Evaluated articles

eLife Assessment

This study focuses on a previously reported positive correlation between translational efficiency and protein noise. Using mathematical modeling and analysis of experimental data the authors reach the valuable conclusion that this phenomenon arises due to ribosomal demand. While some aspects of the work appear to be incomplete, the results have the potential to be of value and interest to the field of gene expression.

eLife Assessment

This study presents a valuable finding on how the interplay between transcription factors SOX2 and OCT4 establishes the pluripotency network in early mouse embryos. The evidence supporting the claims of the authors is solid, although inclusion of additional omics data would further strengthen the study. The work will be of interest to biologists working on embryonic development and gene regulation.

eLife Assessment

This valuable study provides a detailed picture of the synapse distributions for a set of visual projection neurons and their downstream partners, in combination with multi-compartmental modelling fitted to electrophysiological data. The model reveals interesting consequences of synapse topography for neuronal computation. The analysis, however, seems incomplete as the authors only analyze passive models of these spiking neurons, and do not attempt to connect their analysis to the bigger picture at the behavioral level.

eLife Assessment

This important study shows that Toxoplasma gondii uses paracrine mechanisms, in addition to cell-intrinsic methods, to evade the host immune system, with MYR1 playing a key role in transporting effector molecules into host cells. The authors present convincing evidence that in vivo, MYR1-deficient parasites can be rescued by wild-type parasites, revealing a limitation in pooled CRISPR screens, where such paracrine effects may obscure the identification of key parasite pathways involved in immune evasion

eLife Assessment

This study reports an important finding on the mechanism underlying the enhancement of anti-viral immune responses by febrile temperatures, especially the role of the conserved heat-shock factor, HSF-1. The data provide compelling support for the authors' model wherein increased temperature in the shrimp Litopenaeus vannamei activates HSF1, which in turn enhances anti-viral response via up-regulation of the nSWD protein and antibacterial peptides. The work, which will be of interest to virologists, immunologists, and cell biologists, would benefit from more discussion of the function and roles of HSF-1 at 25°C vs. 32°C.

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.

eLife Assessment

This valuable study on Pseudomonas subverting host immunity identifies a new immune evasion strategy. There is solid evidence for the cleavage of VgrG2B by Caspase 11 and the generation of fragments that inhibit activity of the NLRP3 inflammasome. This work should be of interest to immunologists and microbiologists.

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.

eLife Assessment

This important study contributes to our understanding of how epithelial cells establish polarity by identifying a hierarchy in which Par3 acts upstream of centrosome positioning and apical membrane initiation. The evidence supporting the main conclusions is convincing, although several aspects of the model remain only partially supported due to unresolved questions about microtubule organization and the need for clearer integration of quantitative and conceptual points raised in review. The work will be of interest to cell and developmental biologists, but the conclusions would be strengthened by greater precision in methodology, terminology, and interpretation.

eLife Assessment

This study provides important findings that during credit assignment, the lateral orbitofrontal cortex (lOFC) and hippocampus (HC) encode causal choice representations, while the frontopolar cortex (FPl) mediates HC -lOFC interactions when the causality needs to be maintained over longer distractions. This research offers compelling evidence and employs sophisticated multivariate pattern analysis. However, while the task design captures the delayed component, it lacks the full complexity and ambiguity of the credit assignment process observed in real-world scenarios. Moreover, the data indicated that other frontal regions beyond just lOFC were involved in delayed credit assignment. This work will be of interest to cognitive and computational neuroscientists who work on value-based decision-making and fronto-hippocampal circuits.

eLife Assessment

This study provides important insights into the brain activity and connectivity underlying speech comprehension, revealing three brain states. The authors present compelling evidence by leveraging hidden Markov modeling of fMRI data to link brain state dynamics to comprehension scores, though the functional role of these states remains under-explored. These findings advance our understanding of how brain state transitions in narrative comprehension relate to stimulus-specific features.

eLife Assessment

This work provides important findings characterizing potential synaptic mechanisms supporting the role of midline thalamus-hippocampal projections in fear memory extinction in mice. The methods and approaches were considered solid, though some evidence is incomplete as there are some concerns with the analytical approaches used for some aspects of the study. This work will be of interest to those in the field of thalamic regulation and fear memory.

eLife Assessment

This important study investigates how working memory load influences the Stroop effect from a temporal dynamics perspective. Convincing evidence is provided that the working memory load influences the Stroop effect in the late-stage stimulus-response mapping instead of the early sensory stage. This study will be of interest to both neuroscientists and psychologists who work on cognitive control.

eLife Assessment

This important report describes the changing antiviral activity of IFIT1 across mammals and in response to distinct viruses, likely as a result of past arms races. One of the main strengths of the manuscript is the breadth of mammalian IFIT1 orthologs and viruses that were tested, as well as the thoroughness of the positive selection analysis. Overall the evidence is convincing, and the discussion conveys well the limitations due to physical interactions with other IFITs that are not accounted for.

eLife Assessment

This valuable study reports on a novel role of PD-1 in early T cell differentiation, showing that PD-1 stimulation impairs Th2 differentiation more effectively than that of Th1, with implications for the treatment of allergies. However, whereas the series of well-designed experiments using OVA-specific CD4 T cells from DO.11.10 mice and the use of an allergy model generated compelling data, the study is still incomplete since it shows gaps in the rationale for the experimental protocols, contradictory data regarding IFN-gamma and IL-4 production, and the lack of in vivo experiments on Th2 differentiation to further support the main hypothesis. Nonetheless, the reported data would be of interest to immunologists working on T cell differentiation and allergy.

eLife Assessment

Gil Ávila et al. evaluated the aperiodic component in the medial prefrontal cortex using resting-state EEG recordings from 149 individuals with chronic pain and 115 healthy participants. The authors present compelling evidence that the aperiodic component of the EEG does not differentiate between those with chronic pain and healthy individuals. The study was well-designed and rigorously conducted, and the clear and conclusive results provide important insights that can guide future research in the field of pain neuroscience.

eLife Assessment

The presented soft tissue data of pterosaur tail vanes represent a valuable contribution to ongoing research efforts to decipher the flight abilities of pterosaurs in the fields of paleontology, comparative biomechanics, and bioinspired design. The new methods are compelling and give new detail on tail morphology, with a potential to resolve how pterosaurs were able to control and maintain tail stiffness to furnish flight control.

eLife Assessment

This important study presents results for the theory of odor coding in hyperbolic spaces by revealing spiral trajectories in the dynamics of odors during natural, ethologically relevant processes such as ripening. In the current manuscript, the strength of the evidence is solid and would be strengthened by answering several technical points raised by reviewers.

eLife Assessment

This study presents numerical results on a framework for understanding the dynamics of subthreshold waves in a network of electrical synapses modeled on the connectome data of the C elegans nematode. The strength of the evidence presented in favor of interference effects being a major component in subthreshold wave dynamics is inadequate and the approach is flawed. Substantial methodological issues are present, including altering the original network structure of the connectome without a clear justification and providing little motivation for the choice of numerical parameters values that were used.