eLife

Latest preprint reviews

1. Impacts of DNA Methylation on H2A.Z Deposition and Nucleosome Stability

   This article has 4 authors:

   1. Rochelle M Shih
   2. Yasuhiro Arimura
   3. Hide A Konishi
   4. Hironori Funabiki

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable mechanistic insight into the mutually exclusive distributions of the histone variant H2A.Z and DNA methylation by testing two hypotheses: (i) that DNA methylation destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin remodelling complexes. Through a series of well-designed and carefully executed experiments, findings are presented in support of both hypotheses. However, the evidence in support of either hypothesis is incomplete, so that the proposed mechanisms underlying the enrichment of H2A.Z on unmethylated DNA remain somewhat speculative.

   Reviewed by eLife

2. Identifying tissue states by spatial protein patterns related to chemotherapy response in triple-negative breast cancer

   This article has 11 authors:

   1. L.M. Luque
   2. A. Khan
   3. G. Torrisi
   4. Tessa D. Green
   5. D. Hardman
   6. C. Owczarek
   7. T. A. Phillips
   8. D.S. Marks
   9. M. Parsons
   10. C. Sander
   11. L.J. Schumacher

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important work implementing data mining methods on IMC data to discover spatial protein patterns related to the triple-negative breast cancer patients' chemotherapy response. The evidence supporting the claims of the authors is solid, although more detailed methodology clarification and validation are needed. While the accuracy of the methods is not very high, the work shows potential for translational application.

   Reviewed by eLife

3. Molecular and Functional Analysis of Calcium Binding by a Cancer-linked Calreticulin Mutant

   This article has 7 authors:

   1. Ishmael Nii Ayibontey Tagoe
   2. Amanpreet Kaur
   3. Osbourne Quaye
   4. Emmanuel Ayitey Tagoe
   5. Nicole Koropatkin
   6. Leslie S Satin
   7. Malini Raghavan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study investigates low-affinity Ca2+ binding by WT calreticulin and mutant calreticulin associated with type I myeloproliferative neoplasms, as well as the impact on Ca2+ fluxes in suspension cultures of megakaryocyte-like cells in vitro in response to ER Ca2+ ATPase inhibitors that deplete endoplasmic reticulum (ER) Ca2+ store and open plasma membrane Ca2+ channels through STIM1-Orai interactions. The results are important in that they show that Ca2+ binding by calreticulin and store-operated Ca2+ entry are not fundamentally impacted by the type I deletion mutation in calreticulin, which rules out a direct effect of the calreticulin mutation on its own low-affinity Ca2+ binding and any broad impact on ER Ca2+ regulation. The strength of the data and methods used ranges from solid to convincing, although the use of suspension-based flow cytometric assays to investigate ER Ca2+ levels and Ca2+ entry can be challenged. High-affinity Ca2+ binding sites could be further considered, and possible confounding effects of Abl kinase activity in the megakaryocyte-like cell lines could be offset.

   Reviewed by eLife

4. Involuntary feedback responses reflect a representation of partner actions

   This article has 7 authors:

   1. Seth R Sullivan
   2. John H Buggeln
   3. Jan A Calalo
   4. Truc T Ngo
   5. Jennifer A Semrau
   6. Michael J Carter
   7. Joshua GA Cashaback

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study combines a two-person joint hand-reaching paradigm with game-theoretical modeling to examine whether, and how, one's reflexive visuomotor responses are modulated by a partner's control policy and cost structure. The study provides a solid and novel set of behavioral findings suggesting that involuntary visuomotor feedback is indeed modulated in the context of interpersonal coordination. The work will be of interest to cognitive scientists studying the motoric and social aspects of action control.

   Reviewed by eLife

5. Concurrent category-selective neural activity across the ventral occipito-temporal cortex supports a non-hierarchical view of human visual recognition

   This article has 4 authors:

   1. Corentin Jacques
   2. Jacques Jonas
   3. Sophie Colnat-Coulbois
   4. Bruno Rossion

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study addresses a classic debate in visual processing, using a strong method applied to a rare clinical population to evaluate hierarchical models of visual object perception. The paper finds only partial support for the hierarchical model: as expected, neural responses in ventral visual cortex show increased representational selectivity for faces along the posterior-anterior axes, but the onsets of the signals do not show a temporal hierarchy, indicating more parallel processing. The iEEG dataset is impressive, but the evidence for lack of temporal hierarchy is incomplete: essential quality checks need to be performed, and statistical analyses adapted to ensure that the data and analyses would be able to reveal temporal hierarchy if it were present in the data.

   Reviewed by eLife

6. Domain-adaptive matching bridges synthetic and in vivo neural dynamics for neural circuit connectivity inference

   This article has 10 authors:

   1. Kaiwen Sheng
   2. Shanghang Zhang
   3. Shenjian Zhang
   4. Yutao He
   5. Maxime Beau
   6. Peng Qu
   7. Xiaofei Liu
   8. Youhui Zhang
   9. Lei Ma
   10. Kai Du

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This article reports an algorithm for inferring the presence of synaptic connection between neurons based on naturally occurring spiking activity of a neuronal network. One key improvement is to combine self-supervised and synthetic approaches to learn to focus on features that generalize to the conditions of the observed network. This valuable contribution is currently supported by incomplete evidence.

   Reviewed by eLife

7. Improved inference of latent neural states from calcium imaging data

   This article has 4 authors:

   1. Stephen Keeley
   2. David Zoltowski
   3. Adam Charles
   4. Jonathan Pillow

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study provides a practical computational framework for inferring latent neural states directly from calcium fluorescence recordings, bypassing the traditional need for a separate spike deconvolution step. The evidence supporting the method is solid, featuring rigorous validation across multiple latent variable model families (including HMM, GPFA, and LFADS) using both simulated and experimental data. However, the assessment of the method's generality would be further strengthened by application to a broader range of experimental datasets, such as recordings from different brain regions or using different calcium indicators.

   Reviewed by eLife

8. Dopamine and its receptor DcDop2 are involved in the mutualistic interaction between ‘Candidatus Liberibacter asiaticus’ and Diaphorina citri

   This article has 10 authors:

   1. Xiaoge Nian
   2. Jiayun Li
   3. Jilei Huang
   4. Weiwei Yuan
   5. Paul Holford
   6. George Andrew Charles Beattie
   7. Jielan He
   8. Yijing Cen
   9. Yurong He
   10. Songdou Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Insects can act as vectors of plant diseases, hence the study of insect-pathogen interactions is relevant for agriculture. This important study identifies in Diaphorina citri a dopamine receptor responsive to 'Candidatus Liberibacter asiaticus' infection, demonstrate direct regulation of this receptor by a microRNA, and integrate dopamine signaling into an established insect reproductive hormone framework. Multiple complementary experimental approaches convincingly support the findings, but key conclusions rely on correlative data and the mechanistic evidence for the proposed linear signaling cascade is incomplete. This work will be of interest for insect physiology and vector-pathogen biology, and more broadly for citrus agriculture.

   Reviewed by eLife

9. Benchmarking of signaling networks generated by large language models

   This article has 3 authors:

   1. Jeevan Tewari
   2. Benjamin W Dahl
   3. Jeffrey J Saucerman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors address a hard question and propose a pipeline for using Large Language Models to reconstruct signalling networks as well as to benchmark future models. The findings are valuable for a defined subfield, as the proposed framework allows for assessing such approaches systematically. The overall support is solid, although the present evaluation remains limited in scope and would benefit from a wider range of networks and performance metrics.

   Reviewed by eLife

10. Subregional activity in the dentate gyrus is amplified during elevated cognitive demands

    This article has 4 authors:

    1. Charlotte CM Castillon
    2. Shintaro Otsuka
    3. John N Armstrong
    4. Anis Contractor

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This manuscript presents a valuable study of the activity and functional relevance of different circuits in the dentate gyrus of mice performing a pattern separation task. The study is likely to be of interest to those studying the subregional organization and cell type-specific functions of the dentate gyrus. However, the strength of evidence for the study's conclusions is currently incomplete.

    Reviewed by eLife