eLife assessment

This study presents a computational model to explore how neurostimulation could impact hippocampal theta oscillations. The computational model combines a detailed physiologically realistic hippocampus model and an abstract theta oscillator. The study could provide valuable predictions on pathological changes in this network. The modelling is based on convincing approaches that could be improved with experimental validation in future experiments.

eLife assessment

This paper reports the development of SCA-seq, a new method derived from PORE-C for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. Most of the conclusions are supported by convincing data. SCA-seq has the potential to become a useful tool to the scientific communities to interrogate genome structure-function relationships.

eLife assessment

This important study reports on the dynamics of PKA investigated at the single-cell level in vitro and in epithelia in vivo. Using different fluorescent biosensors and optogenetic actuators, the authors dissect the signaling pathway responsible for PKA waves, finding that PKA activation is a consequence of PGE2 release, which in turn is triggered by calcium pulses, requiring high ERK activity. The evidence supporting the claims is solid. At this stage the work is still partly descriptive in nature, and additional measurements would increase the strength of mechanistic insights and physiological relevance.

eLife assessment

This study has important implications for theoretical proposals concerning how language lateralization affects the lateralization of other cognitive functions. The methods are solid, with an appropriate selection of cognitive control tasks that share homotopic regions of the brain with language, comparing participants with typical and atypical organization of language. The participants included in the study were mainly bilinguals, a population previously reported to have a more bilateral organization of cognitive control regions than monolinguals, limiting the generalizability of the results to the general population. Despite this limitation, the results will be of interest to researchers working of brain plasticity and development, in addition to those interested in language and cognitive control.

eLife assessment

This paper presents important findings into the response of epithelial monolayers to the combined effects of surface curvature and hydraulic stress, offering insights into how these cues contribute to epithelial cell extrusion. Most of the evidence is convincing, relying mainly on a combination of imaging-based techniques. This paper is of interest to a broad and growing community of biologists, biophysicists, and engineers interested in cell-geometry interactions.

eLife assessment

The authors use a combination of structural and MD simulation approaches to characterize phospholipid interactions with the pentameric ligand-gated ion channel, GLIC. The general agreement between structures and simulations increases confidence in the description of the lipid interaction poses and provides a solid basis for the prediction of a state-dependent interaction site where lipids could dynamically modulate channel gating. The results will be very useful to understand the nature of phospholipid interactions with pentameric ligand-gated ion channels, although the functional or structural significance of these lipid interactions remains to be verified.

eLife assessment

In this study, neurons were recorded and combined across the parahippocampal area while rats performed a memory-guided spatial navigation task. Sophisticated analytical tools were used to provide convincing evidence that neuronal populations in these areas show behavior-related changes that might indicate the encoding of errors by the system. The valuable results suggest that rate remapping is a likely mechanism to support changes in representations that support memory-guided behavior in these regions, most interestingly in neurons that code head direction.

eLife assessment

This is a potentially important study that deals with the toxic effects of an intermediary in lipid degradation [trans-2-hexadecenal (t-2-hex)] in yeast through modification of mitochondrial protein import via the TOM complex. However, in the current version, the claims are incompletely supported by the data. Lacking is evidence that Tom40 is a direct target of the lipid derivative or causally implicated in the described consequences. Were such evidence forthcoming, the paper would be interesting to a broad audience of molecular and cell biologists.

eLife assessment

This important study reports on the causal role of the inferior frontal gyrus (IFG) in behavioral control. Transcranial ultrasonic stimulation is used to stimulate the IFG in a stop-signal task. The results are compelling while the analyses remain incomplete and some claims are unsubstantiated.

eLife assessment

This is an important biophysical study combining native mass spectrometry with mutant cycles to estimate the thermodynamic components of lipid A binding to the ABC transporter MsbA. Solid evidence supports the binding energies for lipid-protein interactions to MsbA using this approach, which could be later applied to other membrane proteins in general.

eLife assessment

This manuscript characterized signaling pathways for growth control and aflatoxin production in the important plant pathogen Aspergillus flavus. Associating tor and tapA with the control of aflatoxin production would be important. However, the copy number of the tor and tapA genes needs to be more clearly established, and without such work, the evidence remains incomplete.

eLife assessment

This study presents valuable insights into the evolution of the gasdermin family, making a strong case that a GSDMA-like gasdermin that was activated by caspase-1 cleavage was already present in early land vertebrates. Convincing biochemical evidence is provided that extant avian, reptile, and amphibian GSDMA proteins can still be activated by caspase-1 and upon cleavage induce pyroptosis-like cell death - at least in human cell lines. The caspase-1 cleavage site is only lost in mammals, which use the more recently evolved GSDMD as a caspase-1 cleavable pyroptosis inducer. The work will be of considerable interest to scientists working on the evolution of cell death pathways, or on cell death regulation in non-mammalian vertebrates.

eLife assessment

This important research uses an elegant combination of protein-protein biochemistry, genetics, and microscopy to demonstrate that the novel bacterial protein FipA is required for polar flagella synthesis and binds to FlhF in multiple bacterial species. This manuscript is convincing, providing evidence for the early stages of flagellar synthesis at a cell pole; however, the protein biochemistry is incomplete and would benefit from additional rigorous experiments. This paper could be of significant interest to microbiologists studying bacterial motility, appendages, and cellular biology.

eLife assessment

This important study characterizes various cell populations and describes a developmental trajectory using snRNAseq data, highlighting the cell state transitions including periosteal stem cells during bone repair. However, there was a general consensus that the evidence provided is currently incomplete, necessitating the additional data and a more thorough verification of the conclusions. Despite this, the work provides a helpful resource that will be of broad interest to the bone community.

eLife assessment

This valuable study investigates the implementation of an efference copy mechanism in the visual flight control system of Drosophila, a topic of broad interest to sensorimotor neuroscientists. Although the behavioral data and computational analysis are solid, the lack of physiological data, as well as the absence of flight saccades in the model, provide incomplete support for the paper's conclusions.

eLife assessment

The work by O'Reilly and Delis is important to extend the synergy ideas using methods from signal processing and information theory to cluster muscles and task parameters, thereby advancing our understanding of the modular architecture of motor control. The method is innovative, and the findings are compelling from theoretical and practical perspectives. The work will be of broad interest to motor control and neural engineering researchers.

eLife assessment

This study presents valuable new structures of a carbamylation-mimetic K125E mutant of the Cx26 gap junction channel uncovering the cytoplasmic loop structure and information about the closed state of the channel. The cryo-EM maps are in high quality and serve as strong foundations for dissecting the gating mechanism by CO2. However, incomplete functional studies fall short of supporting the proposed mechanism of gap junction channel modulation through carbamylation.

eLife assessment

This important study identifies candidate mitochondrial metabolite carriers in stramenopile protists that may allow these divergent eukaryotes to maintain a compartmentalized glycolytic pathway. This study fills a gap in our understanding of glycolysis evolution and opens avenues for drug design to combat stramenopile parasites. The evidence, based on phylogenetic analysis, thermostability shift assays, and in vitro reconstitution of transport reactions, is convincing, albeit lacking direct in vivo confirmation of the physiological function of these candidates.

eLife assessment

This fundamental study provides insight into the fascinating process of self- and non-self-recognition in the protist Tetrahymena thermophila, a species with seven distinct mating types. Using an elegant combination of phenotypic assays, protein studies, and imaging, the authors present convincing evidence that a large multifunctional protein complex at the cell surface mediates both self- and non-self mating-type recognition. This study extends our understanding of how more than two mating types/sexes may be specified in a species, and it will be relevant for anyone interested in sexual systems and cell-cell communication.

eLife assessment

This valuable study demonstrates the requirement of a DEAD-box helicase DDX6 for the cotranslational mRNA decay pathway in human cells. The authors performed a set of solid experiments, combining DDX6 KO cells with reporter assay and global analysis of mRNA stability/translation efficiency. Although some conclusions drawn by the authors need a more careful examination of alternative possibilities, this study will be of broad interest to RNA biologists working on translational control and mRNA stability.

eLife assessment

In this valuable paper, the authors use an existing theoretical framework relying on information theory and maximum entropy inference in order to quantify how much information single cells can carry, taking into account their internal state. They reanalyze experimental data in this light. Despite some limitations of the data, the study convincingly highlights the difference between single-cell and population channel capacities. This result should be of interest to the quantitative biology community, as it contributes to explaining why channel capacities are apparently low in cells.

eLife assessment

This study provides useful insights into the subcellular localization, interaction with integrins, and functional importance of the cell surface receptor Piezo1 in migrating human T-cells. Whether Piezo1 is critically sensing mechano-physical cues during T-cell migration is however not well supported by direct experimental evidence. The data collected is solid otherwise.

eLife assessment

This important study uses the novel light sheet imaging technique to investigate how different TLR4 agonists regulate Myddosome formation. The data showing that LPS and A-beta can control the kinetic and size of Myddosome assembly are compelling. This work would further benefit from establishing the linkage between these results and downstream signal efficiency. With this aspect strengthened, this paper would be of great interest to the innate immunity field.

eLife assessment

Following small molecule screens, this study provides convincing evidence that 7,8 dihydroxyflavone (DHF) is a competitive inhibitor of pyridoxal phosphatase. These results are important since they offer an alternative mechanism for the effects of 7,8 dihdroxyflavone in cognitive improvement in several mouse models. This paper is also significant due to the interest in the phosphatases and neurodegeneration fields.

eLife assessment

Therapeutic treatments for congenital and acquired craniofacial (CF) bone abnormalities are not well developed. This study provides convincing evidence for an innovative regenerative treatment for pediatric craniofacial bone loss using Jagged1-PEG-MAL hydrogel with pediatric human bone cells. The report is a valuable advance in this field.

eLife assessment

TRPV4 is a unique cation channel that has been demonstrated to play a role in a variety of sensory processes. The authors provide useful new data to indicate that TRPV4 activation occurs in eccrine gland cells. They then show that temperature-dependent perspiration is TRPV4-dependent in mouse skin. This provides new insight, but the data are incomplete in that more orthogonal assays could be used to more comprehensively support the conclusions.

eLife assessment

This so-far most comprehensive, spatially resolved in 2D, dynamical, multicellular model of murine muscle regeneration after injury is is an attempt to combine many contributors to muscle regeneration into one coherent calibrated framework. It has the potential to be a very valuable tool in the areas of tissue morphogenesis, regenerative therapies, quantitative modeling and simulation. However, the presentation of the experimental validation is incomplete.

eLife assessment

This study offers useful insights into the structural architecture of the mammalian egg-sperm fusion synapse, shedding light on the role of specific proteins in fertilization. The strength of the findings lies in the potential identification of a pentameric complex involved in gamete fusion by utilizing a new multimer structure prediction tool, AlphaFold Multimer. The absence of experimental validation weakens the strength of evidence supporting these claims and leaves this work incomplete.

eLife assessment

This study presents a valuable model for the emergence of planar cell polarity from the interplay of local interactions and global gradient. The framework of this model is solid, although the appreciation of its result should in places be more quantitative. A quality of this model is its simplicity and its convenience for experimental testing.

eLife assessment

This useful study introduces the development of Salmonella infection model in zebrafish embryos as an important model to study the interaction between macrophages and Salmonella during in vivo infection. Overall, the data presented are convincing and provide an inventory of genes mediating macrophage cell-cell adhesion and interactions that are useful for dissecting tissue macrophage responses and heterogeneity during intracellular bacterial infection. This is important to characterize the infection outcome and the dynamics of the immune response. The work will be of interest to microbiologists.

eLife assessment

This paper makes a valuable contribution to approaches to studying the stimulus selectivity of sensory neurons. The imaging data that forms the core of the paper is compelling, but the evidence for some of the conclusions reached is limited. A central issue is a reliance on linear measures of stimulus selectivity, which may miss key aspects of retinal coding.

eLife assessment

This valuable study addresses both commonly accepted and alternative hypotheses for the mechanism by which an intercrop supports pest control in push-pull agriculture, a promising and broadly recognized approach for sustainable intensification. The findings address a widely recognized gap in data on the mechanism underlying push-pull systems and thus can be important for work on pest control in agroecology as well as plant-herbivore interactions more generally. The support of claims is solid, combining observations of several different mechanistic aspects in an uncommonly broad range of relevant environments with clear reasoning regarding experimental design, but also using some non-standard approaches that are not as well explained, complicating comparisons to the current state of the art.

eLife assessment

This paper is of interest to a broad audience of cell biologists, and researchers who work in cell death and the role of NETosis in the pathogenesis of chronic diseases. This study presents valuable new insights to support NETosis plays an important role in the development of aristolochic acid nephropathy (AAN). A series of compelling experiments using in vivo and in vitro model supported that AAN induced NET formation via IL-19-IL20-beta receptor can induce inflammation and cell death. This new knowledge of the interaction between kidney cells and neutrophils could have clinical implications in the treatment of AAN.

eLife assessment

In this manuscript the authors describe the expression and regulatory function of a self-cleaving ribozyme in the Cpeb3 gene. This is an important study because although many self-cleaving ribozymes have been identified in the genome, the functions of these RNA enzymes even for molecular control of their target genes is mostly unknown. The manuscript provides solid data for the molecular function of the ribosome in gene regulation and its role in hippocampal learning. The study will be of interest to neurobiologists who study gene regulatory mechanisms in learning.

Universal Summarizer

(Summary generated with Kagi's Universal Summarizer.)

Bandcamp has operated as an online music store for over a decade, providing artists and labels with an easy-to-use platform to sell music directly to fans. While receiving little mainstream attention, Bandcamp has paid out $270 million to artists and maintained a simple, artist-focused design. The platform allows free streaming but encourages direct purchases from artists. Chance the Rapper has been a notable champion of Bandcamp, using it for early mixtapes and helping to bring attention to its role in supporting independent musicians. While other services focus on algorithms and playlists, Bandcamp prioritizes direct artist support through low fees and transparent sales data. It has changed little over the years but provides a niche alternative for direct fan-artist connections without the culture-diluting aspects of other streaming services. Bandcamp's low-key approach has helped it avoid issues faced by competitors while continuing to innovate for artists.

eLife assessment

The finding that Fusicoccin (FC-A) promotes locomotor recovery after spinal cord injury is supported by solid data, and the idea of harnessing small molecules that may affect protein-protein interactions to promote axon regeneration is valuable. The evidence showing that 14-3-3 and spastin interact and that 14-3-3 enhances spastin function and stability in cells is also solid.

eLife assessment

This valuable paper examines gene expression differences between male and female individuals over the course of flower development in the dioecious angiosperm Trichosantes pilosa. Male-biased genes evolve faster than female-biased and unbiased genes, which is frequently observed in animals, but this is the first report of such a pattern in plants. In spite of the limited sample size, the evidence is mostly solid and the methods appropriate for a non-model organism. The resources produced will be used by researchers working in the Cucurbitaceae, and the results obtained advance our understanding of the mechanisms of plant sexual reproduction and its evolutionary implications: as such they will broadly appeal to evolutionary biologists and plant biologists.

eLife assessment

The authors present useful findings on the use of a Drosophila behavioral paradigm for assessing different fly genetic models of neurodegeneration. The experimental design and analyses are solid and can be used for quick behavioral assessment in fly models of various neurodegenerative diseases, especially those having an impact on locomotion. The work will be of interest to Drosophila biologists using behavior as a readout for their studies.

eLife assessment

This valuable study reports the induction of supernumerary inner hair cells in the mouse cochlea upon reducing the expression level of a tight-junction protein (claudin-9). However, the evidence supporting the claims is incomplete and the work would be strengthened by adding several control experiments, resolving inconsistencies and imprecisions in the presentation of the results, and providing more mechanistic insight. The work will be of interest to scientists working in the development and regeneration of hair cells in the inner ear.

eLife assessment

This important study used a new double knockout mouse model to investigate the role of two neuropeptides, substance P and CGRPa, in pain signaling. There is convincing evidence that double knockout of these two molecules, both of which have historically been associated with pain, does not affect nociception or acute pain behaviors in males and females. The conclusions would further benefit from additional validation of the approach, consideration of potential outliers and statistical approach in cases with smaller sample sizes, and consideration of the potential for opposing effects across region or peptide. This paper will be of interest to those interested in the neurobiology of pain and/or neuropeptide function.

eLife assessment

Yang et al. investigate whether distinct sources of conflict are represented in a common cognitive space. The study uses an interesting task that mixes different sources of difficulty and reports that the brain appears to represent these sources as a mixture on a continuum in prefrontal areas. While the findings could be valuable to theory in this area, there are concerns with the analysis, design and results, that raise uncertainty regarding the main conclusion of a shared cognitive space. Thus, the evidence reported here ranges from solid to incomplete.

eLife assessment

This work is of fundamental significance to the field of nervous system development as it advances our mechanistic understanding of axon guidance. The rigorous biochemical and genetic approaches are compelling, experiments are well-controlled, and the major claims are supported by convincing data. The study should be of general interest to the developmental neurobiology community.

eLife assessment

These ingenious and thoughtful studies present important findings concerning how people represent and generalise abstract patterns of sensory data. The issue of generalisation is a core topic in neuroscience and psychology, relevant across a wide range of areas, and the findings will be of interest to researchers across areas in perception, learning, and cognitive science. The findings have the potential to provide compelling support for the outlined account, but there appear other possible explanations, too, that may affect the scope of the findings but could be considered in a revision.

eLife assessment

This valuable study links the "taste" of botanicals to their application as medicines used by the ancient Greco-Roman society. The authors used phylogenetic linear mixed models in a Bayesian framework to test the relationships between taste qualities, intensities, complexities, and therapeutic use. The evidence supporting the conclusions is solid, although there is a minor weakness concerning the somewhat inconsistent method of botanical preparation and presentation to the taster panelists; subjective bias and robustness of the participants' responses might have been overlooked. The study may be of broad interest to pharmacologists and scientists working on drug discovery, particularly those interested in natural products.

eLife assessment

This fundamental study provides compelling evidence to explain how chemical variations within a set of kinase inhibitors drive the selection of specific Erk2 conformations. Conformational selection plays a critical role in targeting medically relevant kinases such as Erk2 and the findings reported here open new avenues for designing small molecule inhibitors that block the active site while also steering the population of the enzyme into active or inactive conformations. Since protein dynamics and conformational ensembles are essential for enzyme function, this work will be of broad interest to those working in drug development, signal transduction, and enzymology.

eLife assessment

This valuable study reports on a new tool that allows for light-controlled protein degradation in Escherichia coli. With the improved light-responsive protein tag, endogenous protein levels can be reduced severalfold. The methodology is convincing and will be of interest to the fields of gene expression regulation in bacteria and, more generally to synthetic biologists.

eLife assessment

This work shows for the first time that the balance of mTOR (mTORC1 and mTORC2) in Sertoli cells regulates the rate of sperm epigenetic aging. The manuscript presents valuable findings that have some theoretical and practical implications. The strength of the evidence is however incomplete: they are limited in some places and the aims are not always fully supported by the results.

eLife assessment

The main idea tested in this work is that host galectin-9 inhibits Mycobacterium tuberculosis (Mtb) growth by recognizing the Mtb cell wall component arabinogalactan (AG) and, as a result, disrupting mycobacterial cell wall structure. Moreover, a similar effect is achieved by anti-AG antibodies. While the hypothesis is intriguing and the work has the potential to make a valuable contribution to Mtb therapy, the evidence presented is incomplete and does not explain several critical points including the dose-independent effect of galectin-9 on Mtb growth and how anti-AG antibodies and galectin-9 access the AG layer of intact Mtb.

eLife assessment

This study offers a useful advance by introducing a cord blood DNA methylation score for maternal smoking effects, with the inclusion of diverse cohorts. However, the overall strength of evidence is deemed incomplete, due to concerns regarding low exposure levels, low statistical power, potential overfitting, and the need for clearer descriptions of statistical methods. Building more directly from the existing evidence base, exploring differences between ancestries, and considering additional health outcomes would help to enhance the study.

eLife assessment

This study presents a valuable finding on the impact of metformin-induced shifts in gut microbial community structure and metabolite levels for drug efficacy in a mouse model of liver injury. The current evidence supporting the claims of the authors is incomplete, although inclusion of additional controls and a revision to clarify the reviewer's methodological concerns could strengthen the study. With revision, this paper could be of broad interest to researchers across multiple disciplines, including the microbiome, liver disease, and pharmacology.

eLife assessment

In this important manuscript, the authors used unbiased approaches to identify somatic mutations in publicly available databases that would disrupt clinically approved antibodies targeting HER2. Using a solid combination of both computational and experimental approaches they identify mutations that could restore therapeutic antibody sensitivity in a series of disease-relevant model systems. Additional cell-based and in vivo assays would strengthen the work and increase the translational and potential clinical relevance of the proposed work.

eLife assessment

This important study presents the validation of an oral delta9-tetrahydrocannabinol (THC) consumption mouse model utilizing highly palatable e-capsule gelatin. The results convincingly demonstrate that oral consumption produced THC behavioral and physiological effects, as well as measurable brain levels. The utility of the model for chronic consumption remains to be determined. The authors have clearly acknowledged limitations of their model and areas for future study and development. As the field of cannabinoid research moves toward application of routes of administration that mimic human use, these model systems will be pivotal in assessing the effects of cannabinoid-based drugs.

eLife assessment

Focusing mainly on var genes, the investigators performed comprehensive computational analyses of gene expression in malaria parasites isolated from patients and assessed changes that occur as these parasites adapt to in vitro culture conditions. The study provides an improved computational pipeline for monitoring var gene expression, and importantly, the study documents changes in expression of the core genome and thus provides insights into metabolic adaptations that parasites undergo while transitioning to culture conditions. The findings are important for their technical advances that are more rigorous than the current state-of-the-art. The solid data analyses, broadly support the claims with only minor weaknesses, tell us to be cautious when interpreting results obtained only from cultured parasites.

eLife assessment

This valuable study highlights how the diversity of the malaria parasite population diminishes following the initiation of effective control interventions but quickly rebounds as control wanes. The data presented is solid and the work shows how genetic studies could be used to monitor changes in disease transmission.

eLife assessment

The work by Han and collaborators describes valuable findings on the role of Akkermansia muciniphila during ETEC infection. If confirmed, these findings will add to a growing list of beneficial properties of this organism. However, as it stands, the strength of the evidence used to justify the conclusions in the manuscript is incomplete.

eLife assessment

This valuable study introduces a new simulation model to explain the wide-spread occurrence of genetic inversions in fruit-fly genomes, based on sexually antagonistic alleles and a trade-off between male reproduction and survival. The evidence supporting the conclusions is currently incomplete, but it might be possible to address this with additional simulations and experiments as well as more rigorous analysis of the model and the data. The work will be of interest to population geneticists beyond the fruit-fly system.

eLife assessment

The manuscript presents an analysis of different factors that are required for release of the lipid-linked morphogen Shh from cellular membranes., which will be useful in the field. The evidence is still incomplete as experiments rely on over-expression of Shh in a single cell line and are sometimes of a correlative nature. The study confirms and extends previous findings and will be of interest to developmental biologists who work on Hedgehog signaling.

eLife assessment

This study represents a valuable addition to the understanding of the DNA replication origin selection process in the budding yeast. The authors provide convincing evidence that the number of possible origins of replication is much higher than previously appreciated, although many of the newly identified origins are likely to only direct replication initiation rarely. This work will be of interest to those studying DNA replication and investigating protein-DNA interactions across the genome.

eLife assessment

This investigation of the changes in gene expression and some of the physiological consequences of sublethal exposures to the neonicotinoid insecticide imidacloprid in honeybee larvae is useful, although numerous experiments were not considered based on technical issues. The methodological design leads to concerns and it is therefore not obvious that all conclusions are justified. The study adds to our understanding of how this insecticide impacts development and growth of honeybees, but the evidence supporting the major claims is incomplete.

eLife assessment

This important study furthers our understanding of the antimicrobial properties of siderophores, and their potential use to battle opportunistic pathogens. The evidence supporting the conclusion is solid, based on rigorous biochemical, growth, and virulence assays. The work would benefit from a more in-depth discussion of the consequences and efficacy of 'siderophore therapy' in more complex communities/environments. The work will be of broad interest to colleagues in the fields of evolutionary ecology, microbiology, and medical sciences.

eLife assessment

This important study uses an innovative set of reporter assays to probe the role of the TnpB protein in IS608 transposition. The work provides independent support for the recently reported homing activity of TnpB, where the transposon is restored following excision, and suggests an additional function for TnpB in enhancing the transposase activity of the TnpA transposase. The overall approach is solid, but the authors should consider how the activity of the TnpB protein used, or the levels of ωRNA, impact their model.

eLife assessment

The manuscript offers useful descriptive insights into the potential influence of whole-brain lactate and pH levels on the manifestation of behavioral phenotypes seen in diverse animal models of neuropsychiatric disorders. However, reviewers have raised concerns about the potential loss of specificity in capturing regional and cell-type-specific effects when relying solely on whole-brain analysis methods. While the evidence supporting the conclusions is largely solid, the robustness of these conclusions could be enhanced by the inclusion of additional data and further analysis.

Editors Assessment: Antimicrobial resistance (AMR) is a global public health threat, and environmental microbial communities can act as reservoirs for resistance genes. There is a need for genomic surveillance could provide insights into how these reservoirs change and impact public health. With that goal in mind this study tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. On average adaptive sampling resulting in a target composition 4x higher than without adaptive sampling, and increased target yield in most replicates. The methods and scripts for this approach were reviewed and curated together, although the scope of this study was limited in terms of communities tested and AMR genes targeted. And the authors improved their analysis by conducting an additional analysis of a diverse microbial community. Demonstrating the method is reusable and its results are promising for developing a flexible, portable, and cost-effective AMR surveillance tool.

*This evaluation refers to version 1 of the preprint *

eLife assessment

This is a compelling study on pro-inflammatory and anti-inflammatory lipids in relation to skeletal muscle injury. It convincingly identifies pro-inflammatory lipids during recovery predisposing to fibrosis, and maresin 1 as an anti-inflammatory lipid reducing fibrosis, improved muscle regeneration, partially restoring contractile function, of fundamental potential clinical application.

eLife assessment

George et al. present a convincing new Python toolbox ("RatInABox") that allows researchers to generate synthetic behavior and neural data specifically focusing on hippocampal functional cell types (place cells, grid cells, boundary vector cells, head direction cells).

This is valuable for theory-driven research where synthetic benchmarks should be used. Beyond just navigation, it can be highly useful for novel tool development that requires jointly modeling behavior and neural data. The authors provide convincing evidence of its utility with well documented and easy to use code and the corresponding manuscript.

eLife assessment

The authors introduce a potentially valuable novel method that provides trial-by-trial probabilistic estimates of learning and decision-making strategies inferred from choice behavior across species. This approach could prove more useful over traditional techniques for arbitrating between strategies and detecting when learning happens, and because it is computationally lightweight. Reviewers identified several concerns that limit the strength of the evidence provided, rendering the findings incomplete.

eLife assessment

This important study combines disparate results from both psychophysics and neural silencing experiments to suggest a new interpretation of how animals and humans represent and interpret recent events in our memory. A key aspect of the model put forward here is the presence of discrete jumps in neural activity within the posterior parietal region of the cortex. The model is distinct from other models, and the authors provide convincing evidence to support it both from existing results as well as from novel experiments.

eLife assessment

This study reports valuable behavioral and computational observations regarding how passive exposure to auditory stimuli can facilitate auditory categorization. The combination of behavioral results in mice with a study of artificial neural network models provides solid evidence for the authors' conclusions. This paper will likely be of broad interest to the general neuroscience community.

eLife assessment

This paper reports valuable results regarding the potential role and time course of the prefrontal cortex in conscious perception. Although the sample size is small, the results are convincing, and strengths include the use of several complementary analysis methods. The behavioral test includes subject report such that the study does not allow for distinguishing between (phenomenal) awareness and conscious access; nevertheless, results do advance our understanding of the contribution of prefrontal cortex to conscious perception.

eLife assessment

This is a valuable study of Eph-Ephrin signaling mechanisms generating pathological changes in amyotropic lateral sclerosis. There are exciting findings bearing on the role of glial cells in this pathology. The study emerges with solid evidence for a novel astrocyte-mediated mechanism for disease propagation. It may help identify potential therapeutic targets.

eLife assessment

This important manuscript investigates the roles of DKK3 in AD synapse integrity. Although previous work has identified the involvement of Wnt and DKK1 in synaptic physiology, this study provides compelling evidence that suppression of DKK3 rescues the changes in excitatory synapse numbers, as well as memory deficits in an established AD model mice. The authors provide both gain and loss of function data that support the main conclusion and advance our understanding of the mechanisms by which Wnt pathway mediates early synaptic dysfunction in AD models.

eLife assessment

This study provides an important starting point for unraveling the molecular basis of the pathological phenotypes of the repeat expansion in the gene associated with open reading frame 72 in human chromosome 9. The coarse-grained simulation method used by the authors goes beyond the state of the art, investigating a compelling number of binding partners. The evidence supporting the claims of the authors is solid, although experimental validation of the results would strengthen the major conclusions of the work. The work will be of broad interest to biophysicists and biochemists.

eLife assessment

In this important study, Guma and colleagues describe the use of structural neuroimaging to assess the cross-species convergence of sex differences in global and regional brain volumes in humans and mice. The goal of the work is to inform to what extent mouse studies of these aforementioned sex differences have relevance to humans. The authors suggest which aspects of brain anatomy (as measured by volume) are conserved or not, across species, which has theoretical and practical implications beyond a single sub-field. The evidence to support the findings is solid, it uses methods and data analysis that are appropriate and validated.

eLife assessment

This important work advances our understanding of how brains flexibly gate actions in different contexts, based on dynamically reconfiguring neural dynamics in motor circuits. The findings, using analyses of many neurons recorded simultaneously during mouse behavior, as well as causal perturbations, are clear and compelling. This work will be of interest to systems neuroscientists and to researchers studying context-dependent computation generally.

eLife assessment

This manuscript reveals important insights into the role of ipsilateral descending pathways in locomotion, especially following unilateral spinal cord injury. The study provides solid evidence that this method improves the injured side's ability to support weight, and as such the findings may lead to new treatments for stroke, spinal cord injuries, or unilateral cerebral injuries. However, the methods and results need to be better detailed, and some of the statistical analysis enhanced.

eLife assessment

This is an important study that investigates BMP signaling mechanisms in the developing chick cerebellum to better understand germinal layer formation, cellular amplification and neuronal differentiation. The data from human tissue is compelling and lends support to the possible links of these processes to medulloblastoma, although these specific statements could be toned down and presented only as part of the discussion. Overall, this is a solid piece of work with beautifully presented findings.

eLife assessment

The manuscript aims to better understand the mechanisms underlying the behavioral responses of C. elegans to hydrogen sulfide, a toxin known to exert remarkable effects on animal physiology in a range of contexts. To this end, the authors provide a series of useful findings regarding the mechanisms by which hydrogen sulfide may be sensed, their relationships to other gas-sensing pathways, and the role of a variety of physiological pathways in responding to hydrogen sulfide exposure. While some of the findings are solid, other aspects of the paper are incomplete, such that some claims are incompletely supported, and an integrated understanding of the authors' observations does not clearly emerge.

eLife assessment

This potentially valuable study provides some evidence that upregulation of sodium-activated potassium channels contributes to neuronal hyperexcitability and seizures following traumatic brain injury. However, the evidence supporting a direct link is incomplete. This work will be of interest to epilepsy and ion channel researchers.

eLife assessment

This important work provides insight into the activity and spatial organization of synapses during early postnatal development in the mouse visual cortex, using state-of-the-art tools to show that synapses are distributed in co-active clusters well before eye opening. The evidence supporting the claims is convincing, although additional methodological details are needed to fully assess the rigor of the analysis. This work is of particular interest to the field of developmental neuroscience and can also be used by computational neuroscientists studying dendritic integration.

eLife assessment

This fundamental study advances substantially our understanding of sound encoding at synapses between single inner hair cells of the mouse cochlea and spiral ganglion neurons. Dual patch-clamp recordings-a technical tour-de force-and careful data analysis provide compelling evidence that the functional heterogeneity of these synapses contributes to the diversity of spontaneous and sound-evoked firing by the neurons. The work will be of broad interest to scientists in the field of auditory neuroscience.

eLife assessment

This valuable study on the molecular and cellular mechanisms of ingestion avoidance of high salt in insects is focused in scope, but the authors present convincing evidence that a specific subset of gustatory receptors in a pair of pharyngeal taste neurons are necessary and sufficient for avoiding ingestion of high salt during feeding. This work will be of interest to Drosophila neuroscientists interested in taste coding and feeding behavior.

eLife assessment

This work presents an important technological advance, in the form of a high throughput platform for Single Particle Tracking allowing us to measure millions of cells and thousands of compounds per day. Analysis of the diffusional behaviour of fluorescently-tagged targets permits the identification of, and differentiation between, small molecules that bind directly or affect the target indirectly. The evidence provided is compelling, although some methodological information is undisclosed.

eLife assessment

This study presents a valuable finding on the distinct subpopulation of adipocytes during brown-to-white conversion in perirenal adipose tissue (PRAT) at different ages. The evidence supporting the claims of the authors is convincing, although specific lineage tracing of this subpopulation of cells and mechanistic studies would expand the work. The work will be of interest to scientists working on adipose and kidney biology.

eLife assessment

The authors have identified a media condition that maintains iPSCs in suspension cultures by inhibiting the PKCβ and Wnt signaling pathways. The manuscript is valuable for the pluripotent stem cell field. This is a solid study with substantial data to support the conclusions in the manuscript.

eLife assessment

This is an important study that develops a method to fluorescently label peptide MHC complexes on live dendritic cells to enable detection of antigen specific T cells in polyclonal populations. Solid evidence that this can be used to effectively identify antigen specific T cells in vitro and in vivo is provided for one model antigen systems (Ova-OTII). The approach has exciting potential as prior single step methods with directly conjugated single peptides have generally failed due to high background. Thus, this approach potentially moves the state of the art forward, but further work is needed to realise and determine the limits and ultimate utility of the approach.

eLife assessment

The study presents a valuable finding on sexually-dimorphic patterns of osteocyte transcriptomics and low calcium diet-induce bone loss. The evidence supporting the claims of the authors regarding the protective role of Irisin/FNDC5-deficiency in lactation and low-calcium diet in female mice is incomplete, due to the relatively modest phenotypes observed and the insufficient link between Irisin/FNDC5 and calcium homeostasis or milk production.

eLife assessment

This important study provides novel strategies to overcome certain limitations when investigating the metabolism of hematopoietic stem cells, mainly due to their low abundance. The study provides compelling evidence suggesting that proliferative hematopoietic stem cells mainly use glycolysis (rather than mitochondrial OXPHOS or TCA cycle) as their primary energy source during emergency hematopoiesis. The article provides direct links between metabolic features and cell proliferation and explores alternative energy sources, and is of great interest to stem cell biologists.

eLife assessment

This is a useful study that shows changes in the chromatin landscape of GABAergic neurons in induced pluripotent stem cells (iPSCs) derived from both Dravet Syndrome (DS) patients and healthy donors. The strength of the evidence is currently incomplete because the authors compared iPSCs from different individuals, rather than isogenic controls, and they did not examine the expression of the gene and encoded protein (SCN1A or Nav1.1) that are thought to be responsible for the majority of DS cases in these iPSCs. The work would be of interest to scientists who study development, developmental disorders, and epigenetic contributions to disease.

eLife assessment

The delineation of MBOAT function is important with theoretical and practical implications in MAFLD, alcohol-induced hepatic steatosis, and lysosomal diseases. The strength of evidence is convincing using methodology in line with current state-of-the-art, with good support for the claims.

eLife assessment

The significance of this work is important in that the authors propose a novel method to therapeutically harness myeloid cells which can be otherwise immunosuppressive and hamper T cell and immunotherapy responses. The strength of evidence is convincing but requires critical pieces of in vivo work to validate the therapeutic efficacy of this approach.

eLife assessment

This important work presents data showing that all non-proneural phenotypes of the Inhibitor of DNA binding (Id) protein emc are mediated through inappropriate non-apoptotic caspase activity. Using the developing Drosophila retina as a model the authors convincingly show that emc acts by transcriptionally regulating the Death-Associated Inhibitor of Apoptosis 1 (diap1) gene, which impacts on Notch signaling by caspase-dependent increase of Delta protein. These findings are interesting for the caspase/apoptosis field as they add more non-apoptotic functions of caspases to the list, as well as for the Id field, which examines how Id proteins inhibit cell differentiation.

Summary

1. 📚 Second Edition Overview: This is the second, revised and expanded edition of the book. The first edition was titled "Como Fazer Anotações Inteligentes. Uma Técnica Simples para Impulsionar a Escrita, Aprendizado e Pensamento - para Estudantes, Acadêmicos e Escritores de Livros de Não Ficção".

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6. 👤 Author's Background: Written by Dr. Sönke Ahrens, a writer and researcher in education and social sciences, known for the award-winning book "Experimento e Exploração: Formas de Revelação do Mundo" (Springer).

7. 🌍 Global Reach: Since its initial release, "Como Fazer Anotações Inteligentes" has sold over 10,000 copies and has been translated into seven languages.

eLife assessment

Through a theoretical approach, this study makes important contributions to our understanding of the evolutionary causes of the ageing process. Using a simple individual-based model and computational simulations, the authors provide convincing evidence that ageing can be a trait under natural selection, opening the door for further discussion in the context of lifespan extension research.

eLife assessment

The fundamental study presents a two-domain thermodynamic model for TetR which accurately predicts in vivo phenotype changes brought about as a result of various mutations. The evidence provided is solid and features the first innovative observations with a computational model that captures the structural behavior, much more than the current single-domain models.

eLife assessment

The work is a valuable contribution to understanding the mechanism of nuclear export of tRNA in budding yeast. The authors present solid evidence that Dbp5 functions in parallel with Los1 and Msn5 in tRNA export, in a manner dependent on Gle1 for activation of its ATPase activity but independently of Mex67, Dbp5's partner in mRNA export. It further presents biochemical evidence that Dbp5 can bind tRNA but that Gle1 and InsP6 are required for activating ATP hydrolysis by the Dbp5-tRNA complex, suggesting a possible mechanism for tRNA export by Dbp5.

eLife assessment

This study presents valuable findings on the contrasting responses of two bacteria to the phytoplankton-derived compound azelaic acid. Metabolomics and transcriptomics evidence convincingly shows the assimilation pathway in one marine bacterium and a stress response in a second bacterium. The study provides evidence that azelaic acid can alter marine microbial community structure in mesocosm experiments, though the mechanisms underlying this shift in community structure remain to be explored in future studies.

eLife assessment

This valuable study considers empirical macroecological patterns in microbiome data across multiple taxonomic scales. The work convincingly shows that the Stochastic Logistic Growth model is a more appropriate choice of null model than the neutral theory of biodiversity. The work will be of particular interest to microbial ecologists.

eLife assessment

The findings of this study are valuable as they provide new insights into the role of acetylcholine in modulating sensory processing in the auditory cortex. This paper reports a systematic measurement of cell activity in the auditory cortex before and after the microiontophoretic application of Ach during an oddball and cascade sequence of auditory stimuli. The evidence presented is convincing, as the study used a rigorous experimental design and statistical analysis. The manuscript will interest researchers in auditory neuroscience and neuromodulation, as well as clinicians and individuals with auditory processing disorders.

eLife assessment

This is an important and interesting account of the ability of Ym1 crystals to promote type 2 immunity in vivo, in mice. The data presented are compelling, building on and significantly advancing evidence this group has previously published on the type 2 immunogenicity of other protein crystals. The work will be of relevant interest to immunologists and researchers working on type 2 inflammatory disease, in the lung and in others tissues.

eLife assessment

The paper represents a novel application of recursion theory to the long call vocalisations of orangutans to demonstrate repetitive, rhythmic sub-structuring. The authors use detailed acoustic analyses to show compelling evidence for self-embedded and nested isochronic motifs. These fundamental results have the potential to significantly advance current approaches used to compare nonhuman communication systems with human language.

eLife assessment

This study presents useful observations about how the human brain uses long-term priors (acquired during our lifetime of listening) to make predictions about expected sounds - an open question in the field of predictive processing. However, the evidence as currently presented is incomplete. Both the theoretical background and analysis approach should be strengthened.

eLife assessment

Overall, this is a significant study, and it is able to highlight mast cells in amphibians and their putative capability to respond to and combat fungal infections. Therefore, this study is important for the field. However, the manuscript is incomplete from the standpoint that there is functional data lacking on how these mast cells are activated and their precise functional properties. Such experiments would add substantial impact and rigor and fully support the conclusions.

eLife assessment

This valuable study applies voltage clamp fluorometry to provide new information about the function of serotonin-gated ion channels 5-HT3AR. The authors convincingly investigate structural changes inside and outside the orthosteric site elicited by agonists, partial agonists, and antagonists, helping to annotate existing cryo-EM structures. This work confirms that the activation of 5-HT3 receptors is similar to other members of this well-studied receptor superfamily. The work will be of interest to scientists working on channel biophysics but also drug development targeting ligand-gated ion channels.

eLife assessment

The authors present a comprehensive set of tools to compactly characterize the time-frequency interactions across a network. The utility of the toolbox is compelling and demonstrated through a series of exemplar brain imaging datasets. This fundamental work adds to the repertoire of techniques that can be used to study high-dimensional data.

eLife assessment

This work uses an interdisciplinary approach combining microfluidics, structural biology, and genetic analyses to provide valuable findings that show that pathogenic enteric bacteria exhibit taxis toward human serum. The data are solid and show that the behavior utilizes the bacterial chemotaxis system and the chemoreceptor Tsr, which senses the amino acid L-serine. The work provides an ecological context for the role of serine as a bacterial chemoattractant and could have clinical implications for bacterial bloodstream invasion during episodes of gastrointestinal bleeding.

eLife assessment

This important study contributes insights into the regulatory mechanisms of a protein governing cell migration at the membrane. The integration of approaches revealing protein structure and dynamics provides convincing data for a model of regulation and suggests a new allosteric role for a solubilized phospholipid headgroup. The work will be interesting to researchers focusing on signaling mechanisms, cell motility, and cancer metathesis.

eLife assessment

In this valuable manuscript, Yao et al. describe new methods for assessing the intracellular itinerary of Botulinum neurotoxin A (BoNT/A), a potent toxin used in clinical and cosmetic applications. The current manuscript challenges previously held views on how the catalytic portion of the toxin makes its way from the endocytic compartment to the cytosol, to meet its substrates. The approach taken is deemed innovative and the experiments are carefully performed, however, they are somewhat incomplete with respect to the drawn conclusions, as it is possible that the scope of their findings could be restricted to the specific neuron model and molecular tools that were used. This paper could be of interest to both cell biologists and physicians.

eLife assessment

In this study, camera trapping and species distribution models are used to show that human disturbance in mountain forests in the eastern Himalayas pushes medium-sized and large mammal species into narrower habitat space, thus increasing their co-occurrence. While the collected data provide a useful basis for further work, the study presents incomplete evidence to support the claim that increased co-occurrence may indicate positive interactions between species.

eLife assessment

This fundamental study addresses a long-standing mystery in splicing regulation: does splicing occur co- or post-transcriptionally? The authors provide compelling evidence demonstrating that splicing can occur post-transcriptionally at a transcription site proximal zone, changing the way we think about splicing.

eLife assessment

This is an important study using 3D mapping of neuronal activation throughout the brain after pair-bonding in the monogamous vole, which can be broadly applied to other species and behaviors. The authors provide compelling evidence that there is some synchrony between male and female partners that have formed a pair bond, the strength of which is based on the number of ejaculations received by the female. Same-sex pairs also form a pair bond and were found to have activation in the same brain regions as mixed sex couples. An overall low level of sex differences in the degree and location of brain activation was observed, which was unexpected. This work will be of interest to those interested in social behavior and its neural mechanisms, or brain systems or behavior more broadly.

eLife assessment

This important study reports on an improved deep-learning-based method for predicting TCR specificity. The evidence supporting the overall method is compelling, although the inclusion of real-world applications and clear comparisons with the previous version would have further strengthened the study. This work will be of broad interest to immunologists and computational biologists.

eLife assessment

Studies of synaptic development and plasticity in the nematode C. elegans have been limited by the difficulty of rapid, accurate assessments of synaptic structure. Here, with a series of convincing studies, the authors introduce and validate a valuable computational pipeline, "WormPsyQi," that allows rapid, reproducible quantitation of fluorescent synaptic puncta while minimizing human error and bias. The authors also describe a new set of strains carrying synaptic markers. Together, these tools should provide groups studying this model system with the ability to quantitatively characterize chemical and electrical synapses, even in densely packed regions in 3D space such as the nerve ring.

eLife assessment

The study is of importance for the cardiac modeling field by developing a novel mathematical model with sex difference. The data are compelling, and the model is helpful for mechanistic understanding, and thus is also important for experimental physiology. The model is based on experimental data and validated against some experimental data.

eLife assessment

The important work by Aballay et al. significantly advances our understanding of how G protein-coupled receptors (GPCRs) regulate immunity and pathogen avoidance. The authors provide convincing evidence for the GPCR NPR-15 to mediate immunity by altering the activity of several key transcription factors. This work will be of broad interest to immunologists.

eLife assessment

BMP signaling plays a vital role in skeletal tissues, and the importance of its role in microtia prevention is novel and promising. This important study will shed light on the role of BMP signaling in preventing microtia in the ear. Solid data broadly support the claims with only minor weaknesses.