Evaluated articles

Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities

1. Swapnesh Panigrahi
2. Dorothée Murat
3. Antoine Le Gall
4. Eugénie Martineau
5. Kelly Goldlust
6. Jean-Bernard Fiche
7. Sara Rombouts
8. Marcelo Nöllmann
9. Leon Espinosa
10. Tâm Mignot

• Curated by eLife

  Evaluation Summary:

  In this work, Panigrahi et. al. develop a powerful deep-learning-based cell segmentation platform (MiSiC) capable of accurately segmenting brightfield, fluorescence, and phase contrast images of bacteria cells densely packed within both homogenous and heterogeneous cell populations. This algorithm, if further optimized and disseminated to the community, will have a large impact in microbial studies in that it will allow for automated analyses of essential every aspect of bacterial cell biology, including cell morphology, cell cycle, cell-cell communications, protein localization dynamics and a variety of cellular processes using time-lapse imaging.

  (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.)

Reviewed by eLife

Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships

1. Jennifer E Jones
2. Valerie Le Sage
3. Gabriella H Padovani
4. Michael Calderon
5. Erik S Wright
6. Seema S Lakdawala

Reviewed by eLife

Expansion of CD10neg neutrophils and CD14+HLA-DRneg/low monocytes driving proinflammatory responses in patients with acute myocardial infarction

1. Daniela Fraccarollo
2. Jonas Neuser
3. Julian Möller
4. Christian Riehle
5. Paolo Galuppo
6. Johann Bauersachs

• Curated by eLife

  Evaluation Summary:

  This paper will be of broad interest to cardiologist and scientists studying acute myocardial infarction (AMI), especially to those focussing on the immune responses during AMI. Using combination of in vivo and in vitro model, as well as tissue from patients, the authors reveal new insights regarding the immune mechanisms during AMI, highlighting the importance of neutrophils and monocytes during the early days of its process. The findings in this paper add to the understanding of how immune mechanisms may contribute to subsequent adverse events after AMI.

  (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)

Reviewed by eLife

T-cell receptor (TCR) signaling promotes the assembly of RanBP2/RanGAP1-SUMO1/Ubc9 nuclear pore subcomplex via PKC-θ-mediated phosphorylation of RanGAP1

1. Yujiao He
2. Zhiguo Yang
3. Chen-si Zhao
4. Zhihui Xiao
5. Yu Gong
6. Yun-Yi Li
7. Yiqi Chen
8. Yunting Du
9. Dianying Feng
10. Amnon Altman
11. Yingqiu Li

• Curated by eLife

  Evaluation Summary:

  PKC-theta is known to regulate T cell activation, and this manuscript reveals a novel function of PKC-theta in the regulation of the nuclear pore complexes. The work by He and colleagues reveals that PKC-theta is recruited to the nuclear pore complex wherein it serves to regulate the assembly of key components of the RanBP2 subcomplex of the NPC, which in turn enables the translocation of AP1, NFkB and NFAT into the nucleus. However, these results need to be substantiated by additional experiments or by limiting the breath of the conclusions.

  (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.)

Reviewed by eLife

Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics

1. Ioannis Galdadas
2. Shen Qu
3. Ana Sofia F Oliveira
4. Edgar Olehnovics
5. Andrew R Mack
6. Maria F Mojica
7. Pratul K Agarwal
8. Catherine L Tooke
9. Francesco Luigi Gervasio
10. James Spencer
11. Robert A Bonomo
12. Adrian J Mulholland
13. Shozeb Haider

• Curated by eLife

  Evaluation Summary:

  This manuscript presents a computational study aiming to understand the allosteric signaling propagation pathway in two class-A beta-lactamases. The results of this study will be of interest to the readers in the fields of beta-lactamase, antibiotic resistance, and enzyme allostery.

  (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. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Reviewed by eLife

Asymptomatic Bordetella pertussis infections in a longitudinal cohort of young African infants and their mothers

1. Christopher J Gill
2. Christian E Gunning
3. William B MacLeod
4. Lawrence Mwananyanda
5. Donald M Thea
6. Rachel C Pieciak
7. Geoffrey Kwenda
8. Zacharia Mupila
9. Pejman Rohani

• Curated by eLife

  Evaluation Summary:

  Overall the reviewers were positive about this manuscript and the importance of this analysis being in identifying the role of asymptomatic transmitters in populations. There are some revisions that will be required and a number of areas for additional analyses and clarifications that would help the reader better put this manuscript in context.

  (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.)

Reviewed by eLife

Enhanced functional detection of synaptic calcium-permeable AMPA receptors using intracellular NASPM

1. Ian Coombs
2. Cécile Bats
3. Craig A Sexton
4. Dorota Studniarczyk
5. Stuart G Cull-Candy
6. Mark Farrant

• Curated by eLife

  Evaluation Summary:

  Here the authors identify that inclusion of intracellular NASPM can fully block Ca-permeable AMPA receptors regardless of association with auxiliary subunits. The distinction between Ca-permeable and Ca-impermeable AMPA receptors is critical to synaptic physiology, and thus these results will be of interest within the field of excitatory synaptic transmission. The data is of high quality and the experimental analysis is rigorous, but the key claim that the approach provides an unambiguous functional measure of CP-AMPAR prevalence has not been fully supported.

  (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.)

Reviewed by eLife

Genetic integration of behavioural and endocrine components of the stress response

1. Thomas M Houslay
2. Ryan L Earley
3. Stephen J White
4. Wiebke Lammers
5. Andrew J Grimmer
6. Laura M Travers
7. Elizabeth L Johnson
8. Andrew J Young
9. Alastair Wilson

• Curated by eLife

  Evaluation Summary:

  This is a timely paper on the genetic integration of behavioral and physiological components of the stress response in guppies. Using evolutionary quantitative genetic approaches, the authors show that genetic variation in the cortisol stress response is associated with genetic variation in stress-related behaviors. This result suggests that physiological and behavioral responses to stress should show correlated evolution in response to natural selection, which is of interest to evolutionary biologists and for animal welfare. The reviewers pointed out several conceptual and methodological issues with the definition of the phenotypes under study and and with the definition strong genetic integration.

  (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.)

Reviewed by eLife

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

1. Eyal Ben-David
2. James Boocock
3. Longhua Guo
4. Stefan Zdraljevic
5. Joshua S. Bloom
6. Leonid Kruglyak

• Curated by eLife

  Evaluation Summary:

  The authors use a pooled single cell sequencing approach to simultaneously genotype and phenotype C. elegans. This allows them to begin to query the genetic architecture of cell specific eQTLs in a multi-cellular organism.

  (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.)

Reviewed by eLife

An agnostic study of associations between ABO and RhD blood group and phenome-wide disease risk

1. Torsten Dahlén
2. Mark Clements
3. Jingcheng Zhao
4. Martin L Olsson
5. Gustaf Edgren

• Curated by eLife

  Evaluation Summary:

  In this manuscript, Dahlen et al. agnostically survey a large transfusion database in Sweden to investigate the association between ABO and RhD blood group and disease occurrence for a large number of clinical phenotypes. The data reported are purely epidemiological associations, with no direct insight into biological mechanism. Nonetheless, these data are a valuable resource for the research community, and offer the potential for a number of important biologic hypotheses and insights for investigation in the future.

  (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.)

Reviewed by eLife

CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning

1. Ryan Conrad
2. Kedar Narayan

• Curated by eLife

  Evaluation Summary:

  This manuscript describes the curation of a training dataset that will be an important resource for developers of new segmentation and deep-learning algorithms for electron microscopy data. The small size of the dataset makes it easy to use, and its broad range of image modalities ensure that the model will be applicable in many situations, making it very useful for 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 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Stress resets ancestral heritable small RNA responses

1. Leah Houri-Zeevi
2. Guy Teichman
3. Hila Gingold
4. Oded Rechavi

• Curated by eLife

  Evaluation Summary:

  In humans, extreme stresses, such as famine, can trigger multi-generational physiological responses through altered metabolism. In C. elegans, environmental stresses, such as heat shock, can similarly promote changes in gene expression and physiology. Here, the authors convincingly show that environmental stress can alter small RNA populations in such a manner that can alter gene expression over multiple generations. The work is beginning to tease out some of the mechanisms by which non-genetic information can regulate descendants biology.

  (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.)

Reviewed by eLife, preLights

Impaired spatial learning and suppression of sharp wave ripples by cholinergic activation at the goal location

1. Przemyslaw Jarzebowski
2. Clara S Tang
3. Ole Paulsen
4. Y Audrey Hay

• Curated by eLife

  Evaluation Summary:

  This paper is of interest for those interested in the roles of cholinergic projections from the medial septum and sharp wave-ripples on reward learning. The work provides compelling evidence showing that activation of septal cholinergic cells at reward zones suppresses sharp wave-ripples and impairs memory performance in freely behaving animals. The work extends our knowledge of the effect of medial septum cholinergic inputs on hippocampal dependent spatial memory formation.

  (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 names with the authors.)

Reviewed by eLife

StormGraph: A graph-based algorithm for quantitative clustering analysis of diverse single-molecule localization microscopy data

1. Joshua M. Scurll
2. Libin Abraham
3. Da Wei Zheng
4. Reza Tafteh
5. Keng C. Chou
6. Michael R. Gold
7. Daniel Coombs

Reviewed by eLife

Systemic inflammation recruits fast-acting anti-inflammatory innate myeloid progenitors from BM into lymphatics

1. Juana Serrano-Lopez
2. Shailaja Hegde
3. Sachin Kumar
4. Josefina Serrano
5. Jing Fang
6. Ashley M. Wellendorf
7. Paul A. Roche
8. Yamileth Rangel
9. Léolène J. Carrington
10. Hartmut Geiger
11. H. Leighton Grimes
12. Sanjiv Luther
13. Ivan Maillard
14. Joaquin Sanchez-Garcia
15. Daniel T. Starczynowski
16. Jose A. Cancelas

• Curated by eLife

  Evaluation Summary:

  The authors demonstrate that acute systemic inflammation induces a new system of rapid migration of granulocyte-macrophage progenitors and committed macrophage-dendritic progenitors but not other progenitors or stem cells from BM to lymphatic capillaries. The cells appear in the lymphatics earlier than in peripheral blood. This type of trafficking is triggered by LPS administration and is anti-inflammatory.

  (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.)

Reviewed by eLife

Distinct higher-order representations of natural sounds in human and ferret auditory cortex

1. Agnès Landemard
2. Célian Bimbard
3. Charlie Demené
4. Shihab Shamma
5. Sam Norman-Haignere
6. Yves Boubenec

• Curated by eLife

  Evaluation Summary:

  Landemard et al. compare the response properties of primary vs. non-primary auditory cortex in ferrets with respect to natural and model-matched sounds, using functional ultrasound imaging. They find that responses do not differentiate between natural and model-matched sounds across ferret auditory cortex; in contrast, by drawing on previously published data in humans, the authors suggest that this is a defining distinction between human and non-human auditory cortex.

  This was found to be a very nice study and with interesting results that are applicable to the general neuroscience community. The analyses are conducted well and a wealth of results are included, including findings for individual subjects and hemispheres (in supplementary figures). Concerns involved the size of the data set (only 2 animals), and some more explanation was needed with respect to data analysis choices.

  (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.)

Reviewed by eLife

Working memory gates visual input to primate prefrontal neurons

1. Behrad Noudoost
2. Kelsey Lynne Clark
3. Tirin Moore

• Curated by eLife

  Summary:

  This is a brief paper documenting the properties of neurons in the frontal eye field (FEF), a cortical brain area traditionally thought to receive visual input and transform it internally to motor commands. The authors used extracellular recordings and electrical microstimulation in behaving non-human primates to add to this view by showing that visual input to FEF from visual area V4 appears to be gated by working -memory activity in FEF. The study was considered well done and interesting, albeit with several important concerns about the interpretation of the findings.

  Reviewer #1 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells

1. Almut S Eisele
2. Jason Cosgrove
3. Aurelie Magniez
4. Emilie Tubeuf
5. Sabrina Tenreira Bento
6. Cecile Conrad
7. Fanny Cayrac
8. Tamar Tak
9. Anne-Marie Lyne
10. Jos Urbanus
11. Leïla Perié

• Curated by eLife

  Evaluation Summary:

  This paper will be of broad interest to readers in the field of cytokine signaling, experimental hematology and clinical hematology. Erythropoietin is one of the most widely used cytokines clinically but the cells it exerts its effects on has been debated. This study has combined clonal lineage tracing and single cell sequencing to understand the cell population that responds to erythropoietin and indicates that erythropoietin acts directly on multipotent progenitors to transiently modulate their output.

  (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.)

Reviewed by eLife

Linguistic processing of task-irrelevant speech at a cocktail party

1. Paz Har-shai Yahav
2. Elana Zion Golumbic

• Curated by eLife

  Summary:

  This study addresses a current and important question: how deeply are "ignored" speech stimuli processed? By imposing a regular rhythm on the to-be-ignored speech and analyzing MEG responses in the frequency domain, you were able to show an increase in power at the phrasal level (1 Hz) of irrelevant speech when It contained structured (linguistic) content, but not at the word level (2 Hz) or the sentence level (0.5 Hz). This finding supports the idea that cortical activity represents syntactic information about the unattended speech. Source analysis shows that the task-irrelevant speech is processed at the sentence level in the left fronto-temporal area and posterior parietal cortex, and in a manner very different from the acoustical encoding of syllables. Though the study is intriguing and well designed, there are some issues that must be addressed to back up the claims of the paper.

  Reviewer #1 and Reviewer #2 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning

1. James A Taylor
2. Yeonee Seol
3. Jagat Budhathoki
4. Keir C Neuman
5. Kiyoshi Mizuuchi

• Curated by eLife

  Evaluation Summary:

  This manuscript reports carefully executed experiments on the dynamics of ParA-ParB and ParB-ParB interactions. Two main findings are presented: a change in stoichiometry of ParA-ParB interactions upon ligand binding and ligand dependent DNA condensation by ParB. The work is solid, the conclusions are generally well supported by the data, however, the relevance of some of the findings could be established more directly.

  (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.)

Reviewed by eLife