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 comment url,comment forum,comment keywords,comment message,comment date,comment username,comment name,paper doi,paper title,paper authors,paper date
+https://www.biorxiv.org/content/10.1101/2024.12.23.630033v1#comment-6618316012,biorxivstage,0,"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.",2024-12-27T03:11:02,samuelyi,samuel Yi,10.1101/2024.12.23.630033,Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms,"Pengfei Ren, Rui Zhang, Yunfeng Wang, Peng Zhang, Ce Luo, Suyan Wang, Xiaohong Li, Zongxu Zhang, Yanping Zhao, Yufeng He, Haorui Zhang, Yufeng Li, Zhidong Gao, Xiuping Zhang, Yahui Zhao, Zhihua Liu, Yuanguang Meng, Zhe Zhang, Zexian Zeng",2024-12-25
+https://www.biorxiv.org/content/10.1101/2024.05.12.593733v1#comment-6618190960,biorxivstage,0,https://uploads.disquscdn.c...,2024-12-26T21:44:40,disqus_tqASSZDsvX,David Schmidt,10.1101/2024.05.12.593733,PTPRS is a novel marker for early tau pathology and synaptic integrity in Alzheimer’s disease,"Alexandre Poirier, Cynthia Picard, Anne Labonté, Isabelle Aubry, Daniel Auld, Henrik Zetterberg, Kaj Blennow, the PREVENT-AD research group, Michel L. Tremblay, Judes Poirier",2024-05-12
+https://www.biorxiv.org/content/10.1101/2024.05.27.594700v1#comment-6618144203,biorxivstage,0,Now has been published in Advanced Science: https://onlinelibrary.wiley.com/share/GRXAEZQFHDVMNTTIKBN8?target=10.1002/advs.202406751,2024-12-26T20:12:49,,Huy Le,10.1101/2024.05.27.594700,JUNB O-GlcNAcylation-mediated promoter accessibility of metabolic genes modulates distinct epithelial lineage in pulmonary fibrosis,"Marie-Therese Bammert, Meshal Ansari, Leoni Haag, Zuhdi Ahmad, Victoria Schröder, Joseph Birch, Diana Santacruz, Werner Rust, Coralie Viollet, Benjamin Strobel, Alec Dick, Florian Gantner, Holger Schlüter, Fidel Ramirez, Muriel Lizé, Matthew J. Thomas, Huy Q. Le",2024-05-30
+https://www.biorxiv.org/content/10.1101/2024.12.18.628574v1#comment-6617912725,biorxivstage,0,Did you include in the sample the microbiome of microscopic animals (e.g. nematodes)?,2024-12-26T11:37:01,,Francisco Rodriguez-Valera,10.1101/2024.12.18.628574,The ketone body β-Hydroxybutyrate mediated epigenetic chromatin β-hydroxybutyrylation protects kidneys,"Juthika Mandal, Sachin Aryal, Ishan Manandhar, Saroj Chakraborty, Xue Mei, Beng San Yeoh, Blair Mell, Andrew Kleinhenz, Ramakumar Tummala, Tao Yang, Piu Saha, William T Gunning, Matam Vijay-Kumar, Venkatesha Basrur, Ivana de la Serna, Bina Joe",2024-12-21
+https://www.biorxiv.org/content/10.1101/2024.11.29.626108v1#comment-6617447013,biorxivstage,0,"One thing I often wonder about when people report transformation efficiencies, or do not have a very detailed protocol, is about the growth phase of the cells that are harvested to make competent cells. I often see something like ""cells are grown overnight"". I suspect harvesting cells in log phase would be most ideal for high transformation, but then a higher volume of cells would be needed and the time incubated in TEL+DTT buffer would likely need to be lowered/optimized. Does the age of the colony used to start the culture matter? If authors spent time optimizing this, it would be a great resource/reference if some of these details were shared.",2024-12-25T08:04:03,phillipkyriakakis,phillip kyriakakis,10.1101/2024.11.29.626108,Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids,"Alexander Pisera, Yutong Yu, Rory L Williams, Chang C Liu",2024-11-30
 https://www.biorxiv.org/content/10.1101/2024.11.11.623134v2#comment-6617349025,biorxivstage,1,"This paper has several useful points, e.g. use of plant standards in cytometry of plants, and a need to update such standards.  It has a major flaw in regarding as complete the recent gapless, telomere-to-telomere (T2T) assemblies of plants, for use as genome size standards.  Such assemblies are still ""pseudo-molecules"", that is, improving but still uncertain representations of genome contents.  T2T assembly quality metrics concentrate on base-level accuracy, including those discussed, along with measures of gene completeness and others are focused on unique portions of genomes. Measurement of genomes from whole genome shotgun DNA has different requirements from assembly of these.  One requirement is unbiased, random coverage of a genome.  This is a problem for assembly of duplicated spans.  Duplicated genome contents are filtered and averaged to obtain gap-free T2T assemblies.  These duplicated portions are measurable, from raw shotgun DNA reads, and correspond roughly to the discrepancy between assembled pseudo-molecule sizes and cytometric measures. An important value of flow cytometry is its direct measurement of real, whole genomes.  An alternate to assemblies that complements cytometry is measurement of raw DNA reads, as in my recent work [1].  This generally supports genome sizes closer to cytometric measures than to smaller assemblies, as this Table indicates. Table G. Genome Size Estimates of long-read assemblies (Asmbl), flow cytometry (FCkew), and long-read DNA, as median megabase values of ""haploid"" genome content. Genome 	Asmbl 	FCkew 	DNA ----------------------------- arath 	136	162	150 rice  	392	431	406 sorghum	757	818	804 cotton 	2305	2450	2492 pea   	3796	4312	4141 FCkew and DNA are not statistically different, while assembly values are significantly lower than both.  Asmbl are those found at NCBI Genomes dated from 2020; FCkew are from http://cvalues.science.kew.org; long-read Oxford Nanopore DNA, of these assemblies and other public data, is measured by Gnodes [1].  Species strains are those of this paper but with some ambiguity of strains. Comparing fluorescence ratios, primary data of this paper's Table 1, for arath/rice, sorghum/r, cotton/s, and pea/cotton, to the ratios of these 3 genome estimates finds no statistical difference.  The rank order of average difference has DNA (0.007) as most similar, then Asmbl (0.009), then FCkew (0.012).  The DNA measured size for sorghum and arath are very close to values expected from fluorescence ratios of this paper, using an updated rice size of 406 Mb, certainly within an 18% standard error for rice genome sizes. Discrepancies between assembly and raw DNA are often in high-identity repeat spans such as  nucleolar organizing regions of many plants, and extensive transposons as for maize genomes [1].  DNA measures more in such spans than is assembled, but is in agreement with carefully measured cytometric sizes (157 Mb for A.t. model plant [2], 2600Mb to 3000Mb for maize isolines [4]). Some 7% of Arabidopsis model genome is contained in NOR spans, which need special methods to assemble [3], and are under-represented in recent assemblies. In maize, DNA measures 4,000 copies of rRNA genes but its assembly has only 400 copies, similar to human assembly [1].  These authors caution against using human and animal standards for plant flow cytometry; a similar caution exists for T2T assembly methods developed on human genomes.  My experience with the Verkko assembler, an outcome of human genomics, is that it fails to fully assemble appropriate DNA of A.t. and maize plants. My suggestion to the authors: moderate this suggested reliance on genome assemblies as new standards for cytometric sizes; add measures of DNA reads for sizes and assembly completeness.  Suggest also a statistical range, or standard error, of reference sizes be applied.  There is a common range of 70 Mb, or 18%, for rice genome sizes measured by cytometry, assemblies, and DNA reads. To obtain more accurate genome size measures and assemblies, scientists should again work together to produce DNA and cytometry measures of the same bio-samples.  One such example,  a recent paper on many A.t. ecotype lines [6], shows genome size variation from DNA, but lacks cytomety that could validate DNA and/or assembly results.  Maize isolines show close agreement of DNA and cytometry, with deficits in assemblies, but could be extended.  Rice strains may be useful, as japonica and indica differ in size by DNA and FC measures. Refs: 1. Gilbert, D.G. (2024). Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it. bioRxiv, doi: 10.1101/2024.10.06.616888 2. Bennett, MD, IJ Leitch, HJ Price and JS Johnston (2003) Comparisons with Caenorhabditis (100Mb) and Drosophila (175Mb) using flow cytometry show genome size in Arabidopsis to be 157Mb and thus 25% larger than the Arabidopsis genome initiative estimate of 125Mb. Ann. Botany, 91, 547-557 doi: 10.1093/aob/mcg057 3. Fultz, D., McKinlay A, Enganti R, Pikaard CS (2023).  Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis.  Sci. Adv. 9, eadj4509; doi: 10.1126/sciadv.adj4509 4. Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, et al. (2018) Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. PLoS Genet 14: e1007162. doi: 10.1371/journal.pgen.1007162 5. Lian, Q et al (2024). A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat. Genet. 56: 982-991; doi: 10.1038/s41588-024-01715-9",2024-12-25T00:21:30,disqus_cnPA852ta0,Don Gilbert,10.1101/2024.11.11.623134,Re-calibration of flow cytometry standards for plant genome size estimation,"Abhishek Soni, Robert J Henry",2024-11-16
 https://www.biorxiv.org/content/10.1101/2024.12.13.628395v1#comment-6616647747,biorxivstage,0,I thought you would be interested in checking out this article on flow cytometry in Galleria mellonella hemocytes (see below). https://pubmed.ncbi.nlm.nih.gov/38357909/,2024-12-23T17:46:28,,Ivan,10.1101/2024.12.13.628395,"A flow cytometric approach to identifying the relative abundance and functional capacities of hemocyte subsets in the American cockroach, Periplaneta americana (L.)","Faith J. Boyer-Millander, Aaron T. Martin, Chadwick A. Hamm, Arthur G. Appel, Elizabeth Hiltbold Schwartz",2024-12-17
 https://www.biorxiv.org/content/10.1101/2024.07.02.601719v1#comment-6616451365,biorxivstage,1,Thank you very much for the comment. The reference is included in the last version we are currently submitting. Cheers!,2024-12-23T11:09:09,josantonioescudero,José Antonio Escudero,10.1101/2024.07.02.601719,Mobile Integrons Encode Phage Defence Systems,"Nicolas Kieffer, Alberto Hipólito, Paula Blanco, Thomas Delobelle, Francisco Manuel Ojeda, Thomas Jové, Dukas Jurenas, Meritxell García-Quintanilla, Pilar Domingo-Calap, José Antonio Escudero",2024-07-02
@@ -93,9 +98,4 @@ https://www.biorxiv.org/content/10.1101/2024.11.25.625233v1#comment-6600076210,b
 https://www.biorxiv.org/content/10.1101/2024.03.06.583669v1#comment-6599369388,biorxivstage,0,"Hello, This article is already published here. https://www.degruyter.com/document/doi/10.1515/mim-2024-0002/html Can I ask you to put the link? Thank you.",2024-11-25T14:04:59,chiekodera,Chie Kodera,10.1101/2024.03.06.583669,Vitrification by high pressure freezing of a wide variety of sample using the HPM Live µ,"Chie Kodera, Yann Bret, Frederic Eyraud, Jérôme Heiligenstein, Martin Belle, Xavier Heiligenstein",2024-03-06
 https://www.biorxiv.org/content/early/2018/08/03/374843#comment-6599367974,biorxivstage,0,"Hello, This article is already published here. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07503-7 Can I ask you to put the link? Thank you.",2024-11-25T14:02:29,chiekodera,Chie Kodera,10.1101/374843,The molecular signatures of compatible and incompatible pollination,"Chie Kodera, Jérémy Just, Martine Da Rocha, Antoine Larrieu, Lucie Riglet, Jonathan Legrand, Frédérique Rozier, Thierry Gaude, Isabelle Fobis-Loisy",2018-08-03
 https://www.biorxiv.org/content/10.1101/2024.11.17.624038v1#comment-6599309579,biorxivstage,0,"Please consider referencing the work done by Herrera et al ( https://pubmed.ncbi.nlm.nih.gov/32565759/) which includes AFA ultrasonication, S-trap sample processing, and DDA of FFPE micro-dissected sections.",2024-11-25T11:52:43,ronan_o_cualain,Ronan O'Cualain,10.1101/2024.11.17.624038,High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue,"Moe Haines, John R. Thorup, Simone Gohsman, Claudia Ctortecka, Chelsea Newton, Dan C. Rohrer, Galen Hostetter, D. R. Mani, Michael A. Gillette, Shankha Satpathy, Steven A. Carr",2024-11-18
-https://www.biorxiv.org/content/10.1101/2024.07.23.604842v1#comment-6599302375,biorxivstage,1,"That is a nice study, well done, although not bringing breakthrough ideas : it is not a great surprise that conjugative plasmids PTUs are more prone to spread AMR genes than non mobile ones, and are also more prone to recombine because they meet more unrelated DNA. At least it is now demonstrated. I however have some doubt about the host range analysis, because the methods applied are not very clear. It is written that the host range was assigned with COPLA (l.159). But I guess that the host range inferred by COPLA includes all  plasmids in their database for each PTU, including some containing AMR genes. So in the last (and most important) section of the manuscript, removing the ARG-carrying plasmids from the AMR+ PTUs will not change the host range classification given by COPLA. This bring an inconsistency between the given host range and the actual plasmids in the 118 ARG-free PTUs investigated. My feeling is that the rare grade V+VI PTUs are actually caused by ARG carriage, bringing a great fitness advantage in very distant bacterial hosts in which plasmids should otherwise struggle to maintain because of maladaptation. It will be necessary I think to calculate the host range only with the data investigated in the study, simply by looking at the plasmid's host taxonomy and not rely on COPLA results. Like this it can be calculated independently for the various sets of PTUs (with/without pAMR). Other samll comment : in figure 2 355 PTUs containing 13,048 plasmids are given in top panl but less than 8000 plasmids and 50 PTUs are given in bottom panel, and it is not indicated what was the display threshold in bottom panel. Please provide the threshold.",2024-11-25T11:32:41,,Sebastien Leclercq,10.1101/2024.07.23.604842,The spread of antibiotic resistance is driven by plasmids amongst the fastest evolving and of broadest host range,"Charles Coluzzi, Eduardo PC Rocha",2024-07-24
-https://www.biorxiv.org/content/10.1101/2024.10.22.619594v1#comment-6599005216,biorxivstage,1,Interesting work. I recommend reading my recent paper prior to final publication. I would love to know whether your conclusions about mammalian MALAT1 and NEAT1 translate to their non-mammalian orthologs. https://doi.org/10.1007/s00239-023-10151-y,2024-11-24T20:45:05,forrestweghorst,Forrest Weghorst,10.1101/2024.10.22.619594,Phylogenetic Study of Long Non-Coding RNA NEAT1 and MALAT1 to Infer Structural-Functional Connection,"Ksenia Arkhipova, Micha Drukker",2024-10-25
-https://www.biorxiv.org/content/10.1101/2023.10.27.563439v1#comment-6598297783,biorxivstage,0,"This paper has now been published in Ecology and Evolution: Fouda, L., Negus, S. R. B., Lockley, E. C., Fairweather, K., Lopes, A., Lopes, A., Correia, S. M., Taxonera, A., Schofield, G., & Eizaguirre, C. (2024). Productive foraging grounds enhance maternal condition and offspring quality in a capital breeding species. Ecology and Evolution, 14, e70137. https://doi.org/10.1002/ece3.70137",2024-11-23T17:12:00,,Leila,10.1101/2023.10.27.563439,Productive foraging sites enhance maternal health and impact offspring fitness in a capital breeding species,"Leila Fouda, Stuart R. B. Negus, Emma C. Lockley, Kirsten Fairweather, Artur Lopes, Anice Lopes, Sandra M. Correia, Albert Taxonera, Gail Schofield, Christophe Eizaguirre",2023-10-29
-https://www.biorxiv.org/content/10.1101/615567v1#comment-6598164110,biorxivstage,0,Published version: https://doi.org/10.1002/ansa.202000111,2024-11-23T12:41:45,disqus_ziRoFF9Nae,Caroline Fernandes Dos Santos ,10.1101/615567,Drug delivery to rodents: how to deal with body mass and water intake fluctuations?,"Gonçalves Leidyanne Ferreira, Fernandes-Santos Caroline",2019-04-23
-https://www.biorxiv.org/content/10.1101/820415v1#comment-6598162192,biorxivstage,0,Published version: https://doi.org/10.33696/diabetes.1.015,2024-11-23T12:36:19,disqus_ziRoFF9Nae,Caroline Fernandes Dos Santos ,10.1101/820415,Perivascular Adipose Tissue: Quantitative analysis by morphometry and stereology in rodents,"Felipe Demani Carneiro, Stephanie Christinne Sinder Mello, Emiliana Barbosa Marques, Rogerio Barbosa Magalhaes Barros, Christianne Bretas Vieira Scaramello, Caroline Fernandes-Santos",2019-10-28
-https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1#comment-6597942524,biorxivstage,0,Nice work! Are the supplementary tables available?,2024-11-23T00:09:48,leebardwell,Lee Bardwell,10.1101/2024.04.09.588596,Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions,"Ernst W. Schmid, Johannes C. Walter",2024-04-12
+https://www.biorxiv.org/content/10.1101/2024.07.23.604842v1#comment-6599302375,biorxivstage,1,"That is a nice study, well done, although not bringing breakthrough ideas : it is not a great surprise that conjugative plasmids PTUs are more prone to spread AMR genes than non mobile ones, and are also more prone to recombine because they meet more unrelated DNA. At least it is now demonstrated. I however have some doubt about the host range analysis, because the methods applied are not very clear. It is written that the host range was assigned with COPLA (l.159). But I guess that the host range inferred by COPLA includes all  plasmids in their database for each PTU, including some containing AMR genes. So in the last (and most important) section of the manuscript, removing the ARG-carrying plasmids from the AMR+ PTUs will not change the host range classification given by COPLA. This bring an inconsistency between the given host range and the actual plasmids in the 118 ARG-free PTUs investigated. My feeling is that the rare grade V+VI PTUs are actually caused by ARG carriage, bringing a great fitness advantage in very distant bacterial hosts in which plasmids should otherwise struggle to maintain because of maladaptation. It will be necessary I think to calculate the host range only with the data investigated in the study, simply by looking at the plasmid's host taxonomy and not rely on COPLA results. Like this it can be calculated independently for the various sets of PTUs (with/without pAMR). Other samll comment : in figure 2 355 PTUs containing 13,048 plasmids are given in top panl but less than 8000 plasmids and 50 PTUs are given in bottom panel, and it is not indicated what was the display threshold in bottom panel. Please provide the threshold.",2024-11-25T11:32:41,,Sebastien Leclercq,10.1101/2024.07.23.604842,The spread of antibiotic resistance is driven by plasmids amongst the fastest evolving and of broadest host range,"Charles Coluzzi, Eduardo PC Rocha",2024-07-24