Evaluated articles

eLife Assessment

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

eLife Assessment

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

eLife Assessment

This valuable work analyzes a large dataset of [NiFe]-CODHs, integrating genomic context, operon organization, and clade-specific gene neighborhoods to discern patterns of diversification and adaptation. A consistent examination of CODH genomic contexts, including CODH-HCP co-occurrence, informs interpretations of enzymatic activity, biotechnological potential, and differential functional roles, in line with current standards in genomic enzymology. With solid support, this work provides a broadly informative contribution to the field.

eLife Assessment

This potentially valuable manuscript focuses on the phosphorylation of residue T495 as a mechanism to inactivate HSP70 and disrupt cell cycle progression in response to DNA damage. The evidence supporting this model is solid, but would be significantly strengthened by additional studies defining the extent of T495 phosphorylation induced by DNA damage, identifying the kinase responsible for phosphorylating T495 of HSP70, and further elucidation of the functional implications of T495 phosphorylation in human cells. This work will be of interest to scientists focused on topics including chaperone biology, proteostasis, cell cycle progression, and DNA damage.

eLife Assessment

This study makes an important contribution by revealing how saccades selectively disrupt spatial working memory while sparing other object features, and by demonstrating how this mechanism is altered in aging and neurodegeneration. The findings are supported by convincing evidence derived from well-controlled eye-tracking experiments and systematic generative model comparisons. Together, the work provides a computationally grounded framework that is of importance for understanding trans-saccadic memory and its clinical relevance.

eLife Assessment

This important study combines optogenetic manipulations with wide-field cortical imaging to investigate the neural basis of context-dependent sensory processing. It provides compelling evidence that the retrosplenial cortex modulates behavioral responses to whisker deflection depending on the behavioral context. The paper will be of strong interest to neuroscientists studying cortical mechanisms of sensorimotor processing.

eLife Assessment

This is an important study showing that movement vigor is not solely an individual property but emerges through interaction when two people are physically linked. The evidence is convincing, supported by a well-controlled experimental design and modeling that closely match the observed behavior. While the authors provided a helpful comparison of several candidate models of human-human interaction dynamics, the statistical power remains limited.

eLife Assessment

This important study reports three experiments examining how the subjective experience of task regularities influences perceptual decision-making. Although the evidence linking subjective ratings to behavioral measures is solid, the study would be strengthened if potential reverse influences of response times on subjective ratings were ruled out and if more comprehensive model comparisons supporting the main claims were performed. The findings will appeal to a wide range of researchers in decision-making and perception.

eLife Assessment

The goal of this useful study is to examine learning-related changes in neural representations of global and local spatial reference frames in a spatial navigation task. Although the study addresses an interesting question, the evidence for neural representations in the hippocampus and retrosplenial cortex remains incomplete because of confounds in the experimental design and partial data analysis. There are further concerns about the framing of the study in the context of the relevant literature as well as the discussion.

eLife Assessment

This fundamental work advances our understanding of the role of kisspeptin neurons in regulating the luteinizing hormone (LH) surge in females. The study uses cutting-edge techniques to provide compelling and rigorous data supporting a critical role of RP3V kisspeptin neurons in the neuroendocrine LH surge process. This research will be of interest to reproductive biologists and neuroscientists studying the female ovarian cycle. Continuing to examine the complexities of the LH surge and the neuronal populations involved, as done in this study, is critical for developing therapeutic treatments for women's reproductive disorders.

eLife Assessment

This study reports important advances in our understanding of how enteropathogenic E. coli (EPEC) interacts at the intestinal interface. Compelling data describe a novel model of spatially coordinated calcium signaling to modulate NF-kB activation. These findings, which integrate imaging, genetics, and computational modeling, provide a new way to consider host-pathogen interactions in EPEC infections that may lead to improved therapies.

eLife Assessment

This study presents compelling new data that combine two FTD-tau mutations, P301L/S320F (PL-SF), that reliably induce spontaneous full-length tau aggregation across multiple cellular systems. The findings are important for the field of neurodegenerative disease. The strength of evidence is solid; however, several conclusions would benefit from more validation.

eLife Assessment

This useful study provides a systematic comparison of sex-biased enteroendocrine hormone expression in Drosophila and suggests that gut-derived peptides may contribute to female-biased triglyceride levels. The revised manuscript includes helpful textual clarifications and an integrative model, but the evidence remains incomplete, because the proposed role of Tk is still over-interpreted relative to authors' stated criterion for statistical significance against both parental controls. The work will be of interest to researchers studying sex differences in metabolism, but the central mechanistic claims require either stronger experimental support or more careful qualification.

eLife Assessment

In this important manuscript, the authors establish a vertebrate model for studying the development of circuits that control heart rate. This contribution uses a combination of experimental techniques to provide compelling information for scientists looking to understand how heart rate regulation emerges during development.

eLife Assessment

This study provides a valuable advance in understanding how decision boundaries may change over time during simple choices by introducing a method that uses information about non-decision components to improve parameter estimates. The evidence supporting the main claims is convincing, with clear demonstrations on simulated and real data, although additional model comparison work would further strengthen confidence. The findings will be of interest to researchers studying human decision processes and the methods used to analyse them.