eLife assessment

This important manuscript uses a machine-learning approach to predict and annotate cis-regulatory elements across insect genomes, helping to address a much-needed gap in comparative genomics. This method does not rely on sequence alignments, thereby allowing functional genomics studies of more distant species, including emerging model organisms. There are nuanced views on the strength of the evidence from the predictions: the pipeline appears to be based on solid evidence, but the methods could be better described. We suggest the manuscript would be much more robust if the code used was accessible for review and validated further.

eLife assessment

Hartman et al.'s important research examines six commonly utilized imaging-based multiplexed transcriptomic techniques and introduces a novel specificity metric, "MECR," to streamline platform evaluations. The authors highlight the crucial influence of cell segmentation methodologies on outcomes, offering insight into the field. Nonetheless, the substantiation for the principal assertions remains incomplete, as the comparisons across platforms seem uneven due to variations in gene panels.

eLife assessment

This is an important study that brings insight into mechanisms that underlie regulation of GABAergic transmission in response to changes in activity. The authors present solid data supporting the premise that action potential firing rather than excitatory synaptic strength is a key determinant of GABAergic synaptic inputs.

eLife assessment

This study demonstrates that neurons receiving inputs from auditory cortex in the inferior colliculus widely encode the outcome of a sound detection task independant of the presence of auditory cortex. This valuable study based on imaging of transynaptically labelled neurons provides convincing evidence that auditory cortex is necessary neither for sound detection, nor to channel information related to behavioral outcome to the subcortical auditory system. This study will be of wide interest for sensory neuroscientists.

eLife assessment

This important study discovered DBT as a novel gene implicated in the resistance to MG132-mediated cytotoxicity and potentially also in the pathogenesis of ALS and FTD, two fatal neurodegenerative diseases. The authors provided convincing evidence to support a mechanism by which loss of DBT suppresses MG132-mediated toxicity via promoting autophagy. This work will be of interest to cell biologists and biochemists, especially in the FTD/ALS field.

eLife assessment

Building on previous toolboxes to distinguish 1/f noise from oscillatory activity, this study introduces an important advancement in neural signal analysis to identify oscillatory activity in electrophysiological data that refines the accuracy of identifying non-sinusoidal neural oscillations. Extensive validation, using synthetic and various empirical data, provides convincing evidence for the accuracy of the method and outlines practical implications for relevant scientific problems in the field.

eLife assessment

This study presents valuable findings regarding the microstructural basis of brain development in the cerebellum and thalamus of rat neonates using diffusion-weighted MRS. The authors present solid evidence of differential development trajectories in the thalamus and the cerebellum through analytical and morphometric biophysical modelling of the diffusion-weighted MRS data, though some aspects such as the validation of the findings against gold-standard techniques and a detailed discussion of methodological choices require further elaboration. The work will be of interest to developmental biologists and neuroscientists seeking noninvasive approaches to probe in vivo neuronal and glial development in the brain.

eLife assessment

This valuable study marks a significant advancement in brain aging research by centering on Asian populations (Chinese, Malay, and Indian Singaporeans), a group frequently underrepresented in such studies. It unveils solid evidence for anatomical differences in brain aging predictors between the young and old age groups. Overall, this study broadens our understanding of brain aging across diverse ethnicities.

eLife assessment

The authors use a synthetic approach to introduce synaptic ribbon proteins into HEK cells and analyze the ability of the resulting assemblies to cluster calcium channels at the active zone. The use of this ground-up approach is valuable as it establishes a system to study molecular interactions at the active zone. The work relies on a solid combination of super-resolution microscopy and electrophysiology, but would benefit from: (i) additional ultrastructural analysis to establish ribbon formation (in the absence of which the claim of these being synthetic ribbons might not be supported; (ii) data quantification (to confirm colocalization of different proteins); (iii) stronger validation of impact on Ca2+ function; (iv) in depth discussion of problems derived from the use of an over-expression approach.

eLife assessment

The authors provide an important step forward in understanding how brain-derived hormones modulate behavior, using medaka fish as a model system. Knockout lines present convincing evidence from multiple mutant lines, showing that estrogens play a significant role in male social behavior, and that lacking aromatase changes brain gene expression. The conclusions for females are less substantiated, and the conclusions regarding sexual differentiation should be considered carefully.

eLife assessment

This important study reports that glutamate signaling in LepRb PMv neurons is necessary for leptin-dependent fertility. The data supporting the conclusion is solid. This work will be of interest to researchers in the fields of both reproductive and metabolic biology.

eLife assessment

This work describes important updates to qFit, the state-of-the art tool for modeling alternative conformations of protein molecules based on high resolution X-ray diffraction or Cryo-EM data. The authors provide some convincing analyses of qFit's performance in selected test cases. This manuscript will be of interest to structural biologists and protein biochemists, since the adoption of qFit in structural refinement may lead to new mechanistic insights into protein function.

eLife assessment

Urofacial syndrome is a rare early-onset lower urinary tract disorder characterized by variants in HPSE2, the gene encoding heparanase-2. This study provides a useful proof-of-principle demonstration that AAV9-based gene therapy for urofacial syndrome is feasible and safe at least over the time frame evaluated, with restoration of HPSE2 expression leading to re-establishment of evoked contraction and relaxation of bladder and outflow tract tissue, respectively, in organ bath studies. The evidence is, however, still incomplete. The work would benefit from evaluation of additional replicates for several endpoints, quantitative assessment of HPSE2 expression, inclusion of in vivo analyses such as void spot assays or cystometry, single-cell analysis of the urinary tract in mutants versus controls, and addressing concerns regarding the discrepancy in HPSE2 expression between bladder tissue and liver in humans and mice.

eLife assessment

This important study develops a machine learning method to reveal hidden unknown functions and behavior in gene regulatory networks by searching parameter space in an efficient way. The evidence for some parts of the paper is still incomplete, needing systematic comparison to other methods and to the ground truth, but the work will nevertheless be of broad interest to anyone working in biology of all stripes, since the ideas put forward by the authors extend beyond gene regulatory networks to revealing hidden functions in any complex system with many interacting parts.

eLife assessment

Despite the importance of long-lived plasma cells (LLPCs), particularly for the infection and vaccination field, it is still unclear how they acquire their longevity. With a solid genetic approach, the authors demonstrate quite convincingly a requirement for chemokine/chemokine receptor-mediated interaction in LLPC longevity. The data are very valuable for the development of new types of vaccines.

eLife assessment

This study presents an important finding on the molecular mechanism for transduction of environmentally induced polyphenism. The evidence supporting the claims of the author is incomplete due to limited sample sizes and inadequate analysis. This paper would be of interest to those studying aphids wing dimorphism.

eLife assessment

This important study presents a new quantitative imaging pipeline that describes with high temporal precision and throughput the movements of late-stage Drosophila embryos, a critical moment when motion first appears. A new approach is used to explore the role of miRNAs in motion onset and presents solid evidence that shows a role for miR-2b-1 and its target Motor in embryonic motion. The data are well supported even if the mechanistic insight into the emergence of movement remains to be explored.

eLife assessment

The study makes a valuable empirical contribution to our understanding of visual processing in primates and deep neural networks, with a specific focus on the concept of factorization. The analyses provide convincing evidence that high factorization scores are correlated with neural predictivity. This work will be of interest to systems neuroscientists studying vision and could inspire further research that ultimately may lead to better models of or a better understanding of the brain.

eLife assessment

This important study assesses a novel in silico neoantigen prediction algorithm combined with in vivo validation to determine important parameters of neoantigen immunogenicity and tumor control. The strength of evidence is compelling. This study contributes to the field and will aid in the development of improved personalized cancer vaccines.

eLife assessment

This study presents a valuable finding on sperm flagellum and HTCA stabilization. The evidence supporting the authors' claims is incomplete. The work will be of broad interest to cell and reproductive biologists working on cilium and sperm biology.

eLife assessment

This manuscript highlights single-stranded DNA exo- and endo-nuclease activities of ExoIII as a potential caveat and an underestimated source of decreased efficiency in its use in biosensor assays. The data present solid evidence for the ssDNA nuclease activity of ExoIII and identifies residues that contribute to it. The findings are useful, but some aspects in the study remain incomplete.

eLife assessment

The study offers a compelling molecular model for the organization of rootlets, a critical organelle that links cilia to the basal body, ensuring proper anchoring. While previous research has explored rootlet structure and organization, this study delivers an unprecedented level of resolution, valuable to the centrosome and cilia field. This research marks a significant step forward in our understanding of rootlets' molecular organization.

eLife assessment

Hepatocellular carcinoma (HCC) is a particularly aggressive form of cancer, with an increasing number of treatment options approved for use in patients over the past decade. However, the biology of HCC and identifiable therapeutic targets have not been as clear, even in the era of molecular oncology. Likewise, the cellular biology of HCC, including the role of intercellular communication, has not been well elucidated. In this compelling study, Dantzer et al. provide fundamental insight into the role of beta-catenin on intercellular communication occurring via extracellular vesicles, with implications for immune evasion in a cancer increasingly being treated using immuno-oncologic agents.

eLife assessment

The study elucidates a detailed molecular mechanism of the initial stages of transport in the medically relevant Na+-coupled GABA neurotransmitter transporter GAT1 and thus generates useful new insights into this protein family. In particular, it presents convincing evidence for the presence of a "staging binding site" that locally concentrates Na+ ions to increase transport activity, whilst solid evidence for how Na+ binding influences larger scale dynamics.

eLife assessment

In this potentially important study, the authors report results of QM/MM simulations and kinetic measurements for the phosphoryl-transfer step in adenylate kinase. The results point to the mechanistic proposal that the transition state ensemble is broader in the most efficient form of the enzyme (i.e., in the presence of Mg2+ in the active site) and thus a different activation entropy. With a broad set of computations and experimental analyses, the level of evidence is considered solid by some reviewers. On the other hand, there remain limitations in the computational analyses, especially regarding free energy profiles using different methodologies and the activation entropy, leading some reviewers to the evaluation that the level of evidence is incomplete.

eLife assessment

This study provides valuable new insights on how a prevailing model of hippocampal sequence formation can account for recent data, including forward and backward sweeps, as well as constant cycling of sweeps across different arms of a T-maze. The convincing evidence presented in support of this work relies on classical analytical and computational techniques about continuous attractor networks.

eLife assessment

This solid study assesses a novel mitochondrial inhibitor in combination with the BCL-2 inhibitor venetoclax, with the aim to increase its activity in acute myeloid leukemia. It provides valuable findings of combinatorial efficacy using preclinical models, confirming the overall importance of targeting oxidative phosphorylation to overcome venetoclax resistance in acute myeloid leukemia, and could be strengthened through mechanistic studies demonstrating drug specificity, pharmacodynamic efficacy studies in vivo to test clinical utility and extended statistical analyses of the results. The study is of interest to hematologists because it addresses a key biomedical issue in acute myeloid leukemia (venetoclax resistance) and provides data regarding the safety and activity of a novel inhibitor of the mitochondrial polymerase addressed in combination with venetoclax.

eLife assessment

This valuable study aims to present a mathematical theory for why the periodicity of the hexagonal pattern of grid cell firing would be helpful for encoding 2D spatial trajectories. The idea is supported by solid evidence, but some of the comparisons of theory to the experimental data seem incomplete, and the reasoning supporting some of the assumptions made should be strengthened. The work would be of interest to neuroscientists studying neural mechanisms of spatial navigation.

eLife assessment

Notch1 is expressed uniformly throughout the mouse endocardium during the initial stages of heart valve formation, yet it remains unclear how Notch signaling is activated in specific regions to induce valve formation. To answer this question, the authors used a combination of in vivo and ex vivo experiments in mice to demonstrate ligand-independent activation of Notch1 by circulation induced-mechanical stress and provide partially convincing evidence for stimulation of a novel mechanotransduction pathway involving post-translational modification of mTORC2 and Protein Kinase C (PKC) upstream of Notch1. While these findings represent an important advance in our understanding of Notch1-mediated valve formation, data supporting the main claims are incomplete.

eLife assessment

In this fundamental work, the authors demonstrated that maternal choline supplementation improved spatial memory, reduced hyperexcitability, and restored NeuN expression in a familial Alzheimer's disease mouse model. Interestingly, choline deficiency increased mortality, while paradoxically reduced hyperexcitability. Through behavioral, electrophysiological, and histological measures, the authors present convincing evidence supporting the significant role of maternal choline supplementation in protecting hippocampal functions vulnerable to Alzheimer's disease.

eLife assessment

In this important work, a quantitative analysis method for three-dimensional morphogenetic processes during embryonic development is introduced. The proposed method is a pipeline combining several methods, allowing quantitative analysis of developmental processes without cell segmentation and tracking. Upon application of their method, the authors obtain convincing evidence that ascidian gastrulation is a two-step process. This work should be of interest to a broad range of developmental biologists who aim to obtain a quantitative understanding of morphogenesis.

eLife assessment

This important study describes a neural circuit contributing to two behavioral processes affecting pathogen avoidance in the nematode C. elegans. The method used to identify specific contributing neurons is innovative and the experimental evidence supporting the major claims is solid. This study will be of interest to neuroscientists studying behavior, in particular in C. elegans.

eLife assessment

This potentially useful study involves neuro-imaging and electrophysiology in a small cohort of congenital cataract patients after sight recovery and age-matched control participants with normal sight. It aims to characterize the effects of early visual deprivation on excitatory and inhibitory balance in the visual cortex. While the findings are taken to suggest the existence of persistent alterations in Glx/GABA ratio and aperiodic EEG signals, the evidence supporting these claims is incomplete. Specifically, small sample sizes, lack of a specific control cohort, and other methodological limitations will likely restrict the usefulness of the work, with relevance limited to scientists working in this particular subfield.

eLife assessment

This study by Cuaya et al. reveals and characterizes two distinct forms of spike timing-dependent long-term depression (t-LTD) at the synapses between excitatory afferents from lateral (LPP) and medial (MPP) perforant pathways to granule cells (GC) of the dentate gyrus (DG) in mice. The findings are valuable for the field of synaptic physiology and are based on solid electrophysiological data. The study extends current knowledge by elucidating additional plasticity mechanisms at PP-GC synapses, complementing existing literature.

eLife assessment

In this important study, the authors use a genetically engineered mouse model to reveal a tumor suppressive role for focal adhesion kinase in right-sided colon cancer. The evidence in support of the authors' claims is generally solid, although the data supporting the mechanism through which FAK deletion promotes tumorigenesis are incomplete. This work will be of interest to cancer researchers and others studying the biological consequences of tuning signal transduction pathways.

eLife assessment

The findings of this study are valuable as they challenge the dogma regarding the link between lowered bacterial metabolism and tolerance to aminoglycosides. The authors propose that the well-known tolerance to AG of mutants such as those of complexes I and II is not due to a decrease in the proton motive force and thus antibiotic uptake. The results presented here are convincing.

eLife assessment

In this useful study, Wang and colleagues investigate the potential probiotic effects of Bacillus velezensis in a murine model. They provide solid evidence that B. velezensis limits the growth of Salmonella typhimurium in lab culture and in mice, together with beneficial effects on the microbiota. The overall presentation of the manuscript and logical flow requires improvement and the work will be of interest to infectious disease researchers.

eLife assessment

Duan et al analyzed brain imaging data in UKBK and divided structural brain aging into two groups, revealing that one group is more vulnerable to aging and brain-related diseases compared to the other group. Such subtyping could be valuable and utilized in predicting and diagnosing cognitive decline and neurodegenerative brain disorders in the future. This discovery, supported by solid evidence, harbors a substantial impacts in aging and brain structure and function.

eLife assessment

This study presents an important dataset that captures the transition from epiblast to amnion using a novel in vitro model of human amnion formation. The supporting evidence for the authors' claims is convincing. Key strengths of the study include the efficiency and purity of the cell populations produced, a high degree of synchrony in the differentiation process, comprehensive benchmarking with single-cell data and immunocytochemistry from primate embryos, and the identification of critical markers for specific differentiation phases. A notable limitation, however, is the model's exclusion of other embryonic tissues.

eLife assessment

This study investigates plant-microbe interactions for an invasive plant, Ageratina adenophora. The findings are valuable in advancing our understanding of how leaf and soil microbes separately affect its performance, with solid experimental evidence revealing the importance of litter microbes in shaping A. adenophora populations. The work will be of interest to invasion biologists.

eLife assessment

Through a genome-wide screen for functional alternative transcription start sites (TSS) in Arabidopsis, the authors provide evidence for widespread transcription of potential microproteins from previously annotated protein-coding genes. Functional analysis of AtHB2-miP, derived from the C-terminal region of transcription factor AtHB2 and predicted to form non-productive dimers with ATHB2, suggested that this microprotein could affect AtHB2 functions in shade responses, root growth, and iron homeostasis. The work is valuable as a case study of how new microproteins could act to modulate gene regulation in response to environmental change, but the focus on a single gene, the lack of precision in AtHB2-miP measurement and missing controls, and the relatively minor phenotypic effects mean that data supporting microprotein production as a vital regulatory strategy are incomplete.

eLife assessment

This valuable study reports a novel function of ATG14 in preventing pyroptosis and inflammation in oviduct cells, thus allowing smooth transport of the early embryo to the uterus and implantation. However, the data supporting the main conclusion remain incomplete. This work will be of interest to reproductive biologists and physicians practicing reproductive medicine.

eLife assessment

This study is a computational analysis using publicly available deep sequencing datasets and the findings support the models that propose widespread gene transfer amongst DNA viruses. The evidence supporting the claims of the authors is solid, but reproducing the analysis based only on the information as presented in the Materials and Methods would be difficult as the data are currently presented. A Flow chart that details the process would help. This is an almost entirely computational study without experimental evidence but one that has the potential to become a fundamental resource for virus hunters - an activity of increasing importance.

eLife assessment

This study investigates the role of queuosine (Q) tRNA modification in aminoglycoside tolerance in Vibrio cholerae and presents convincing evidence to conclude that Q is essential for the efficient translation of TAT codons, although this depends on the context. The absence of Q reduces aminoglycoside tolerance potentially by reprogramming the translation of an oxidative stress response gene, rxsA. Overall, the findings point to an important mechanism whereby changes in Q modification levels control the decoding of mRNAs enriched in TAT codons under antibiotic stress.

eLife assessment

This study provides valuable new insights into insect cognition and problem-solving in bumblebees. The authors present convincing evidence that bumblebees lack causal understanding in a string-pulling task, although evidence that bumblebees instead use image-matching for this task, which would benefit from further experiments, is currently incomplete.

eLife assessment

This study provides a single-cell atlas for syngnathid fishes (seahorses, pipefishes, and seadragons), a valuable new resource to investigate the molecular basis of the many unique characters that define the pipefish embryo. The findings are generally supported by solid arguments, but whereas the single-cell RNA-sequencing analysis appears to be of good quality, the spatiotemporal expression data only incompletely support the authors' arguments. Additional computational analyses on cell identity and developmental trajectories would allow a deeper examination of the current data from these unconventional model organisms, to provide new insights into understanding the extraordinary adaptations of the Syngnathidae family. If appropriately improved, the work could be of broad interest for evolutionary developmental biology, particularly for fishes.

eLife assessment

This valuable study proposes that protein secreted by colon cancer cells induces cells with Paneth-like properties that favor colon cancer metastasis. The evidence supporting the conclusions is incomplete and would benefit from more direct experiments to test the functional role of Paneth-like cells and to monitor metastasis from colon tumors. The work will be of interest to researchers studying colon cancer metastasis.

eLife assessment

This study makes a connection between cellular metabolism and proteostasis through MAGIC, a previously proposed protein quality control pathway of clearance of cytosolic misfolded and aggregated proteins by importing into mitochondria. The authors reveal the role of Snf1, a yeast AMPK, in preventing the import of misfolded proteins to mitochondria for MAGIC controlled by the transcription factor Hap4, depending on the cellular metabolic status. The key message is important, although the evidence for physiological relevance of MAGIC for overall cellular proteostasis and its molecular regulation by Snf1 remains incomplete.

eLife assessment

This useful paper addresses a novel exercise mimetic agent on muscle exercise and performance. While the data provided are interesting, the evidence is incomplete, as much of it is correlative.

eLife assessment

The paper presents valuable insights into the success of the parasitoid Trichopria drosophilae on Drosophila suzukii, elucidating the importance of both molecular adaptations, such as specialized venom proteins and unique cell types, ecological strategies, including tolerance of intraspecific competition and avoidance of interspecific competition. Through convincing methodological approaches, the authors demonstrate how these adaptations optimize nutrient uptake and enhance parasitic success, highlighting the intricate coordination between molecular and ecological factors in driving parasitization success.

eLife assessment

The authors discuss an effect, "diffusive lensing", by which particles would accumulate in high-viscosity regions – for instance in the intracellular medium. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention. The "lensing effect" discussed is a direct consequence of the choice of the Ito convention without spurious drift which has been discussed before and its adequacy for the intracellular medium is insufficiently discussed and relatively doubtful. Consequently, the relevance of the presented results for biology remain unclear and based on incomplete evidence.

eLife assessment

This important study provides deep insight into a ubiquitous, but poorly understood, phenomenon: synaptic noise (primarily due to failures). Through a combination of theoretical analysis, simulations, and comparison to existing experimental data, this paper makes a compelling case that synapses are noisy because reducing noise is expensive. It touches on probably the most significant feature of living organisms -- their ability to learn -- and will be of broad interest to the neuroscience community.

eLife assessment

This important study reveals the use of an allocentric spatial reference frame in the updating perception of the location of a dimly lit target during locomotion. The evidence supporting this claim is compelling, based on a series of cleverly and carefully designed behavioral experiments. The results will be of interest not only to scientists who study perception, action and cognition but also to engineers who work on developing visually guided robots and self-driving vehicles.

eLife assessment

This valuable study presents a novel analysis of a large human intracranial electrophysiological recording dataset. The study challenges the traditional view that neural responses to word lists exhibit smoothly drifting contexts over time, showing that items just after a boundary have a characteristic response that occurs repeatedly. The evidence is incomplete, however, leaving open the possibility for alternative explanations.

eLife assessment

This study presents valuable intracranial findings on how two types of natural auditory stimuli - speech and music - are processed in the human brain, and demonstrates that speech and music largely share network-level brain activities, thus challenging the domain-specific processing view. The evidence supporting the claims of the authors is solid. The work will be of broad interest to speech and music researchers as well as cognitive scientists in general.

eLife assessment

This important work substantially advances our understanding of episodic memory in individuals with aphantasia, and sheds light on the neural underpinnings of episodic memory and mental imagery. The evidence supporting the conclusions is convincing, including evidence from a well-established interview paradigm complemented with fMRI to assess neural activation during memory recall. The work will be of broad interest to memory researchers and mental imagery researchers alike.

eLife assessment

This manuscript is useful to researchers with an interest in cervical cancers because it provides scRNA-seq data from a diverse cohort of 15 early-stage cervical cancer patients. While the dataset could be of use to the research community, the key claims of the paper around the immunosuppressive microenvironment associated with specific tumour cell clusters (and the properties/importance of those clusters) are incomplete. Additional experiments will be required to substantiate these claims.

eLife assessment

This important work illuminates the dynamics of BRAF in both its monomeric and dimeric forms, with or without inhibitors, combining traditional techniques and sophisticated computational analyses. The evidence presented is convincing and suggests a potential allosteric effect, though substantiating the exact mechanism will require further studies. The work has implications for understanding kinase signaling and the development of potential drug candidates. This study will be of interest to structural biologists, medicinal chemists, and pharmacologists.

eLife assessment

This study presents valuable findings on the ligand- and ion-dependent structural dynamics of a transcriptional riboswitch. The single-molecule data presented are solid and prompts intriguing hypotheses and models, which will undoubtedly stimulate future structural analyses. These findings are of considerable interest to biochemists and biophysicists engaged in the study of RNA structure and riboswitch mechanisms.

eLife assessment

This study presents a valuable finding on the relationship between brain activity related to sustained attention and substance use in adolescence/early adulthood with a large longitudinal dataset. The evidence supporting the claims of the authors is solid, although the inclusion of more details of methods, results, and data analyses would have strengthened the study. The work will be of interest to cognitive neuroscientists, psychologists, and clinicians working on substance use or addiction.

eLife assessment

This interesting study reports that muscle contains fibro-adipogenic progenitor cells (FAPs) that promote regeneration following injury of peripheral neurons. These novel results indicate that several known growth factors are involved in the process of regeneration. This is an important contribution, however the analysis is incomplete since additional experimental data is needed to support the main conclusions.

eLife assessment

Cancer treatments are not just about the tumor - there is an ever-increasing need for treating pain, fatigue, and anhedonia resulting from the disease. Using an implantable oral tumor model in the mouse, the authors provide valuable information showing that nerve fibers are transmitting sensory signals to the brain that reduce pleasure and motivation. These findings are in part supported by anatomical and transcript changes in the tumor that suggest sensory innervation, neural tracing, and neural activity measurements; however, the study is incomplete in its current form.

eLife assessment

The authors show that short bouts of chemical ischemia lead to presynaptic changes in glutamate release and long-term potentiation, whereas longer bouts of chemical ischemia lead to synaptic failure and presumably cell death (which could be confirmed experimentally). This solid work relies on rigorous electrophysiology/imaging experiments and data analysis. It is valuable as it provides new mechanistic details on chemical ischemia, though its implications for ischemic stroke in vivo remain to be determined.

eLife assessment

This important study sheds new light on cargo movement within the Golgi apparatus, challenging the cisternal progression model by providing convincing evidence for a velocity decrease from cis to trans Golgi and variable speeds within cisternae, suggesting a more stable compartmental nature. While these findings propose refinements to the classic model, they prompt further exploration of recent models like rapid partitioning and rim progression, necessitating additional experimental approaches to account for cargo expression variations and HeLa cell-specific effects.

eLife assessment

This important work provides interesting datasets of myofiber differentiation. The evidence supporting the involvement of SRF2 in selected biological processes is convincing, however, additional evidence to pin-point the major action of SRF2 during muscle differentiation is appreciated. The work will be of broad interest to developmental biologists in general and molecular biologists in the field of gene regulation.

eLife assessment

This study describes the application of machine learning and Markov state models to characterize the binding mechanism of alpha-Synuclein to the small molecule Fasudil. The results suggest that entropic expansion can explain such binding. However, the simulations and analyses in their present form are inadequate.

eLife assessment

This valuable study establishes a method for live-cell imaging, tracking, and quantification of Alu elements marking euchromatic regions of the nucleus. The method will help characterize the relationship between chromatin dynamics and transcriptional activity. While the findings are largely consistent with previous reports, characterization of the technique is incomplete and could benefit from additional controls.

eLife assessment

This study provides valuable initial characterization of a verterbrate embryonic system that demonstrates aspects of an optogenetically inducible hyperplasia model. Although the evidence provided is incomplete to conclude that the system is demonstrating tumor initiation from a single cell that is metastasizing that can be quantitatively assessed, the authors propose a mechanism whereby reactivation of re-programming factors correlates with the increased likelihood of a mutant cell undergoing malignant transformation. This work will be of interest to developmental and cancer biologists mainly for the novel genetic tools described.

eLife assessment

The authors show in vitro that TAK1 overexpression reduces tumor cell migration and invasion, while TAK1 knockdown promotes a mesenchymal phenotype and enhances migration and invasion. The work is a valuable addition to the field of tumor biology of esophageal squamous cell carcinoma. Although minor limitations exist, the overall evidence is solid. The data aligns with previous findings by the same researchers and others.

eLife assessment

In the current study, the authors describe how sex and age affect the consequence of traumatic brain injury in Drosophila. They find that females are more sensitive than males, and mated females are sensitive whereas virgin females are not. This fundamental work substantially advances our understanding of how sex-dependent response to traumatic brain injury occurs, by identifying the Sex Peptide and the immune system as modulators of sex differences. The authors provide a compelling set of results, showing that female Sex Peptide signaling in Drosophila adversely affects late-life neurodegeneration after early-life exposure to repetitive mild head injury.

eLife assessment

This manuscript describes an AI-automated microscopy-based approach to characterize both bacterial and host cell responses associated with Shigella infection of epithelial cells. The methodology is compelling and should be helpful for investigators studying a variety of intracellular pathogens. The authors have acquired valuable findings regarding host and bacterial responses in the context of infection, which should be followed up with further mechanistic-based studies.

eLife assessment

This valuable work characterized a new set of small molecules targeting the interaction between ELF3-MED23, with one of the reported compounds representing a promising novel therapeutic strategy, The evidence supporting the conclusions is solid, although including characterization with breast and lung cancer cell models would strengthen the study. This article will be of interest to medical and cell biologists working on cancer and, particularly, on HER2-overexpression cancers.

eLife assessment

This manuscript describes a method for genetic manipulation of Leishmania species which should be sufficiently efficient to enable genome-wide genetic screens. The authors improved numerous aspects of their previously described method, which is based on sequence-specific genome editing to introduce premature stop codons using a CAS9-cytidine deaminase variant. The work is thoroughly described, with convincing data, and will be very important for Leishmania researchers, as well as perhaps suggesting the use of similar approaches in other organisms in which genetic manipulation is challenging.

eLife assessment

This important chronobiological study in mice suggests that light modulated activity of Cdk5 activity on the PKA-CaMK-CREB signaling pathway provides missing molecular mechanistic details to understand light- induced circadian clock phase delays during the early night, but not for phase advances in the morning. The authors provide overall convincing evidence bridging from behavioral to molecular/cellular experiments to neural activity imaging.

eLife assessment

This paper presents H3-OPT, a deep learning method that effectively combines existing techniques for the prediction of antibody structure. This work, supported by convincing experiments for validation, is important because the method can aid in the design of antibodies, which are key tools in many research and industrial applications.

eLife assessment

This important study, using three bioactive compounds as a model, demonstrates that estimating the intake of food components based on food composition databases and self-reported dietary data is highly unreliable. The authors present convincing data showing the differences in the estimated quantile of intake of three bioactive compounds between biomarker and 24-hour dietary recall with food-composition database. The work will be of broad interest to the clinical nutrition research community.

eLife assessment

This useful article provides evidence of the potential neuropathogenicity of Bacillus cereus serovar anthracis in wild chimpanzees. The authors provide an extensive characterization of four chimpanzees that died acutely from anthrax. The study provides incomplete traditional histopathologic evidence of neuroinvasion since the meninges could not be evaluated, which weakens the authors' conclusions. The work will be of interest to infectious disease researchers.

eLife assessment

This valuable biomechanical analysis of kangaroo kinematics and kinetics across a range of hopping speeds and masses is a step towards understanding a long-standing problem in locomotion biomechanics: the mechanism for how, unlike other mammals, kangaroos are able to increase hopping speed without a concomitant increase in metabolic cost. Based on their suggestion that kangaroo posture changes with speed increase tendon stress/strain and hence elastic energy storage/return, the authors imply (but do not show quantitatively or qualitatively) that the greater tendon elastic energy storage/return counteracts the increased cost of generating muscular force at faster speeds and allows for the invariance in metabolic cost. The methods are impressive, but there is currently only limited evidence for increased tendon stress/strain at faster speeds, and the support for any conclusion metabolic energy expenditure is inadequate.

eLife assessment

This important manuscript follows up on previous findings from the same lab supporting the idea that deficits in learning due to enhanced synaptic plasticity are due to saturation effects. Compelling evidence is presented that behavioral learning deficits associated with enhanced synaptic plasticity in a transgenic mouse model can be rescued by manipulations designed to reverse the saturation of synaptic plasticity. In particular, the finding that a previously FDA-approved therapeutic can rescue learning could provide new insights for biologists, psychologists, and others studying learning and neurodevelopment.

eLife assessment

This study conducted fMRI experiments in an inbred rat model of absence seizures. The results provide new information suggesting reduced brain responsiveness during this type of seizure. The reviewers had divergent opinions but on average thought the study was valuable and the conclusions were solid.

eLife assessment

In this manuscript, the authors tested the hypothesis that Aβ42 toxicity arises from its proven affinity for γ-secretases. The authors provide useful findings, showing convincingly that human Abeta42 inhibits gamma-secretase activity. The data will be of interest to all scientists working on neurodegenerative diseases.

eLife assessment

This important study explores infants' attention patterns in real-world settings using advanced protocols and cutting-edge methods. The presented evidence for the role of EEG theta power in infants' attention is solid. The study will be of interest to researchers working on the development and control of attention.

eLife assessment

This valuable manuscript reveals sex differences in bi-conditioning Pavlovian learning and conditional behavior. Males learn hierarchical context-cue-outcome associations more quickly, but females show more stable and robust task performance. These sex differences are related to cellular activation in the orbitofrontal cortex. Although the evidence for the claims is convincing, the claim of sex differences in context-dependent discrimination behaviour is overstated in places. Nevertheless, the results will be of interest to many behavioural neuroscientists, particularly those who investigate sex-specific behaviours.

eLife assessment

This important study shows that a high autism quotient in neurotypical adults is associated with suboptimal motor planning and visual updating after eye movements, suggesting a disrupted efference copy mechanism. The implication is that abnormal visuomotor updating may contribute to sensory overload - a key symptom in autism spectrum disorder. The evidence presented is convincing, with few limitations, and should be of broad interest to neuroscientists at large.

eLife assessment

This study offers a useful advance by introducing a cord blood DNA methylation score for maternal smoking effects, with the inclusion of cohorts from diverse backgrounds. However, the overall strength of evidence is deemed incomplete, due to concerns regarding low exposure levels and low statistical power, which hampers the generalisability of their findings. The study provides an interesting basis for future studies, but would benefit from the addition of more cohorts to validate the findings and a focus on more diverse health outcomes.

eLife assessment

This important manuscript shows that axonal transport of Wnd is required for its normal degradation by the Hiw ubiquitin ligase. These are interesting findings supported by solid data. However, the summary and conclusions are over-interpreted and how Rab11 is involved in Golgi processing or axonal transport of Wnd is not resolved and would require additional experiments to support the claims. Alternatively, the authors should dial back on their interpretation.

eLife assessment

Manley and Vaziri introduce an important new method for brain-wide imaging of cellular activity in zebrafish and provide evidence for the applicability of this technique. They use this method to explore the question of how neural variability gives rise to variability in behavior. The analyses used are mostly convincing, with some central results that are currently incomplete and difficult to interpret.

eLife assessment

This is a potentially valuable study suggesting that neuronal-specific loss of function of the RNA splicing factor Ptbp1 in striatal neurons induces dopaminergic markers and alleviates motor defects in a 6-hydroxydopamine (6-OHDA) mouse model of Parkinson's Disease. If properly replicated, the claims of the manuscript are remarkable and identify a straightforward mechanism with therapeutic relevance for the treatment of motor deficits in Parkinson's Disease. However, while the rescue of motor deficits with Ptbp1 manipulation is solid, the strength of the evidence supporting the induction of a dopaminergic neuronal identity is incomplete. The study nevertheless addresses recent controversial literature on cell reprogramming in Parkinson's Disease and will be of interest to researchers with a focus on the application of gene therapy to rescue neurodegeneration.

eLife assessment

This valuable study provides insights and strategies for assessing laminar structure in vivo in the visual cortex of the macaque monkey with high-density linear electrode arrays. The paper provides solid evidence demonstrating that signals in higher frequency bands, related to the discharge of action potentials, are of substantially better use for achieving well-resolved cortical layer identification than are signals in lower frequency bands typically associated with local field potentials and standard-practice Current Source Density (CSD) analyses. These findings are of interest to electrophysiologists seeking to make comparisons between cortical layers.

eLife assessment

This important study uses state-of-the-art, multi-region two-photon calcium imaging to characterize the statistics of functional connectivity between visual cortical neurons. The evidence supporting the conclusions is incomplete; currently, alternative interpretations of the results cannot be ruled out. With new analyses strengthening the conclusions, the work would be of broad interest to neuroscientists interested in the visual cortex and inter-area communication.

eLife assessment

The authors expand the concept of a new layer to training immunity, which is currently being highlighted by several colleagues in the field. The work provides important hints to understand end-stage renal disease. Overall, the rational approach leads to experimental results that are solid.

eLife assessment

This important study expands generally upon our understanding of the role of hnRNP proteins in lncRNA function through analysis of ASAR genes that are present on all chromosomes and of profound significance. The findings provide convincing evidence linking ASARs with the phenomenon of RNA retention on chromosomes, including X inactivation, thereby providing an expanded context for studies in these areas. This manuscript will be of interest to researchers studying gene regulation and the interactions and functional roles of hnRNP and lncRNAs.

eLife assessment

The author use an approach that is in principle useful, comparative meta-analysis, to contribute to our understanding of life history evolution. The advance remains limited, as both the meta-analysis and the theoretical model are incomplete, and proper statistical and mechanistic descriptions of the simulations are lacking. A major concern is that the interpretation does not properly take into account the effect of well-characterised complexities in the relationship between clutch size and fitness in birds.

eLife assessment

This valuable paper presents a new protocol for quantifying tRNA aminoacylation levels by deep sequencing. The improved methods for discrimination of aminoacyl-tRNAs from non-acylated tRNAs, more efficient splint-assisted ligation to modify the tRNAs' ends for the following RT-PCR reaction, along with the use of an error-tolerating mapping algorithm to map the tRNA sequencing reads provide new tools for anyone interested in tRNA concentrations and functional states in different cells and organisms. The results and conclusions are solid, with well-designed tests to optimize the protocol under different conditions.

eLife assessment

This useful studying implicates TRPV4 as a mediator of sweat, potentially based on TRPV4's expression and function on sweat glands. The data and methods are solid, with some limitations in terms of the approach. Overall, the work lends new insight into the physiologic basis of sweating using data from mice and humans.

eLife assessment

This study provides a useful set of experiments showing the relative contribution of the Neurodrenergic system in reversing the sedation induced by midazolam. The evidence supporting the claims of the authors is solid, although specificity issues in the pharmacology and neural-circuit investigations narrow down the strengths of the conclusions. After dealing with these limitations, the paper will be of interest to medical biologists working on the neurobiology of anesthesia.

eLife assessment

Münker and colleagues use an optical tweezer setup to apply oscillatory forces to endocytosed/phagocytosed glass beads over a wide frequency range (from ~1 to 1000 Hz) and probe cytoplasmic material properties at multiple time scales in six different cell types. Using statistical methods and principal component analysis, they find that the active and passive mechanical properties of cells can be described by 6 parameters (from power law fits) that allow characterizing the viscous and elastic nature of the cytoplasmic material as well as an effective active energy driven by cellular metabolism. Overall, this is very well done and important work, using convincing and state-of-the-art methods, albeit with some limitations related to the way the beads are internalized.

eLife assessment

This valuable manuscript sets out to identify sleep/arousal phenotypes in larval zebrafish carrying mutations in Alzheimer's disease (AD)-associated genes. The authors provide detailed phenotypic data for F0 knockouts of each of 7 AD-associated genes and then compare the resulting behavioral fingerprints to those obtained from a large-scale chemical screen to generate new hypotheses about underlying molecular mechanisms. The data presented are solid, although extensive interpretation of pharmacological screen data does not necessarily reflect the limited mechanistic data. Nonetheless, the phenotypic characterization presented is comprehensive, and the authors develop a well-designed behavioral analysis pipeline that will provide considerable value for zebrafish neuroscientists.

eLife assessment

This study addresses an important, understudied question using approaches that link molecular, circuit, and behavioral changes. The findings that Netrin-1 and UNC5c can guide dopaminergic innervation from the nucleus accumbens to the cortex during adolescence are solid. The data showing that the onset of Unc5 expression is sexually dimorphic in mice, and that in Siberian hamsters environmental effects on development are also sexually dimorphic are also solid. Reviewers identified significant gaps in evidence for specificity of Netrin-1 expression, which, if filled, would strengthen the evidence for some of the claims. Future work would also benefit from Unc5C knockdown to corroborate the results and investigation of the cause-effect relationship. This paper will be of interest to those interested in neural development, sex differences, and/or dopamine function.

eLife assessment

van Vliet and colleagues show a correlation between internal states of a convolutional neural network (CNN) trained on visual word stimuli with three specific components of evoked MEG potentials during reading in humans. The findings are useful, but the current results remain incomplete, without evidence that the CNN can produce any of the phenomena that the human visual system is known to have (e.g., feedback connections, sensitivity to word frequency), or that the model has comparable performance to human behaviour (i.e., similar task accuracy with a comparable pattern of mistakes).

eLife assessment

This study provides useful insights for anyone focusing on exonic regions when looking into the investigation of DNA fragmentation patterns (fragmentomics) for circulating tumor DNA (ctDNA) data for cancer detection. The method expands the DELFI method of Cristiano and colleagues (2019), but the datasets chosen are not ideal and the analysis remains incomplete.

eLife assessment

Supported by solid evidence, this work provides valuable insights into theanine metabolism and regulation at single-cell resolution. The study paves the way for addressing the multicellular compartmentation of secondary metabolites in various plant systems, making it a valuable resource for future research.

eLife assessment

The authors present an important resource to quantify mitochondrial function across many organs in mice. The convincing conclusions are supported by the identification of processes that specifically differ between young and old, or between male and female mice. All reviewers point to the merit of this study in providing a comprehensive resource to contextualize mitochondrial functions across the body. Some further suggestions are made to clarify conclusions in terms of data normalization, interpretations of comparative analyses between organs.

eLife assessment

This valuable study partially succeeds in providing evidence to support the therapeutic potential of the plant-derived compound eugenol for ameliorating symptoms associated with Type 1 Diabetes, identifying Nuclear factor E2 - related factor (Nrf2) as a mediator of the effects induced by eugenol. Although the study provides some interesting data, the evidence for the proposed mechanism is currently incomplete.

eLife assessment

This valuable simulation study proposes a new coarse-grained model to explain the effects of CpG methylation on nucleosome wrapping energy and nucleosome positioning. The evidence to support the claims in the paper looks solid, although the novelty of the findings should be discussed in connection with the previous works. This work will be of interest to the researchers working on gene regulation and mechanisms of DNA methylation.

eLife assessment

This study presents valuable findings linking circHMGCS1 and miR-4521 in diabetes-induced vascular endothelial dysfunction. The evidence supporting the claims of the authors is solid, but addressing concerns around how certain experiments were performed and controlled could enhance clarity and further strengthen the study. The work will be of interest to biomedical scientists working with cardiovascular and/or RNA biology, particularly those studying diabetes.

eLife assessment

This useful manuscript presents an interesting multi-modal omics analysis of lung adenocarcinoma patients with distinct clinical clusters, mutation hotspots, and potential risk factors identified in cases linked to air pollution. The findings show potential for high clinical and therapeutic impact. However, some of the conclusions are incomplete as they are based on correlative or suggestive findings, and would benefit from further functional investigation and validating approaches.

eLife assessment

This valuable work provides novel insights into the substrate binding mechanism of a tripartite ATP-independent periplasmic (TRAP) transporter. The structural analysis is convincing, but evidence to support some of the conclusions regarding the mechanism is incomplete. This study will be of interest to the membrane transport and bacterial biochemistry communities.

eLife assessment

This important manuscript presents several structures of the Kv1.2 voltage-gated potassium channel, based on state-of-the-art cryoEM techniques and algorithms. The authors present solid evidence for structures of DTX-bound Kv1.2 and of Kv1.2 in potassium-free solution (with presumably sodium ions bound within the selectivity filter). These structures advance our knowledge of the molecular basis of the channel inactivation process.

eLife assessment

This structural and biochemical study of the mouse homolog of acidic mammalian chitinase (AMCase) enhances our understanding of the pH-dependent activity and catalytic properties of mouse AMCase, and it sheds light on its adaptation to different physiological pH environments. The methods and analysis of data are solid, providing several lines of evidence to support the development of mechanistic hypotheses. While the findings and interpretation will be valuable to those studying AMCase in mice, the broader significance, including extension of the results to other species including human, remain less clear.

eLife assessment:

This paper characterises a novel gene (Spar), and presenting valuable findings in the field of insect biology and behaviour. The experiments are well designed, with attention to detail, showcasing the potential of the Drosophila melanogaster model and the use of online resources. The mixed approach presents a convincing argument for a genetic interaction between Alk and Spar.

eLife assessment

Receptor tyrosine kinases such as ALK play critical roles during appropriate development and behaviour and are nodal in many disease conditions, through molecular mechanisms that weren't completely understood. This manuscript identifies a previously unknown neuropeptide precursor as a downstream transcriptional target of Alk signalling in Clock neurons in the Drosophila brain. The experiments are well designed with attention to detail, the data are convincing, and the findings will be valuable to those interested in events downstream of signalling by receptor tyrosine kinases.

eLife assessment

The authors present evidence suggesting that MDA5 can substitute as a sensor for triphosphate RNA in a species that naturally lacks RIG-I. The key findings are potentially important for our understanding of the evolution of innate immune responses. Compared to an earlier version of the paper, the strength of evidence has improved but it is still partially incomplete due to a few key missing experiments and controls.

eLife assessment

The authors provide compelling evidence that MSP1 inhibition (leading to chromosomal instability or CIN in the cancer cells) increases phagocytosis and that tumors with CIN respond better to macrophage therapeutics. In this important study, they demonstrate particularly impressive survival rates for mouse models of CIN B16 tumors treated with adoptively transferred macrophages, CD47-SIRPα blockade, and anti-Tyrp1 IgG.