Evaluated articles

eLife assessment

In this paper, the authors introduce fundamental work on mathematical methods for inferring evolutionary parameters of interest from RNA data in healthy tissue and during hematopoiesis. By combining single cell and bulk sequencing analyses, the authors use a stochastic process to inform different aspects of genetic heterogeneity; the strength of evidence in support of the authors' claim is exceptional. The work will be of broad interest to cell biologists and theoretical biologists.

eLife assessment

This important manuscript investigates the role of a subpopulation of glutamatergic neurons in the suprammamillary nucleus that projects to the pre-optic hypothalamus area in active coping but not locomotor activity. They provide solid evidence from experiments using fibre photometry or photostimulation during threatening tasks that these neurons allow animals to produce flexible behaviours in response to stress. This work will be of interest to behavioural and systems neuroscientists.

eLife assessment

This important study advances our understanding of how listeners understand speech when there are multiple talkers by showing that the content of the speech affects acoustic processing. The evidence is generally solid, although additional details on the methods to allow replication would strengthen the study. The work will be of use to researchers interested in the neuroscience of speech and language processing.

eLife assessment

This important study identifies a spatial pattern of neural activity that corresponds to trust in an investment game. It provides a compelling assessment of the validity of this pattern by assessing its expression, or lack thereof, in a variety of datasets. This work, and the "neurometrics" approach it proposes, will be of broad interest to psychology researchers more generally.

eLife assessment

This is an important study that improves gene models for the ferret genome and identifies neural progenitors that are comparable to those found in developing human brains. The data are convincing and clearly presented. Of particular interest to the field, the work identifies enriched expression of FOXJ1 in late truncated radial glia, strongly indicating that towards the end of neurogenesis, these cells likely give rise to ependymal cells. The work is of interest to anyone studying the development of the nervous system, especially colleagues studying the evolution of development.

eLife assessment

This manuscript will provide a valuable method to evaluate the safety of MR in patients with orthopaedic implants, which is required in clinics. A strength of the work is that the in-silicon testbed is solid, based on the widely available human project, and validated. In addition, the toolbox will be open for clinical practice.

eLife assessment

This fundamental study advances our understanding of the cell specific treatment of cone photoreceptor degeneration by Txnip. The evidence supporting the conclusions is compelling with rigorous genetic manipulation of Txnip mutations. The work will be of broad interest to vision researchers, cell biologists and biochemists.

eLife assessment

This important study presents a new way to selectively activate a cell signaling pathway in a specific cell type by designer ligands that link signaling co-receptors to a marker specific to the target cells. Convincing experimental results demonstrate that the agonist molecules activate Wnt signaling in target cells expressing the marker as intended. More broadly, this concept could be used to induce Wnt signaling or another pathway initiated by co-receptor association in a cell type-specific manner. In vitro results in this study could be further strengthened by assessing the biological consequences of Wnt activation in target cells.

eLife assessment

This is an important demonstration of how the false-positive rate of high-resolution 2D template matching to find particles of a given target structure in 2D cryo-EM images (2DTM) relates to overfitting the data towards the template. The authors present new methods to measure the amount of model bias that gets introduced in high-resolution features of such maps, with compelling evidence that high-resolution features that are not present in the template can still be reconstructed in 3D from images obtained by 2DTM.

eLife Assessment

This valuable study presents findings on the role of the small GTPase Rab3A in homeostatic plasticity. While the study provides solid evidence for a requirement of Rab3A in homeostatic up-scaling in cultured mouse neurons, it does not provide a model of how Rab3A is involved in homeostatic plasticity. The work will be of interest to researchers in the field of synaptic transmission and synaptic plasticity.

eLife assessment

This is an important study that addresses a significant question in microbiome research. The authors provide convincing evidence that certain bacterial groups within the fly microbiome have critical functions for host development. Additionally, dietary aspects such as microbial community progression in a natural food source are integrated into their host-microbe interaction analyses.

eLife assessment

Necarsulmer et al describe an interesting new mouse model of TDP-43 proteinopathy in which gene editing was used to introduce a K145Q acetylation-mimic mutation previously shown to impair RNA-binding capacity and induce downstream misregulation of target genes. Mice homozygous for this mutation are convincingly shown to display cognitive/behavioral impairment, TDP-43 phosphorylation and insolubility, and changes in gene expression and splicing. This novel mouse model replicates some key hallmarks of human frontotemporal lobar degeneration and will be an important contribution to the field.

eLife assessment

The authors use point light displays to measure biological motion (BM) perception in children (mean = 9 years) with and without ADHD, and relate it to IQ, social responsiveness scale (SRS) scores and age. They report that children with ADHD were worse at all three BM tasks, but that those tasks loading more heavily on local processing relate to social interaction skills and those loading on global processing relate to age. There are still some elements of the results that need clarification with future work, but nevertheless, the important and solid findings extend our limited knowledge of BM perception in ADHD, as well as biological motion processing mechanisms in general.

eLife assessment

In this important study, the authors develop a promising experimental approach to a central question in ecology: What are the contributions of resource use and interactions in the shaping of an ecosystem? For this, they develop a synthetic ecosystem set-up, a variant of SELEX that allows very detailed control over ecological variables. The evidence is convincing, and the work should be of broad interest to the ecology community, leading to further quantitative studies.

eLife assessment

This important study indicates a role for linker Histone H1 in protecting heterochromatic regions from certain types of repression. The experiments and data analysis that support the model for the role of linker Histone H1are solid, although additional experiments could provide a deeper mechanistic understanding. The study will be of broad interest to those interested in the role of chromatin in eukaryotic gene expression.

eLife assessment

This study tests the effects of using neurofeedback, in the form of reward delivery when large sharp wave-ripples (SWRs) are detected, on neurophysiological and behavioral measures. The results are important, and the authors provide convincing evidence that the rate of SWRs increased prior to reward delivery and decreased in the period after reward delivery, with no significant effect on memory performance. The ability to manipulate SWR rate in a naturalistic way is an exciting new tool for studies that seek to understand the function of SWRs.

eLife assessment

The study is of importance for the cardiac modeling field by developing a novel mathematical model with sex difference. The data are compelling, and the model is helpful for mechanistic understanding, and thus is also important for experimental physiology. The model is based on experimental data and validated against some experimental data.

eLife Assessment

This valuable study focuses on the regulation of Notch signaling during the immune response in Drosophila. The authors provide solid evidence in support of roles for Su(H) and Pkc53E-induced phosphorylation in Drosophila immunity. The work will be of interest to colleagues in immunity and receptor signaling.

eLife assessment

This important study points out discrepancies between the clinical diagnosis of Clostridioides difficile infection and the lack of detectable C. difficile in gut microbiome samples, as well as different relationships between asymptomatic C. difficile carriage and adult or infant gut microbiota compositions. While the solid analysis of a comprehensive and diverse metagenomic dataset suggests an over-diagnosis of C. difficile infection and an under-diagnosis of other putative enteric pathogens, the work requires addressing the detection limitations of the approach to be more convincing. This work will interest microbiologists and clinicians concerned with understanding the role of C. difficile in gut microbiota health and dysbiosis.

eLife assessment

This important study uses a combination of computational modeling and glutamate imaging to show how a particular synaptic organization referred to as space-time wiring contributes minimally to a dendritic computation that occurs in the retina. The evidence supporting the claims of the authors is compelling, incorporating new findings regarding dynamic receptive field properties, an improvement over previous modeling and experimental results based on static visual stimuli. The work will be of interest to retinal neurobiologists and neurophysiologists interested in dendritic computations.