60 ± 2.27 mL/min to 4.17 ± 2.10 mL/min, P = 0.005) owing to reduced regurgitant cranially directed CSF flow velocity. On BOLD, this paralleled increased low-frequency (0.0614 to 0.0887 Hz) CSF fluctuations ( P = 0.0138), which were inversely correlated with gray matter fluctuations during FA meditation. Findings suggest that mindfulness meditation may represent a nonpharmacological, waking state capable of modulating neurofluid dynamics in a directionally similar manner to sleep and opposite to aging and neurodegeneration.

Unravelling the evolution of wood-feeding in termites with 47 high-resolution genome assemblies

Reconstructing Waddington’s landscape from data

The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate the interactions within developmental signaling networks that coordinate these hierarchical cell fate transitions are difficult to interpret or fit to data. An alternative approach models the cellular decision-making process as a flow in an abstract landscape whose signal-dependent topography defines the possible developmental outcomes and the transitions between them. Prior applications of this formalism have built landscapes in low-dimensional spaces without explicit maps to gene expression. Here, we present a computational geometry framework for fitting dynamical landscapes directly to high-dimensional single-cell data. Our method models the time evolution of probability distributions in gene expression space, enabling landscape construction with minimal free parameters and precise characterization of dynamical features, including fixed points, unstable manifolds, and basins of attraction. We demonstrate the applicability of this framework to multicolor flow-cytometry and RNA-seq data. Applied to a stem cell system that models ventral neural tube patterning, we recover a family of morphogen-dependent landscapes whose valleys align with canonical neural progenitor types. Remarkably, simple linear interpolation between landscapes captures signaling dependence, and chaining landscapes together reveals irreversible behavior following transient morphogen exposure. Our method combines the interpretability of landscape models with a direct connection to data, providing a general framework for understanding and controlling developmental dynamics.

A mechanistic understanding of the varying yields of highly oxygenated organic molecules

Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics

Although histologically normal, esophageal preneoplastic cells harbor early genetic alterations and likely exhibit lineage plasticity. However, their origins and trajectories remain unclear. To address this, we combined genetic barcoding with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells. We identified a distinct progenitor-like cell population with high plasticity. Through a scoring system, these high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. This approach uncovers molecular markers, including Nfib and Qk , that define these precursor cells, validated by spatial transcriptomics and a Trp53 Cdkn2a Notch1 mouse model. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early detection and therapeutic targets of esophageal squamous cell cancer. By elucidating the cellular dynamics underlying esophageal preneoplasia, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches.

Nitrogen deposition reveals global patterns in plant and animal stoichiometry

Correction for Greenberg et al., Sex and age differences in “theory of mind” across 57 countries using the English version of the “Reading the Mind in the Eyes” Test

Exploring the resting habits of invasive Aedes albopictus mosquitoes in Southern France

NMDA receptors coordinate brain vascular development via neuron-to-endothelial tip cell crosstalk in zebrafish

Structural insights into the role of eIF3 in translation mediated by the HCV IRES

The genomes of various RNA viruses and a subset of human genes contain structured RNA elements termed internal ribosomal entry sites (IRESs) to initiate translation in a cap-independent manner. The well-studied IRES from Hepatitis C virus (HCV) binds to eukaryotic initiation factor 3 (eIF3), but how the HCV IRES harnesses eIF3 for viral translation remains unclear. Here, we determined multiple cryo-EM structures in which the HCV IRES binds simultaneously to the ribosome and eIF3, covering steps from initiation to elongation. The eIF3 core subunits are displaced from the ribosome by binding more tightly to subdomain IIIb of the HCV IRES. However, cross-linking mass spectrometry suggested that the eIF3 noncore subunits in the HCV-IRES-mediated elongation complex remain in similar positions on the ribosome to those observed in the cap-mediated initiation complex. This currently determined configuration of eIF3 core and noncore subunits reveals the mechanisms through which the HCV IRES overcomes the competition with the host mRNA and promotes viral mRNA translation by utilizing eIF3. Interestingly, cryo-EM structures also revealed that the N-terminal domain of the eIF3 c-subunit (eIF3c-NTD) binds to the large ribosomal subunit (60S) during elongation. These findings suggest that eIF3 contributes to HCV IRES–mediated translation not only during initiation but also elongation and potentially in reinitiation. The interaction between the eIF3c-NTD and the 60S ribosome is likely to occur in general translation processes as well, contributing to 60S joining or eIF3 stabilization on the elongating ribosome.

Efficacy of rocket and mustard oils and their nano-emulsions as alternatives to chemical herbicides for controlling weeds associated faba bean

Abstract Weeds are one of the most well-known biotic environmental stresses in crop ecosystems. They negatively affect plant growth by competing for essential natural resources, leading to adverse impacts on physiological and biochemical processes. Chemical herbicides are also considered as abiotic stress and negatively affect on human and animal health as well as the surrounding environment. So, we shed light on natural products as rocket salad and mustard oils and their nano-emulsions as alternatives to chemical herbicides. Two pot experiments in greenhouse along the winter seasons of 2021/2022 and 2022/2023. Treatments involved foliar spray of rocket and mustard oils and their nano-emulsions at successive concentrations (2.5, 5.0 and 7.5%). Healthy uninfected faba bean plants and unweeded control treatments were applied for comparison. Recorded results revealed that all applied weed control treatments significantly decreased canary grass and cheeseweed growth parameters. Mustard oil was more efficient than rocket oil in suppressing both investigated weeds. This recorded reduction was directly proportional to concentration. Nano-emulsions applications recorded better results than pure oils (without nano-emulsions). Hence, Mustard oil nano-emulsions at 7.5% recorded notified inhibition for both weeds. The reduction of weeds’ biotic stress is positively reflected in turn on faba bean plants. In this respect, rocket oil showed a stimulatory effect on faba bean plants higher than mustard oil. Meanly, rocket oil at 7.5% scored the highest growth traits and photosynthetic pigment at both growth ages. Rocket and mustard oils at the highest concentration (7.5%) progressed on healthy faba bean in scoring the high yield traits and seed quality as compared to the unweeded control. GC-mass fractionation of both oils identified eight fatty acids, namely: palmitic, palmitoleic, stearic, oleic, linoleic, linolenic, behenic and erucic fatty acids. Inhibitory response of weeds and stimulatory response of faba bean plants may be attributed to these phenolic acids. Rocket and mustard oils and their nano-emulsions achieved our hypothesis in having herbicidal properties as they have a high phytotoxic effect on growth and physiological processes of the weeds.

Breathing mode in Nd-CoOx for active and stable proton exchange membrane water electrolysis

Guiding esophagectomy with intraoperative NIR-II fluorescence video imaging and rapid computation

Preclinical shortwave infrared/near-infrared II (SWIR/NIR-II, 1,000 to 3,000 nm) fluorescence imaging has shown superior contrast, resolution, and penetration depth compared to traditional near-infrared I (NIR-I, 700 to 900 nm) imaging, owing to reduced light scattering and tissue autofluorescence. Here, we carried out clinical translation of NIR-II fluorescence imaging to guide esophagectomy through intraoperative video imaging and rapid analysis of blood perfusion in the gastric conduits (GC) of esophageal cancer patients, following intravenous administration of indocyanine green (ICG). Within <1 min, NIR-II video imaging clearly visualized the spatial and temporal blood flow features, and importantly, intraoperative principal component analysis (PCA) of the video revealed distinct perfusion patterns in GC. This led to rapid, subjective decision-making for targeted resection of poorly perfused tissue and informed reconstruction of the GC to reduce the risk of life-threatening anastomotic leakage. This approach enhances surgical precision and improves outcomes by providing operator-independent intraoperative guidance.

Enhancing tumor deepfake detection in MRI scans using adversarial feature fusion ensembles

Abstract The proliferation of AI-generated medical deepfakes, such as tumor insertions or removals in diagnostic scans, threatens patient safety and healthcare integrity. Existing detection methods often lack robustness against adversarial attacks or fail to integrate multimodal feature representations. To address these gaps, we propose AFFETDS (Adversarial Feature Fusion Enhanced Tumor Detection System), a novel ensemble framework combining adversarial training, feature fusion, and weighted voting. AFFETDS leverages adversarial attack methods (PGD, FGSM) to harden the model, fuses high-level ResNet50 features with handcrafted HOG descriptors, and employs an SVM-based ensemble classifier. Evaluated on a curated dataset of 1378 MRI scans (774 real, 604 manipulated) from TCIA and ADNI repositories, AFFETDS achieves state-of-the-art performance with 91.5% accuracy, 90.7% precision, and 91.2% recall, outperforming baseline models (SVM: 86.2%, CNN: 88.4%). The framework’s ROC-AUC (0.80) and calibrated confidence scores demonstrate superior generalization across diverse imaging conditions. The ability of combining the adversarial techniques with multimodal feature fusion, our proposed AFFETDS framework improves the detection of subtle tumor manipulations, presenting an important safeguard to maintain the authenticity of medical images. The findings of research work underscore the urgent need of proactive defenses against growing deepfake threats in healthcare applications.

Optically-controlled phonon-specific phase transitions from graphite to diamond

Restoring institutional confidence in backsliding democracies: Evidence from Mexico

Declining confidence in public institutions afflicts many democracies, a trend apparently exacerbated by backsliding leaders. These are leaders who gradually undermine the institutions that sustain democratic competition and accountability. Does the rhetoric of backsliders undermine the public’s confidence in the institutions under attack and can rebuttals of presidential diatribes restore this confidence? We explore the impact of backsliding leaders’ anti-institutional rhetoric in the context of Mexico. With text-as-data analyses, we demonstrate the harshness of President Andrés Manuel López Obrador’s (2018–2024) anti-institutional diatribes against the agency that oversees national elections. With survey experiments, we demonstrate that these diatribes can indeed undermine public confidence. Yet our research also uncovers the potential for rebuttals to restore confidence. Counternarratives offered by organizations viewed as above the fray of Mexican politics restored public confidence—surprisingly, even among the president’s supporters. Our findings suggest strategies for breaking out of the cage of intense partisanship and countering democracy-degrading rhetoric. Though presidential haranguing of democratic institutions can have a powerful effect, there remains room for public confidence to be restored by more positive accounts.

Generation and characterization of a tamoxifen-inducible, Cre driver rat for transgene expression in microglia

Abstract Microglia are the resident immune cells of the central nervous system (CNS) and display diverse functions under both physiological and pathological conditions. The past decade has seen burgeoning interest in microglia function, with a variety of transgenic tools developed for specific genetic manipulation of microglia in various injury, disease, and developmental models. Although many of these models have been developed in mice, the ability to manipulate microglia in rats provides additional advantages to studying microglial function in the brain especially related to complex behavior. Using BAC transgenesis, our lab created a transgenic rat (Cx3cr1-CreERT2) that expresses a tamoxifen inducible Cre recombinase (CreERT2) under control of the microglial/macrophage specific fractalkine C-X3-C Motif Chemokine Receptor 1 ( Cx3cr1 ) promoter. In mice, CreERT2 and other transgenes have been expressed in microglia using the Cx3cr1 promoter, however, this is the first demonstration in rats. Importantly, these rats exhibit similar cognitive behaviors compared to their wildtype (WT) controls. Microglial specificity of inducible Cre expression was confirmed by breeding the novel Cx3cr1-CreERT2 +/− rat with a previously reported double floxed inverse open reading frame (DIO)-mCherry +/− reporter rat to show tamoxifen inducible mCherry expression that colocalizes with the microglial marker Iba1. In addition, we utilized flow cytometry to demonstrate time- and Cre-dependent differences in recombination of Cx3cr1 + cells in the spleen, peripheral blood, and brain at two- and eight-weeks post-tamoxifen treatment. Overall, we have created a novel transgenic rat model for researchers to employ in understanding microglial and peripheral immune cell function in rats.

K isotopes trace temporal silicate weathering intensity

Abstract Silicate weathering alters the biogeochemical compositions of the lithosphere, hydrosphere, and atmosphere, and thereby regulates both nutrient cycling and habitable temperatures on Earth, but tracing silicate weathering effectively remains a challenge. Potassium (K) isotopes have been proposed as a tracer of silicate weathering intensity spatially, but there is a significant gap in how and why K isotopes trace silicate weathering temporally. Here we investigate seasonal variations in dissolved K isotopes in the middle Yellow River, which drains a large area of homogeneous loess that represents the average geochemical composition of the upper continental crust, and experiences significant climatic seasonality driven by the East Asian monsoon. We find that K isotopes show strong seasonality as a function of aluminosilicate neoformation following silicate dissolution, and thus could serve as a tracer of silicate weathering intensity. We derive an empirical relationship of δ 41 K rw  = −0.07 × ln(W/D) − 0.38, where W(silicate chemical weathering)/D(denudation) refers to silicate weathering intensity.

Conscious awareness, sensory integration, and evidence accumulation in bodily self-perception

Conscious awareness refers to the subjective experience of perceiving, thinking, and feeling and the ability to report these experiences. These perceptions and thoughts are experienced as bound to an individual self. A fundamental aspect of this self-consciousness is the sense of bodily self—the experience of one’s physical presence distinct from the external world, serving as the spatial reference point for conscious perceptions. A key component of the bodily self is body ownership, the experience of the body as one’s own. Research shows this sense involves integrating signals from different sensory modalities, including vision, touch, and proprioception, into a coherent multisensory percept. However, the relationship between body ownership and conscious awareness remains unclear. To investigate this, we developed a psychophysical paradigm to objectively quantify multisensory integration, conscious awareness, and their relationships within a bodily illusion manipulating body ownership perception. Using signal-detection analysis, metacognitive computational modeling, and drift–diffusion modeling, we found conscious awareness reports closely matched objective discrimination of body ownership. This relationship remained consistent across different levels of multisensory integration and evidence accumulation. A visuotactile control experiment revealed that this strong conscious access is specific to body ownership, not general to multisensory integration. These findings suggest that conscious awareness has continuous and prioritized access to body ownership, implying that the self-related form of multisensory integration supporting body ownership is largely implemented at the level of conscious processing. This provides theoretical insight into how conscious awareness and the bodily self are intertwined, with wide-reaching implications for consciousness and body representation research.