Latest preprint reviews

1. Scale matters: Large language models with billions (rather than millions) of parameters better match neural representations of natural language

   This article has 16 authors:

   1. Zhuoqiao Hong
   2. Haocheng Wang
   3. Zaid Zada
   4. Harshvardhan Gazula
   5. David Turner
   6. Bobbi Aubrey
   7. Leonard Niekerken
   8. Werner Doyle
   9. Sasha Devore
   10. Patricia Dugan
   11. Daniel Friedman
   12. Orrin Devinsky
   13. Adeen Flinker
   14. Uri Hasson
   15. Samuel A Nastase
   16. Ariel Goldstein

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study investigates how the size of an LLM may influence its ability to model the human neural response to language recorded by ECoG. Overall, solid evidence is provided that larger language models can better predict the human ECoG response. Further discussion would be beneficial as to how the results can inform us about the brain or LLMs, especially about the new message that can be learned from this ECoG study beyond previous fMRI studies on the same topic. This study will be of interest to both neuroscientists and psychologists who work on language comprehension and computer scientists working on LLMs.

   Reviewed by eLife

2. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2402.07252v3

3. Synapse weakening-induced caspase-3 activity confers specificity to microglia-mediated synapse elimination

   This article has 4 authors:

   1. Zhou Yu
   2. Andrian Gutu
   3. Namsoo Kim
   4. Erin K O’Shea

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important finding on the involvement of a Caspase 3-dependent pathway in the elimination of synapses for retinogeniculate circuit refinement and eye-specific territory segregation. This work fits well with the concept of "synaptosis" which has been proposed in the past but lacked in vivo support. Despite its elegant design and many strengths, the evidence supporting the claims of the authors is incomplete, particularly regarding whether Caspase-3 expression can really be isolated to synapses vs locally dying cells, whether microglia direct or instruct synapse elimination, and whether astrocytes are also involved. The work will be of interest to investigators studying cell death pathways, neurodevelopment, and neurodegenerative disease.

   Reviewed by eLife

4. Characterization of direct Purkinje cell outputs to the brainstem

   This article has 4 authors:

   1. Christopher H. Chen
   2. Zhiyi Yao
   3. Shuting Wu
   4. Wade G. Regehr

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable paper provides an unbiased landscape for the cerebellar cortical outputs to the brainstem nuclei. By conducting anatomical and physiological analyses of the axonal terminals of Purkinje cells, the data provide convincing evidence that Purkinje cells innervate brainstem nuclei directly. The results show that in addition to previously known inputs to vestibular and parabrachial nuclei, Purkinje cells synapse onto the pontine central grey nucleus but have little effect on the locus coeruleus and mesencephalic trigeminal neurons.

   Reviewed by eLife

5. Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression

   This article has 4 authors:

   1. Shengze Yao
   2. Yesu Jeon
   3. Barry Kesner
   4. Jeannie T Lee

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study addresses potential roles of the master regulator of X chromosome inactivation, the Xist long non-coding RNA, in autosomal gene regulation. Using data from mouse cells, the authors propose that Xist can coat specific autosomal promoters, which in turn leads to the attenuation of their transcriptional activity, complementing recently published results from humans. While the evidence from individual genes is suggestive, shortcomings in the data and statistical analyses leave the evidence currently incomplete. The work would be of interest to anyone studying gene regulation and noncoding RNAA

   Reviewed by eLife

6. Crystal structure and catalytic mechanism of PL35 family glycosaminoglycan lyases with an ultrabroad substrate spectrum

   This article has 12 authors:

   1. Lin Wei
   2. Hai-Yan Cao
   3. Ruyi Zou
   4. Min Du
   5. Qingdong Zhang
   6. Danrong Lu
   7. Xiangyu Xu
   8. Yingying Xu
   9. Wenshuang Wang
   10. Xiu-Lan Chen
   11. Yu-Zhong Zhang
   12. Fuchuan Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript reports on the crystal structures of two glycosaminoglycan (GAG) lyases from the PL35 family, along with in vitro enzyme activity assays and comprehensive structure-guided mutagenesis. While the study provides structural insights into the broad substrate specificity of these enzymes, the incomplete structural models, lack of key data such as Mn²⁺ binding confirmation, and reliance on basic docking methods diminish the overall impact. Although the work is useful for specialists in carbohydrate-active enzymes, additional data, and more rigorous analysis are required to present a complete study.

   Reviewed by eLife

7. LAPTM4B Alleviates Pulmonary Fibrosis by Enhancing NEDD4L-Mediated TGF-β Signaling Suppression

   This article has 12 authors:

   1. Kai Xu
   2. Xiaoyue Pan
   3. Hui Lian
   4. Yaxuan Wang
   5. Ruyan Wan
   6. Zhongzheng Li
   7. Xin Pan
   8. Yajun Li
   9. Juntang Yang
   10. Ivan Rosas
   11. Lan Wang
   12. Guoying Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this valuable manuscript, the authors propose that the lysosomal protein LAPTM4B plays a role in suppressing the TGF-β/SMAD signaling pathway and suggest that enhancing LAPTM4B function could be a potential therapeutic strategy for alleviating bleomycin-induced lung fibrosis. The findings will be of interest to the lung disease field, and the data presented to support the authors' conclusions is solid. However, it remains unclear whether the suppressive effect of LAPTM4b on idiopathic pulmonary fibrosis is mediated by Nedd4l.

   Reviewed by eLife

8. Phosphodiesterase 1A physically interacts with YTHDF2 and reinforces the progression of non-small cell lung cancer

   This article has 9 authors:

   1. Chong Zhang
   2. Zuoyan Zhang
   3. Yuchen Wu
   4. Jing Cheng
   5. Kaizhi Luo
   6. Zhidi Li
   7. Manman Zhang
   8. Jian Wang
   9. Yangling Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript provides valuable mechanistic insight into NSCLC progression, both in terms of tumour metastasis and the development of chemoresistance. The authors draw upon a range of techniques and assays and although the evidence shown is solid, suggestions by the two reviewers will strengthen the message. The work presented will be of interest to cancer biologists and more broadly to those interested in NSCLC translational studies.

   Reviewed by eLife

9. HIV integrase compacts viral DNA into biphasic condensates

   This article has 14 authors:

   1. Pauline J Kolbeck
   2. Marjolein de Jager
   3. Margherita Gallano
   4. Tine Brouns
   5. Ben Bekaert
   6. Wout Frederickx
   7. Sebastian F Konrad
   8. Siska Van Belle
   9. Frauke Christ
   10. Steven De Feyter
   11. Zeger Debyser
   12. Laura Filion
   13. Jan Lipfert
   14. Willem Vanderlinden

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The manuscript by Kolbeck and co-workers is an important contribution to understanding the physical mechanism that controls a key step in the retroviral infectious cycle. The authors employ a wide range of experimental techniques, complemented with Montecarlo simulations, that result in convincing evidence of compaction of HIV DNA by the viral integrase. This manuscript would benefit from in-depth discussion and analysis of the biophysical implications of the results.

   Reviewed by eLife

10. Image-based identification and isolation of micronucleated cells to dissect cellular consequences

    This article has 5 authors:

    1. Lucian DiPeso
    2. Sriram Pendyala
    3. Heather Z Huang
    4. Douglas M Fowler
    5. Emily M Hatch

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This valuable paper reports image analysis pipelines for the automated segmentation of micronuclei and the detection and sorting of micronuclei-containing cells, which could be powerful tools for researchers studying micronuclei. While the development of the pipelines is solid, a proof-of-principle experiment is not entirely conclusive and leaves open the possibility that additional refinements are required, which would be facilitated by a more detailed explanation of the methods used.

    Reviewed by eLife