- Feb 2025
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study reports a detailed computational analysis of the CFTR ion channel's permeation mechanism, advancing our understanding of its structure-function relationship. The conclusions are based on extensive molecular dynamics simulations and thorough analysis, but the use of an approximate chloride ion model, known to underestimate key ion-protein interactions, leaves them incomplete without experimental or alternative computational validation. The work will be of interest to biophysicists working on CFTR and cystic fibrosis.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Rennert et al. developed a valuable thermodynamic framework to study the force response of branched actin networks from the crucial and unexplored perspective of energetic cost. They used the fact that the entropy production rate must be positive to derive inequalities that set limits on the maximum force produced by branched actin networks, and speculate that the dissipative cost beyond that required to move the load may be necessary to maintain an adaptive steady state. This work is highly innovative, but remains incomplete until the hypotheses of the model are better justified and the conclusions about the dissipative cost of the system are better established.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents a potentially fundamental analysis of the original color of a fossil feather from the crest of a 125-million-year-old enantiornithine bird, using sophisticated 3D microscopic and numerical methods to conclude that the feather was iridescent and brightly colored, possibly indicating that this was a male bird that used its crest in sexual displays. At present, the strength of evidence supporting the authors' conclusions is considered incomplete based on methodological incompleteness and questions about taphonomy.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This fundamental manuscript comprehensively examines the roles of nine structural proteins in herpes simplex virus 1 (HSV-1) assembly and nuclear egress. By integrating cryo-light microscopy and soft X-ray tomography, the study presents an innovative approach to investigating viral assembly within cells. The research is thoroughly executed, yielding compelling data that explain previously unknown functions of these structural proteins. This work is of broad interest to virologists, cellular biologists, and structural biologists, offering a robust, contextually rich methodology for studying large protein complex assembly within the cellular environment, serving as an excellent starting point for high-resolution techniques.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides important insights into the regulation of type-I interferon signaling and anti-tumor immunity, demonstrating that ORMDL3 promotes RIG-I degradation to suppress immune responses. The evidence is convincing, with well-executed mechanistic experiments and in vivo validation in syngeneic tumor models. These findings have significant implications for cancer immunotherapy, highlighting ORMDL3 as a potential therapeutic target.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study addresses an important and longstanding question regarding the molecular mechanism of protein misfolding in Ig light chain (LC) amyloidosis (AL), a life-threatening condition. By combining advanced techniques, including small-angle X-ray scattering, molecular dynamics simulations, and hydrogen-deuterium exchange mass spectrometry, the authors provide convincing evidence that the "H state" distinguishes amyloidogenic from non-amyloidogenic LCs. These findings not only offer novel insights into LC structural dynamics but also hold promise for guiding therapeutic strategies in amyloidosis and will be of particular interest to structural biologists, biophysicists, and many others working on amyloid diseases.
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eLife Assessment
This study addresses an important and longstanding question regarding the molecular mechanism of protein misfolding in Ig light chain (LC) amyloidosis (AL), a life-threatening condition. By combining advanced techniques, including small-angle X-ray scattering, molecular dynamics simulations, and hydrogen-deuterium exchange mass spectrometry, the authors provide convincing evidence that the "H state" distinguishes amyloidogenic from non-amyloidogenic LCs. These findings not only offer novel insights into LC structural dynamics but also hold promise for guiding therapeutic strategies in amyloidosis and will be of particular interest to structural biologists, biophysicists, and many others working on amyloid diseases.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors present three transgenic models carrying three representative exon deletions of the dystrophin gene. The findings presented are valuable to the field of muscle diseases, particularly muscular dystrophies. The evidence provided in the manuscript is convincing, with rigorous biochemical assays and state-of-the-art microscopy methods.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable work provides solid evidence that a neuronal metallothionein, GIF/MT-3, incorporates metal-persulfide clusters. A variety of well-designed assays support the authors' hypothesis, revealing that sulfane sulfur is released from MT-3. The biological role of the persulfidated form is not yet clearly defined. There are caveats to the findings that limit the study, but the work will nevertheless prompt major follow-up work.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This fundamental article significantly advances our understanding of FGF signalling, and in particular, highlights the complex modifications affecting this pathway. The evidence for the authors' claims is convincing, combining state-of-the-art conditional gene deletion in the mouse lens with histological and molecular approaches. This work should be of great interest to molecular and developmental biologists beyond the lens community.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this valuable report, the authors investigated the effect of mitochondrial transplantation on post-cardiac arrest myocardial dysfunction (PAMD), which is associated with mitochondrial dysfunction. They convincingly demonstrated that mitochondrial transplantation enhanced cardiac function and increased survival rates after the return of spontaneous circulation (ROSC). They have also shown that myocardial tissues with transplanted mitochondria exhibited increased mitochondrial complex activity, higher ATP levels, reduced cardiomyocyte apoptosis, and lower myocardial oxidative stress post-ROSC.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
These useful findings assigned a novel functional implication of histone acylation, crotonylation. Although the mechanistic insights have been provided in great detail regarding the role of the YEATS2-GCDH axis in modulating EMT in HNC, the strength of evidence for the manuscript is incomplete. The patient cohort is very small, with just 10 patients; to establish a significant result the cohort size should be increased. Furthermore, the functional implication of p300 is also to be looked into.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this important study, the authors advance our understanding of copper uptake by chalkophores and their targeted metalloproteins in Mycobacterium tuberculosis. These convincing data demonstrate that chalkophore-acquired copper is solely incorporated into the Mtb bcc:aa3 copper-iron respiratory oxidase under low copper conditions, and that chalkophore-mediated protection of the respiratory chain is critical to Mtb virulence. These findings may be leveraged for drug discovery and will be of broad interest to those studying bacterial pathogenesis.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript reports fundamental discoveries on how necrotic cells contribute to organ regeneration through apoptotic signalling to produce cells with non-lethal apoptotic caspase activity that contribute to the regenerated tissue. These findings will be of broad interest to those who study wound repair and tissue regeneration. The strength of the evidence is solid and has been improved in the revised version.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript establishes a mathematical model to estimate the key parameters that control the repopulation of planarian stem cells after sublethal irradiation as they undergo fate-switching as part of their differentiation and self-renewal process. The findings are valuable for future investigation of stem cell division in planarians. The methods are solid, integrating modeling with perturbations of key transcription factors known to be critical for cell fate decisions, but the authors have only shown that this is the case for a small number of stem cell types.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides evidence that single-cell multi-omics profiling can reveal key regulators of HIV-1 persistence and early immune dysregulation, particularly implicating KLF2 and Th17 cells as major players in viral reservoir dynamics. The findings are solid, supported by rigorous integration of scRNA-seq and scATAC-seq data, but are limited by sample size and lack of validation with external datasets. Overall, this work makes a valuable contribution to understanding HIV-1 immune evasion and highlights potential therapeutic targets for reservoir eradication.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study describes a software package in R for visualizing metabolite ratio pairs. The evidence supporting the claims of the authors is solid and broadly supports the authors' conclusions. This work would be of interest to the mass spectrometry community.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides valuable information on the single nucleus RNA sequencing transcriptome, pathways, and cell types in pig skeletal muscle in response to conjugated linoleic acid (CLA) supplementation. Based on the comprehensive data analyses, the data are considered compelling and provide new insight into the mechanisms underlying intramuscular fat deposition and muscle fiber remodeling. The study contributes significantly to the understanding of nutritional strategies for fat infiltration in pig muscle.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study reveals that disrupting fatty acid metabolism in macrophages significantly restricts the growth of Mycobacterium tuberculosis, showing that impaired lipid processing triggers various antimicrobial responses. Overall, the approach is robust, utilizing CRISPR-Cas9 knockout of multiple genes involved in lipid metabolism which yielded convincing data. This work highlights how host lipid metabolism affects the ability of tubercle bacilli to thrive intracellularly, pointing to potential new therapeutic targets.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript establishes a mathematical model to estimate the key parameters that control the repopulation of planarian stem cells after sublethal irradiation as they undergo fate-switching as part of their differentiation and self-renewal process. The findings are important for future investigation of stem cell division in planarians and have implications for analyzing stem cell biology in other systems. The methods are convincing, integrating modeling with perturbations of key transcription factors known to be critical for cell fate decisions, but the authors have only shown that this is the case for a small number of stem cell types.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important and well-written study uses functional neuroimaging in human observers to provide compelling evidence that activity in the early visual cortex is suppressed at locations that are frequently occupied by a task-irrelevant but salient item. This suppression appears to be general to any kind of stimulus and also occurs in advance of any item actually appearing. The work will be of great interest to psychologists and neuroscientists examining attention, perception, learning and prediction.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable work presents how PRDM16 plays a critical role during colloid plexus development, through regulating BMP signaling. Solid evidence supports the context-dependent gene regulatory mechanisms both in vivo and in vitro. The work will be of broad interest to researchers working on growth factor signaling mechanisms and vertebrate development.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors utilize a valuable computational approach to exploring the mechanisms of memory-dependent klinotaxis, with a hypothesis that is both plausible and testable. Although they provide a solid hypothesis of circuit function based on an established model, the model's lack of integration of newer experimental findings, its reliance on predefined synaptic states, and oversimplified sensory dynamics, make the investigation incomplete for both memory and internal-state modulation of taxis.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study examines the role of pericytes in patterning the zebrafish blood-brain barrier (BBB) and controlling its permeability. Using pdgfrb mutant zebrafish models lacking brain pericytes, the authors report that pericyte-deficient cerebrovasculatures are ill-patterned, yet display unaltered restrictive BBB permeability properties at larval and juvenile stages. More severe phenotypes are detected in adults, with focal leakage sites associated with hemorrhages and aneurysms. Using solid and beautifully documented imaging, the authors suggest that, contrary to the situation described in rodent models, pdgfrb-dependent pericytes are not required to maintain the BBB in the zebrafish brain; these unexpected and intriguing findings reshape our understanding of BBB permeability regulation in vertebrates.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important manuscript proposes a new strategy for the identification of new mechanisms of drug resistance based on SAturated Transposon Analysis in Yeast (SATAY), a powerful transposon sequencing method in Saccharomyces cerevisiae. This method allows us to uncover loss- and gain-of-function mutations conferring resistance to 20 different antifungal compounds. The method is convincing, allowing the authors to identify a novel interaction of chitosan with the cell wall mannosylphosphate, and show that the transporter Hol1 concentrates the novel antifungal ATI-2307 within yeast.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study seeks to examine the relationship between pupil size and information gain, showing opposite effects dependent upon whether the average uncertainty increases or decreases across trials. Given the broad implications for learning and perception, the findings will be of broad interest to researchers in cognitive neuroscience, decision-making, and computational modelling. Nevertheless, the evidence in support of the particular conclusion is at present incomplete - the conclusions would be strengthened if the authors could both clarify the differences between model-updating and prediction error in their account and clarify the patterns in the data.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study analyzes a large dataset of Salmonella gallinarum whole-genome sequences and provides findings regarding the population structure of this avian-specific pathogen. The convincing results indicate regional adaptation of the mobilome-driven resistome and a role in the evolutionary trajectory of this pathogen that will interest microbiologists and researchers working on genomics, evolution, and antimicrobial resistance.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this valuable study, Tutak and colleagues set out to identify factors that mediate Repeat Associated Non-AUG (RAN) translation of CGG repeats in the FMR1 mRNA which are implicated in toxic protein accumulation that underpins ensuing neurological pathologies. The authors provide solid evidence that RPS26 may be implicated in mediating the RAN translation of FMR1 mRNA. This article should be of broad interest to researchers in the variety of disciplines including post-transcriptional regulation of gene expression and neurobiology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study uses a massive and long-term experimental data set to provide solid evidence on how tree diversity affects host-parasitoid communities of insects in forests. The work will be of interest to ecologists working on biodiversity conservation, community ecology, and food webs.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study provides new insights into the mechanisms that underlie perceptual and attentional impairments of conscious access. The paper presents convincing evidence of a dissociation between the early stages of low-level perception, which are impermeable to perceptual or attentional impairments, and subsequent stages of visual integration which are susceptible to perceptual impairment but resilient to attentional manipulations. This study will be of interest to scientists working on visual perception and consciousness.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important 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 authors address most reviewer concerns in their revised version, providing invaluable new analyses. Phenotypic characterization presented is comprehensive, and the authors develop a well-designed behavioral analysis pipeline that will provide considerable value for zebrafish neuroscientists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study examined how multidimensional social relationships influence social attention in rhesus macaques, linking individual and group-level behaviors to attentional processes. The findings that oxytocin altered social attention and its relationship to both social tendencies and dyadic relationships are important, as recent technological advances allow for the exploration of neuronal activities and mechanisms in free-moving macaques. This work is convincing and will be of interest to those studying the interplay between social dynamics and information processing in primates.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study reveals a novel mechanism of glutamine synthetase (GS) regulation in Methanosarcina mazei, demonstrating that 2-oxoglutarate (2-OG) directly promotes GS activity by stabilizing its dodecameric assembly. Using mass photometry, activity assays, and cryo-electron microscopy, the authors show that GS transitions from a dimeric, inactive form at low 2-OG concentrations to a fully active dodecameric complex at saturating 2-OG levels, highlighting 2-OG as a key effector in C/N sensing. The findings are valuable, supported by solid data, and provide new insights into archaeal GS regulation, though further clarification of interactions with known partners like Glnk1 and sp26 is needed.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important paper reports functional interactions between L1TD1, an RNA binding protein (RBP), and its ancestral LINE-1 retrotransposon which is not modulated at the translational level. The evidence for the association between L1TD1 and LINE-1 ORF1p is solid. The work implies that the transposon-derived RNA binding protein in the human genome can interact with the ancestral transposable element from which this protein was initially derived. This work spurs interesting questions for cancer types, where LINE1 and L1TD1 are aberrantly expressed.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The study reports valuable findings from a very rich EEG-fMRI dataset including 107 participants, which was collected during nocturnal naps. The authors link activity in memory-related brain regions (e.g., hippocampus, thalamus, and medial prefrontal cortex), and their functional connectivity, to the occurrence of canonical sleep rhythms, namely spindles and slow oscillations in non-rapid eye movement sleep. This work could contribute to further understanding of sleep neural dynamics, although the evidence for some of the main claims is incomplete at present.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors use deep mutational scanning to assess the effect of ~6,600 protein-coding variants in MC4R, a G protein coupled receptor associated with obesity. They develop new, more precise approaches to deep mutational scanning, enabling them to probe molecular phenotypes directly relevant to the development of drugs that target this receptor. In this important work, the authors provide compelling evidence that variants impact signaling through MC4R in different ways, that some defective variants are amenable to a corrector drug and that deep mutational scanning data could guide compound optimization.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript describes an important study of the giant virus Jyvaskylavirus. The characterisation presented is compelling. The work will be of interest to virologists working on giant viruses as well as those working with other members of the PRD1/Adenoviridae lineage.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript presents solid evidence suggesting that the loss of ZNRF3 and RNF43, two E3 ubiquitin ligases, leads to dysregulation of EGFR signaling in cancer. The authors propose that EGFR is a direct substrate of ZNRF3/RNF43. While the authors provide immunoprecipitation data showing increased detection of ubiquitinated species, this evidence does not definitively establish that EGFR itself is ubiquitinated by RNF43/ZNRF3. The absence of direct evidence for EGFR ubiquitination is a major limitation, although the findings are useful as they may provide novel insights into the mechanisms underlying EGFR-driven cancers and open new therapeutic avenues.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript presents a clever and powerful approach to examining differential roles of Nav1.2 and Nav1.6 channels in excitability of neocortical pyramidal neurons, by engineering mice in which a sulfonamide inhibitor of both channels has reduced affinity for one or the other channels. Overall, the results in the manuscript are compelling and give important information about differential roles of Nav1.6 and Nav1.2 channels. Activity-dependent inactivation of NaV1.6 was also found to attenuate seizure-like activity in cells, demonstrating the promise of activity-dependent NaV1.6-specific pharmacotherapy for epilepsy.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study provides a novel framework for leveraging longitudinal field observations to examine the effects of aging on stone tool use behaviour in wild chimpanzees. However, the analysis and interpretation are currently incomplete and would benefit from a more robust consideration of additional sources of variance for the data (e.g., foraging ecology, nut and tool properties, etc.). Despite the low sample size of five individuals, this study is of broad interest to ethologists, primatologists, archaeologists, and psychologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The conclusions of this work are based on valuable simulations of a detailed model of striatal dopamine dynamics. Establishing that a lower dopamine uptake rate can lead to a 'tonic' level of dopamine in the ventral but not dorsal striatum, and that dopamine concentration changes at short delays can be tracked by D1 but not D2 receptor activation, is of value and will be of interest to dopamine aficionados. However, the simulations are incomplete, providing only partial support for the key claims. Several things can be done to strengthen the conclusions, including, for example, but not exclusively, a demonstration of how the results would change as a function of changes in D2 affinity.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study provides convincing evidence that specific proteins on the surface of cancer cells undergo a particular form of recycling and are redirected toward the cell-cell contact with T cells, a type of immune cell. However, the characterization of the consequences of T cell activation resulting from perturbing the recycling pathway is incomplete. Furthermore, relevant literature has not been sufficiently cited.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents valuable insights into the role of two proteins, Rab27A and SYTL5, which control vesicle transport and delivery. While the data is clear, the overall evidence is somewhat incomplete. Strengthening the mechanistic aspect would enhance the study, making it of greater interest to cell biologists studying membrane trafficking and mitochondria.
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eLife Assessment
This important study characterizes the mechanics and stability of bolalipids from archaeal membranes using molecular dynamics simulations. A mesoscale model of bolalipids is presented and evaluated across a series of membrane configurations. The evidence supporting the conclusions is convincing, demonstrating that mixtures of bolalipids and regular bilayer lipids in archaeal membranes enhance fluidity and stability.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study explores the commander-independent function of COMMD3-Arf1 in endosomal recycling. The evidence supporting the authors' claims is solid; however, the inclusion of additional validation experiments and control conditions would have further strengthened the study. The findings will be of significant interest to cell biologists working on membrane trafficking.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript makes a valuable contribution to the field by uncovering a molecular mechanism for miRNA intracellular retention, mediated by the interaction of PCBP2, SYNCRIP, and specific miRNA motifs. These findings advance our understanding of RNA-binding protein-mediated miRNA sorting and provide deeper insights into miRNA dynamics. While the conclusions are supported by solid experimental evidence, additional controls and clarification of the precise intracellular interactions would further strengthen the study.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study explores the conserved role of IgM in both systemic and mucosal antiviral immunity in teleosts, challenging established views on the differential roles of IgT and IgM. The findings have theoretical and practical implications for immunology and aquaculture. However, the strength of the evidence is incomplete due to insufficient validation of the monoclonal antibodies used to deplete IgM, which limits confidence in the main claims. Addressing these methodological weaknesses would significantly enhance the study's impact.
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eLife Assessment
This study reveals that PRMT1 overexpression drives tumorigenesis of acute megakaryocytic leukemia (AMKL) and that targeting PRMT1 is a viable approach for treating AMKL. While the evidence, based largely on one cell line, is convincing, further validations in additional experiment settings will solidify the conclusion. These findings have important implications for the treatment of AMKL with PRMT1 over expression in the future.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This useful study reports analyses of Neuropixel recordings in the medial prefrontal cortex and hippocampus of rats in a spatial navigation trial, focusing on classifying prefrontal neurons based on SWR modulation and anatomical location. However, the evidence for claims of a clear link between SWR modulation and neuronal encoding, and the evidence for anatomical organization, is currently incomplete. Further analyses might strengthen the evidence for some conclusions, and some of the strong claims of the paper should likely be moderated.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Using electrophysiological recordings in freely moving rats, this valuable study investigates the role of different gamma frequency bands in the development of spatial representations in the hippocampus. Solid evidence supports the idea that gamma-modulated neurons are crucial for generating specific neuronal sequences. These findings will be of interest to neuroscientists studying spatial navigation and neuronal dynamics.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The Twin Domain model proposed by Lui and Wang proposing that twin supercoiling domains of DNA emerge during transcription were first described decades ago, but direct experimental evidence has been challenging to obtain. Here, the authors make a fundamental contribution by directly measuring DNA torsion in cells using a photoactivatable intrastrand cross-linker compared to controls. They gather compelling data using this clever method, which provides direct evidence in support of the twin-supercoiled domain model, for torsional effects at transcription start and end sites, and thereby uncover novel features of higher order structure of chromatin in yeast. These data are exciting, and the tools will be of interest to anyone studying chromosome structure and gene regulation.
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arxiv.org arxiv.org
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eLife Assessment
This useful paper uses a quantitative modeling approach to explore a putative mechanism underlying a well-studied behavioral transition in the nematode C. elegans. The premise, that what has been considered a two-state behavior can instead be described as a process whose parameters are smoothly modulated within a single state, is intriguing. However, in the paper's current state, concerns about the model and its fit to empirical data make the support for this idea inadequate.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The study presents valuable findings on the molecular mechanisms of glucose-stimulated insulin secretion from pancreatic islets, focusing on the main regulatory elements of the signaling pathway in physiological conditions. While the evidence supporting the conclusions is solid, the study can be strengthened by the use of a beta cell line or knockout mice. The work will be of interest to cell biologists and biochemists working on diabetes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This paper presents miniML, an AI-based framework for the detection of synaptic events. Benchmark results presented in the paper are compelling, demonstrating the superiority of miniML over current state-of-the-art alternatives. The performance of miniML is demonstrated across various experimental paradigms, showing that miniML has the potential to become a valuable tool for the analysis of synaptic signals.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript describes a novel approach for assessing cognitive function in freely moving mice in their home-cage, without human involvement. The authors provide convincing evidence in support of the tasks they developed to capture a variety of complex behaviors and demonstrate the utility of a machine learning approach to expedite the acquisition of task demands. This work is important given its potential utility for other investigators interested in studying mouse cognition. However, additional information (e.g., detailed construction manual, code) is needed to allow other investigators to implement this system independently and use it widely.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors have undertaken a useful study to update an existing niche model of highly pathogenic avian influenza. However, there are issues regarding the conceptualisation of the ecological niche of highly pathogenic avian influenza transmission that the modelling aims to capture, raising concerns about the strength of evidence used to support the findings. There are a number of modelling assumptions that are incompletely justified. Combined with shortcomings in the communication, this dilutes the strength of the key findings of this work.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides valuable findings on the effects of mating experience on sweet taste perception. The data as presented provide solid evidence that the dopaminergic signaling-mediated reward system underlies this mating state-dependent behavioral modulation. The work will interest neuroscientists, particularly those working on neuromodulation and the effects of internal states on behavior.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This useful study presents a virtual reality-based contextual fear conditioning paradigm for head-fixed mice. The approach provides a way to perform multiphoton imaging of neural circuits during behaviors that have traditionally been studied in freely moving animals. However, evidence supporting key claims is currently incomplete, particularly regarding elicitation and detection of freezing behaviors, and the impact of the study would be increased by articulating what this initial exploration of parameters offers over existing approaches.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents a valuable finding regarding how partner preference formation and pair bonding behavior are related to the oxytocin receptor gene expression in the NAc and paraventricular nucleus of the hypothalamus in prairie voles. The evidence supporting this claim is solid but could benefit from clarity in the framing, approach, and results. This study will be of interest to social scientists and neuroscientists who work on pair bonding and oxytocin.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This multimodal neuroimaging study leverages fMRI, PET, and deep learning to predict memory performance. The authors introduce the brain-cognition gap to link these different imaging modalities to cognition and evaluate their results in two independent cohorts. The results are a valuable addition to the literature and will be of interest to neuroscientists working at the interface of cognition, neuroimaging, and computational modeling. However, the evidence supporting the conclusions remains incomplete.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is a well-written important paper on the recovery of fauna and flora following the end-Permian extinction event in several continental sites in northern China. The convincing conclusion, a rapid recovery in tropical riparian ecosystems following a short phase of hostile environments and depauperate biota, is supported by an impressive amount of data from sedimentology, body fossils of animals and plants, and especially trace fossils.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The manuscript addresses the 3D chromatin architecture in monocytes from patients with alcohol-associated hepatitis and its relationship to enhanced transcription of innate immune genes. While the concept and methodological approach are appealing, the evidence is incomplete as a result of insufficient sample sizes as well as other significant analytical concerns.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study combined whole-head magnetoencephalography (MEG) and subthalamic (STN) local field potential (LFP) recordings in patients with Parkinson's disease undergoing deep brain stimulation surgery. The paper provides convincing evidence that cortical and STN beta oscillations are sensitive to movement context.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study by Wong et al. addresses a longstanding question in the field of associative learning regarding how a motivationally relevant event can be inferred from prior learning based on neutral stimulus-stimulus associations. The research provides convincing behavioral and neurophysiological evidence to address this question. The manuscript will be interesting for researchers in behavioral and cognitive neuroscience.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important work investigates the mechanism that underlies the switch between feeding and mating behaviors in the oriental fruit fly, Bactrocera dorsalis. Using a variety of approaches, the authors show that this switch is mediated by the neuropeptide, sulfakinin, acting peripherally through the sulfakinin receptor 1 to regulate the expression of antennal odorant receptors. The evidence is solid in support of the hypothesis that sulfakinin signaling mediates changes in the periphery, although additional sites of action may also contribute to these changes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important work combines molecular genetics and behavioral analyses to identify inhibitory neurons in the female medial preoptic area as a neural locus that is activated following male ejaculation and whose prolonged activity plays a key role in the regulation of female sexual motivation. These experiments are rigorous and well-performed. The data are compelling and demonstrate that a subpopulation of neurons in the medial preoptic area are selectively activated following the completion of mating in females. The medial preoptic area has long been implicated as critical to sexual behavior in both sexes; however the use of a self-paced mating assay for females provides fine control over manipulating and monitoring cellular activity in this region during more naturalistic behavior. In addition, this study may act to inspire others to further explore the additional brain regions found to show upregulation of neural activity (Fos) during mating completion in females using the datasets generated here.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Yamamoto and Matano provide convincing evidence that a G63E/R CD8+ T-cell escape mutation in the accessory viral protein Nef promote the induction of neutralizing antibody (nAb) responses in rhesus macaques infected with SIVmac239, which is usually largely resistant to neutralization. Functional analyses support that this mutation specifically impairs Nef`s ability to stimulate PI3K/Akt/mTORC2 signalling. This important study suggests that the accessory viral protein Nef impairs B cell function and effective humoral immune responses and is of interest for researchers and physicians interested in HIV/AIDS and vaccine development.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study presents data suggesting the critical roles of two ancient proteins, XAP5 and XAP5L, in regulating the transcriptional program of ciliogenesis during mouse spermatogenesis. The supporting data are solid, and this work will be of interest to biomedical researchers studying ciliogenesis and reproduction.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study employed multiple orthogonal techniques and tissue samples to investigate the interaction between the NRL transcription factor and RNA-binding proteins in the retina. The findings are convincing to support an interaction between NRL and the DHX9 helicase. The significance of the study could be enhanced with functional experiments of NRL-R-loop interactions in the developing retina and their potential role in photoreceptor health and gene regulation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study is a valuable contribution to the field of neuronal modeling by way of providing a method for rapidly obtaining neuronal physiology parameters from electrophysiological recordings. While the approach seems promising, in its current form it is incomplete since the generated models often diverge from the data and the comparison with existing methods has concerns.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents valuable findings on the role of the small GTPase Rab3A in homeostatic plasticity. While the study demonstrates that Rab3A is required for homeostatic scaling, the evidence supporting the model put forward by the authors is incomplete. The work will be of interest to researchers in the field of synaptic transmission and plasticity.
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www.biorxiv.org www.biorxiv.org
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Evaluation Statement (5 February 2025)
Pannexin (Panx) channels are a family of poorly understood large-pore channels that mediate the release of substrates like ATP from cells, yet the physiological stimuli that activate these channels remain poorly understood. The preprint by Henze et al. describes an elegant approach wherein activity-guided fractionation of mouse liver led to the discovery that lysophospholipids (LPCs) activate Panx1 and Panx2 channels expressed in cells or reconstituted into liposomes. The authors provide evidence that LPC-mediated activation of Panx1 is involved in joint pain and that Panx1 channels are required for the established effects of LPC on inflammasome activation in monocytes, suggesting that Panx channels play a role in inflammatory pathways. Overall, this important study reports a previously unanticipated mechanism wherein LPCs directly activate Panx channels.
Biophysics Colab recommends this study to scientists investigating phospholipids, Panx channels, purinergic signalling and inflammation.
Biophysics Colab has evaluated this study as one that meets the following criteria:
- Rigorous methodology
- Transparent reporting
- Appropriate interpretation
(This evaluation refers to version 3 of this preprint, which has been revised in response to peer review of versions 1 and 2.)
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides valuable information on a novel gene that regulates meiotic progression in both male and female meiosis. The evidence supporting the conclusions of the authors is solid. This study will be of interest to developmental and reproductive biologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study identifies a new key factor in orchestrating the process of glial wrapping of axons in Drosophila wandering larvae. The evidence supporting the claims of the authors is convincing and the EM studies are of outstanding quality. However, the quantification of the wrapping index, the role of Htl/Uif/Notch signaling in differentiation vs growth/wrapping, and the mechanism of how Uif "stabilizes" a specific membrane domain capable of interacting with specific axons might require further clarification or discussion. The work will be of interest to neuroscientists working on glial cell biology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this important study, the authors test the model that a type of vascular lesion caused by the inactivation of one gene in the cells that line blood vessels requires the activity of a second gene for the lesions to form. The evidence supporting the conclusions is solid.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This comprehensive scRNAseq atlas of the cranial region during neural induction, patterning, and morphogenesis provides a fundamental demonstration of how different cell fates are organized in specific spatial patterns along the anterior-posterior and medial-lateral axes within the developing neural tissue. The compelling data are analyzed with a rigorous computational approach, and the data revealed both known and novel genes differentially expressed along rostro-caudal and medio-lateral axes. This will be a helpful resource for researchers studying brain development.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This fundamental work demonstrates the importance of considering overlapping modes of functional organization (i.e. gradients) in the hippocampus, showing associations with aging, dopaminergic receptor distribution and episodic memory. The evidence supporting the conclusions is convincing, although not all analyses were performed in a replication sample. The work will be of broad interest to basic and clinical neuroscientists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors present an valuable and intriguing observation challenging current views on DNA methylation dynamics, revealing earlier-than-expected de novo methylation with significant implications for gene regulation in early embryonic development. However, the study's significance is difficult to ascertain due to incomplete evidence supporting the conclusions. Moreover, the observed changes in DNA methylation across promoter regions is modest, leaving its relevance open to alternative interpretations.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is a valuable study of the role that life history differences might play in determining population size and demography. While concerns about generation times and population structure leave the evidence for the claims in parts incomplete, the work is of considerable interest to anyone who tries to understand evolutionary consequences of life history changes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This fundamental study further validates DNAH12 as a causative gene for asthenoteratozoospermia and male infertility in both humans and mice. Compelling evidence supports the notion that DNAH12 is essential for proper axonemal development. This work will be of interest to reproductive biologists studying spermatogenesis and sperm biology, as well as andrologists focusing on male fertility.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This work presents potentially important findings suggesting that a combination of transcranial stimulation approaches applied for a short period could improve memory performance after administration. However, the evidence supporting the conclusions is currently incomplete. The work, if replicated in larger samples and animal models or clinical populations, will have both theoretical and practical implications for non-invasive enhancement of cognitive function.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study reports the transcriptomic and proteomic landscapes of the oviducts at four different preimplantation stages during natural fertilization, pseudopregnancy, and superovulation. The supporting data are convincing. This work will be of interest to reproductive biologists and clinicians practicing reproductive medicine.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The manuscript presents valuable data suggesting that enalapril elevates pSmad1/5/9 signaling, reduces cellular senescence, and enhances physiological functions in aged mice. However, the in vivo evidence remains incomplete, as studies blocking pSmad1/5/9 or using NAC to negate enalapril's purported benefits are lacking, and no lifespan extension data are shown. While in vitro findings support Smad1/5/9 as a key mediator, additional experiments - including BMP receptor inhibition and comprehensive senescence markers - are necessary to validate its essential role in vivo. Overall, the study provides promising insights into enalapril's anti-senescence potential but requires further rigorous investigation to fully substantiate its mechanism and therapeutic impact.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript provides convincing evidence derived from diverse state-of-the-art approaches to suggest that non-dopaminergic projection neurons in the ventral tegmental area (VTA) make local synapses. These important findings challenge the prevailing wisdom that VTA interneurons exclusively form local synaptic contacts and instead reveal that VTA neurons expressing interneuron markers also form long-range projections to forebrain targets such as the cortex, ventral pallidum, and nucleus accumbens. Given the importance of VTA interneurons to many models of VTA-linked behavioral functions, these findings have significant implications for our understanding of the neural circuits underlying reward, motivation, and addiction.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This work uses enhanced sampling molecular dynamics methods to generate potentially useful information about a conformational change (the DFG flip) that plays a key role in regulating kinase function and inhibitor binding. The focus of the work is on the mechanism of conformational change and how mutations affect the transition. The evidence supporting the conclusions is incomplete.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This useful study provides a novel perspective on assessing the generalizability of meta-analytic findings by introducing prediction intervals (and distributions) as tools to evaluate whether future studies will likely yield non-zero effects. The methodology is generally solid, with a thorough exploration of a large set of published meta-analyses that broadens our understanding of between-study heterogeneity. However, some critical details are incomplete, requiring refinement to ensure statistical rigor.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study demonstrates the potential of synthetic gene circuits to detect and target aberrant RAS activity in cancer cell lines. The circuit design is novel and the evidence supporting the claims is convincing. As a proof-of-concept, this will be of broad interest. Testing the system with other KRAS mutations and clinically relevant output proteins, as well as gaining a better understanding of the underlying molecular mechanism, will both strengthen the study and help translate the technology toward clinical applications in cancer therapeutics.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents a valuable nonlinear mathematical model that addresses how cell shape transitions in response to ECM stiffness. The evidence supporting the claims of the authors is solid, although additional work is required to improve the manuscript. For instance, the authors should improve the overall readability of the text and amend the experimental validation section. The work will be of interest to scientists working on a spectrum of fields including cell mechanics, cell behaviors, and cancer research.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is an important and solid study that examines the role of TFAM, a protein that helps maintain mtDNA, in mtDNA mutator mice. The authors have demonstrated that TFAM's counteractive role in mtDNA mutator mice is tissue-specific. Minor revisions will enhance the clarity and discuss some of the findings for the broader audience.
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www.researchsquare.com www.researchsquare.com
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eLife Assessment
The manuscript by Qi et al. provides valuable insights into the structural basis of RNA methylation by the METTL3-METTL14 complex, revealing a novel cryptic pocket critical for m6A recognition. The solid experimental approach, integrating crystallography, molecular simulations, and functional assays, supports a proposed two-step mechanism for enzymatic activity. Refining structural data and addressing binding kinetic inconsistencies would further enhance clarity and impact. This manuscript will interest researchers in RNA modification, cancer biology, and therapeutic drug development.
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eLife Assessment
This study presents a valuable finding on the signaling mechanisms underlying Treg cell homeostasis by identifying the simultaneous requirement of diacylglycerol (DAG) kinases (DGK) alpha and zeta for Foxp3+ Treg cell function and follicular responses, with implications for the pathogenesis of some autoimmune diseases. Whereas data based on the characterization of double knock-out mice (for DGK alpha and zeta) is solid, showing the emergence of autoimmune manifestations, the study has gaps in its experimental approaches since it is not clear what can be attributed to the simultaneous DKGα and ζ deficiency, versus the individual deficiency of either one. Experiments on the pathogenic potential of the DKO Tregs in the absence of other T-cells were not presented and results on the role of CD25 downregulation and CD28-independent activation of Treg cells were not properly discussed. Nonetheless, the reported data would be of interest to immunologists working on T-cell intracellular signaling and autoimmunity.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study proposes a useful assay to identify relative social ranks in mice incorporating the competitive drive for two basic resources - food and living space. Using this new protocol, the authors provide solid evidence of stable ranking among male and female pairs, while reporting more fluctuant hierarchies among triads of males. The evidence is, however, incomplete in providing ethologically based validation, assessment of the influence of competitor recognition, rigorous analysis of training data, and proof of concept of application to neuroscience. With these concerns addressed, this manuscript will be of interest to those interested in social behavior and related neuroscience.
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eLife Assessment
Veiga et al demonstrate the importance of incorporating RNAseq and machine learning approaches for neoantigen prediction. The evidence is convincing, and these findings contribute important information towards the selection of neoantigens for personalized antitumor vaccination.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
By using molecular tools, electrophysiology, and ultrastructural reconstructions, this manuscript investigates the role of the Nogo/RTN4 receptor homolog RTN4RL2 at the afferent synapses between the sensory inner hair cells and spiral ganglion neurons and proposes that this regulates key aspects of hearing. The study is important because it provides insights into potential therapeutic targets for hearing loss related to synaptic dysfunction. The experimental data, based on the use of excellent tools, is solid and could be further improved with additional experiments that strengthen the validity of the findings and their interpretation, described in detail in the reviewers' comments.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this important study, the authors reconstruct the evolutionary history of a large and widespread group of freshwater fishes (Nemacheilidae) across Eurasia since the early Eocene, based on molecular phylogenetic analysis with very comprehensive samplings including 471 specimens belonging to 250 living species. The authors convincingly infer that range expansions of the family were facilitated by tectonic connections, favorable climatic conditions, and orogenic processes, adding to our understanding of the effects of climatic change on biodiversity during the Cenozoic. This work is of interest to evolutionary biologists, ichthyologists, paleontologists, and general readers.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study investigates the signaling pathways regulating retinal regeneration. Convincing evidence shows that the sphingosine-1-phosphate (S1P) signaling pathway is inhibited following retinal injury. Small-molecule activators and inhibitors support a model in which S1P signaling must be inhibited to generate Müller glial progenitor cells-a key step in retinal regeneration. The presented results support the major conclusions. However, whether the drug treatments directly or indirectly affect the Müller cells remains unclear.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study reports the developmental dynamics and molecular markers of the rete ovarii during ovarian development. The data supporting the main conclusions are convincing. This study will be of interest to developmental and reproductive biologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study focused on characterizing clonally derived MSC populations from the synovium of normal and osteoarthritis (OA) patients, demonstrating their potential to regenerate cartilage in vivo. Although the strength of evidence is solid, further work is needed to fill the gaps in the CD47Hi cell characterization and the in vivo response assessment. The study will be of interest to scientists advancing MSC based regenerative medicine approaches.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study presents a mouse gastruloid model that can be used to generate hematopoietic progenitors as well as leukemic cells. However, in its current form, the manuscript is inadequate because the primary claims are not supported. Overall, the hematopoietic progenitor cells generated in this system need to be better defined.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important article describes a meticulously-developed improved strategy for generation of functionally null mutants in Leishmania spp. via cytosine base editing, with reduced background toxicity and enhanced efficiency relative to a previously-described method. The authors show use of the strategy in a small-scale loss-of-function screen, providing compelling evidence that large-scale screens will be possible. The newly developed tools will be of great interest to researchers working with Leishmania and beyond.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study uses a comprehensive observational dataset to provide solid evidence on how genetic diversity and species diversity differentially affect multiple ecosystem functions within and across multi-trophic levels in an aquatic ecosystem. The work will be of interest to ecologists working on multi-trophic relationships and biodiversity.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides important observations about the role of Hebbian synapse rewiring (which predicts that correlated activity between neurons begets stronger synapses) on brain connectivity development, by examining a naturally emerging case where Hebbian predictions can be tested because neurons with differing activity undergo development under otherwise similar conditions (albino mouse lateral geniculate nucleus [LGN], where retinal ganglion cells [RGCs] from the contralateral retina form inappropriate projections alongside a majority of ipsilateral RGCs). The evidence supporting the conclusions is compelling, with combined confocal imaging and serial electron microscopy (EM) reconstructions showing complete synaptic isolation of aberrantly projecting RGCs onto LGN thalamocortical projection neurons, and mixed connectivity onto LGN local interneurons. The morphological descriptions of connectivity presented here will be of interest to researchers studying synaptic connectivity and plasticity during development.
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eLife Assessment
This important paper provides an unbiased landscape for the cerebellar cortical outputs to the brainstem nuclei. By conducting anatomical and physiological analyses of the axonal terminals of Purkinje cells, the data provides convincing evidence that Purkinje cells innervate brainstem nuclei directly. The results show that in addition to previously known inputs to vestibular and parabrachial nuclei, Purkinje cells synapse onto the pontine central grey nucleus but have little effect on the locus coeruleus and mesencephalic trigeminal neurons.
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eLife Assessment
This fundamental study comprehensively characterizes insulin producing cells (IPCs) resident in the Drosophila melanogaster brain. A compelling experimental tour de force, the combination of connectomics, mapping of receptors for neuromodulators, electrophysiological recordings, Calcium imaging and optogenetics demonstrates that IPCs operate as a functionally heterogeneous population, as necessary to address continuously changing metabolic demands. These findings will be of interest to both neuroscientists and physiologists seeking to study context-dependent neuroendocrine regulation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study highlights the novel role of RSPO mimetic SZN-043 in the activation of hepatic WNT signaling and promoting hepatocyte regeneration. The authors provided solid evidence of SZN-043 increasing hepatocyte proliferation in various mouse models, including a humanized mouse liver model, ALD model, and CCL4 fibrosis model, although mechanistic characterization of liver pathology remains incomplete. This study will be of interest to researchers in liver regeneration and repair mechanisms.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Nold et al. examined exercise-induced pain modulation in a pharmacological within-subject fMRI study using the opioid-antagonist naloxone and different levels of aerobic exercise and pain. This study provides valuable findings showing that the intensity of exercise does not seem to impact the hypoalgesic effect; however, the evidence is incomplete for the claims relating to the overall effect of exercise on pain, since they cannot be tested with the proposed experimental design.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Lloyd et al. used an evolutionary comparative approach to study DNA damage repair associated with low sleep duration in Astyanax mexicanus, highlighting how the cavefish population has evolved a reduced DNA damage response. The results presented here have important implications. Their results are generally solid however, the evidence suggesting that sleep differences are linked to DNA damage response is missing and this hypothesis remains to be fully tested.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this useful study, the authors perform voltage imaging of CA1 pyramidal cells in head-fixed mice running on a track while local field potentials (LFPs) are recorded. The authors conclude that synchronous ensembles of neurons are differentially associated with different types of LFP patterns, namely theta and ripples. However, evidence for the claims remains incomplete, due to caveats of the experimental approach that were not acknowledged and strong claims that are based on a sparse data set.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study substantially advances our understanding of the neural circuits that regulate social behavior by identifying a population of hypothalamic neurons in the preoptic area that promote social interactions following short-term isolation. The evidence supporting the authors' claims is solid, with well-designed experiments using validated activity-dependent tagging and manipulation methods, though some differences in outcomes between experiments highlight limitations of the tagging approach. The work will be of broad interest to neuroscientists studying social behavior, neural circuit function, and hypothalamic mechanisms and will represent a meaningful contribution to the field.
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eLife Assessment
The authors provide a thorough investigation of the interaction of megakaryocytes (MK) with their associated extracellular matrix (ECM) during maturation; they provide evidence that the existence of a dense cage-like pericellular structure containing laminin γ1 and α4 and collagen IV is key to fixing the perisinusoidal localization of MK and preventing their premature intravasation. Adhesion of MK to this ECM cage is dependent on integrin beta1 and beta3 expressed by MK. This strong and solid conclusion is based on the use of state-of-the art techniques such as the use of primary murine bone marrow MK cultures, mice lacking ECM receptors, namely integrin beta1 and beta3 null mice, as well as high-resolution 2D and 3D imaging. The study provides valuable insight into the role of cell-matrix interactions in MK maturation and provides an interesting model with practical implications for the fields of hemostasis and thrombosis.
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eLife Assessment
In this valuable study, the authors used rats to determine the receptor for a food-related perception (kokumi) that has been characterized in humans. They employ a combination of behavioral, electrophysiological, and immunohistochemical results to provide solid support for their conclusion that ornithine-mediated kokumi effects are mediated by the GPRC6A receptor. They complemented the rat data with some human psychophysical data. The results are intriguing, but there are some deficiencies.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this important study, the authors use zebrafish to examine protein absorption in the gut. Using a combination of imaging and single-cell RNA-seq, they characterize a population of lysosome-rich enterocytes that are important for protein uptake. They find that the microbiome impacts the ability of these cells to uptake protein. The RNA-seq provides a rich dataset for future functional experiments, which makes a convincing case for the importance of these cells.
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eLife Assessment
This study presents fundamental findings that could redefine the specificity and mechanism of action of the well-studied Ser/Thr kinase IKK2 (a subunit of inhibitor of nuclear factor kappa-B kinase (IkB) that propagates cellular response to inflammation). Solid evidence supports the claim that IKK2 exhibits dual specificity that allows tyrosine autophosphorylation and the authors further show that auto-phosphorylated IKK2 is involved in an unanticipated relay mechanism that transfers phosphate from an IKK2 tyrosine onto the IkBa substrate. The findings are a starting point for follow-up studies to confirm the unexpected mechanism and further pursue functional significance.
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archive.org archive.org
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Hurd, Cuthbert C., ed. Proceedings: IBM Computation Seminar December 1949. New York: Internation Buisiness Machines Corporation, 1951. http://archive.org/details/bitsavers_ibmproceedeminarDec49_14295048.
In a variety of context here the idea of "cards" could be held to be synonymous with "notes".
Collision cards (though used in a physics setting) could be a bit hilarious with the idea of "atomic notes" and the idea of "combinatorial creativity".
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Understanding how the divisome is assembled in Chlamydia trachomatis, a bacterial pathogen, is crucial since this bacterium has a non-canonical cell wall and lacks the master regulator of cell division, FtsZ. This important study shows that a DNA translocase, FtsK, is an early and essential component of the Chlamydia trachomatis divisome. The evidence presented is convincing, leveraging the elegant use of genetics and fluorescence microscopy. As this role of FtsK is distinct relative to most other bacteria, these findings should be of significant interest to bacterial cell biologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this study, the authors use the zebrafish to investigate how the microbiome affects a specialized gut cell called the lysosome rich enterocyte. They use a combination of functional assays for protein absorption, gnotobiotic manipulations and single-cell RNA-seq. The findings in the paper are considered important and the results are convincing.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The important manuscript presents convincing evidence of temporal correlations during specific oscillatory activity between the prefrontal cortex, thalamic nucleus reuniens, and the hippocampus, in naturally sleeping animals. Such correlations represent solid evidence to support the notion that the thalamic nucleus reuniens participates in the hippocampal and prefrontal cortex dialogue subserving memory processes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This work presents an important mouse model for a liver-specific depletion of the Survival Motor Neuron (SMN) protein, where the liver retains 30% of functional full-length SMN protein. The authors provide a profile of phenotypic changes in liver-specific SMN depleted mice with convincing evidence supporting their claims.
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eLife Assessment
This important body of work uses state-of-the-art quantitative methods to characterize and compare behaviors across five different fish species to understand which features are conserved and which ones are differentiated. The convincing results from this study will be of interest to ethologists and also have potential utility in understanding the neural mechanisms leading to these behaviors.
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eLife Assessment
This study presents solid evidence for distinct neurotransmitter release modalities between two subclasses of dopaminergic neurons in the olfactory bulb, highlighting an important finding that dendritic neurotransmitter release in anaxonic neurons and axonal neurotransmitter release in axon-bearing neurons, and GABAergic self-inhibition in anaxonic neurons emphasizes the functional differences between these neuronal subtypes. However, some experiments looked incomplete with a relatively small sample size (low n). The conclusion would benefit significantly from additional validations.
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eLife Assessment
The authors adapt a previously-established method that permits detection of in vivo extracellular levels of two distinct enkephalin opioid peptides in response to stressful experiences in mice. The present study highlights the potential of measuring actual peptides by microdialysis-LC-MS. They use this approach in conjunction with fiber photometric calcium imaging to correlate enkephalin neuron activity and enkephalin release in response to repeated stress, providing convincing evidence that this improved approach can provide new insights into opioid signaling in-vivo. This important study provides a means to understand various behavioral states controlled by endogenous opioids and the nucleus accumbens, including hedonic and stress responses, in health and disease. This work will be of broad interest to the neuroscientific community.
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eLife Assessment
This study provides valuable observations indicating that human pyramidal neurons propagate information as fast as rat pyramidal neurons despite their larger size. Convincing evidence demonstrates that this property is due to several biophysical properties of human neurons. This study will be of interest to neurophysiologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents valuable findings to the field interested in inattentional blindness (IB), the phenomenon that participants fail to notice salient stimuli when their attention is directed elsewhere. This study reveals that participants who indicate no awareness of unexpected stimuli through yes/no questions ("did you notice anything unusual?"), may still show above-chance sensitivity to specific properties of these stimuli through follow-up forced-choice questions (e.g., regarding its location or color). By introducing absent trials where no IB stimulus is presented, the authors show that this is because participants are generally conservative and biased to report not noticing in inattentional blindness experiments. The evidence supporting these conclusions is convincing, the samples sizes are large and the analysis protocol is novel.
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eLife Assessment
This work provides an important framework for understanding the primary causes of disease. While the theoretical results rely on strong assumptions about the underlying causal mechanisms, the authors provide solid empirical evidence that the framework is robust to modest violations of these assumptions.
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eLife Assessment
This valuable study investigates how inter-organ communication between the tracheal stem cells and the fat body plays a key role in the directed migration of tracheal stem cells in Drosophila. The evidence supporting the claims of the authors is solid. The work would be of interest to researchers in the fields of developmental biology and cancer biology.
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eLife Assessment
This important work demonstrates the application of Pro-PRIME, a large language model, to engineer VHH antibodies with enhanced stability for extreme industrial environments. The evidence is convincing, showing through two rounds of design and experimental validation that AI-guided approaches can outperform traditional rational design methods. The solid methodology and results establish a foundation for further exploration of LLM-assisted protein engineering.
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eLife Assessment
The preliminary data presented in this manuscript seem valuable. The data are currently incomplete and there are numerous technical concerns, some of which may arise from insufficient description of methodologies used.
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eLife Assessment
This study reports an approach for restoring sperm motility in mice. The strength lies in in the novelty of the methodology being developed, but the evidence for the success of the method or its mechanism is inadequate. Additional experimental support would be required to support the conclusions of the authors.
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eLife Assessment
This valuable work presents an interpretable protein-DNA Energy Associative (IDEA) model for predicting binding sites and affinities of DNA-binding proteins. The study provides a detailed description of the method, making it reproducible. However, the generalizability of the prediction model presents certain concerns, and the supporting evidence appears incomplete. Nonetheless, with a thorough re-examination of the training and testing procedures, this model can be widely applicable for predicting genome-wide protein-DNA binding sites.
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eLife Assessment
This important study measures the functional specialization of distinct subregions within the mouse posterior parietal cortex (PPC) using mesoscopic two-photon calcium imaging during visual discrimination and choice history-dependent tasks. It presents compelling evidence supporting the existence of functional specialized subregions within the PPC. The work will be of interest to system and computational neuroscientists interested in decision-making, working memory, and multisensory integration.
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eLife Assessment
This study is important as it highlighted how IL-4 regulates the reactive state of a specific microglial population by increasing the proportion of CD11c+ microglial cells and ultimately suppressing neuropathic pain. It provided convincing evidence on the pain-resolving roles of microglia. However, the authors are encouraged to clarify data interpretation and integrate the study's findings into the existing knowledge about microglia, monocytes, and macrophages.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study shows that the activity of hypothalamic hypocretin/orexin neurons (HONs) correlates with body movement over multiple behaviors. Sophisticated techniques and analyses showcase this link which appears to be unique to HONs. Evidence for this correlation is, however, incomplete as the confound of arousal with movement needs to be resolved since orexin also plays a key role in arousal. This work should be of interest to scientists studying peptidergic neurons, movement, energy regulation, and brain-body coordination.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents a valuable finding that C238 in vimentin regulates long non-coding RNA XIST to suppress EMT and thereby Xist may be a therapeutic target in breast cancer. The evidence supporting the claims of the authors is solid, although the improvement of data visibility and presentation would have strengthened the study. The work will be of interest to scientists working in the field of BCs.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is an important study that provides CCR7-APEX2 proximity labelling mass spectrometry data that is expected to provide new insights into CCR7 signaling partners and pathways. The study is technically easy to follow and the data is convincing. It will be interesting in the future to have complementary studies in lymphocytes/dendritic cells that endogenously express CCR7. This is of value to the community, and there are likely multiple opportunities to use the APEX2 data set to extend these findings, strengthen some claims, and even explore a new pathway identified in the APEX2 data set.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Working with a diverse panel of rice accessions grown in field conditions, this valuable study measures changes in transcript abundance, tests for patterns of selection on gene expression, and maps the genetic basic of variation in gene expression in normal and elevated salinity treatments. The manuscript provides solid evidence that mean gene expression levels are further from the optimum abundance for more genes under the elevated salinity treatment compared to normal treatment, and that a relatively small number of genes are hotspots that harbor genetic variants which affect broader genome-wide patterns of natural variation in gene expression under high salinity conditions. However, the design, clarity, and interpretation of several statistical analyses can be improved, some opportunities for integration among datasets and analyses could yet be realized, and genetic manipulation is required to confirm functional involvement of any specific genes in regulatory networks or organismal traits that confer adaptation to higher salinity conditions. The manuscript will be of interest to evolutionary biologists studying the genetics of complex traits and a resource for plant biologists studying mechanisms of abiotic stress tolerance.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is an important study examining the role of conserved PCH-2 protein at different stages of C. elegans meiosis. The authors use elegant molecular genetic approaches to provide convincing evidence to support their claims. The work will be of interest to scientists studying meiosis, DNA recombination, and chromosome segregation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study unravels the mechanisms underlying mammalian sperm-oocyte recognition and penetration, shedding light on cross-species interactions. It provides solid evidence that exposure of sperm to oviductal fluid or OVGP1 proteins from bovine, murine, or human sources imparts species-specific zona pellucida (ZP) recognition, ensuring that only sperm from the corresponding species can penetrate the ZP, regardless of its origin. These findings hold significant potential for reproductive biology, offering insights to enhance porcine in vitro fertilization (IVF), which frequently suffers from polyspermy, as well as advancing human IVF through improved intrinsic sperm selection.
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www.researchsquare.com www.researchsquare.com
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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 solid. This paper would be of interest to those studying aphids wing dimorphism.
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eLife Assessment
This manuscript focuses on the identification of RNA crosslinks within the HIV RNA genome under different conditions i.e. in infected cells and in virions using a new method called HiCapR. These cross-links reveal long-range interactions that can be used to determine the structural arrangement of the viral RNA, providing valuable data that show differences in the genomic organization in different conditions. The data analysis, however, is incomplete and based on extensive computational analysis from a limited number of datasets.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This work presents valuable data demonstrating that a camelid single-domain antibody can selectively inhibit a key glycolytic enzyme in trypanosomes via an allosteric mechanism. The claim that this information can be exploited for the design of novel chemotherapeutics is solid but limited by the modest effects on parasite growth, as well as the lack of evidence for cellular target engagement in vivo.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study investigates the propensity of the intravacuolar pathogen, Leishmania, to scavenge lipids which it utilizes for its accelerated growth within macrophages. Although some of the data compellingly links increased lipid acquisition to parasite growth, data to support the underlying mechanism to describe the proposed model is incomplete. The study adds to other work that has implicated pathogen-derived processes in the selective recruitment of vesicles to the pathogen-containing vacuole, based on the content of the cargo.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors present a useful agent-based model to study the tensile force generated by myosin mini-filaments in actin systems (bundles and networks); by numerically solving a mechanical model of myosin-II filaments, the authors provide insights into how the geometry of the molecular components and their elastic responses determine the force production. This work is of interest to biophysicists (in particular theoreticians) investigating force generation of motor molecules from a biomechanical engineering and physics perspective. The authors convincingly show that cooperative effects between multiple myosin filaments can enhance the total force generated, but not the efficiency of force generation (force per myosin) if passive cross-linkers are present. This work would benefit from a more extensive discussion of the relevance of the results in view of the existing experimental literature.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This useful study uses the MMTV-Neu-YD5 mouse model for HER2-dependent breast cancer to generate transcriptomic and proteomic datasets from extracted primary tumour samples. The data sets generated appear to be solid and will be of interest to the community. However, mechanistic studies to support the conclusion that mitochondrial function is increased in the tumours remain incomplete and would benefit from experiments that would directly interrogate aspects such as cellular heterogeneity, and signalling.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study combines compelling experiments with optogenetic actuation and convincing theory to understand how signalling proteins control the switch between cell protrusion and retraction, two essential processes in single cell migration. The authors examine the importance of the basal concentration and recruitment dynamics of a guanine exchange factor (GEF) on the activity of the downstream effectors RhoA and Cdc42, which control retraction and protrusion. The experimental and theoretical evidence provides a model of RhoA's involvement in both protrusion and retraction and shows that these complex processes are highly dependent on the concentration and activity dynamics of the components.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Using experiments in the white fly, this manuscript provides evidence that the bacterial symbiont Wolbachia can be transmitted from parasitoid wasps to their insect hosts. Characterizing the transfer of Wolbachia between insect species is a valuable attempt to explain the widespread of this intracellular bacterium. This paper is incomplete as it does not furnish sufficient data to support several of its claims for which additional methods and data are necessary.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides a convincing explanation for why HIV-1 Vif causes a qualitatively different cell cycle arrest to its accessory gene counterpart Vpr. The authors use elegant time-dependent microscopy reporter assays in immortalized tumor cell models to show that HIV-1 Vif causes a pseudo-metaphase arrest rather than a G2 arrest. The metaphase arrest correlates with dysregulation of the kinetochore that could be explained by the loss of phosphatase functions that determine chromosome-microtubule interactions. These valuable findings lay the groundwork for additional studies examining the mechanisms and consequences of this Vif-dependent phenotype in the viral life cycle and in primary cells more relevant to HIV-1 pathogenesis.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study reports important findings about pre-saccadic foveal prediction and the extent to which it is influenced by the visibility of the saccade target relative to its background. The results and research methodology are solid, although the neural substrates of oscillatory pre-saccadic enhancement for high-opacity targets remain unclear. This work should be of broad interest to visual neuroscientists, as well as those aiming to understand perception in the context of eye movements and modeling of visually guided actions.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is an interesting and important paper that grew from a careful clinical assessment of an unusual patient with hypoparathyroidism whose parathyroid glands synthesize and secrete a mutant form of PTH made. This mutant PTH (R25C-PTH), when studied in mice and in vivo, has interesting properties. It can homodimerize and can raise blood calcium and lower blood phosphate levels: the opposite to the human phenotype in the index patient. These investigators perform a careful and convincing comparison of native PTH (1-34), an anabolic drug for osteoporosis treatment, and this R25C-mutant of PTH for their effects on bone mass, strength, microarchitecture, and metabolic activity. This dimeric mutant of PTH has anabolic properties raising the possibility that such forms of PTH could be developed as potent therapies for low bone mass states.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this manuscript the authors established a novel three-dimensional culture system for stratified epithelia that allows epithelial cells to undergo epithelial-to-mesenchymal transition (EMT) and subsequent mesenchymal-to-epithelial transition (MET) while migrating through a membrane with 3.0-µm micropores, and, thus, provides a valuable tool to study EMT and possibly wound regeneration or metastasis. Furthermore, a set of experiments provides solid data suggesting that TGF beta signaling and actin polymerization promote movement of epithelial cells into the pores, while Piezo1 and Keratin 6 prevent keratinocyte migration and EMT.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This work represents an important contribution to our understanding of how membrane energetics influence protein conformation and function in mechano-sensitive channels. Through extensive molecular dynamics simulations and energetic analysis, the study demonstrates how the channel structure is shaped by a balance of protein and membrane-induced forces, effectively reconciling experimental data from different membrane environments. However, while much of the computational data is convincing, some aspects of the energetic analysis and models employed remain incomplete.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important work substantially advances our understanding of the interaction among gut microbiota, lipid metabolism, and the host in type 2 diabetes. However, some evidence is incomplete, particularly in the mouse experiments with FMT. Additional experiments will be required to strengthen the authors' interesting findings.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The study presents important findings on inositol-requiring enzyme (IRE1α) inhibition on diet-induced obesity (overnutrition) and insulin resistance where IRE1α inhibition enhances thermogenesis and reduces the metabolically active and M1-like macrophages in adipose tissue. The evidence supporting the conclusions is convincing and the work will be of interest to cell biologists and biochemists working in metabolism, insulin resistance, and inflammation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study describes the impact of mycobacterial genetic diversity on host-infection phenotypes by assessing the effect of different M. tuberculosis lineages on granulomatous inflammation using a 3D in vitro granuloma model. Despite being descriptive and showing mostly correlative relationships, the useful findings and data provide some solid support regarding the functional impact of M. tuberculosis natural diversity on host-pathogen interactions. The study will interest researchers working on mycobacteria and how genetic diversity influences virulence and immunity outcomes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript describes the impact of modulating signaling by a key regulatory enzyme, Dual Leucine Zipper Kinase (DLK), on hippocampal neurons. The results are interesting and will be important for scientists interested in synapse formation, axon specification, and cell death. The authors have carefully addressed the comments made by the reviewers and the findings are convincing in large part due to the use of extensive mouse genetics, detailed gene expression of enriched genes, and recognition of neuron vulnerability.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents important findings on the function of enteric glia expressing proteolipid protein 1 (PLP1+ glia). The evidence supporting the claims of the authors is solid, although the inclusion of additional data showing the mechanisms by which PLP1+ enteric glia acts on Paneth cells would have strengthened the study. The work will be of interest to colleagues studying intestinal biology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study on mouse Ly49 receptors expressed on natural killer (NK) cells shows that Ly49A, in the presence of the corresponding MHC Class I allele, can lead to NK cell licensing, thereby providing valuable insights into the mechanisms of NK cell modulation by Ly49 receptors. The work may have significant implications for studies of human Killer-cell immunoglobulin-like receptors (KIR) expressing and other NK cells. Overall, the study was well-developed with convincing evidence.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Zanetti et al use convincing biophysical and cellular assays to investigate the interaction of the birnavirus VP3 protein with the early endosome lipid PI3P. The study provides valuable insights and will be of interest to virologists. In future studies, it would be interesting to demonstrate that VP3-PIP3P is a specific interaction and not a general interaction with other PIPs.
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www.biorxiv.org www.biorxiv.org
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eLife assessment
These important findings stand out from other similar studies via some convincing demonstration of behavioural and neural relationships between two helping tasks – one focusing more on social perception, one more on its influence on social behaviour – that were performed more than 300 days apart. The claims however would be stronger with a larger sample size.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents a useful finding that targeting amino acid metabolism can overcome Trastuzumab resistance in HER2+ breast cancer. The evidence supporting the claims of the authors is solid and the authors may want to validate their results in additional cell lines to strengthen their conclusions. Moreover, the authors should clarify the source of patient samples and why the manuscript focused on epigenetic regulations instead of major transcription factors. The work will be of interest to scientists working in the field of breast cancer.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This is an important study reporting that activation of the presynaptic GPR55 receptor suppresses synaptic transmission by modulating GABA release through the reduction of the readily releasable pool without affecting the presynaptic AP waveform and calcium influx. The evidence supporting this claim is compelling and based on an impressive array of techniques including patch-clamp recordings from the axon terminals of cerebellar Purkinje cells and fluorescent imaging of vesicular exocytosis. However, a few technical issues leave some questions open, these include uncertainty regarding the specificity of pharmacological agents and the nature of the endogenous process that would activate this pathway in vivo. In the current form, the evidence indicating that synaptic vesicles become insensitive to VGCC activation in the presence of GPR55 is weak and would need to be supported with additional experimental data.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
Overall, this is an important work: the new methodology of hamFISH is a key additional tool for the assessment of the expression of multiple genes simultaneously. The authors provide convincing evidence of the utility of this approach on Medial Amygdala (MeA) tissue leveraging previous a transcriptomic dataset for gene selection. The authors also present a deeper dive into putative relationships between the on-tissue expression of subsets of genes and connectivity and behavioral regulation. The putative biological insights are intriguing, although preliminary, but notably they set up questions for future studies.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
In this valuable contribution, the authors present an approach based on a complex systems theoretical framework to characterize diet-host-microbe interactions and to develop targeted bacteriotherapies using a three-phase workflow. Overall, the solid results provide a reference for microbial community research and insights to guide future studies. However, the theoretical systems approach would benefit from further description, and some claims regarding oxalate bacterial metabolism in complex microbial communities could be strengthened. This study will interest researchers working on gut microbiomes specifically those seeking to modulate host-microbial interactions.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study investigates the function of a critical regulator of human early cardiac development. The convincing examination of GATA6 function is thorough and well-executed. The study will be of interest to scientists working on how the human heart acquires its identity.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The study by Pudlowski et al. shows that a previously-identified protein complex, composed of delta- and epsilon-tubulin together with TEDC1 and TEDC2, functions in generating centriolar triplet microtubules, and that this is crucial for the proper formation of centriolar subdomains and the stability of centrioles throughout the cell cycle. This is an important study that advances our understanding of centriole biogenesis and structure and is supported by convincing evidence based on knockout cell lines, immunoprecipitation, and ultrastructure expansion microscopy. The work is of interest to cell biologists, in particular researchers with interest in centrosome biology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript describes an important finding of the transcriptional control of a chimeric gene transfer agents (GTA) cluster in Bartonella by a processive anti-termination factor (BrrG). The evidence provided is solid. This manuscript will interest researchers working on transcriptional regulation, horizontal gene transfer, and phages.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study presents findings on DNA methylation as an efficient epigenetic transcriptional regulating strategy in bacteria. The authors utilized single-molecule real-time sequencing to profile the DNA methylation landscape across three model pathovars of Pseudomonas syringae, identifying significant epigenetic mechanisms through the Type-I restriction-modification system, which includes a conserved sequence motif associated with N6-methyladenine. The evidence presented is solid and the study provides novel insights into the epigenetic mechanisms of P. syringae, expanding the understanding of bacterial pathogenicity and adaptation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript offers valuable theoretical predictions on how horizontal gene transfer (HGT) can lead to alternative stable states in microbial communities. Using a modeling framework, solid theoretical evidence is provided to support the claimed role of HGT. However, given that the model has many degrees of freedom, a more comprehensive analysis of the role of different parameters could strengthen the study. Additionally, potential interactions between plasmids that carry out HGT are not discussed in the model. This paper would be of interest to researchers in microbiology, ecology, and evolutionary biology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study combines virology experiments and mathematical modeling to determine the nuclear export rate of each of the eight RNA segments of the influenza A virus, leading to the proposal that a specific retention of mRNA within the nucleus delays the expression of antigenic viral proteins. The proposed model for explaining the differential rate of export is compelling, going beyond the state of the art, but the experimental setup is only in partial support and further studies will be needed to confirm the proposed mechanism.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study reports a model of 8 somatosensory areas of the rat cortex consisting of 4.2 million morphologically and electrically detailed neurons. The authors carry out simulation experiments aimed at understanding how multiscale organization of the cortical network shapes neural activity. While the reviewers found the results to be solid, they note that they could have likely been obtained using a much smaller portion of the model. Nonetheless, the release of the modeling platform represents a significant contribution to the field by providing a valuable resource for the scientific community.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study investigates the implications of human endogenous retrovirus (HERV) activity in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and fibromyalgia (FM). These findings indicate significant associations that coincide with previous literature, which has suggested roles for differential HERV activity in degenerative, inflammatory, and aging-related pathologies of the central nervous system (CNS), as well as neurotropic infections. These seminal studies can be strengthened with minor improvements to the methodologies of characterizing differential HERV activity, further characterizing downstream mechanisms by which HERV activity impacts disease and by an expansion of the datasets utilized to include additional cohorts. These compelling findings are of immediate importance to clinicians, policymakers, and researchers interested in the underlying etiology of human health and disease.
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www.medrxiv.org www.medrxiv.org
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eLife Assessment
This study investigated the influence of genomic information and timing of vaccine strain selection on the accuracy of influenza A/H3N2 forecasting. The authors utilised appropriate statistical methods and have provided solid evidence that is an important contribution to the evidence base. While the study addresses a key aspect of public health, the impact is rather limited by its exclusive reliance on predictive methods using genomic information, without incorporating phenotypic data.
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Editors Assessment:
DNA has huge potential as a data storage medium because of its incredibly high storage density and stability. This work addresses the potential of modified bases, specifically 5-methylcytosine (5mC), in enhancing DNA data storage systems. This paper introduces a transcoding scheme named R+, which incorporates this modified 5mC base to increase information density beyond the standard limits. By encoding various file types into DNA sequences of between 1.3 to 1.6 kb in size, this method achieves an average recovery rate of 98.97% (with reference), validating the effectiveness of the method. On top of a wet-lab protocol (hosted in protocols.io) for the experimental validation of the transcoding scheme, it also includes open source code for in-silico simulation tests. Peer review scruitinising the protocols and validation are reusable and provide convincing results. As nanopore sequencing has enabled reading of these modified bases, it is timely making them applicable as extra letters in the molecular alphabet for DNA data storage
This evaluation refers to version 1 of the preprint
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors report how a previously published method, ReplicaDock, can be used to improve predictions from AlphaFold-multimer (AFm) for protein docking studies. The level of improvement is modest for cases where AFm is successful; for cases where AFm is not as successful, the improvement is more significant, although the accuracy of prediction is also notably lower. The evidence for the ReplicaDock approach being more predictive than AFm is particularly convincing for the antibody-antigen test case. Overall, the study makes a valuable contribution by combining data- and physics-driven approaches.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript reports important findings that the methyltransferase METTL3 is involved in the repair of abasic sites and uracil in DNA, mediating resistance to floxuridine-driven cytotoxicity. Convincing evidence shows the involvement of m6A in DNA based on single cell imaging and mass spec data. The authors present evidence that the m6A signal does not result from bacterial contamination or RNA, but the text does not make this overly clear.
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www.biorxiv.org www.biorxiv.org
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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.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study examines the variability in spacing and direction of entorhinal grid cells, providing convincing evidence that such variability helps disambiguate locations within an environment. This study will be of interest to neuroscientists working on spatial navigation and, more broadly, on neural coding.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study reports a detailed quantification of the population dynamics of Salmonella enterica serovar Typhimurium in mice. Bacterial burden and founding population sizes across various organs were quantified, revealing pathways of dissemination and reseeding of the gastrointestinal tract from systemic organs. Using various techniques, including genetic distance measurements, the authors present compelling evidence to support their conclusions, thus presenting new knowledge that will be of broad interest to scientists focusing on infectious diseases.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The current human tissue-based study provides compelling evidence correlating hippocampal expressions of RNA guanine-rich G-quadruplexes with aging and with Alzheimer's Disease presence and severity. The results are fundamental and will rejuvenate our understanding of aging and AD's pathogenesis.
[Editors' note: this paper was reviewed by Review Commons.]
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study provides information on the TMEM16 family of membrane proteins, which play roles in lipid scrambling and ion transport. By simulating 27 structures representing five distinct family members, the authors captured hundreds of lipid scrambling events, offering insights into the mechanisms of lipid translocation and the specific protein regions involved in these processes. However, while the data on groove dilation is compelling, the evidence for outside-the-groove scramblase activity without experimental validation is inadequate and is based on a limited set of observed events.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study presents valuable data on the increase in individual differences in functional connectivity with the auditory cortex in individuals with congenital/early-onset hearing loss compared to individuals with normal hearing. The evidence supporting the study's claims is convincing, although additional work using resting-state functional connectivity in the future could further strengthen the results. The work will be of interest to neuroscientists working on brain plasticity and may have implications for the design of interventions and compensatory strategies.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This fundamental study provides a critical challenge to a great many studies of the neural correlates of consciousness that were based on post hoc sorting of reported awareness experience. The evidence supporting this criticism is compelling, based on simulations and decoding analysis of EEG data. The results will be of interest not only to psychologists and neuroscientists but also to philosophers who work on addressing mind-body relationships.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
The authors investigated the mechanisms underlying the pause in striatal cholinergic interneurons (SCINs) induced by thalamic input, identifying that Kv1 channels play a key role in this burst-dependent pause. The valuable study provides mechanistic insights into how burst activity in SCINs leads to a subsequent pause, highlighting the involvement of D1/D5 receptors. The experimental evidence is solid; however, the reviewers suggest further clarifying the mechanism by which clozapine reduces D5R ligand-independent activity in the L-DOPA-off state.
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www.researchsquare.com www.researchsquare.com
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eLife Assessment
This useful study investigates the impact of disrupting the interaction of RAS with the PI3K subunit p110α in macrophage function in vitro and inflammatory responses in vivo. Solid data overall supports a role for RAS-p110α signalling in regulating macrophage activity and so inflammation, however for many of the readouts presented the magnitude of the phenotype is not particularly pronounced. Further analysis would be required to substantiate the claims that RAS-p110α signalling plays a key role in macrophage function. Of note, the molecular mechanisms of how exactly p110α regulates the functions in macrophages have not yet been established.
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eLife Assessment
This manuscript reports important findings that the methyltransferase METTL3 is involved in the repair of abasic sites and uracil in DNA, mediating resistance to floxuridine-driven cytotoxicity. The presented evidence is conclusive for the involvement of m6A in DNA involving single cell imaging and mass spectrometry data. The authors present convincing evidence that the m6A signal does not result from bacterial contamination or RNA.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This paper addresses the important question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are predictable based on the wild-type phenotype. However, these potentially interesting claims are inadequately supported by the analysis, because measurement noise is not accounted for, arbitrary cutoffs are used, and global nonlinearities are not sufficiently considered. If the results continue to hold after these major improvements in the analysis, they should be of interest to all biologists working in the field of fitness landscapes.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study makes a valuable contribution to understanding Bayesian inference in dynamic environments by demonstrating how humans integrate prior beliefs with sensory evidence, revealing an overestimation of environmental volatility while accurately tracking noise. The evidence is solid, supported by robust model fitting and principled factorial model set analyses, though limitations in sample size and inconclusive findings on memory capacity tradeoffs reduce the overall impact. Future work should expand validation across datasets, enhance model comparisons, and explore the generalizability of reduced Bayesian frameworks to strengthen the conclusions and broader relevance of the study.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This manuscript presents a useful mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space. The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, but also raise questions about their justifications and the degree to which the results agree with experiments as well as direct numerical simulations. Therefore, the evidence for the utility of this approach is at present incomplete.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study uses diffusion magnetic resonance imaging to non-invasively map the white matter fibres connecting the zona incerta and cortex in humans. The authors present convincing evidence to indicate that these connections are organized along a rostro-caudal axis. The findings will be of interest to researchers interested in neuroanatomy and cortico-subcortical connectivity.
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eLife Assessment
This important work proposes a neural network model of interactions between the prefrontal cortex and basal ganglia to implement adaptive resource allocation in working memory, where the gating strategies for storage are adjusted by reinforcement learning. Numerical simulations provide convincing evidence for the superiority of the model in improving effective capacity, optimizing resource management, and reducing error rates, as well as for its human-like performance. This work will be of broad interest to computational and cognitive neuroscientists, and may also interest machine-learning researchers who seek to develop brain-inspired machine-learning algorithms for memory.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This report 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. This finding is fundamental, as it challenges the hypothesis that these peptides are essential for pain transmission, even when targeted together. This paper will be of interest to those interested in the neurobiology of pain and/or neuropeptide function.
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eLife Assessment
This important study provides convincing data from in vitro models and patient-derived samples to demonstrate how modulation of GSK3 activity can reprogram macrophages, revealing potential therapeutic applications in inflammatory diseases such as severe COVID-19. The study stands out for its clear and systematic presentation, strong experimental approach, and the relevance of its findings to the field of immunology.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides valuable insights into the behavioral, computational, and neural mechanisms of regime shift detection, by identifying distinct roles for the frontoparietal network and ventromedial prefrontal cortex in sensitivity to signal diagnosticity and transition probabilities, respectively. The findings are supported by solid evidence, including an innovative task design, robust behavioral modeling, and well-executed model-based fMRI analyses, though claims of neural selectivity would benefit from more rigorous statistical comparisons. Overall, this work advances our understanding of how humans adapt belief updating in dynamic environments and offers a framework for exploring biases in decision-making under uncertainty.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable study implicates a specific Wolbachia gene in driving the male-killing phenotype in a moth: This is a contribution to a growing body of literature from the authors in which they authors have nicely teased apart the loci responsible for male killing across diverse insects. The conclusions are supported by solid evidence.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study provides compelling data regarding the molecular characterization of a rare tumor type with few treatment options. This fundamental work significantly advances our mechanistic understanding of solitary fibrous tumours, a critical first step towards targeted precision medicine approaches. The results of this study will be of broad interest to cancer biologists and experimental oncologists.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This valuable contribution combines high-resolution histology with magnetic resonance imaging in a novel way to study the organisation of the human amygdala. The main findings convincingly show the axes of microstructural organisation within the amygdala and how they map onto the functional organisation. Overall, the approach taken in this paper showcases the utility of combining multiple modalities at different spatial scales to help understand brain organisation.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study provides insights into the role of the cerebellum in fear conditioning, addressing a key gap in the literature. The evidence presented is solid overall, although the theoretical framing and clarity of the results can be improved and some concerns remain about the reliability of results based on small numbers of trials. This work will be of interest to both the extinction learning and cerebellar research communities.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This research addresses an important and timely topic in cancer treatment, as the authors present a novel computational tool, 'retriever,' which has the potential to revolutionize personalized cancer treatment strategies by predicting effective drug combinations for triple-negative breast cancer. The strength of the evidence presented is solid, as evidenced by the systematic testing of 152 drug response profiles and 11,476 drug combinations.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This important study provides new evidence on the role of norepinephrine (NE) release in the hippocampus in response to environmental transitions (event boundaries), providing a potential link between NE signaling and the segmentation of episodic memories. The work is solid, employing innovative techniques such as fiber photometry with the GRAB-NE sensor for NE measurement, the analysis of public electrophysiology hippocampal datasets, and well-controlled experiments. While further analysis could strengthen some claims, this work offers insights into memory, neuromodulation, and hippocampal function.
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www.biorxiv.org www.biorxiv.org
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eLife Assessment
This study examined the important question of how neurons code temporal information across the hippocampus, dorsal striatum, and orbitofrontal cortex. Using a behavioral task in the rat that requires discrimination between short and long time intervals, the authors conclude that time intervals are represented in all three regions and that synchronized activity of time-coding cells across the brain regions is coordinated by theta rhythms. However, several weaknesses are noted, and in its current form, the study provides incomplete evidence for understanding how temporal information is processed and coordinated throughout these brain networks.
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