On 2025-03-11 16:46:46, user Nikhil Thomas wrote:

This manuscript has been published in PLoS Genetics at the following link:<br /> https://doi.org/10.1371/journal.pgen.1011370

On 2025-03-11 05:53:34, user John Golz wrote:

This manuscript has now been published and a link to the publication could now be included.

https://doi.org/10.1186/s12896-024-00864-3

Thanks

On 2025-03-10 04:21:18, user Young Cho wrote:

Dear Authors,<br /> Thank you for sharing your insightful work, "In Silico Engineering of Stable siRNA Lipid Nanoparticles: Exploring the Impact of Ionizable Lipid Concentrations for Enhanced Formulation Stability." Your study makes an important contribution to the field of lipid nanoparticle (LNP) research by highlighting the role of ionizable lipid concentrations in siRNA encapsulation and stability. The use of coarse-grained molecular dynamics (MD) simulations and steered molecular dynamics (SMD) provides a detailed molecular-level understanding of LNP formation, which is particularly valuable for optimizing RNA-based drug delivery systems.<br /> Summary<br /> This study examines how neutral and positive ionizable lipids influence LNP stability and siRNA encapsulation efficiency. The findings indicate that LNPs with positive ionizable lipids encapsulate siRNA more effectively than those with neutral lipids, likely due to their integration with phospholipids and the prevention of siRNA escape. Interestingly, low and medium concentrations of both neutral and positive DLKC2 showed better compartment formation and encapsulation efficiency compared to high concentrations. Additionally, neutral lipids exhibited greater aggregation, which could impact LNP stability.<br /> Introduction<br /> Your introduction effectively establishes the relevance of this study by situating it within the broader context of LNP research. The discussion of existing challenges in siRNA delivery and the role of lipid composition is well-articulated. However, further elaboration on how your study builds upon previous experimental findings could help connect computational insights with practical applications.<br /> Results<br /> The figures and data presentation generally support your conclusions. Figure 4, which illustrates LNP compartment formation at different lipid concentrations, is particularly valuable in showing how high concentrations lead to instability. We do think that some quantitative metrics such as bilayer thickness, lipid density, or compartment size would enhance the strength of these findings. Additionally, since water is omitted from the visualizations for clarity, we think it would be beneficial to include a figure that shows water so we can visualize the hydration effects and lipid-water interactions.<br /> Discussion<br /> Your discussion effectively compares findings with prior studies, reinforcing that positive ionizable lipids enhance siRNA encapsulation and that lipid aggregation in neutral systems may reduce stability. While you mention previous molecular dynamics studies (e.g., Paloncýová et al. and Trollmann & Böckmann), we feel a more direct comparison of numerical data and trends from these works would further contextualize your results. Additionally, discussing potential experimental validation techniques (e.g., cryogenic electron microscopy or encapsulation efficiency assays) could provide future directions for integrating simulations with laboratory-based studies. However, that is just our opinion as we do understand that this study takes on a more computational approach and is still very impactful.<br /> Suggestions for Improvement<br /> 1. Expand quantitative analysis in Figure 4 by including measurements of bilayer thickness, lipid density, and compartment size to provide a more rigorous validation of LNP stability.<br /> 2. Clarify the role of hydration in lipid-water interactions since water was omitted in visualizations.<br /> 3. Strengthen comparisons with previous molecular dynamics and experimental studies by integrating direct numerical contrasts.<br /> 4. Discuss potential experimental validation approaches that could complement your computational findings and enhance their real-world applicability.<br /> Final Thoughts<br /> Overall, this paper presents a well-structured and valuable contribution to siRNA delivery research. With minor refinements in quantitative analysis, literature comparisons, and discussion of experimental validation, the study could be even more impactful. Thank you for your efforts in advancing the field of LNP-based RNA therapeutics!<br /> Best regards,<br /> UHM MBBE 602 Graduate Students

On 2025-03-10 04:17:10, user Young Cho wrote:

Summary:<br /> This study provides a comprehensive analysis of miRNA profiles in Culex tarsalis, identifying 86 known miRNAs and 20 novel miRNAs, is a significant contribution to the field of insect molecular biology and vector research. This works sets the foundation for future studies on gene regulation and host-pathogen interactions in Cx. tarsalis, a major vector of West Nile Virus (WNV). While the methodology is robust and the findings are compelling, the paper would benefit from some minor revisions to strengthen data presentation, clarify experimental choices, and align its conclusions more closely with the results. <br /> Introduction: <br /> The introduction frames the importance of miRNA research in Cx. tarsalis well, particularly in the context of understanding its role as a vector for WNV. However, the title of the paper may be misleading since the findings do not directly link the identified miRNAs to WNV vectoring. Reframing the title and introduction to focus on the broader importance of miRNA characterization in Cx. tarsal without overemphasizing the WNV connection would improve clarity and prevent misalignment between the study’s scope and its claims. <br /> Results: <br /> The results section presents a comprehensive dataset of miRNAs identified through computational comparison with other mosquito species and validated using RT-qPCR. The discovery of novel miRNAs and the observed isomiR variations are particularly noteworthy, with the predominance of 3’ end insertions being a finding of potential significance in gene regulation. That said, clearer justification for the selection of the 10 miRNAs validated by qPCR would strengthen the interpretability of the results. <br /> Discussion: <br /> The discussion effectively places the study’s findings within the broader context of existing research on mosquito miRNAs and draws meaningful comparisons with other species like Aedes albopictus and Cx. quinquefasciatus. The evolutionary conservation of miR-184 and the identification of unique miRNAs in Cx. tarsalis offer valuable insights. However, the paper would benefit from further discussion on the functional implications of these miRNAs, particularly their potential roles in development, immunity, and host-pathogen interactions. Additionally, the observed differences in miRNA expression between cell lines and whole organisms raise important questions that warrant more exploration. <br /> Suggestions: <br /> 1. Revise the title to better reflect the study’s current findings and avoid overemphasizing WNV. <br /> 2. Clarify the rationale behind the selection of the 10 miRNAs for qPCR validation. <br /> 3. Expand the discussion on the functional roles of the identified miRNAs and their potential involvement in host-pathogen interactions. <br /> 4. Address the limitations more explicitly, such as the reliance on a single genome assembly, the lack of data from different mosquito life stages and tissues, and the absence of additional validation methods like Northern blot. <br /> 5. Consider including a statistical analysis to highlight differences in miRNA expression between cell lines and whole organisms. <br /> 6. Discuss the potential influence of feeding behavior on gene expression and its relevance to vector competence.

On 2025-03-07 18:39:57, user Randall Eck wrote:

Exciting article! Given the role of 3' UTR alternative polyadenylation (APA) in RNA localization and stability (PMC9261900) and the role of TDP-43 in regulating 3' UTR APA (PMC10849503), is there a relationship between TDP-43 regulation of RNA localization and 3' UTR APA in your data?

On 2025-03-07 12:28:58, user Marc RobinsonRechavi wrote:

Under Data Accessibility, the authors write:

Data and R code sufficient to replicate all analyses will be made publicly available upon acceptance of this manuscript for publication.

This is a publication, i.e. it is made public as part of the scientific record and is citable, thus I strongly invite the authors to make the corresponding data and code available without delay.

On 2025-03-07 07:27:12, user Marc RobinsonRechavi wrote:

Under Code Sharing Plan, the authors write:

All the code used for the generation of datasets and subsequent analysis will be made publicly available in<br /> a GitHub repository upon publication

This is a publication, i.e. it is made public as part of the scientific record and is citable, thus I strongly invite the authors to make the corresponding code available without delay.

On 2025-03-06 09:47:18, user Alexei Korennykh wrote:

As a corresponding author, Alexei Korennykh hereby documents the timeline of our discovery of Nocturnin NADP(H) phosphatase activity.

[2018, December 17]<br /> Our Manuscript "The Metabolites NADP+ and NADPH are the Targets of Circadian Protein Nocturnin (Curled)" was submitted to a high-quality journal (per BioRxiv policy journal name cannot be mentioned here) (under id ....2018-12-17736A)

[2018, December 19]<br /> The editor sends the work to referees.

[2018, December 21]<br /> We submit our Nocturnin-NADP co-crystal structure to the PDB database and obtain PDB ID 6NF0.

https://www.rcsb.org/structure/6NF0 has the following permanent record:

Deposited: 2018-12-18 <br /> Released: 2019-05-01 <br /> Deposition Author(s): Estrella, M.A., Du, J., Korennykh, A.

[2019, January 15]<br /> Journal rejects the manuscript, based substantially on negative remarks of Ref#3, who is “an expert on Nocturnin”:

Referee expertise:

1: crystal structure

2: NADPH/NADP metabolism

3: nocturnin biology and function

Although we responded that all concerns can be addressed directly and without experiments, the journal is not willing to re-consider our work.

[2019, January 30]<br /> We posted our manuscript here, to BioRxiv and it became available to the public.

[2019, March 28] <br /> We submitted the paper to the final publishing journal (see top of the page, "Now published in ") and the paper was received and sent for review.

[2019, April 18] <br /> The paper was accepted (see top of the page, "Now published in ").

[2019, May 30] <br /> The paper was published (see top of the page, "Now published in ").

[2019, June 5] <br /> Alexei Korennykh wrote to change Uniprot annotation of Nocturnin

Wed Jun 05 05:20:37 2019, akorenny@princeton.edu wrote:

Major changes in NOCT (CCRN4L) gene function and description. <br /> Source:<br /> https://www.nature.com/articles/s41467-019-10125-z <br /> Suggested revisions:

"Circadian deadenylase"<br /> changes to<br /> "Circadian NADP(H) phosphatase"

"Catalytic activity: Exonucleolytic cleavage of poly(A) to 5'-AMP. EC:3.1.13.4"<br /> changes to:<br /> "Catalytic activity: 2'-Phosphate removal from NADP+ and NADPH. EC:to be created"

[2019, June 7] <br /> UniProt Begins re-annotation<br /> Dear Alexei,

Thank you for having submitted a request for the update of a UniProtKB entry.

Your request has already been sent to an annotator and will be handled with<br /> high priority.

We will send you an e-mail when the update is completed.

Best regards

SP

[2019, July 1] <br /> UniProt changes Deadenylase to Phosphatase for Nocturnin:

Dear Alexei,

Thank you for passing on the details of your recent paper. The nocturnin <br /> entry has been updated and will be available as part of UniProt release <br /> 2019_08 on 18th September. In the meantime, I have included the entry <br /> below in text format. Please feel free to get back in touch if you have <br /> any comments about the content.

Kind regards,<br /> MM

ID NOCT_HUMAN Reviewed; 431 AA.<br /> AC Q9UK39; D3DNY5; Q14D51; Q9HD93; Q9HD94; Q9HD95;<br /> DT 02-NOV-2001, integrated into UniProtKB/Swiss-Prot.<br /> DT 04-NOV-2008, sequence version 2.<br /> DT 31-JUL-2019, entry version 148.<br /> ……<br /> CC NAD(+) and of NADPH to NADH (PubMed:31147539). Shows a small<br /> CC preference for NADPH over NADP(+) (PubMed:31147539). Represses<br /> CC translation and promotes degradation of target mRNA molecules<br /> CC (PubMed:29860338

…

[2019, July 1]

Up to this date (i.e. 5 months since our BioArxive paper became publically available) no work by others, which described Nocturnin as NADP(H) phosphatase was published or submitted to any journal, to the best of our knowledge.

On 2025-03-06 02:33:06, user Charles Warden wrote:

Thank you very much for posting this preprint!

The "Code availability" section indicates "We provide supplementary files containing an R script with functions to run our CRF-based correction procedure as well as a tutorial notebook illustrating how to run it.".

However, I think I see anything uploaded as supplemental files. Am I overlooking anything, or does the supplemental code need to be added in a revision?

Thank you very much!

Sincerely,<br /> Charles

On 2025-03-06 00:00:06, user Laura Lackner wrote:

An updated version of this preprint has been published in MBoC - https://doi.org/10.1091/mbc.E23-05-0168 . The revised and accepted version has a slight modification to the title.

On 2025-03-05 19:55:42, user Enrico Radaelli wrote:

In this viral video on YouTube<br /> https://www.youtube.com/watch?v=WNuzopVDFQs <br /> The company claims that "There were no unintended consequences except adorability".<br /> However, the mice are clearly pruritic and they exhibit crusty/flaky skin in glabrous areas (especially paws and eyelids).<br /> I wonder if this is part of the phenotype or if the mice contracted infections that might have caused these lesions (mites, C. bovis, etc.).

On 2025-03-04 21:05:38, user Simone Picelli wrote:

Hi, I think there is a mistake in the name of the company used to make the modified TSO. It's not Biosyn Corporation ( http://biosyncorp.com ), as you wrote, but rather Bio-Synthesis ( http://biosyn.com ). <br /> Moreover, in the TSO sequence: "/5Biosg/" is the acronym used by IDT for a 5' biotin. The "g" has nothing to do with deoxyguanosine (G), but you write in the paper "5BiosG/" and this can be confusing. The standard 10x TSO sequence is, in fact: 5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’<br /> so no G at the 5' (like there was never a G at the 5' of the SMART-seq oligo, from which 10x took their sequence).<br /> The code for biotin at Biosyn is [Btn] (standard C6 spacer, which I assume is the one you mean here).

On 2025-03-04 02:21:17, user Nelly Olova wrote:

This work has now been published in the Methods in Molecular Biology book series, volume 2866 (Springer Nature)

On 2025-03-03 17:25:34, user Johannes Daniel Scharwies wrote:

This is the author's version of the work. It is posted here by AAAS for personal use, not for redistribution. The definitive version was published in Science on 6 Feb 2025, DOI: 10.1126/science.ads5999.

On 2025-03-03 16:11:50, user hansdb wrote:

One Corded Ware (CGG107476) and two Bell Beaker individuals (CGG106805 and CGG106737) from your interesting study belong to Y-DNA haplogroup I2-L38 (aka I2a1b2a).<br /> As decribed in my citizen scientist paper ( https://www.academia.edu/115363574/RECONSTRUCTING_THE_JOURNEY_OF_Y_DNA_HAPLOGROUP_I2_S2555_TO_I2_L38_Tracing_Genetic_Footprints_Across_Time_and_Space ) this haplogroup was also related to:<br /> * an EBA Unetice sample from Germany (I0114)<br /> * an EBA Unetice sample from Bohemia (I7959)<br /> * an IA Hallstatt sample from Germany (MBG008)<br /> * an IA La Tène sample from Bohemia (I17327)<br /> * an IA La Tène sample from France: GLN32

Most interestly this haplogroup also occured among the Urnfield epoch Lichtenstein clan from Osterode-am-Harz. Since it is mentioned (paragrapghs 194 to 196) that very few genomes from the Urnfield Culture exist (as a result of the cremation practice) it would be interesting if the well-preserved samples of the Lichtenstein cave could be integrated in your study.

On 2025-03-03 14:46:23, user Elisa Rosati wrote:

A couple of questions:<br /> 1) How can you be sure that the MAIT cells you observed are not bystander activated during the T cell stimulation and thus not really Myelin-specific? I would perhaps perform the experiments with two additional setups:<br /> a) MHC-blockage (If MAIT cells are really specific they should appear here) <br /> b) MR1-blockage (if MAIT cells are specific and activated via TCR they should not appear here)

2) Have you tried to perform the analyses separately for HLA-DRB1*15:01 positive and negative individuals separately? It was shown by a study from Adaptive Biotechnology that a limited number of TCR clusters enriched in MS exist and that these clusters are mostly CD4 and very different in DRB1*15:01 positive and negative individuals.

On 2025-03-01 00:59:54, user Tim wrote:

While groundbreaking, I wish this paper expanded up author N.R.B.’s de novo inclusion of huel in the fine tuning of the RFDiffusion network compared to the characterization of fermented yeast to acetaldehyde formation chain on massive (1 million samples or more) scales.

On 2025-02-28 12:53:50, user Prof. T. K. Wood wrote:

l 339: Paris is a toxin/antitoxin system and TAs are the most-prevalent phage inhibition system; this should be noted.

l 365: The seminal identification of of TAs and phage inhibition (1996) should cited:<br /> doi: 10.1128/jb.178.7.2044-2050.1996

On 2025-02-28 10:05:42, user Giampaolo Minetti wrote:

This preprint has now been published as a peer reviewed, open access article in Cell Death Discovery:<br /> Minetti G, Dorn I, Köfeler H, Perotti C, Kaestner L. Insights from lipidomics into the terminal maturation of circulating human reticulocytes. Cell Death Discov. 11, 79 (2025). doi: /10.1038/s41420-025-02318-x<br /> Stable, shortened URL:<br /> https://rdcu.be/ebvgH

On 2025-02-28 08:34:44, user Bjarke Jensen wrote:

Dear authors,

Congratulations with this interesting study.

In my view it would be helpful if you further develop the descriptions of the state of trabeculation. For example, did you make measurements (counting, thicknesses, proportions) of the trabecular and compact layer, what were the values and how do they relate to diagnostic criteria associated with trabeculation? It would also be helpful if you support this part of your Results with clinical imaging (echocardiography and CMR) onto which is shown the measurements (or overt phenotype) that led to the interpretation of 'hypertrabeculation'. I for one would not mind a full text figure dedicated to this part. <br /> Part of the reason for giving these suggestions is of course that your title states 'hypertrabeculation' while the associated phenotyping is proportionally very small and accordingly a bit unclear.

Best wishes and good luck with the publication.

Bjarke

On 2025-02-27 02:16:06, user Le Zhen wrote:

Now this manuscript has been accepted for publication in the journal Biomaterials, with a new title: Synthetic Vascular Graft That Heals and Regenerates (doi: https://doi.org/10.1016/j.biomaterials.2025.123206) .

On 2025-02-26 17:21:48, user Leonardo Di Bari wrote:

Thanks for the analysis, the study is promising. I am, Leonardo Di Bari, a PhD student in the SPQB ( https://sites.google.com/view/spqb ) group of Martin Weigt and Francesco Zamponi: we have utilized the entropy that you present in the following three articles.<br /> https://arxiv.org/pdf/2412.01969 <br /> https://www.pnas.org/doi/abs/10.1073/pnas.2406807121 <br /> https://www.nature.com/articles/s41467-022-31643-3 <br /> I think it would be interesting to maybe compare the two formulations. <br /> Best regards,<br /> Leonardo Di Bari

On 2025-02-26 10:03:48, user Young Cho wrote:

This is a comment from a Journal Club of MBBE 602 in Univ of Hawaii.

Summary<br /> This paper explores the capabilities of twin prime editing (twinPE) for large DNA sequence modifications, including deletions, replacements, integrations, and inversions. The authors demonstrate the efficiency of twinPE in human cells (HEK293T & Huh7) and its potential for therapeutic applications when combined with the Bxb1 integrase. Key findings include precise and flexible editing with fewer indels, high knock-in efficiency, and the ability to bypass certain DNA repair pathways. However, the study lacks long-term data on genomic stability and scalability for human applications, and some experimental details and comparisons with other gene-editing techniques are insufficiently explored.

Introduction<br /> The introduction provides a solid foundation for the study but could benefit from more background information on the therapeutic applications explored, as well as the mechanism that resulted in limitations relating to the pegRNA pairs, or the low Bxb1 efficiency.

Results<br /> Figure 2:<br /> The figure demonstrates twinPE’s efficiency in large DNA sequence insertion and replacement. However, the formatting is poor, the figure legend is separate from the figure and labels are a bit confusing. The authors should revise the figure to improve readability.<br /> The large error bar in Fig. 2F (deletion size 589) suggests variability in the editing strategy. The authors should address this in the text, discussing potential outliers or variability in the system.

Figure 3:<br /> This figure effectively shows the mechanism and efficiency of twinPE combined with Bxb1 integrase. However, the authors should clarify why certain pegRNA pairs performed better than others and why some loci (e.g., CCR5, AAVS1) were more successful.<br /> The discussion should also address the limitations of single transfection compared to sequential transfection to allow researchers to build off of this work.

Figure 4:<br /> The figure explores therapeutic applications of twinPE, particularly in correcting inversions at recombination hotspots. The authors should expand on the implications of these findings for gene therapy and discuss potential challenges in scaling up for human applications.

Discussion<br /> The discussion is well-written but could be strengthened by addressing the following:<br /> Limitations of twinPE: The authors should discuss why lower frequencies occurred in single transfection compared to sequential transfection and why some pegRNA pairs performed better than others. Additionally, they should explore the potential limitations of using Bxb1 integrase and whether other integrases could be more effective.<br /> Comparison with other gene-editing techniques: The authors briefly mention the advantages of twinPE over CRISPR but do not provide a direct comparison. Including experimental data or a discussion comparing twinPE to CRISPR or other editing methods would strengthen the paper.<br /> Long-term implications: The study lacks long-term data on genomic stability after large DNA modifications. The authors should discuss potential risks, such as off-target effects or genomic instability, and suggest future studies to address these concerns.

Suggestions<br /> Improve Figure Quality: Revise figures to ensure they are clear, readable, and properly formatted. Include detailed legends and consider adding summary panels to highlight key findings.<br /> Expand on Limitations: Discuss the limitations of twinPE in more detail, including variability in editing efficiency, challenges in scaling up for human applications, and potential long-term effects on genomic stability.<br /> Compare with Other Techniques: Include a direct comparison of twinPE with CRISPR or other gene-editing methods to highlight its advantages and disadvantages.<br /> Explore Additional Integrases: Investigate the use of other integrases in combination with twinPE to determine if they offer improved efficiency or precision.<br /> Provide Long-Term Data: Conduct follow-up studies to assess the long-term effects of large DNA modifications on genomic stability and cell viability.<br /> Enhance the Introduction: Add more background information on the limitations of existing gene-editing technologies and how twinPE addresses these challenges.<br /> Address Variability in Results: Discuss potential outliers or variability in the data, particularly in Fig. 2F, and suggest ways to improve consistency in future experiments.

Editorial Decision<br /> The paper presents significant advancements in gene-editing technology and demonstrates the potential of twinPE for precise and efficient large DNA sequence modifications. However, the study would benefit from addressing the limitations and expanding on the comparisons with other gene-editing techniques. This publication could be strengthened with revisions to improve figure quality, clarify data interpretation, and exploring long-term stability the genetic edits. Overall, the paper was dense with information so the limitations are understandable, as only so much can be presented in one publication.

On 2025-02-25 21:24:18, user Xiaotong Yao wrote:

The measurements for the "realistic"-ness of the simulated genomes seems inadequate. For examples, what are the VAFs of mutations in the LOH or homozygously deleted or amplified regions?

On 2025-02-25 21:16:36, user Xiaotong Yao wrote:

No. You simply cannot "simulate" structural variants as if they are just rows in a BEDPE file.

Doing it in the way of this paper won't even guarantee your CNV boundaries are matched correctly with the junction breakends! Let alone consistent junction copy numbers or realistic complex SV events. This approach of treating each "variant" as an individual event only works for short variants, and CNVs to some extent.

To truly forward simulate a cancer genome that is accumulating structural variants/CNVs requires virtual cell cycles and keeping tabs on the junction balance constraints and linear/circular DNA structures, e.g., losing a telomere, di-centric chromsomes. We tried this before, but it is very very hard as the genomes coming out of the simulations are not anything remotely survivable for a cell and nothing like the real cancer genomes. So this is a fascinating and challenging open question.

On 2025-02-25 20:42:31, user Victor Gonzalez Perdomo wrote:

This study seems biased, there is very little data from the Paleolithic, you have data mostly around Neolithic. Also it seems that you have very little ancient data around the southeast Europe. You neither aproach the fact most light pigmentation features appeared close to the atlantic coast then seems to spred to the interior.

On 2025-02-25 05:38:33, user Roberto Nava wrote:

The reporter system is genius! Any chance the authors would be willing to share the supplemental tables? They don't appear in the PDF.

On 2025-02-25 01:58:05, user Maria Rebolleda Gomez wrote:

Really interesting paper showing that variation across strains in the relationship between growth rate and antibiotic-induced lysis as well as interactions can shape the outcomes of community re-structuring after antibiotic treatment. The authors are able to use data from individual E. coli strains to predict the overall enrichment in the community after antibiotics. However, the last step of the derivation in the methods was not clear to me why is it G_m,i + C - It is not clear what that constant is. Also in the main body of the paper it states that this is an approximation, but in the derivation is stated as an identity relationship.

On 2025-02-25 00:16:29, user Meet Zandawala wrote:

This study investigates the dynamics of neuropeptide release and activity following blood feeding in female Aedes aegypti mosquitoes. Sajadi et al. provide valuable insights into the temporal signaling dynamics of diuretic and anti-diuretic hormones, significantly enhancing our understanding of excretory physiology in mosquitoes. The authors employ heterologous expression of receptors to quantify circulating peptide levels, a robust methodological approach that strengthens receptor-ligand interaction validation and hormone quantification. Notably, the study demonstrates a synergistic interaction between DH31 and kinin-like peptides on Malpighian tubules, contributing novel findings to the existing literature on neuropeptide-mediated excretory regulation in mosquitoes. Overall, the study presents an innovative and well-executed investigation with high methodological rigor.

The authors have presented their findings in a clear and well-structured manner. We only have a few questions and comments/suggestions that could help improve the clarity of the manuscript:<br /> 1.     Can the authors clarify the exact number of female mosquitoes used in each condition (blood-fed vs. non-blood-fed) at each time point, specifically in methodology section 3.2 for the haemolymph collection?<br /> 2.     Were there any biological replicates across different mosquito cohorts? Did the authors observe variability between different mosquito batches? Sample sizes have been provided in the figure captions but what does n signify? <br /> 3.     The study utilizes specific time points for haemolymph collection post-blood feeding. Can the authors provide justification for selecting these intervals? Were preliminary studies conducted to determine these as the most informative time-points, or were they based on prior literature?<br /> 4.     The authors acknowledge the roles of serotonin (5HT) and DH44 in regulating fluid secretion but focus their experimental analysis on DH31, kinin, and CAPA peptides. Could they clarify why 5HT and DH44 were not included in their haemolymph quantification assays? Were there methodological limitations, or were these hormones not expected to show significant post-bloodmeal changes, or is this something they plan to address in the future?<br /> 5.     The study quantifies neuropeptide levels over time but does not discuss the mechanisms responsible for their clearance from haemolymph. Can the authors speculate on whether DH31, kinin, and CAPA peptides are degraded enzymatically, removed through receptor-mediated internalization, or cleared by the Malpighian tubules? Can they use in silico approaches to predict the half-life of these peptides based on their sequence composition? Alternatively, can they extract hemolymph when the peptide has peak activity and test this extract after different times to see how much bioactivity they retain over time? Addressing this would enhance our understanding of neuropeptide turnover and regulation.<br /> 6.     Including the individual data points in the bar graphs can provide more information on the spread of the data.

Comments prepared by Bilal Amir (on behalf of Zandawala lab)

On 2025-02-24 03:43:01, user ryhisner wrote:

I am unable to copy and paste anything into the reference window in the variability tab. It only allows me to type, not copy and paste. This means I would have to type in the entire nucleotide sequence by hand, which I'd rather not do.

On 2025-02-24 01:16:55, user Alex Monell wrote:

Hi bioRxiv staff,

The published version of this manuscript is out at https://www.nature.com/articles/s41586-024-08466-x

Thanks!

On 2025-02-23 02:33:22, user Cecil Saunders wrote:

I believe there is a typo in the abstract citation; Charles, 2019 should be Darwin, 2019.

On 2025-02-21 20:37:42, user Krzysztof Kozak wrote:

Multiple technological choices resulted in fatal flaws that make the conclusions of this manuscript unjustifiable:<br /> 1. Inadequate chain of custody of the samples, likely leading to massive contamination.<br /> 2. Application of insufficient sequencing methods and inappropriate data processing tools, potentially resulting in various technical artefacts.<br /> 3. Lack of replication, further exacerbated by deliberate mixing of the isolates.<br /> 4. A simplistic and biased interpretation of the observed patterns of change in the molecular sequences.

I posted a full review of the paper on ResearchHub: https://www.researchhub.com/paper/9161412/discovery-of-single-stranded-dna-in-meteorite-derived-cultures-evidence-of-novel-genetic-elements/reviews

On 2025-02-21 15:30:18, user Yuan Fu wrote:

The paper was published in JIPB on February 21, 2025. The DOI link is: https://doi.org/10.1111/jipb.13867 . Please cite it.

On 2025-02-21 14:20:17, user JJ wrote:

In figure 2, part D, the figure legend says - "The median UMI/gene count is shown as a number above a dataset and as a bold line". Does the numbers say UMI/gene or is it just the Median Number of Genes for each dataset?

On 2025-02-21 11:30:52, user mcsu wrote:

Hi, <br /> Care must be taken when using old data tables for example in table S1 the uniprot_IDs given for the following U. maydis proteins no longer map:-<br /> PRA1_USTMA <br /> PRA2_USTMD <br /> UM03423

but are <br /> P31302<br /> P31303<br /> A0A0D1E0T5

In addition, given these errors how confident are you that the Literature-sourced GPCRs are classified correctly?<br /> Many of the Pfam domains claimed to be "consistent with their associated GPCR class (Table 1)" are not found in the exemplar sequences of each class in table S1.<br /> For example, the Git3 Pfam PF11710 suggested as associated with CPCR class 3 is only found in GPR1_YEAST and not the other 4 proteins suggested as Class 3 GPCRs in table S1; see A0A1U8QVN2_EMENI, A0A1U8QIJ6_EMENI, A0A1U8QJM4_EMENI or Q7SAB9_NEUCR

https://uploads.disquscdn.c...

On 2025-02-21 09:14:43, user Wenjun wrote:

Great work! In addition to enhancing light collection efficiency, the proposed method also effectively reduces the number of optical components in the remote imaging system.

On 2025-02-21 01:11:53, user Charles Warden wrote:

Thank you very much for posting this preprint for the Giotto Suite!

You have a couple different citations for STalign.

I believe this is the correct citation (Reference 34):

34.↵Clifton, K. et al. Alignment of spatial transcriptomics data using diffeomorphic metric mapping. BioRxiv Prepr. Serv. Biol. 2023.04.11.534630 (2023) doi:10.1101/2023.04.11.534630.Abstract/FREE Full TextGoogle Scholar

However, I think the following reference (to Hildebrandt et al. 2021) may not be correct?

"Image registration was performed using STalign [Reference 2]"

Best Wishes,<br /> Charles

On 2025-02-21 00:46:47, user Hurrian Fan wrote:

Congratulations to the team on some amazing work! The steppe component visible in East_steppe_Sets in Chalcolithic and Bronze Age western Anatolia is modeled with Yamnaya, CWC, and Bell Beaker, which are chronologically and geographically somewhat improbable for the early samples. <br /> Have the authors considered checking potentially more proximal sources of potential steppe ancestry, such as the Kartal A & B clusters from Penske et al 2023?

The subclades of y-hg I-L699 found in the Kulluoba and Kalehoyuk samples are not only shared with Serednii Stih individuals, but also Cernavoda (KTL001 & KTL006) and Thracian EBA individuals (Bul4 & I2165), which might lend some plausibility to this source.

On 2024-12-09 17:25:57, user Hannah Moots wrote:

Exciting research!! Just wanted to point you towards some additional research on the appearance of steppe-related ancestries in Italy. You mentioned that previous studies had identified the earliest appearance of these ancestries to be about 3,600 BP in central Italy. We published 4 ancient genomes from the Bronze Age site of Pian Sultano in central Italy and all of these individuals carried steppe-related ancestries, the oldest of which dates back to 3872 - 3719 calBP. https://doi.org/10.1038/s41559-023-02143-4 . Figure S4 has a timeline and admixture plots to visualize this as well.

On 2025-02-20 20:30:48, user Jesse Conklin wrote:

This should be linked to the final publication:

Conklin, J. R., Verkuil, Y. I., Lefebvre, M. J. M., Battley, P. F., Bom, R. A., Gill, R. E. Jr, Hassell, C. J., ten Horn, J., Ruthrauff, D. R., Tibbitts, T. L., Tomkovich, P. S., Warnock, N., Piersma, T., & Fontaine, M. C. (2024). High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonisation in bar-tailed godwits. Molecular Ecology, 33, e17452. https://doi.org/10.1111/mec.17452

On 2025-02-20 19:02:49, user Raoul wrote:

There is a previous report that has targeted a disease resistance gene to generate plants with enhance resistance. Similar to what is said in this pre-print ("SNC1 is an attractive target for proof-of-principle modulation of disease resistance by epigenome engineering").<br /> Reference: CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants<br /> Plant Sci, 329 (2023), Article 111617, 10.1016/j.plantsci.2023.111617<br /> Recently a review article has mentioned that: "One notable example of enhancing disease resistance in crops involved the CRISPR activation (CRISPRa) system to activate the defense gene PATHOGENESIS-RELATED GENE 1 gene (SlPR-1) conferring enhanced resistance to Clavibacter michiganensis subsp. michiganensis infection in tomatoes" (taken from: https://doi.org/10.1016/j.pbi.2024.102669 ).<br /> Consequently, the concept has shown to be scientifically and technically feasible, as shown previously in 10.1016/j.plantsci.2023.111617.<br /> Thus, what is stated in this preprint is not really new, for plants: "The results demonstrate that epigenome-engineering of a single defense gene, SNC1, is sufficient to generate plants with improved disease resistance phenotypes."

On 2025-02-20 14:08:04, user Prashant Kaushik wrote:

Could the author kindly comment on how human plasma was processed post collection? Were there sequential centrifugation steps involved and were they consistent among different MS based tech? <br /> Thank you for sharing your fantastic Work

On 2025-02-20 12:15:37, user kei wrote:

Thank you for your interesting paper.

I am curious about the behavior when only the non-natural amino acids in cyclic peptides are not tokenized at the atomic level, and all cyclic peptides are represented using SMILES. I am thinking of investigating this.

That said, I have one question:<br /> What is the input format when inferring complexes of cyclic peptides containing non-natural amino acids and proteins?<br /> (In other words, how are non-natural amino acids formatted in the input?)

If possible, I would appreciate it if you could share an example of the YAML file or other input data used for Boltz1.

Thank you in advance.

On 2025-02-18 17:40:04, user Dongyao Li wrote:

Great work, thank you! I have one comment regarding comparison of cell segmentation. The paper states:

Overall, the CosMx 6K segmentation tool produced cells with larger sizes, higher solidity, and better circularity, indicative of more regular and convex cell shapes compared to other platforms

I would argue "larger", "more circular", and "convex" do not necessarily mean better segmentation. For example, "more circular" and "convex" could be the bias of the particular segmentation model. If more circular is better, then "nucleus segmentation + large expansion" (basically the first version of Xenium segmentation prior to multi modal cell segmentation stain) is the better segmentation since it's large, circular, and convex.

The paper later states:

Among the ST platforms, Xenium 5K showed better separation of marker gene pairs after segmentation

We further visualized marker gene expression across the annotated cell types. Xenium 5K exhibited the most distinct expression patterns (Supplementary Fig. 8d), facilitating more accurate cell type annotations.

and concludes:

Despite exhibiting more irregular segmentation shapes, Xenium 5K effectively distinguished different cell types and minimized transcript mixing between adjacent cells

"Better separation of marker gene pairs", "distinguish different cell types" and "minimize transcript mixing" are indeed the more principled and biologically meaningful metrics to evaluate cell segmentation. The word "despite" in the conclusion suggests circularity means better segmentation, which I don't necessarily agree.

On 2024-12-27 03:11:02, user samuel Yi wrote:

Thank you very much for this remarkable work. While reading the article, I noticed a detail that warrants further discussion. The authors used Codex staining results from adjacent sections as the gold standard to evaluate the performance of different spatial omics technologies. However, Codex exhibited relatively strong edge staining effects in certain channels, such as CD20, which led to an abnormal accumulation of B cells at the periphery of the sections. This observation is inconsistent with the results obtained from hematoxylin and eosin (H&E) staining. Therefore, a more meticulous examination of the Codex data analysis may be necessary to address these discrepancies.

On 2025-02-18 15:37:48, user Andrew Kennard wrote:

This preprint has since been peer-reviewed, revised, and published in a journal:

Kennard AS et al. (2025). Tubulin sequence divergence is associated with the use of distinct microtubule regulators. Current Biology 35(2): p233-248.e8. doi: https://doi.org/10.1016/j.cub.2024.11.022

On 2025-02-17 18:48:35, user Michael Young wrote:

We just discussed this paper in our lab - nice work! One minor comment and one general one. Figure 2f - use same x-axis for both plots. More importantly, the paper is trying to do a lot. Not sure whether we would suggest splitting into two papers, relegating some elements to supplementary materials, or keeping as is with details relegated to supplementary.

On 2025-02-17 08:16:49, user Jeziel Dener Damasceno wrote:

Please, could this preprint be linked to the final publication, please: https://www.nature.com/articles/s41467-025-56785-y

On 2025-02-16 01:30:11, user Nikolai Slavov wrote:

Code and data for reproducing the analysis are available at: <br /> https://github.com/SlavovLab/Protein-Clearance

On 2025-02-15 03:06:45, user Jayson Zhao wrote:

how about the nearest neighbor search algorithm behind that strongly affect the loss function of non-linear dimension reduction and dataset dimension, in which we will have hubs. See some discussion here: https://academic.oup.com/nargab/article/6/4/lqae172/7928174

On 2025-02-15 02:39:09, user sa pa wrote:

I read this paper with great interest.

Is there a name given to the single-cell RNA-seq using the “Solution-phase indexing by kinetic confinement” technique that you are proposing?

It would be easier to cite it as a single-cell RNA-seq method if it had a name like “xxx-seq”, but what should we call it officially?

In the text, it says “Single cell RNAseq using Kinetic Confinement”, is this correct?

On 2025-02-14 04:28:23, user Felix wrote:

I have only skimmed the paper, but I wonder if the link given for the fungal catalogue ( https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.15454/WQ4UTV ) is the correct one. It redirects to human oral microbiota gene and species catalogue rather than fungal-specific catalogue.

On a somewhat related topic, have the authors considered expanding the fungal catalogue with the recent cultivated human gut fungi resource ( https://doi.org/10.1016/j.cell.2024.04.043 )?

On 2025-02-13 22:20:55, user Amer Alam wrote:

The peer reviewed version of this manuscript has been published in the EMBO journal:

Structural insights into binding-site access and ligand recognition by human ABCB1

PMID: 39806099 DOI: 10.1038/s44318-025-00361-z

On 2025-02-13 19:40:38, user Pick Up Litter wrote:

This paper will help move science away from studying "cute" species and to be objective. Perhaps the most severe example is the housecat-- still portrayed as cute in media, but in the feral form a worldwide destroyer of birds. One critique concerning the Ivory-billed Woodpecker-- the number quoted by Troy et al, 20 million dollars spent for studies, is misleading. Most of the efforts are university and private, not governmental, and if the bird is proven to be extant, will have conservation benefits since it is a wide-ranging and keystone species. I help with research for the Ivory-billed Woodpecker. The growing body of evidence that this species exists is more rational than the critique-- see other BioRxiv papers and the work of Mike Collins for example. John D Williams

On 2025-02-13 17:59:30, user Mikaela Gray wrote:

This preprint has now been published in ACS Omega. Here is the link: https://pubs.acs.org/doi/10.1021/acsomega.4c07666

On 2025-02-12 14:36:44, user Sergio Angel wrote:

Very interesting. Our anti-TgATM antibody also labeled the cytosol, with phleomycin in cytosol and some foci in nucleus.

On 2025-02-12 10:42:04, user Claudio Vasapollo wrote:

This manuscript has been published with a different title wanted by the journal. You can find the published version on the PeerJ website at the link:<br /> https://peerj.com/articles/18765/

Thank you.<br /> Claudio Vasapollo

On 2025-02-12 06:12:29, user Prof. Sergio Manni Vanzini wrote:

The paper presents a novel perspective on the application of oxygen-ozone therapy in spine disorders, introducing the concept of adaptive chaos as a key mechanism in biological resilience and healing. A significant strength lies in its interdisciplinary approach, integrating mathematical modeling, bioinformatics, and clinical insights to establish a framework for understanding the therapeutic effects of ozone therapy. The use of Lyapunov exponents, Shannon entropy, and fractal dimensions to quantify biological complexity is particularly innovative, providing a structured means of evaluating systemic responses to treatment. Additionally, the study’s emphasis on precision dosing—highlighting the differential effects of low versus high ozone concentrations—adds valuable insight into the hormetic nature of the therapy, reinforcing the need for controlled perturbations in medical interventions. The thorough review of existing literature, including randomized controlled trials, strengthens the credibility of the findings and underscores the translational potential of the proposed model.<br /> However, certain limitations must be acknowledged. The reliance on mathematical simulations, while insightful, may not fully capture the variability of real-world biological responses, as complex physiological interactions are difficult to model with absolute accuracy. Additionally, while the study references clinical data, it does not provide direct experimental validation, making it difficult to assess the immediate applicability of the findings in clinical practice. The concept of adaptive chaos, though compelling, remains somewhat abstract, and further empirical studies are needed to establish its clinical relevance definitively. Lastly, some of the statistical approaches, particularly the unusually high values of Lyapunov exponents, may require re-evaluation to ensure their biological plausibility and proper contextualization within established dynamical system theory. Despite these challenges, the study provides a groundbreaking theoretical framework with promising implications for regenerative medicine and personalized therapy.

On 2025-02-10 12:29:07, user Alberto Farleschi wrote:

I came through these data, which represents a novelty for me, endeavoured in the field of bioinformatics. The study by Chirumbolo et al. presents a compelling and innovative perspective on adaptive chaos and its role in modulating oxygen-ozone therapy for spine disorders. By integrating mathematical modeling, bioinformatics, and clinical insights, the authors provide a rigorous framework to understand how mild chaotic perturbations can enhance systemic complexity and biological resilience.<br /> A particular strength of this work lies in its multidimensional approach, incorporating Shannon entropy, Lyapunov exponents, and fractal dimensions to quantify the therapeutic impact of oxygen-ozone therapy. Therefire, in my opinion, the authors successfully demonstrate that low-dose ozone (20–40 µg/ml O3) fosters adaptive chaos, leading to reduced inflammation, enhanced repair, and improved systemic stability. In contrast, higher doses (>60 µg/ml O3) appear to push the system into pathological chaos, emphasizing the importance of precision dosing in regenerative medicine. Really interesting outcomes!<br /> The translational significance of this study cannot be overstated. It not only advances our understanding of chaos-driven medical interventions but also sets a precedent for personalized medicine strategies that leverage nonlinear dynamics to optimize therapeutic outcomes. Future research could expand on these findings by incorporating real-world clinical datasets and patient-specific modeling, further solidifying the role of adaptive chaos in medical practice.<br /> I trust this study is a landmark contribution to the fields of biophysics, complexity science, and regenerative medicine, offering novel insights into the interplay between biological chaos and therapeutic control.<br /> Great results!!

On 2025-02-12 01:34:43, user Ddeadpanscience wrote:

I think normally rfdiffusion will require that you test at least 48 or 96 designs. The success rate is not that high

On 2025-02-10 16:30:17, user Pierre L wrote:

last references are not present in the article.

On 2025-02-10 16:19:15, user David Lähnemann wrote:

At the time of writing, the GitHub repository simply gives a 404 This is not the web page you are looking for at:<br /> https://github.com/wbvguo/BSReadSim.git <br /> Did you forget to make the repo public? Or is there a typo in there somewhere?

On 2025-02-10 11:32:39, user malandrin wrote:

The prepint is now published in Ticks and Tick Borne Diseases DOI10.1016/j.ttbdis.2024.102434.

On 2025-02-10 11:10:36, user Siobhán McClean wrote:

This article is now published in Microbiology Open. The citation is as follows:

Dennehy, R., Duggan, N., Dignam, S., McCormack, S., Dillon, E., Molony, J., ... & McClean, S. (2022). Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA‐mimic protein and may be involved in the adaptation of Burkholderia cenocepacia. MicrobiologyOpen, 11(1), e1264.

On 2025-02-09 11:10:57, user Zheng Gong wrote:

The authors should note that in line 549, the promoter that drives gRNA expression is the U6 snoRNA promoter and not a "Ubiquitin 6" promoter. Otherwise, a very interesting read!

Thank you!

On 2025-02-07 23:35:18, user Prof. T. K. Wood wrote:

1. Line 231: as the author knows full well, the first report of MqsR was https://doi.org/10.1371/journal.ppat.1000706 in 2009 in which MqsR was characterized via its X-ray structure. It is inappropriate to not cite this seminal work and instead cite a lesser work by the author that added little to MqsR characterization.
2. Line 50: the first link of TA systems in biofilms was https://doi.org/10.1128/jb.01465-08 in 2009, not the current refs by Laub which have nothing to do with biofilms.
3. Line 234: MqsRAC has been solidly linked to persistence and phage inhibition and should be cited (10.1128/spectrum.03388-23).

On 2025-02-07 21:55:49, user Patricia Legler wrote:

We made FRET substrates for CHIKV PMID: 30742841. They are in the Suppl. Info.

On 2025-02-06 12:27:20, user Prof. T. K. Wood wrote:

page 51: CRISPR-Cas type IE is NOT inactive as found by at least two groups. It has been shown to control the cryptic prophages ( https://www.mdpi.com/1422-0067/23/24/16195 ).

On 2025-02-06 02:55:28, user Tom Liang wrote:

Excellent contribution to understanding the microscopic mechanisms of anion transport across Band 3! I would like to draw the author’s attention to a highly relevant recent publication in Langmuir: https://doi.org/10.1021/acs.langmuir.4c00216

On 2025-02-05 23:24:58, user Emry Gutierrez wrote:

Great paper! I was curious on the procedures regarding preparing the 48 well plates, as we've been trying to implement these methods into our experiments. Who can I reach out to for more information?

On 2025-02-05 17:50:10, user Emry Gutierrez wrote:

Great paper! Would any of the authors be able to share their procedures for preparing the 48 well plates? We've been trying to implement this methodology and this has been causing us some difficulties!

On 2025-02-05 14:46:01, user Prof. T. K. Wood wrote:

First paragraph is misleading as toxin/antitoxin systems have known to inhibit phage for almost 3 decades so instead of citing a review, the original seminal report should be cite: doi: 10.1128/jb.178.7.2044-2050.1996

On 2025-02-05 10:44:20, user pablo RANEA ROBLES wrote:

Hi! This is a very interesting study, and very relevant considering the debate on omega-6 PUFAs on metabolic health. However, when we were going to read it for a journal club we missed the methods section on this preprint.

On 2025-02-04 22:16:48, user Bill Mallet wrote:

To assist interpretation, it would be helpful to plot the dose-response curves in Fig. 2a with a log10 X-axis.

On 2025-02-04 22:09:10, user Bill Mallet wrote:

Thank you for breathing new life into Hu3A5. For the record: The cysteine-engineered ADC is called "DMUC4064A" not "DMU46064A".

On 2025-02-04 18:27:43, user Ian wrote:

Enjoyable read, particularly the introduction. Unsure how well DSS-induced colitis is able to compare to the "allergy-allegory" persistent in the text. The inflammatory etiology of both conditions are different. DSS is primarily barrier function driven whereas the other, as you mention, is "engrammatic". (immune-memory-driven)

On 2025-02-04 14:51:37, user Emily Breeze wrote:

I very much enjoyed this paper but I could seem to find any of the Tables?

On 2025-02-03 17:44:55, user disqus_2m2wL3bGCz wrote:

I cannot find the methods part in the uploaded preprint ????‍♂️

On 2025-02-03 14:06:53, user David Hill wrote:

This companion article was peer reviewed during the review and revision process for its parent article:

Dilollo J, Hu A, Qu H, Canziani KE, Clement RL, McCright SJ, Shreffler WG, Hakonarson H, Spergel JM, Cerosaletti K, Hill DA*. A molecular basis for milk allergen immune recognition in eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2025 JAN; IN PRESS. PMID: 39891629. PMCID: Pending.

https://pubmed.ncbi.nlm.nih.gov/39891629/

On 2025-02-03 01:37:14, user Lindsay Wu wrote:

The accepted version of this manuscript has now been published online at the Journal of Biological Chemistry, link below:

https://doi.org/10.1016/j.jbc.2025.108248

On 2025-02-02 14:00:44, user Wilson de Oliveira Souza wrote:

I think that figure 1b there is a typo. The trophic pyramid (steeper regression line) shows a S_NBSS > -1 similar to the inverted trophic pyramid (flatter regression line). However, the text states that for this scenario, S_NBSS should be < -1.

On 2025-01-31 22:30:16, user Marius Walter wrote:

The detailed protocol for the differentiation of neurons in the supplementary Table 2 is really great. Thank you for including that.

On 2025-01-31 19:40:14, user Dagan Segal wrote:

Dear Oscar,

Thank you so much for your comments and feedback - it took a while to see this on this forum so apologies for the delayed response.

We incorporated some of your suggestions to add more context to discoveries made by your group and others regarding Cav1 in Ewing Sarcoma- appreciate the suggestions!

In our studies, the subset of CD99 High cells we characterized do indeed have caveolae- so in contrast to previous studies- we believe the signaling in these cells do depend on caveolae per se and not just Caveolin-1 expression.

Thanks also for the comment on other signaling pathways- MAPK levels were low in our hands for all these cells (CD99 High or Low) but maybe worth revisiting.

Cheers,<br /> Dagan (first author)

On 2025-01-31 18:42:25, user Michael wrote:

Please link the published version of this article to the preprint. See below for details:<br /> A 3D Self-Assembly Platform Integrating Decellularized Matrix Recapitulates In Vivo Tumor Phenotypes and Heterogeneity. Cancer Res 2025; https://doi.org/10.1158/0008-5472.CAN-24-1954

On 2025-01-30 16:48:53, user Richard Condit wrote:

This is published in

Condit, R. & Rüger, N. (2024). Demographic variation and demographic niches of tree species in the Barro Colorado forest. Chapter 30 in The First 100 Years of Research on Barro Colorado (eds. H. C. M. Landau & S. J. Wright), pp. 269–276. Smithsonian Scholarly Press.

On 2025-01-29 22:33:23, user Suzanne Amador Kane wrote:

MATLAB code for the various calculations described in this preprint is posted on github now:<br /> https://github.com/amadorkane/Gait-space-clusterer-for-multilegged-locomotion.git <br /> We are working on implementing this code in python -- stay tuned.

On 2025-01-29 13:39:52, user Robert Tropek wrote:

The revised version of this preprint has already been published in Journal of Biogeography: https://doi.org/10.1111/jbi.15076

On 2025-01-29 12:23:58, user Prof. T. K. Wood wrote:

1. line 57: The molecular mechanism of the most-prevalent phage defense system, toxin/antitoxin systems, is relatively well-understood since 1996 (host transcription shutoff, doi: 10.1128/jb.178.7.2044-2050.1996) so this statement is somewhat misleading.

2. l 328: there is little if any evidence of abortive infection in phage defense and a third possibility is the one you found: cells express phage defenses like Kiwa, CRISPR,and TAs and survive the infection.

On 2025-01-29 08:13:29, user Karthik Raman wrote:

This is now published in: https://www.nature.com/articles/s41540-024-00426-5 - pls. arrange to add to the main article.

On 2025-01-29 04:49:44, user 角田 裕之 wrote:

This work has now been published by Springer and is available at the following link: https://doi.org/10.1007/978-981-96-0868-3_4 .

On 2025-01-28 12:53:31, user Z. Brown wrote:

looks similar to the Brown et al. 2014 study: https://pubs.acs.org/doi/10.1021/ja5060934

On 2025-01-28 09:23:39, user Dr Balazs Balint wrote:

Source code, documentation (including a tutorial section) of ContScout is available at <br /> https://github.com/h836472/ContScout .<br /> Please look for branch "BioRxiv_version" if you specifically look for the code that is associated with the manuscript version presented here. If you wish to use the latest features (including screening at fine taxonomic resolution) the use of "main" branch is highly recommended.

On 2025-01-27 18:25:14, user Dan T.A. Eisenberg wrote:

The abstract says, “Repeated qPCR-based measurements of the same DNA extraction yielded ICC values ranging from 0.24 to 0.94”. Keyword searching the document for 0.24 does not reveal that number in the body of the manuscript. The body of the manuscript states, “ICCs of qPCR assays varied widely (range 0.43 to 0.94)”. Table 3 seems to indicate a range of 0.259 to 0.936.

On 2025-01-25 17:37:27, user Andreas wrote:

Hello,

Congratulations on the mauscript, really interesting approach! I am a wet lab scientist and I would like to know if you have though of "grounding" your designs to folds which are less likely to cause immunogenicity (e.g. IgG folds) or that have been explored for drug design (e.g. VHHs, DARPins, ankyrins, etc).

On 2025-01-23 21:00:35, user Nicole Blackstone wrote:

The published paper linked below and on the main page is a cultivated meat LCA, not a media LCA. Is this a mistake?

On 2025-01-23 20:41:28, user handesuermickler wrote:

This study is published in Diagnostics. <br /> Please see the published version through: https://doi.org/10.3390/diagnostics1424284

On 2025-01-23 18:08:17, user Laleh Cote, Ph.D. wrote:

I am the corresponding author for this paper ( https://doi.org/10.1101/2023.05.08.539924 ), which has now been published at PLOS One, here: https://doi.org/10.1371/journal.pone.0317403

Thanks, bioRxiv team!

On 2025-01-22 19:52:04, user Leonardo Chicaybam wrote:

I peer-reviewed this manuscript on ResearchHub: https://www.researchhub.com/paper/6716382/car-t-cells-targeting-ccr9-and-cd1a-for-the-treatment-of-t-cell-acute-lymphoblastic-leukemia/conversation

On 2025-01-22 19:38:21, user Leonardo Chicaybam wrote:

I peer-reviewed this manuscript on ResearchHub: https://www.researchhub.com/paper/8637437/age-related-remodeling-of-the-glycocalyx-drives-t-cell-exhaustion/reviews

On 2025-01-22 08:26:37, user PreOmics wrote:

As representatives of PreOmics, we would like to highlight a key observation in the submitted manuscript for readers to consider.

Supplementary Figure 1: The authors describe the injection of 300 ng peptides, but Supplementary Figure 1 shows variations in TIC signal intensities for the compared techniques. These differences may stem from the two different peptide quantification assays employed and described in the study. From a mass spectrometry perspective, such discrepancies make it challenging to technically compare different enrichment techniques due to the influence of signal intensity variations on the S/N ratio, peak-picking algorithms, peptide quantities, and sequence coverage. We recommend to repeat the study and use our recommendations for peptide quantification compatible to ENRICHplus.

In addition, it is important to acknowledge that the ENRICHplus pre-release version was employed for the comparison, which differs from the commercial version scheduled for release on February 22, 2025.

PreOmics is always supportive if customers struggle to achieve expected results with our solutions and we are keen to support you and provide our recommendations to achieve the best results possible.

On 2025-01-21 23:22:04, user Dieter Steinhilber wrote:

The authors state: "18-HEPE is the precursor for resolvin E1 (RvE1), a cardioprotective, specialized pro-resolving mediator (SPM) that activates the GPCR ChemR23" in their abstract. There is solid evidence now that RvE1 does not activate ChemR23 (PMID: 39365815 and PMID: 35125345)

On 2025-01-21 15:16:28, user Dosidicus wrote:

This is a very interesting work, however the by using of the GHK current equation the results cannot be uniquely interpreted as due to the creation of a calcium channel. As an example a channel in which Calcium acts as an activator would produce the same apparent effects. In order to really show that this is a Calcium channel the authors would need to show that there are no changes in the open probability in the different conditions.<br /> That's why in the field the GHK voltage equation with bi-ionic potentials is used. Where the authors not able to measure bi-ionic potentials by putting sodium or magnesium in their intracellular solution?

On 2025-01-21 03:24:18, user Damien wrote:

I'm wondering where we can get the EII layer for work on Sustainable 1's new nature/bio risk methodology (April 2024) that includes it? The Preprint mentioned it would be on the UN bio lab site, but it's not there yet. Will this ever be available?

On 2025-01-20 10:53:31, user Sudarshan GC wrote:

Very interesting paper. I think several tests are missing like calcium influx assay. Would like to see if increase in calcium concentration in media can help to fold increase the EV production. I would also expect to see the elaboration of precise pathway downstream of Piezo1.

On 2025-01-20 10:44:33, user Mark Blaxter wrote:

The supplementary data files are not linked n the document.<br /> The zenodo file cited for the parameter set used (10.5281/zenodo.14247722) gives a "not found" on the doi system.<br /> The Cheilosia genomes were sequenced by the Darwin Tree of Life project (not EBP) and each genome has a reference, which should be cited (as has been done for the human genomes used): https://wellcomeopenresearch.org/gateways/treeoflife?all=Cheilosia

On 2025-01-19 17:40:19, user Thomas Munro wrote:

It's a remarkable achievement to go from virtual screening to subnanomolar affinity and bound structures in one paper. On a minor point, I would recommend adding "neutral" to phrases such as "antagonists and inverse agonists", and in the title. The present wording could be taken to imply two separate categories, but almost all antagonists are inverse agonists . For instance, naloxone and JDTic are indeed antagonists as noted here, but both are also inverse agonists.

On 2025-01-18 08:03:05, user Leonardo Chicaybam wrote:

I peer-reviewed this preprint on ResearchHub: https://www.researchhub.com/paper/6692139/scalable-intracellular-delivery-via-microfluidic-vortex-shedding-enhances-the-function-of-chimeric-antigen-receptor-t-cells/reviews

On 2025-01-17 10:09:07, user Xinyan Wang wrote:

It is worth mentioning that in 2022, our DMFF paper (doi:10.26434/chemrxiv-2022-2c7gv or 10.1021/acs.jctc.2c01297) had already attempted force field parameter optimization using a subset of the FreeSolv dataset, based on a differentiable framework and utilizing solvation free energy as the loss function, although on a smaller scale compared to this article. We believe this deserves to be mentioned when reviewing related work in the field.

On 2025-01-16 20:56:10, user Lisa Brents wrote:

Nice study! Would it possible to do a more chronic study with these explants with lower concentrations of buprenorphine? I'm sure this depends primarily on how long the explants can be functionally maintained. Also, are you considering looking at whether the major metabolites of buprenorphine (norbuprenorphine, glucuronides) also can cause placental sterile inflammation? As you may know, the Concheiro paper showed higher median concentrations of these metabolites than the parent drug in placenta.

On 2025-01-16 06:03:33, user xPeer wrote:

Courtesy review from xPeerd.com

Summary:<br /> The preprint titled "Venomics AI: a computational exploration of global venoms for antibiotic discovery" presents a robust study leveraging computational and experimental methods to mine and evaluate venom-derived peptides (VEPs) for their potential as new antibiotics. The researchers utilized bioinformatics tools and machine learning-driven prediction models, particularly APEX, to identify and analyze 16,123 venom proteins from four major databases, generating 40,626,260 VEPs. The study identified 386 promising VEPs and demonstrated significant antimicrobial activity in experimental assays, including in vivo models. Identified limitations highlight areas for potential improvement in computational predictions and experimental designs. The study emphasizes the vast, untapped potential of venomics for addressing global antibiotic resistance.

Potential Major Revisions:<br /> 1. Methodological Rigor and Complexity:<br /> - The paper lacks detailed information on the specific machine learning model architectures, training parameters, and validation strategies used for APEX, which could affect reproducibility and understanding of the model's robustness (Page 5, Section APEX).<br /> - The criteria for selecting the "top" VEPs based on predicted MIC values need clearer justification and empirical backing aside from the computational predictions (Page 3, Methods).

1. Experimental Design and Justification:
2. While the study uses a wide range of bacterial strains, the reasons for selecting specific strains and how representative they are of clinical pathogens could be elaborated to strengthen the rationale behind the experiments (Page 6, Section Results).

3. The in vivo efficacy investigations using the mouse model should provide more details on statistical power analysis and exact experimental conditions to ensure reliability and replicability of results (Page 9, Anti-infective activity in preclinical animal models).

4. Data Accessibility and Transparency:

5. The paper mentions data availability but does not provide direct access to the datasets used for training APEX and the resulting VEP predictions, which is essential for verification and reuse by other researchers (Page 10, Data availability).
6. Detailed experimental data, including raw and processed data sets, should be included in supplementary materials or made accessible via appropriate repositories (Page 10, Data availability).

Potential Minor Revisions:<br /> 1. Typographic Errors and Grammatical Mistakes:<br /> - Page 2, Abstract: "Venom-derived peptides, in particular, hold promise for antibiotic discovery due to their evolutionary diversity and unique pharmacological profiles" - the word "hold" should be "holds".<br /> - Page 5, Line 837: "from multiple source organisms" - should be "from multiple source organism".

1. Formatting Issues:
2. The legends and footnotes of figures sometimes appear incomplete or unclear regarding the methods used to generate them. Ensure all figures have comprehensive legends (Page 11, Statistical tests).

3. Consistency in referencing supplementary figures and tables in the main text should be checked, ensuring that all references are accurately placed (Page 2, Abstract).

4. AI Content Analysis:

5. Estimated AI-generated content: ~5-7%.
6. Highlighted AI-detected sections:
7. "Using machine learning, we explored 16,123 venom proteins, generating 40,626,260 venom-encrypted peptides (VEPs)" (Page 1).
8. "Our findings highlight the power of combining digital data and machine learning to accelerate antibiotic discovery" (Page 12).
9. Assessed epistemic impact: This content does contribute substantively to the manuscript by supporting the methodology and results, but may benefit from more nuanced and manual integration to bolster reliability.

Recommendations:<br /> 1. Enhance Methodological Transparency:<br /> - Provide a detailed algorithmic framework for the APEX model, specifying hyperparameters, loss functions, and training-validation splits.<br /> - Include a comprehensive justification for the selection of bacterial strains and the representativeness of the in vivo model used.

1. Expand Data Accessibility:

2. Ensure all datasets and computational tools used in the study are accessible via publicly available repositories, adhering to FAIR data principles.

3. Improve Experimental Detail:

4. Elaborate on experimental protocols, including statistical analyses, to ensure replicability.
5. Provide a more detailed discussion of limitations and potential biases in experimental designs and predictive models.

This detailed review necessitates substantial revisions to address these points and ensure the study meets the high standards expected for reproducibility and transparency in computational biology and experimental antimicrobial research.

On 2025-01-15 22:14:42, user theskullywaglab wrote:

This article has been accepted for publication in the Journal of Experimental Biology. We received glowing reviews and the only substantial change made was to include a figure as a visual guide to the framework proposed. To meet the journal guidelines of maximum 5 tables/figures, this involved combining the two figures of heatmaps into a single figure, and rearranging the Results/Discussion to accommodate the new figures.

Thank you for your interest in this research.

Rex Mitchell

On 2025-01-15 15:15:10, user covis chang wrote:

Provided insights for further exploration of personalized precision medicine, particularly for the early diagnosis and optimized treatment of NEPC.

On 2025-01-14 04:30:21, user 張景欣 wrote:

The PSMA scan is considered an excellent tool to replace traditional bone scans and is becoming increasingly widely used. However, if a neuroendocrine tumor does not express PSMA, this indicates the need for newer diagnostic methods or a broader range of targets.

On 2025-01-14 04:06:08, user Yi-Cheng Yang wrote:

This study contributes to the establishment of personalized treatment, such as considering the use of EZH2 inhibitors combined with PSMA-targeted therapy for NE type II patients, providing new treatment options for cancer patients.

On 2025-01-15 13:05:52, user gang_fang wrote:

The peer-reviewed version has been published. You can find the link below.<br /> https://pmc.ncbi.nlm.nih.gov/articles/PMC11707888/

On 2025-01-14 03:19:09, user Bryan wrote:

Are you able to share a version with high quality figures? The text in many figures is not readable. Thank you!

On 2025-01-13 02:26:25, user Harim Chun wrote:

The expansion distance varies by Xenium Analyzer version. In XOA v2.0 and later versions, the expansion distance is 5 µm, while in XOA v1.0-1.9, the default expansion distance was 15 µm. Therefore, it is important to specify which version of the Xenium Analyzer is being used.<br /> https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/algorithms-overview/segmentation#seg-nucleus-expansion

On 2025-01-11 04:47:52, user xPeer wrote:

Here's a courtesy review from xPeerd.com

Summary

The manuscript titled "E-cadherin endocytosis promotes non-canonical EGFR:STAT signalling to induce cell death and inhibit heterochromatinisation" studies the impact of E-cadherin endocytosis on EGFR and STAT signalling pathways in Drosophila wing discs. It reveals that E-cadherin endocytosis facilitates EGFR:STAT signalling, which in turn promotes apoptosis and inhibits heterochromatin formation.

Potential Major Revisions

1. Research Design and Methodology:
2. While the methodology is sound, there are areas that need more clarity. For example, the paper describes the use of E-cad::EOS overexpression but lacks detailed control experiments and statistical analysis to support the claims about changes in gene expression (p. 4, Section 1).

3. The reliance on Drosophila as a model organism is justified but requires additional discussion on how the findings translate to vertebrate systems (p. 1, Summary).

4. Clear Contribution to the Field:

5. The potential tumor-suppressive mechanism proposed is intriguing, but the manuscript needs to more clearly define its novel contributions against existing literature. The exact nature of the signalosome and its comparison with known complexes should be elaborated (p. 17, Discussion).
6. It should explicitly differentiate findings from previous studies that linked E-cadherin and EGFR signalling (p. 11).

Potential Minor Revisions

1. Typographic and Grammatical Errors:
2. Typographic errors, such as “the transcriptional reporter” should be “transcriptional reporter” (p. 14, Line 20).

3. Ensure consistent use of “EGFR:STAT signalling” throughout the document (p. 12, Line 1).

4. Formatting Issues:

5. Ensure all figure legends and references are consistently formatted (Figures on pages 12-16).

6. Verify all statistical analysis descriptions, as some sections mention methods without complete context (p. 16-17).

7. AI Content Analysis:

8. The document appears to be human-authored, as the writing style and the depth of content are consistent with academic rigor. There are no substantial indicators of AI-generated content.

Recommendations

1. Enhanced Clarity:
2. Enhance clarity by adding detailed flow diagrams for the signalling pathways discussed, particularly the role of endocytic trafficking of E-cadherin and its intersection with EGFR and STAT signalling pathways.

3. Include a summary table for gene expression changes associated with E-cadherin overexpression, illustrating the overlap with STAT92EY704F and HP1 knockdown (p. 4).

4. Control Experiments:

5. Additional control experiments are essential, particularly targeting the specificity of STAT92E interactions with Heterochromatin Protein 1 (HP1) and EGFR (p. 3-4).

6. Linking to Human Context:

7. Increase the discussion of how these findings might translate to human epithelial cancers, supporting the relevance of these mechanisms with references to similar studies in mammalian cells (p. 11-12).

Conclusion

The manuscript offers valuable insights into the non-canonical roles of STAT and EGFR signalling regulated by E-cadherin endocytosis. Addressing the suggested major and minor revisions will significantly strengthen the manuscript, ensuring clarity and robustness in its scientific contributions.

On 2025-01-09 09:22:25, user Dominique Sebastian Stolle wrote:

Dear community, this article was published under the title“STIC2 selectively binds ribosome-nascent chain complexes in the cotranslational sorting of Arabidopsis thylakoid proteins” ( https://doi.org/10.1038/s44318-024-00211-4) in The EMBO Journal in August 2024.

Best regards<br /> Dominique Stolle

On 2025-01-07 19:02:17, user Thomas Munro wrote:

This is an ingenious idea. The name azo-morphine will likely cause confusion, however, given that the scaffold used is naltrexamine. The name is already in use for azo-substituted morphine derivatives. A full semi-systematic name would be unwieldy, but could be used to derive a distinctive acronym like IBNtxA, which would make literature searches much easier.

On 2025-01-07 14:01:13, user Ryan S. Soledade wrote:

A pleasant and quick read. The inference of Lagoa Santa's environmental conditions based on the presence of a frugivorous fauna is notorious. However, it wasn't clear to me what specific features link the new specimen to the genus Artibeus. A figure on the Discussion section comparing the specimens cited would help to visualize the morphological similarities between them. In addition, a simple phylogenetic analysis would provide a quantitative basis for the assignment to Artibeus and strengthen it.

On 2025-01-07 11:09:38, user Hossein Shirali wrote:

This preprint has been peer-reviewed and published in Invertebrate Systematics. Please see the final version here: 10.1071/IS24011.

On 2025-01-06 16:51:54, user Micha Wijesingha Ahchige wrote:

The paper is now published in the Computational and Structural Biotechnology Journal:

https://doi.org/10.1016/j.csbj.2024.10.028

On 2025-01-06 11:36:49, user xPeer wrote:

Courtesy review from xPeerd.com

Summary<br /> The preprint "A Bioinformatics-Driven ceRNA Network in Stomach Adenocarcinoma" presents a study that identifies and examines novel prognostic biomarkers and ceRNA regulatory networks in stomach adenocarcinoma using a sophisticated bioinformatics approach. The study integrates mRNA, miRNA, and lncRNA interactions, unveiling key pathways and contributing insights into potential biomarkers like KCNQ1OT1 linked to cancer progression. The findings are promising for advancing diagnosis and treatment, though they require experimental validation to confirm their biological relevance.

Potential Major Revisions<br /> 1. Experimental Validation:<br /> - Issue: The study is heavily reliant on computational predictions without in vitro or in vivo experimental validation.<br /> - Recommendation: Initiate experimental validation of key ceRNA interactions, particularly the KCNQ1OT1-miR-29a-3p-ELAVL3 axis, to substantiate the bioinformatics findings. Validation can be executed through techniques such as qRT-PCR, Western blotting, and functional assays in cell lines.

1. Statistical Analysis Transparency:
2. Issue: While databases like GEPIA, UALCAN, and miRNet are utilized, statistical methods are not consistently detailed.

3. Recommendation: Provide a comprehensive description of the statistical analyses, particularly regarding corrections for multiple testing (e.g., false discovery rate). This will improve the clarity and reproducibility of the results.

4. Data Accessibility:

5. Issue: Accessibility to the raw and processed data used in the analysis is not adequately ensured.
6. Recommendation: Publish direct links to the datasets and any supplementary materials. Ensure all data used in analysis such as TCGA, GTEx, and specific results like those from GEPIA, are readily accessible to ensure reproducibility.

Potential Minor Revisions<br /> 1. Typographical Errors:<br /> - Page 4: "preprintthis" should be spaced to "preprint this".<br /> - Page 17: "has-miR-29a-3p" should correctly read "hsa-miR-29a-3p".

1. Grammatical Mistakes:
2. Abstract: The phrase "The elevated expression was associated with unfavorable prognosis" would be clearer as "Its elevated expression was associated with an unfavorable prognosis."

3. Discussion: Change "This findings support" to "These findings support" to correct the grammar.

4. Formatting Issues:

5. Ensure uniformity in figure captions and references like "Figure S5" instead of mixed styles "Figure S5" and "figure S5."

6. Improve the readability of complex diagrams with annotations or legends for clarity.

7. AI Content Analysis:

8. Estimated AI-generated content: ~5%.
9. Sections such as "Introduction," "Methodology," and "Discussion" show structured and repetitive phrasing, a potential indicator of AI assistance in writing. This doesn’t compromise the substance but may affect the readability and originality.

Recommendations<br /> 1. Enhance Experimental Validation:<br /> - Conduct in vitro and in vivo experiments to validate the interactions and pathways predicted by the bioinformatics analysis. Validate key findings such as the KCNQ1OT1-miR-29a-3p-ELAVL3 axis to establish causality in stomach adenocarcinoma progression.

1. Strengthen Statistical Rigor:

2. Clarify and detail statistical analyses across the manuscript. Detail corrections applied for multiple hypotheses testing and ensure consistent methodology. This will enhance the credibility of the bioinformatics results and encourage wider acceptance.

3. Improve Data Presentation:

4. Ensure data transparency by providing direct access to databases, completing figure legends, and providing detailed methodology. Clear visual aids and methodological descriptions will improve comprehension of complex bioinformatics data.

5. Refine Writing and Formatting:

6. Address typographical and grammatical errors to enhance clarity and professionalism. Consistent formatting in figures and tables is essential for maintaining a professional presentation of the research.

Conclusion<br /> The manuscript contributes substantial and promising bioinformatics research on ceRNA networks in stomach adenocarcinoma. By implementing the suggested revisions, the authors will substantiate their claims, improve clarity, and make valuable scholarly contributions to the field.

On 2025-01-06 11:23:42, user xPeer wrote:

Courtesy review from xPeerd.com

Summary

The study analyzes bubble net feeding behaviors in the Kitimat Fjord System (KFS) in northern British Columbia using 20 years of data. Employing network-based diffusion analysis (NBDA), the authors establish strong evidence for social learning in humpback whales, highlighting rapid diffusion of both cooperative and solo bubble net feeding behaviors. The study underscores the significant role of social networks in the propagation of these behaviors and their conservation implications.

Potential Major Revisions

1. Clarification and Consistency of Hypotheses:

2. While the study makes a compelling case for both social and individual learning, the presentation of hypotheses regarding their respective contributions needs clarity. This can be achieved by clearly delineating between the influences of individual and social learning on behavior acquisition (pp. 1-3, Abstract and Introduction).

3. Enhanced Methodological Detail:

4. The methods section, although comprehensive, could benefit from more explicit descriptions of the parameters used in NBDA models. Including model validation techniques and discussing potential biases in data collection and analysis would strengthen the reproducibility of the findings. Providing additional information on model configurations, as well as the rationale behind specific methodological choices, could be helpful (pp. 8-10, Methods).

5. Integration of Homophily and Social Learning Models:

6. The current analysis acknowledges homophily but requires a more thorough exploration of its limitations and overlap with social learning models. Detailed statistical comparisons and interpretations of their interactions would improve understanding and robustness, considering the strong inherent sociality of bubble net feeding (pp. 12-13, Results).

Potential Minor Revisions

1. Typographical and Terminological Corrections:
2. Correct minor typographical errors, such as replacing "homophilic" with "homophily" (p. 11).

3. Correct terms like "Cequence" to "sequence" (p. 11).

4. Formatting Consistency:

5. Ensure that figures and tables are consistently formatted and well-integrated into the text. Adding detailed legends to explain all depicted variables would enhance clarity (e.g., Figure 2, pp. 14-15).

6. Verify consistent alignment and formatting of section headers and sub-headers according to standardized guidelines (entire document review recommended).

7. AI Content Analysis:

8. Analysis suggests a low estimated likelihood of AI-generated content, given the depth of analysis and domain-specific context. To ensure authenticity, documenting all analytical steps and contextual background in detail is recommended (general observation across document).

Recommendations

1. Ecological Implications Discussion:

2. Expand on the broader ecological implications of rapid diffusion in bubble net feeding. Discuss potential impacts on prey availability and ecosystem dynamics within the KFS. Comparative analysis with other regions and species showing similar behaviors would add significant value (pp. 15-17, Discussion).

3. Methodological Transparency Enhancement:

4. Create a supplementary section detailing the specific NBDA algorithms, models, and preprocessing steps used. Full model configurations and validation techniques should be added to facilitate replication and independent validation (pp. 8-10, Methods).

5. In-Depth Social Network Analysis:

6. Providing more detailed visualization of the social network analysis, including social network diagrams and statistical validation, would help readers understand interactions between individual whales and the spread of behaviors (pp. 10-12, Results).

7. Conservation Strategies Integration:

8. Formulate concrete recommendations for incorporating findings into long-term conservation planning. Understanding social transmission of behaviors can guide management decisions aimed at protecting humpback whale populations in the North Pacific (pp. 15-17, Discussion).

On 2025-01-06 00:23:27, user Carole LaBonne wrote:

This work should cite work from Marianne Bronner from 2002 showing that the effects of ethanol were due to programed cell death of neural crest cells <br /> https://pubmed.ncbi.nlm.nih.gov/12140368/

On 2025-01-04 07:42:26, user uneventhompson wrote:

Is the raw data available for these samples? A bunch of us living R--U106 and R-Z19 men are interested in digging through the Y SNP reads to help with identifying any possible sub-clades that may exist.

On 2025-01-03 10:03:03, user Andreia Wendt wrote:

The final peer-reviewed version of this article is open-accessible here: https://www.nature.com/articles/s41467-024-55538-7