Evaluated articles

eLife Assessment

The authors examined the evolution of hepatitis C virus (HCV) in a cohort of 14 subjects with recent HCV infections. They showed that viral fitness declines as the virus mutates to escape the immune response and can rebound later in infection as HCV accumulates additional mutations. The study contributes to an important aspect of viral evolution. The combination of approaches contributes to a convincing study.

eLife Assessment

This important study provides evidence for the role of neutrophil extracellular traps in chronic kidney damage (CKD) induced by chemotherapy and suggests a therapeutic approach to mitigate the kidney pathology caused by the NETs. The study utilizes a sound murine in vivo model of CKD with low-dose administration cisplatin and a genetic model for impairment of NET formation by deletion of the enzyme Pad4. In its current form, the study was seen as incomplete as there is not yet formal demonstration of NET production by neutrophils in the model of CKD used. Additionally, the accuracy and clarity of data presentation could be improved.

eLife Assessment

The manuscript by de La Forest Divonne et al. offers an important and detailed exploration of the immune cells in the oyster Crassostrea gigas, by correlating distinct hemocyte morphotypes with specific single-cell transcriptional profiles. The evidence supporting the conclusion is convincing, deriving from the comprehensive dataset that not only captures unicellular diversity but also associates these cells with distinct immune roles, making it an invaluable resource for the broader research community.

eLife Assessment

This is a valuable study of the physiological mechanisms promoting network activity during fever in the mouse neocortex. The supporting evidence is solid, and has improved with revision, along with increased clarity of presentation.

eLife Assessment

This study presents an important computational framework, FLiSimBA (Fluorescence Lifetime Simulation for Biological Applications), for modeling experimental limitations in Fluorescence Lifetime Imaging Microscopy (FLIM). FLiSimBA is readily available in MATLAB and Python, enables users to simulate effects of noise and varying sensor expression levels, and provides practical guidance for both lifetime imaging experiments and biosensor development. The analyses are robust, and the evidence supporting the tool's utility in distinguishing between multiple lifetime signals is compelling, indicating strong potential for multiplexed dynamic imaging. However, users should also consider that the tool's effectiveness depends on the suitability of a two-component discrete exponential model.

eLife Assessment

This valuable study describes how trains of mossy fiber stimulation control cerebellar unipolar brush cell discharges. The dissection of the contributions of relevant glutamate receptors to these transformations is convincing. Overall, the study broadens our understanding of temporal processing in the cerebellar cortex.

eLife Assessment

This study provides important observations about the role of Hebbian synapse rewiring (which predicts that correlated activity between neurons begets stronger synapses) on brain connectivity development, by examining a naturally emerging case where Hebbian predictions can be tested because neurons with differing activity undergo development under otherwise similar conditions (albino mouse lateral geniculate nucleus [LGN], where retinal ganglion cells [RGCs] from the contralateral retina form inappropriate projections alongside a majority of ipsilateral RGCs). The evidence supporting the conclusions is compelling, with combined confocal imaging and serial electron microscopy (EM) reconstructions showing complete synaptic isolation of aberrantly projecting RGCs onto LGN thalamocortical projection neurons, and mixed connectivity onto LGN local interneurons. The morphological descriptions of connectivity presented here will be of interest to researchers studying synaptic connectivity and plasticity during development.

eLife Assessment

The microbiome field is constantly providing insight on various health-related properties elicited by the commensals that inhabit their mammalian hosts. Harnessing the potential of these commensals for knowledge about host-microbe interactions, as well as properties with therapeutic implications, will likely remain a fruitful field for decades to come. In this valuable study, Wang et al use various methods, encompassing classic microbiology, genomics, chemical biology, and immunology, to identify a potent probiotic strain that protects nematode and murine hosts from Salmonella enterica infection. The authors provide compelling evidence identifying gut metabolites that are correlated with protection, and show that a single metabolite can recapitulate the effects of probiotic administration.

eLife Assessment

This study presents valuable findings related to seasonal brain size plasticity in the Eurasian common shrew (Sorex araneus), which is an excellent model system for these studies. The evidence supporting the authors' claims is convincing. The work will be of interest to biologists working on neuroscience, plasticity, and evolution.

eLife Assessment

This study developed a novel continuous dot-motion decision-making task, in which participants can see another player's responses as well as their own, to measure perceptual performance and confidence judgments in a social context. The study is a valuable contribution to social decision-making primarily by introducing a new task and offering convincing evidence on how participants are impacted by others' decisions during continuous perceptual choices. The manuscript delivers clear evidence that participants judgements are driven by metacognitive confidence over simpler primary uncertainty.

eLife Assessment

This valuable study uses consensus-independent component analysis to highlight transcriptional components (TC) in high-grade serous ovarian cancers (HGSOC). The study presents a convincing preliminary finding by identifying a TC linked to synaptic signaling that is associated with shorter overall survival in HGSOC patients, highlighting the potential role of neuronal interactions in the tumour microenvironment. This finding is corroborated by comparing spatially resolved transcriptomics in a small-scale study; a weakness is it being descriptive, non-mechanistic, and requires experimental validation.

eLife Assessment

This study presents a valuable finding on the molecular mechanisms that govern GABAergic inhibitory synapse function. The authors propose that Endophilin A1 serves as a novel regulator of GABAergic synapses by acting as a component of the inhibitory postsynaptic density. The findings are convincing and likely to interest a broad audience of scientists focusing on inhibitory synaptic transmission, the excitation-inhibition balance, and its disruption in disorders such as epilepsy.

eLife Assessment

Computational simulation of neuron function depends on a collection of morphological properties and ion channel biophysics. This manuscript introduces DendroTweaks, a valuable web application and Python library that eases interactive exploration, development, and validation of single-neuron models in an easily installable and well-documented package. The authors provide a convincing demonstration that their software aids with building intuition and rapid prototyping of biophysical models of neurons, which improves the accessibility of dendritic simulation.

eLife Assessment

This important paper takes a novel approach to the problem of automatically reconstructing long-range axonal projections from stacks of images. The key innovation is to separate the identification of sections of an axon from the statistical rules used to constrain global structure. The authors provide compelling evidence that their method is a significant improvement over existing measures in circumstances where the labelling of axons and dendrites is relatively dense.

eLife Assessment

This revised paper provides valuable findings that altruistic tendency during moral decision-making is gain/loss context-dependent and oxytocin can restore the absence of altruistic choices in the loss domain. The methods and analyses are solid, yet the study could still benefit from better overall framing and more clarity and precision in the definition of key constructs, as pointed out by reviewers. If these concerns are addressed, this study would be of interest to social scientists and neuroscientists who work on moral decision-making and oxytocin.

eLife Assessment

The study presents important findings on inositol-requiring enzyme (IRE1α) inhibition on diet-induced obesity (overnutrition) and insulin resistance where IRE1α inhibition enhances thermogenesis and reduces the metabolically active and M1-like macrophages in adipose tissue. The evidence supporting the conclusions is convincing. The work will be of interest to cell biologists and biochemists working in metabolism, insulin resistance and inflammation with a broad eLife readership.

eLife Assessment

This study provides important insights as to how interacting brain areas produce movement during the execution of a skilled multi-directional reaching task. Using a combination of single neuron and neural population analysis, optogenetic stimulation, and computational models, the authors provide convincing evidence of an asymmetrical influence between mouse premotor and motor cortex during the execution of a well-practiced behaviour. This asymmetry can only be captured by some but not all population analysis methods, which is a key lesson to the field in and of itself. Analyzing how activity that is shared and private to these areas relates to different aspects of movements, and why different methods provide different outcomes regarding the nature of inter-area interactions would further strengthen this work.

eLife Assessment

This valuable study combined whole-head magnetoencephalography (MEG) and subthalamic (STN) local field potential (LFP) recordings in patients with Parkinson's disease undergoing deep brain stimulation surgery. The paper provides convincing evidence that cortical and STN beta oscillations are sensitive to movement context.

eLife Assessment

The authors provide a valuable contribution by documenting the role of microglia in pruning the axon terminals of AgRP neurons. The analysis of microglial axonal pruning is solid; however, the analysis of the effects inhibiting microglia on subsequent food consumption is not fully complete.

eLife Assessment

This study aims to clarify the effects of cochlear neural degeneration on auditory processing in listeners with normal audiograms (sometimes referred to as 'hidden hearing loss'). The authors provide important new data demonstrating associations between cochlear neural degeneration, non-invasive assays of auditory processing, and speech perception. Based on a cross-species comparison, the findings pose compelling evidence that cochlear synaptopathy is associated with a significant part of hearing difficulties in complex environments.