Evaluated articles

eLife Assessment

This paper represents a valuable contribution to our understanding of how LFP oscillations and beta band coordination between the hippocampus and prefrontal cortex of rats may relate to learning. Enthusiasm for the reported results was moderated by the concern that some key analyses need to be done, and highly relevant details about task, data, and statistics were missing. Consequently, the reviewers considered the evidence to be incomplete in this version of the manuscript.

eLife Assessment

The authors combine a modeling approach, using a digital twin, with electrophysiological evidence in two species to assess the role of inhibition in shaping selectivity in the visual cortex. The results provide an important advance beyond the classic view of sensory coding by proving compelling evidence that many neurons in visual areas exhibit dual-feature selectivity. Overall, the work exceptionally showcases how in silico experiments can generate concrete hypotheses about neuronal coding that are difficult to discover experimentally.

eLife Assessment

This important study, which tackles the challenge of analyzing genome integrity and instability in unicellular pathogens by introducing a novel single-cell genomics approach, presents compelling evidence that this new tool outperforms standard whole-genome amplification techniques. While thorough and rigorous, the work's impact would increase by providing scripts and data, as well as a description of the biological relevance that would make this method more appealing to the broad community studying genetic heterogeneity in diverse organisms.

eLife Assessment

This important study employs a closed-loop, theta-phase-specific optogenetic manipulation of medial septal parvalbumin-expressing neurons in rats and reports that disrupting theta-timescale coordination impairs performance of challenging aspects of spatial behaviors, while sparing hippocampal replay and spatial coding in hippocampal place cells. The findings are expected to advance theoretical understanding of learning and memory operations and to provide practical implications for the application of similar optogenetic approaches. The experiments were viewed as technically rigorous, but the strength of evidence provided in the current version of the manuscript was viewed as incomplete, mostly due to limited analyses and the descriptions of some of the experimental protocols.

eLife Assessment

This is a useful study that investigates the role of the long non-coding RNA Dreg1 for the development, differentiation, or maintenance of group 2 ILC (ILC2). The authors generate Dreg1-/- mice and show a reduction of group 2 innate lymphoid cells (ILC2). However, the strength of evidence supporting the impact of Dreg1 on Gata3 expression, a transcription factor required for ILC2 cell fate decisions, and the cell-intrinsic requirement of Dreg1 for ILC2 remain incomplete. This study will be of interest to immunologists.

eLife Assessment

This manuscript proposes a lateralized, lobe-specific brain-liver sympathetic neurocircuit regulating hepatic glucose metabolism and presents anatomical evidence for sympathetic crossover at the porta hepatis using viral tracing and neuromodulation approaches. While the topic is of important significance and the methodologies are, in principle, state-of-the-art, significant concerns regarding experimental design, incomplete methodological reporting, sparse and ambiguous labeling, and overi-nterpretation of the data substantially weaken support for the study's central conclusions, thereby limiting the study's completeness. The work will be of interest to biologists, clinicians, and physiologists.

eLife Assessment

In this useful study, the authors conducted an impressive amount of atomistic simulations with a realistic asymmetric lipid bilayer to probe how the HIV-1 envelope glycoprotein (Env) transmembrane domain, cytoplasmic tail, and membrane environment influence ectodomain orientation and antibody epitope exposure. The simulations convincingly show that ectodomain motion is dominated by tilting relative to the membrane and explicitly demonstrate the role of membrane asymmetry in modulating the protein conformation and orientation. However, due to the qualitative nature of the conducted analyses, the evidence for the coupling between membrane-proximal regions and the antigenic surface is considered incomplete. With stronger integration of prior experimental and computational literature, this work has the potential to serve as a reference for how Env behaves in a realistic, glycosylated, membrane-embedded context.

eLife Assessment

This study provides a useful application of computational modelling to examine how people with chronic pain learn under uncertainty, contributing to efforts to link pain with motivational processes. However, the evidence supporting the main claims is incomplete, as the modelling differences are not reflected in observable behaviour or pain measures, and the interpretation extends beyond what the data can substantiate. The conclusions would benefit from a clearer explanation of the behavioural differences that underlie the computational findings.

eLife Assessment

This important study establishes a workflow based on environmental sampling for the discovery of bacteriophages capable of infecting antibiotic-resistant pathogens. The experimental design, analysis, and results demonstrating the effectiveness of the workflow are convincing, although a broader sampling scheme and more careful framing of the data within the current limitations of viral taxonomy could strengthen the work. This study will interest researchers working on bacterial infections, environmental microbiology, and phage-based alternatives for addressing antimicrobial resistance.

eLife Assessment

This important study provides the first direct neuroimaging evidence for the integration-segregation theory of exogenous attention underlying inhibition of return, using an optimized IOR-Stroop fMRI paradigm to dissociate integration and segregation processes and to demonstrate that attentional orienting modulates semantic- and response-level conflict processing. Although the empirical evidence is compelling, clearer justification of the experimental logic, more cautious framing of behavioral and regional interpretations, and greater transparency in reporting and presentation are needed to strengthen the conclusions. The work will be of broad interest to researchers investigating visual attention, perception, cognitive control, and conflict processing.

eLife Assessment

This important work contributes a transcriptional dataset that identifies potential genes involved in axon initial growth and axon regrowth, followed by a characterization of axon phenotypes after knockdown of a subset of these genes. Focused experiments on a single gene, Pmvk, highlight the potential role of the mevalonate pathway in axon regrowth. The methods are convincing, though partially incomplete. The data establish a basis for further studies on axonal development and will be of interest to both developmental neurobiologists and those seeking to develop molecular tools to target, monitor, and manipulate axon morphology and function.

eLife Assessment

This important work shows that a history of cocaine self-administration disrupts the orbitofrontal cortex's ability to encode similarities between distinct sensory stimuli that possess identical task information - hidden states. The evidence supporting these conclusions is compelling, with methods and analyses spanning self-administration, a novel 'figure 8' sequential odor task, recordings from 3,881 single units, and sophisticated firing analyses revealing complex orbitofrontal representations of task structure. These results will be of broad interest to psychologists, neuroscientists, and clinicians.

eLife Assessment

This is a potentially important paper attempting to identify neutral correlates of memory engram expression in humans, and how they change during forgetting. The questions posed are clear and novel. The methods employed, namely behavioral analysis, high-resolution functional magnetic resonance imaging, and representational similarity analysis, are advanced, integrative, and appropriate. The experiments are well designed and combine analysis of recollection and familiarity of object/face associations. However, substantial questions remain as to the validity of the incomplete statistical analyses applied to the imaging data, as well as the parsing of and interpretation of the behavioral data.

eLife Assessment

This valuable study links psychological theories of chunking with a physiological implementation based on short-term synaptic plasticity and synaptic augmentation. The theoretical derivation for increased memory capacity via hierarchical chunking is solid. However, the model robustness and biological grounding of the mechanism - including many aspects that were hard-wired, chunking cues, and parameter ranges - as well as its evaluation in the task settings that motivated the study, are incomplete. Additional simulations to test robustness in more cognitively and biologically realistic settings, a systematic parameter analysis, and stronger links to prior work would substantially strengthen the manuscript and increase its impact across disciplines.

eLife Assessment

The study presents data on the possible connection of respiratory pathologies like pneumonia in a cohort of dolphins with altered composition and concomitant perturbed biophysical properties of pulmonary surfactant complexes. Overall, it is a valuable contribution that could be of interest to scientists in the field. However, the study as it is appears somewhat incomplete and additional clarification and discussions are required in order to explain a few methodological questions that may limit the impact of the work considerably.

eLife Assessment

This important study examined age-related changes in cerebellar function by testing a large sample of younger and older adults, including 30 over 80 years old, on motor and cognitive tasks linked to the cerebellum and conducting structural imaging. Their findings show that cerebellar-dependent functions are mostly maintained or even enhanced across the lifespan, with cerebellar-mediated motor abilities remaining intact despite degeneration, in contrast to non-cerebellar measures. Overall, the authors provide solid evidence in support of preserved cerebellar function with age. These results highlight the resilience and redundancy of cerebellar circuits and offer key insights into aging and motor behavior.

eLife Assessment

Using their unique Fish-On-Chips optofluidics platform, the authors make three important findings: the presence of precise coupling between saccades and tail flips can be used to discriminate between turning or gliding behaviours; aversive and appetitive chemosensory cues differentially modulate these behaviours; transformation from cue valence to behaviour is encoded by the pallium. The evidence supporting these findings is solid. The work advances our understanding of the ancient interplay between chemosensation and motor output through the modulation of eye-body coordination.

eLife Assessment

The presented findings are important for the field of cell-cycle control. They provide new insights into the origin of cell size variability in budding yeast. The strength of evidence is solid. However, the conclusions could be more strongly supported by additional analysis.

eLife Assessment

This important study employs functional magnetic resonance spectroscopy (fMRS) to demonstrate that GABAergic inhibition in the parietal cortex actively suppresses goal-irrelevant distractors, thereby facilitating goal-directed visual tracking. The data and analyses are solid, and the methodology is validated. However, the link between the metabolic changes and the purported functional mechanisms is incomplete due to concerns with experimental design and interpretations. The study will be of interest to researchers studying goal-directed behavior and neurochemical dynamics in cognitive processing.

eLife Assessment

This valuable work demonstrates that M. tuberculosis protein PPE2 perturbs adipose tissue biology by modulating adipogenesis, lipolysis, and inflammatory remodeling, thereby contributing to fat loss and insulin resistance during TB. Using M. smegmatis overexpression strains, PPE2-deficient Mtb mutants, and mouse models, the study links PPE2 to downregulation of PPAR-γ, C/EBP-α, adiponectin, and broader transcriptional changes in host fatty acid metabolism. These findings convincingly highlight, for the first time, a direct role for a bacterial virulence factor in TB-associated wasting. However, despite strong associative evidence, the mechanistic basis of PPE2-mediated regulation remains unresolved.