Neuroscience

eLife Assessment

This work describes a useful computational tool for automated morphometry of dynamic organelles from microscope images. However, the supporting evidence and novelty of the manuscript as presented are incomplete and could be improved. The work will be of interest to microscopists and bioimage analysts who are non-experts but wish to improve quantitative analysis of cellular structures.

eLife Assessment

This valuable study tests whether prediction error or prediction uncertainty controls how the brain segments continuous experience into events. The paper uses validated models that predict human behavior to analyze multivariate neural pattern changes during naturalistic movie watching. The authors provide solid evidence that there are overlapping but partially distinct brain dynamics for each signal.

eLife Assessment

The authors investigate how dominance hierarchy shapes defensive strategies in mice under two naturalistic threats: a transient visual looming stimulus and a sustained live rat. This study provides important insights into how social context and dominance hierarchy modulate innate defensive behaviors across distinct naturalistic threats. The strength of evidence is convincing, with detailed classification and analysis of behaviors.

eLife Assessment

This work represents a valuable finding of how single-trial functional connectivity may be used to infer different cognitive states involved in speech perception and production. Although the data and analyses are overall convincing, the theoretical advance and novelty of the finding are less clear. With a clearer idea of the functional significance of the connectivity data, the paper would be of interest to those interested in brain networks and communication.

eLife Assessment

This important study is of relevance for the fields of predictive processing, perception and learning, with a well-designed paradigm allowing the authors to avoid several common confounds in investigating predictions, such as adaptation. Using a state-of-the-art multivariate EEG approach, the authors test the opposing process theory and find evidence in support of it. Overall, the empirical evidence is solid, however, some conclusions rest on limited evidence and need further work to reconcile the present results with previous studies.

eLife Assessment

This important study by Bartas and colleagues examined how patterns of monosynaptic input to specific cell types in the ventral tegmental area are altered by drugs of abuse. The authors applied a dimensionality reduction approach (principal component analysis) and showed that various drugs of abuse, and somewhat surprisingly the anesthesia alone (ketamine/xylasin), caused changes in the distribution of inputs labeled by the transsynaptic rabies virus. The evidence supporting the conclusions is overall convincing and provides foundational information, as well as a cautionary note on the interpretation of rabies virus-based tracing experiments.

eLife Assessment

This study provides valuable findings on how the activity of the E3 ubiquitin ligase Highwire (Hiw/Phr1) is regulated and its impact on synaptic growth. The authors propose that impaired endocytosis leads to condensation of Hiw, resulting in increased synaptic growth. They also integrate such a mechanism within the known JNK (c-JUN N-terminal Kinase) and BMP (Bone Morphogenetic Protein) signalling pathways involved in synapse regulation. While the work raises an interesting mechanistic framework, several aspects of the experimental design and methodology are incomplete, and key conclusions, particularly those regarding the liquid-liquid phase separation of the E3 ubiquitin ligase, are not fully supported by the presented data.

eLife Assessment

This valuable study examined how sensory adaptation supports visual perception in the presence of noise. The authors used a combination of human psychophysics, electroencephalography (EEG), and deep neural networks to show that adaptation to noise can improve perception. The results are solid but are, at present, weakened by a number of concerns, including some related to the experimental design and some regarding the interpretation of the results in terms of particular mechanisms. With these concerns adequately addressed, the study and conclusions would be likely to be of broad interest to the neuroscience community.

eLife Assessment

This study presents a valuable and well-documented computational pipeline for the scalable analysis and spike sorting of large extracellular electrophysiology datasets, with particular relevance for high-density recordings such as Neuropixels. The authors demonstrate the pipeline's utility for benchmarking spike sorter performance and evaluating the effects of data compression, supported by thorough testing, clear figures, and openly available code. The workflow is reproducible, portable, and practical, providing concrete guidance on computational cost and runtime. Overall, the evidence supporting the pipeline's performance and output quality is compelling, and this work will be of broad interest to the systems neuroscience community.

eLife Assessment

This manuscript presents a novel investigation of organizational principles governing brain activity at both global and local scales during naturalistic viewing paradigms, an important advance for theoretical neuroscience, functional neuroimaging, and neurology. The authors demonstrate that brain activity during naturalistic viewing is dominated by two anti-correlated states that toggle between each other with a third transitional state mediating between them. The evidence supporting this finding is compelling, with the successful replication across three independent datasets (StudyForrest, NarrattenTion, and CamCAN) a particular strength.