Evaluated articles

Evaluation Summary:

The current manuscript will be of interest to researchers working in aging, diabetes, and neurocognition. This work emphasizes the role of diabetes in brain aging and cognitive functions that are considered an hourly need due to the increasing trend in the prevalence of diabetes around the world. This article provides valuable information about specific brain regions altered during aging and diabetes. Further, this article reports how T2DM accelerates the aging-associated decline in cognition and brain function. Extensive analysis of human datasets and comparison with published data from other researchers support the conclusion of this study. However, as mentioned by the authors, certain decisions like diabetic interventions that do not rescue brain damage need further validation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript addresses mechanisms by which bacteria are able to survive and evade killing by antibiotics. Using fluorescent versions of antibiotics it studies whether if entry/efflux of the drug itself is a significant contributor to the observed variability of antibiotic activity. This study will be of interest to microbiologists and clinicians for design of better antibiotic therapies.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript is of interest to molecular neurobiologists studying Nicotinic acetylcholine receptors (nAChRs) or other membrane bound receptors. The paper highlights several different and complementary techniques relevant for studying membrane proteins in native conditions, which are relevant and useful to a wide audience.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This work reports the structure of the photosystem I of Gloeobacter, a cyanobacterium that does not contain low energy absorbing chlorophylls, the so-called red forms. By comparing this structure to those of other cyanobacteria that contain red forms, the authors aim to identify the chlorophylls responsible for low-energy absorption in PSI. Their second aim is to understand the role of the red forms. The topic is interesting, the structural data are very good, but the conclusions regarding the role of the red forms are not supported by data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is of broad interest to those interested in the relationship between mind wandering and reading, at the behavioral and neural levels, including when both processes occur at the same time. As such, this manuscript has important implications for clarifying how the experience of mind wandering while reading may occur. The results partially support the proposed theoretical framework that mind wandering during reading disrupts processing of visual input, however, not all of the authors' claims appear to be supported by the experimental design and data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is of broad interest to the neuroimaging community. It establishes a detailed reference model of human brain development and lifespan trajectories based on a very large data set, across many cortical and subcortical brain regions. The model not only explains substantial variability on test data, it also successfully uncovers individual differences on a database of psychiatric patients that, in addition to group-level analyses, may be critical for diagnosis, thereby demonstrating high clinical potential. It presents a clear overview of the data resource, including detailed evaluation metrics, and makes code, models and documentation directly available to the community.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper builds on a previously published computational model of the insect central complex developed to generate a biologically plausible neural circuit for producing visually guided navigation behavior to show how the same model can be used to produce navigation behavior in response to multimodal sensory information. In particular, the authors show that olfactory navigation as well as wind-guided navigation can be seamlessly integrated with visual behaviors. The work is significant, valuable and of broad interest to circuit and computational neuroscientists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study examines genetic and non-genetic factors influencing immune responses in type 1 diabetes Key findings are: 1) age and season affect immune cell traits and cytokine production upon stimulation; 2) certain genetic variants that determine susceptibility to T1D significantly affect T cell composition, notably the CCR region that is associated with CCR5+ regulatory T cells; and 3) 15 genetic loci that influence immune responses in T1D, most of which have not been seen previously in healthy populations. The results suggest mechanisms of T1D-specific genetic regulation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is a tour de force study, with elegant mouse genetics and potentially clinically relevant rescue results using a small molecule inhibitor that can aleriorate cleft palate in a mutant mouse model. The work will be of interest to the craniofacial biology community and to the broader developmental biology community, as well as to all those devoted to the study of the epigenetic and transcriptional regulation of morphogenesis and organogenesis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Phosphoinositide phosphates (PIPs) are lipids that can convey distinct identities to different cellular membranes via different phosphorylation patterns. Here, Doumane and co-authors document the effects of the previously-characterized sac9 mutant, affecting a putative PIP-5-phosphatase in Arabidopsis, on PIP localization and endocytic trafficking. This work confirms that disrupting PI(4,5)P2 localization can affect endocytic trafficking in plants and will be of interest to the plant and cell biology research fields.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Olfactory coding is still an open question in neuroscience. Therefore, this paper is of potential interest to a broad audience of neuroscientists. It undertakes a thorough investigation of how olfactory sensory neurons drive avoidance or attraction in flies and also addresses how combinations of active ORNs can become behaviorally meaningful. It has great potential value for clarifying how animals map sensory input to valence.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This study is of interest to scientists working in the field of genetic control of glial cell differentiation, myelination and repair. The data are extensive, of high quality, support their main conclusions, and provide novel insights into regulation of genetic compensatory mechanisms. The presentation and interpretation of the data can be improved.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Tissue microarrays (TMA) have become a mainstay in clinical and basic research, for both discovery and validation of biomarkers. This manuscript provides relevant methodologic considerations for cancer researchers investigating tissue-biomarkers using TMAs. A comprehensive investigation was conducted using a combination of analytic approaches using empirical data and simulated data to support key findings and conclusions. The authors approach the possible sampling variation in a thoughtful way, not only quantifying the issue systematically, but working towards a solution.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Sugawara et al describe a new interactive tool for 3D cell tracking in time that allows the user to retrain models quickly with updated labels. The utility of a tool like this for biologists is great: many experiments require tracking cell division over time or cell movements. With clear comparison to the latest developments in cellular segmentation and an improved procedure enabling the use of the tool, this paper would make an interesting contribution to the image analysis field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

Mika and colleagues reconstruct the evolution of uterine endometrial transcriptomes during pregnancy from 23 diverse species of mammals that differ with respect to their degree of placental invasiveness. Through this analysis the authors infer that the eutherian mammal ancestor had an invasive mode of placentation and that the degree of invasiveness of placentation is reflected on uterine endometrial gene expression during pregnancy. Thus, phylogenetic analysis of gene expression profiles of different mammals groups them on the basis of degree of placental invasiveness, a quite striking finding.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Diminishing returns on sampling new variable sites with increasing samples sizes is a classic limitation of population genomics and one that limits the power of population genomic approaches to make site-specific inferences of natural selection. This timely study demonstrates that methylated CpG sites, which have a mutation rate an order of magnitude higher than other sites in the genome, are saturated with polymorphisms in modern human genomic datasets. They can thus serve as a starting point for understanding the effects of natural selection at the resolution of single nucleotide sites. The manuscript is a clearly written presentation of the state of the field and the claims are supported by a variety of thoughtful analyses. Additional work will be needed to take full advantage of the insights from this study.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper will be of interest to electrophysiologists, systems neuroscientists and neural engineers. The authors describe a framework for evaluating the comparison between LFP dynamics and spikes and perform this comparison for several datasets recorded from motor, premotor, and sensory areas of cortex in rhesus macaque monkeys. These results serve as an important benchmark for the information content of LFP recordings, which is relevant to data collection in neuroscientific investigations and to designing brain computer interfaces.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper examines the effects of amylospheroids, highly neurotoxic assemblies of β-amyloid, on aortic function and on cultured cells. The authors propose that the interaction of amylospheroids with the sodium pump in endothelial cells induces production of reactive oxygen species to ultimately comprise nitric oxide generation. The study provides some new insight into mechanisms underlying brain blood vessel dysfunction and will be interesting neuroscientists who study neurovascular contribution to neurodegenerative diseases. The conclusions of the manuscript are supported by the data, but alternative approaches would make the study stronger.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to oncologists and dermatologists and has high clinical relevance. It reveals a novel mechanism of EGFR inhibitor-induced rash which be may closely related to atrophy of dermal white adipose tissue (dWAT). A series of experimental manipulations dissect the mechanism with a murine model, supporting the major claims of the paper.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors identify a novel compound called Dwn1 that suppresses the expression of Npas2, a key gene that delays wound healing. In doing so, they identify a novel treatment strategy for incisional surgical wounds that may have broader application to the treatment of scars in general.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)