November 2024 - Consensus - lists.biobrillouin.org

FW: [EXTERN] arXiv New submission -> 2411.11712 in physics.optics from Kareem.elsayad@meduniwien.ac.at
by Kareem Elsayad Nov. 19, 2024

Nov. 19, 2024

On 19.11.24, 04:00, "e-prints(a)arxiv.org <mailto:e-prints@arxiv.org>" <e-prints(a)arxiv.org <mailto:e-prints@arxiv.org>> wrote: Your submission submit/6002321 has been assigned the permanent arXiv identifier 2411.11712 and is available at: http://arxiv.org/abs/2411.11712 <http://arxiv.org/abs/2411.11712> The paper password for this article is: peexv Please share this with your co-authors. They may use it to claim ownership. Abstract will appear in today's mailing as: ------------------------------------------------------------------------------ \\ arXiv:2411.11712 From: Kareem Elsayad <Kareem.elsayad(a)meduniwien.ac.at <mailto:Kareem.elsayad@meduniwien.ac.at>> Date: Mon, 18 Nov 2024 16:37:33 GMT (2451kb) Title: Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials Authors: Pierre Bouvet, Carlo Bevilacqua, Yogeshwari Ambekar, Giuseppe Antonacci, Joshua Au, Silvia Caponi, Sophie Chagnon-Lessard, Juergen Czarske, Thomas Dehoux, Daniele Fioretto, Yujian Fu, Jochen Guck, Thorsten Hamann, Dag Heinemann, Torsten J\"ahnke, Hubert Jean-Ruel, Irina Kabakova, Kristie Koski, Nektarios Koukourakis, David Krause, Salvatore La Cavera III, Timm Landes, Jinhao Li, Jeremie Margueritat, Maurizio Mattarelli, Michael Monaghan, Darryl R. Overby, Fernando Perez-Cota, Emanuele Pontecorvo, Robert Prevedel, Giancarlo Ruocco, John Sandercock, Giuliano Scarcelli, Filippo Scarponi, Claudia Testi, Peter T\"or\"ok, Lucie Vovard, Wolfgang Weninger, Vladislav Yakovlev, Seok-Hyun Yun, Jitao Zhang, Francesca Palombo, Alberto Bilenca, Kareem Elsayad Categories: physics.optics physics.bio-ph physics.ins-det Comments: Main Text & Supplementary Text: 56 pages, 3 Figures, 2 Supplementary Figures, 1 Supplementary Table License: http://creativecommons.org/licenses/by/4.0/ <http://creativecommons.org/licenses/by/4.0/> \\ Brillouin Light Scattering (BLS) spectroscopy is a non-invasive, non-contact, label-free optical technique that can provide information on the mechanical properties of a material on the sub-micron scale. Over the last decade it has seen increased applications in the life sciences, driven by the observed significance of mechanical properties in biological processes, the realization of more sensitive BLS spectrometers and its extension to an imaging modality. As with other spectroscopic techniques, BLS measurements not only detect signals characteristic of the investigated sample, but also of the experimental apparatus, and can be significantly affected by measurement conditions. The aim of this consensus statement is to improve the comparability of BLS studies by providing reporting recommendations for the measured parameters and detailing common artifacts. Given that most BLS studies of biological matter are still at proof-of-concept stages and use different--often self-built--spectrometers, a consensus statement is particularly timely to assure unified advancement. \\ Contains: CONSENSUS_ArXiv_v2.pdf: 2510309 bytes

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consensus manuscript on arXiv
by Kareem Elsayad Nov. 16, 2024

Nov. 16, 2024

Dear All, Per request from several of you we have uploaded the manuscript to the arXiv preprint server. Due to the formatting constraints of arXiv (which makes it difficult to have supp mat) we have combined supp text with the main text and put other supp mat on figshare. I took this opportunity to also make some edits people sent me after submission (most notably grammar corrections, the affiliations of some of you, and indexing and titles in supp text to make more readable/coherent). I uploaded this (arXiv) submitted version here: https://drive.google.com/file/d/1q194xOFTzMG9VF96M8J0dre4_dRl-aUG/view?usp=… (.pdf version) https://docs.google.com/document/d/1SyLc7Ef7eM7N4Hd_j11cO3DVmnwisAYN/edit?u… (.docx version) arXiv just wrote me the following.. Your article is currently scheduled to be announced at Tue, 19 Nov 2024 01:00:00 GMT. Updates before Mon, 18 Nov 2024 19:00:00 GMT will not delay announcement. As such, in case you would still like any (minor) changes please let me know asap and very latest by Monday 18th Nov. 15:00 GMT Thanks and all the best, Kareem

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Consensus statement (submitted)
by Kareem Elsayad Nov. 13, 2024

Nov. 13, 2024

Dear All, We finally submitted the manuscript earlier this afternoon (I have yet to receive any confirmation email – which is a bit strange, but online it says submitted and editor assigned). The final manuscript files (Main Text and Supplementary Text) can be found here: https://drive.google.com/file/d/1rGMNPmpbKGXNSCoa6obnj_ZyrhTy3JGM/view?usp=… https://drive.google.com/file/d/1y70F3Rf44Legs85xM-74UDr7Pgh5DEuS/view?usp=… (also submitted were the reporting tables in zipped format, and template thereof) I hope we managed to respect/implement your edits/suggestions.. In some cases, compromises had to be made -- but I don’t think these were major. Eitherway, we should have another round to discuss things when we get it back. About author order. I was checking through what convention is in consensus statements. In the end, I have put Pierre Bouvet and Carlo Bevilacqua up front since they really in my opinion did an exceptional amount of work behind the scenes in making manuscript what it is. I then listed everybody in alphabetic order. I understand some contributed more than others, but please understand we cannot rank contributions of >40 people without going insane (and making someone unhappy). At the end I tack Francesca, Alberto and myself as this was initially planned by us in communication with the editor. I have seen this type of author ordering applied previously in numerous consensus statements (such as recent ones in Nature Energy and Nature Medicine). Less frequently used alternatives are everybody in alphabetic order (more usual for very large consortia), or ranking in terms of contribution (more usual for smaller author lists). I hope this is acceptable for everyone. If anyone has issues with this though let me know and I am ofcourse happy to discuss on amending for resubmission. In the end it was I think a great group effort (if at times exhausting – it took me forever to enter all your affiliations & info online!). I wanted to thank you all again for your valuable contributions and time - I think we have something quite important that we can all be proud of! All the best (& I’ll keep you posted with any news on this front), Kareem

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Re: Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials
by Kareem Elsayad Nov. 8, 2024

Nov. 8, 2024

Dear All, Thank you for going through the manuscript and providing corrections/suggestions. We have already started addressing a number of these. From tomorrow noon I will take the manuscript offline to implement these properly with references and modified figures. If you have not yet entered your affiliation and email please do not forget to do so before Monday morning in the excel doc. Here is the link again: https://docs.google.com/spreadsheets/d/1YP-5kgcZcC3FViogO44GN-vm7JDSmjZk/ed… Also IMPORTANTLY, I completely forgot, I will also need a statement if you have any conflicts of interests. I created an extra column in the above excel file to enter if you do. Please enter a full sentence explaining any conflicts of interest you think relevant to report. If you do not have any, then no action is needed here. The specific statement on the submission pages reads as follows: the authors have competing interests as defined by Nature Portfolio, or other interests that might be perceived to influence the results and/or discussion reported in this paper. These interests are listed in a paragraph at the end of the manuscript. You can find a list of what Nature consider constitutes conflicts of interests here: https://www.nature.com/nature-portfolio/editorial-policies/competing-intere… I paste the relevant section from this webpage at the bottom of this message. Also do not forget to send me any updated reporting tables by Sunday. Very finally, I received a lot of requests to include additional references to people’s work (both per email and as comments in document). It may not be possible to include all due to space. We will prioritize the ones that are needed to illustrate/justify an already discussed point and relevant to the concept of journal/article and its expected readership… ….while, when possible, trying to respect contributions from different labs. I ask for your understanding in advance though, that we likely cannot include every suggested reference. If you have any important comments, please feel free to write ofcourse. I may spontaneously contact some of you over the weekend if there are any burning questions. But I think we are good for the most part, and you will probably hear next from me when we submitted on Monday! All the best, Kareem CONFLICTS OF INTEREST: In the interests of transparency and to help readers form their own judgements of potential bias, Nature Portfolio journals' require authors to declare any competing financial and/or non-financial interests in relation to the work described. The corresponding author is responsible for submitting a competing interests' statement on behalf of all authors of the paper. Definition For the purposes of this policy, competing interests are defined as financial and non-financial interests that could directly undermine, or be perceived to undermine the objectivity, integrity and value of a publication, through a potential influence on the judgements and actions of authors with regard to objective data presentation, analysis and interpretation. Financial competing interests include any of the following: Funding: Research support (including salaries, equipment, supplies, and other expenses) by organizations that may gain or lose financially through this publication. A specific role for the funder in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript, should be disclosed. Employment: Recent (while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through this publication. Personal financial interests: Stocks or shares in companies that may gain or lose financially through publication; consultation fees or other forms of remuneration (including reimbursements for attending symposia) from organizations that may gain or lose financially; patents or patent applications (awarded or pending) filed by the authors or their institutions whose value may be affected by publication. For patents and patent applications, disclosure of the following information is requested: patent applicant (whether author or institution), name of inventor(s), application number, status of application, specific aspect of manuscript covered in patent application. It is difficult to specify a threshold at which a financial interest become significant, but note that many US universities require faculty members to disclose interests exceeding $10,000 or 5% equity in a company (see, for example, B. Lo et al. New Engl. J. Med. 343, 1616-1620; 2000). Any such figure is necessarily arbitrary, so we offer as one possible practical alternative guideline: "Any undeclared competing financial interests that could embarrass you were they to become publicly known after your work was published." We do not consider diversified mutual funds or investment trusts to constitute a competing financial interest. Non-financial competing interests: Non-financial competing interests can take different forms, including personal or professional relations with organizations and individuals. We would encourage authors and referees to declare any unpaid roles or relationships that might have a bearing on the publication process. Examples of non-financial competing interests include (but are not limited to): Unpaid membership in a government or non-governmental organization Unpaid membership in an advocacy or lobbying organization Unpaid advisory position in a commercial organization Writing or consulting for an educational company Acting as an expert witness From: Kareem Elsayad <kareem.elsayad(a)meduniwien.ac.at> Date: Tuesday, 5. November 2024 at 12:29 To: "consensus(a)biobrillouin.org" <consensus(a)biobrillouin.org> Subject: Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials Dear All, You are receiving this email as you are part of the author list of the BLS consensus statement we are now finalizing for Nature Photonics. We have finally managed to cut the manuscript down (by a factor of >5) to fit into the required format and tried our best to make it into a somewhat coherent story, while accommodating most requests. We would like to submit it on Monday next week. Please take a read through the Manuscript (Main Text) and Supplementary Text here and add any comments you see relevant. When doing so, remember we are tight on space, and we can have at times up to almost 40 different opinions (approx. number of authors), but we will do our best to accommodate. It would be really great if you could provide your comments before the weekend so we can implement course of Sat & Sun. Here are the main files, which you should also have access to edit: Main Text: https://docs.google.com/document/d/1mdSDVePGOB8y0B4mCZpiKr_pFvF5WDeZ/edit?u… Supplementary Text: https://docs.google.com/document/d/1d5wA-QFlYJNiVtgA20ENMZnhJUSRzjO5/edit?u… Also, for the submission we will have to enter all your affiliations and any requested mentions of funding sources, etc. To not write everyone individually, could you please be sure to fill in the following online excel sheet before Monday: Affiliation and funding .xlsx file: https://docs.google.com/spreadsheets/d/1YP-5kgcZcC3FViogO44GN-vm7JDSmjZk/ed… If you submitted any data (and especially if you see your image in the manuscript) please double check the completeness of the Minimum Reporting Table you submitted with the data, and as needed send me an updated version. These will be provided with the manuscript as Supplementary Data. Neither we (nor the journal) will edit what you entered further, so please make sure it is as you would like to see it in print online. (FYI the Minimum Reporting Table file is still available here: https://docs.google.com/spreadsheets/d/1i-bz6QJ0l3LZl8YUgCw7b3hkzdWrtW_v/ed…) Last but not least, since there are so many authors (and I cannot send to all at once in cc/bcc using my University account – it thinks I have been hacked!), I created this mailing list consensus(a)biobrillouin.org If you would like to write all the authors you may also post to this, but please do not send files to this mailing list or everybody gets them (and it will clog everyones mailbox). If you share any files, the best option is to upload here: https://drive.google.com/drive/folders/1zBkQajxKTgjzUju19fdrFPFZC1r5O5Kq?us… and send me a quick email stating you have uploaded something and what it is you have uploaded. All the best, Kareem

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Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials
by Kareem Elsayad Nov. 5, 2024

Nov. 5, 2024

Dear All, You are receiving this email as you are part of the author list of the BLS consensus statement we are now finalizing for Nature Photonics. We have finally managed to cut the manuscript down (by a factor of >5) to fit into the required format and tried our best to make it into a somewhat coherent story, while accommodating most requests. We would like to submit it on Monday next week. Please take a read through the Manuscript (Main Text) and Supplementary Text here and add any comments you see relevant. When doing so, remember we are tight on space, and we can have at times up to almost 40 different opinions (approx. number of authors), but we will do our best to accommodate. It would be really great if you could provide your comments before the weekend so we can implement course of Sat & Sun. Here are the main files, which you should also have access to edit: Main Text: https://docs.google.com/document/d/1mdSDVePGOB8y0B4mCZpiKr_pFvF5WDeZ/edit?u… Supplementary Text: https://docs.google.com/document/d/1d5wA-QFlYJNiVtgA20ENMZnhJUSRzjO5/edit?u… Also, for the submission we will have to enter all your affiliations and any requested mentions of funding sources, etc. To not write everyone individually, could you please be sure to fill in the following online excel sheet before Monday: Affiliation and funding .xlsx file: https://docs.google.com/spreadsheets/d/1YP-5kgcZcC3FViogO44GN-vm7JDSmjZk/ed… If you submitted any data (and especially if you see your image in the manuscript) please double check the completeness of the Minimum Reporting Table you submitted with the data, and as needed send me an updated version. These will be provided with the manuscript as Supplementary Data. Neither we (nor the journal) will edit what you entered further, so please make sure it is as you would like to see it in print online. (FYI the Minimum Reporting Table file is still available here: https://docs.google.com/spreadsheets/d/1i-bz6QJ0l3LZl8YUgCw7b3hkzdWrtW_v/ed…) Last but not least, since there are so many authors (and I cannot send to all at once in cc/bcc using my University account – it thinks I have been hacked!), I created this mailing list consensus(a)biobrillouin.org If you would like to write all the authors you may also post to this, but please do not send files to this mailing list or everybody gets them (and it will clog everyones mailbox). If you share any files, the best option is to upload here: https://drive.google.com/drive/folders/1zBkQajxKTgjzUju19fdrFPFZC1r5O5Kq?us… and send me a quick email stating you have uploaded something and what it is you have uploaded. All the best, Kareem

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