Evaluated articles

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.

eLife Assessment

This valuable study identifies a novel regulator of stress-induced gene quiescence in C. elegans: the multi-Zinc-finger protein ZNF-236. The work provides evidence for an active mechanism that maintains the repressed state of inducible genes under basal conditions in the absence of stress. The claims for discovery made in the title and abstract are supported by solid experimental data. However, a deeper investigation into the mechanisms of ZNF-236 action could substantially enhance the manuscript's impact and value.

eLife Assessment

This study addresses an important problem in gene regulation, namely, which features of chromatin regulate potential RNA Polymerase 2 activity at a locus. The authors provided evidence that specific post-translational modifications of histones within the gene body are correlated with Pol II transcription, that these modifications are dynamic, and that they can be regulated by Pol II activity. The manuscript contributes to the concept of "fragile nucleosomes" as a unifying framework for key epigenetic drivers of transcription; however, the quality of the evidence provided is inadequate in support of the claims made, and further evidence teasing out the mechanistic aspects of the work would strengthen its impact. This work will be of interest to the fields of transcriptional regulation, chromatin structure, and epigenetics.

eLife Assessment

This important work advances our understanding of the development of the visual system. The data presented is compelling and provides a detailed single-cell atlas of post-natal anterior chamber development in mice, highlighting the trabecular meshwork and Schlemm's canal.

eLife Assessment

This study presents important findings on how cardiac regenerative capacity diverges across species by examining heart repair in two species of livebearers, platyfish and swordtails. In contrast to zebrafish, the livebearer species show persistent scarring after cryo-injury, and the work highlights how lineage-specific anatomical and immunological traits may constrain regenerative competence. The study is compelling, the data are convincing, and the results contribute to our understanding of the mechanisms underlying heart regeneration across vertebrates.

eLife Assessment

This is an important study on the sensory roles of Cerebrospinal fluid-contacting neurons (CBF-cn) in mammals. The authors identify PKD2L1 as the predominant pH-sensing channel CBF-cn and show how the apical extension is used as an amplifier of chemical changes in the content of the Cerebrospinal fluid. The evidence is solid in experimental design but limited in mechanistic interpretation, as the electrophysiological analyses require re-evaluation.

eLife Assessment

This important study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides solid evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

eLife Assessment

This fundamental work substantially advances our understanding of a major research question: whether collagen can be directly imaged with MRI. The evidence supporting the conclusion is compelling, with methods, data, and analyses that are more rigorous than those currently considered state-of-the-art. The work will be of high interest to MR physicists and clinicians, as collagen is the most abundant protein in the human body and plays an essential role in health.

eLife Assessment

Rickert and colleagues demonstrate that the host peptidoglycan-binding protein PGLYRP1 has both beneficial and detrimental effects on Bordetella pertussis infection in mice. Using a solid array of techniques, the study provides useful insights into how peptidoglycan species may alter host immune responses. The data on the bactericidal effects on B. pertussis are incomplete, and further experiments are needed to draw conclusions on this question.