Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: A retrospective study

Jorge Enrique Machado-Alba; Manuel E. Machado-Duque; Andres Gaviria-Mendoza; Carolina Duarte-Rey; Andrés González-Rangel

doi:10.1371/journal.pone.0285889

Peer Review History

Original SubmissionMay 20, 2022
13 Jul 2022 Decision Letter - Nasser Hadal Alotaibi, Editor PONE-D-22-14695Clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in ColombiaPLOS ONE Dear Dr. Machado-Alba, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Aug 27 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Nasser Hadal Alotaibi Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. 2. Thank you for stating the following in the Competing Interests section: This study received funding from GSK. The funder had the following involvement with the study: GSK did not participate in the management or data analysis of the study information. CDR and AGR are GSK employees; JMA, AGG and MMD have developed studies funded by GSK, Pfizer, Biotoscana, Sanofi, Sanofi-Pasteur, Abbot, Tecnoquímicas, Bayer, Novartis. Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: No ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: General comments There are a lot of abbreviations where they were not full explained before they first appear The methods part is not well written; I believe this needs to be majorly revised again The paper overall needs major revision with a grammars and needs to be clearly written Introduction It is well written and the background and statement of the problem is given well Methods ICD- mention this first before indicating the abbreviation applies to others too Design and patients section is not well written please revise this paragraph. Why did you include all patients irrespective of age? (any implication you see on the result)? Does SLE not differ by age? Very young and very old? How do you see their comparison? Why did you remove those who were only 3 month diagnosed/or cared? Give justification Why did you only include 12 months? This seems short period? Any implication on your result What do you mean by the data was monitored for one year? (re-write this sentence). Why have not applied ICD 11 instead of 10? On line 119 what do you mean by trained physician? Specify it very well? Make a detail explanation how your data collectors were trained for your study? Was there a supervisor? On line 150 can you mention a reference? The sample size calculation is not clear at all? How can you insure representativeness? Where did you get the estimate? It needs a reference Line 161-162 is not clear. Please clearly state the methods used to test normality If you use Kaplan mayor this study cannot be a descriptive study… The methods lack quality assurance, tools used for data collection, what did you do with missing data? How did you clean the data? Results Any statement you want to mention about incomplete data you found? How did you handle it? How many did you review (how many data was available in the mentioned duration) What you wrote on the first paragraph of the result and on the sample size determination is different. Did you have 373 or 413 sample size? On costs associated with care; can you mention the frequency and percentage? Line number 236’ You have not reported anything related with Kaplan-Meier survival result? If you did please specify very well… Line 326 what do you mean by certain cases? Can you quantify? Line 327 why was it not possible to establish the frequency of emergency department visits, as well as the costs associated with hospital care. Line 328 why were costs calculated according to fee schedules? Line 329 why didn’t you make the follow up period longer then? Conclusion Line 337 Why did you mention a reference here. the concussion part should be your own words no reference is needed here What is DMARD? Reviewer #2: In this manuscript, the authors aimed to assess the clinical characteristics and health care resource utilization in a Colombian SLE outpatient cohort. The study is interesting, but a number of issues should be addressed before its publication. Major issues 1. How was sample size calculated? Try to elaborate the method used for calculation of the sample size. 2. Sampling design used in the study was not specified. Try to specify how the patients was selected from the source population. 3. I did not see any recommendation in the main text. Thus, a ‘recommendation’ should be added after the ‘conclusion’ section of the main text. Minor issues 1. The full form of the abbreviated word ‘SLEDAI’ should be properly written. 2. I suggest the authors’ to add a recommending sentence within the conclusion part of the abstract. 3. I suggest the authors’ to rename the sub-section ‘Design and patients’ within the method section of the main text to ‘Study design and setting’. Moreover, a new sub-section ‘source and study population’ should be added (this can include the study population and the exclusion criteria which is already explained within the sub-section ‘Design and patients’). 4. Try to add the main statistical tools used in the study in the method of the abstract section. 5. Ethical approval sound appropriate. Please detail ethical approval body with address. Add Reference number of approval letter. 6. Most of your findings were compared with the findings of developed countries only. I also recommend the authors’ to compare their findings with that of the developing countries. 7. I suggested the title of the article to be renamed as “Assessment of clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in Colombia: a retrospective study”. 8. Referencing style need adjustment. It should be in compliance with the PLOSONE guidelines. 9. Your manuscript does not follow PLOS ONE’s manuscript preparation guidelines. Try to revisit the guidelines and adjust the whole manuscript accordingly. 10. Coherence and readability of this manuscript need improvement. English editing is required. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Tsion Afework Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0285889.r001
Revision 1
10 Aug 2022 Author Response PONE-D-22-14695R1 Clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in Colombia: a retrospective study Dear Edrian Nim Tolentino PLOS ONE We have reviewed all your concerns and we respond to each of them. 1. Thank you for stating the following in the Competing Interests section: This study received funding from GSK. The funder had the following involvement with the study: GSK did not participate in the management or data analysis of the study information. CDR and AGR are GSK employees; JMA, AGG and MMD have developed studies funded by GSK, Pfizer, Biotoscana, Sanofi, Sanofi-Pasteur, Abbot, Tecnoquímicas, Bayer, Novartis. Response/ Thank you. Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Response/ confirmed, we add “This does not alter our adherence to PLOS ONE policies on sharing data and materials” Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. Response/ confirmed, we add “This does not alter our adherence to PLOS ONE policies on sharing data and materials” in cover letter. 2. Please provide additional details regarding participant consent. In the Methods section, please ensure that you have specified (1) whether consent was informed and (2) what type you obtained (for instance, written or verbal). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information. Response/ we add in Ethics statement According to Colombian regulations (Decree 8430 of 1993), risk-free research that takes information from clinical records does not require informed consent. The research was endorsed by the Bioethics Committee of the Universidad Tecnológica de Pereira in the risk-free category (Approval code: CBE 132018). The principles established by the Declaration of Helsinki were respected. No personal data from any of the research participants were considered. 3. We note your current Data Availability statement is: "Yes - all data are fully available without restriction" "This text is appropriate if the data are owned by a third party and authors do not have permission to share the data." Response/ ok, we will make the correction in the journal application. We also note you included the following, additional information in your response to reviewers: "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s." The name of the information repository is: protocols.io Code availability: dx.doi.org/10.17504/protocols.io.bzufp6tn” PLOS journals require authors to make the minimal data set publicly available without restriction at the time of publication. PLOS defines the “minimal data set” as consisting of the data set used to reach the conclusions drawn in the manuscript with related metadata and methods, and any additional data required to replicate the reported study findings in their entirety. This includes: - The values behind the means, standard deviations and other measures reported; - The values used to build graphs; - The points extracted from images for analysis. Can you please address the following and clarify where the relevant data are located: a.) Can you please clarify whether the minimal dataset for this study are uploaded to protocols.io and available via the provided DOI (dx.doi.org/10.17504/protocols.io.bzufp6tn)? Response/ Yes, the minimal dataset for this study are uploaded to protocols.io and available via the provided DOI (dx.doi.org/10.17504/protocols.io.bzufp6tn) b.) If not, are the data third party data (i.e., data not owned or collected by the author(s))? If these are indeed third party data, please explain how others can access these datasets and confirm that others would be able to access these data in the same manner as the authors. Please also confirm that the authors did not have any special access privileges that others would not have. Response/ All data is owned by the authors. In addition, the data was correctly anonymized. as it says in methods, where it is indicated " The principles established by the Declaration of Helsinki were respected. No personal data from any of the research participants were considered”. c.) If not, but there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive information) and who has imposed them (e.g., a governmental body, an ethics committee, etc.). Please also provide non-author contact information* for a data access committee, ethics committee, or other institutional body to which data requests may be sent. Response/ N/A * PLOS’ Data Policy states that authors cannot be the sole named individuals responsible for ensuring data access (https://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions). Response/ The anonymized data are public since the manuscript was written and are available at the corresponding link for anyone who wants to consult them. We will update your Data Availability statement on your behalf using the information you provide. The authors Attachments Attachment Submitted filename: Response to reviewers LES (10-08-2022).docx https://doi.org/10.1371/journal.pone.0285889.r002
6 Oct 2022 Decision Letter - Nasser Hadal Alotaibi, Editor PONE-D-22-14695R1Clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in Colombia: a retrospective studyPLOS ONE Dear Dr. Machado-Alba, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Nov 20 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Nasser Hadal Alotaibi Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: No ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Overall the paper is well revised; I just have few comments On Line 39 and line 101 please re-write again, don’t put full stops before finishing a sentences, re-write it again. Why didn’t you give any recommendation for the missing variables (or incomplete) like emergency department visits, costs associated with hospital care, ambulatory health records Do you think you have measured economic burden well? Can you say something about that on the paper? On the data source can you describe the time frame of your data collection. Reviewer #2: Minor Comment -English editing is required. Coherence and readability of the manuscript need an improvement. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Nuru Abdu ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: comment for PLOS.docx https://doi.org/10.1371/journal.pone.0285889.r003
Revision 2
18 Oct 2022 Author Response Response to reviewers Dear Editor Journal: PLOS ONE Manuscript ID number: PONE-D-22-14695R1 Title: Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective study We have reviewed the manuscript and responded to each concern. In addition, AJE, who performed the translation, was asked to review the coherence and readability. Reviewer #1: Overall the paper is well revised; I just have few comments On Line 39 and line 101 please re-write again, don’t put full stops before finishing a sentences, re-write it again. Response: We corrected the sentences on lines 39 and 101 regarding the study design. Why didn’t you give any recommendation for the missing variables (or incomplete) like emergency department visits, costs associated with hospital care, ambulatory health records Response: In the conclusions section, we added a sentence recommending future studies that include these variables. Ambulatory health records were the main source of information in the study. Do you think you have measured economic burden well? Can you say something about that on the paper? Response: We think that economic burden was adequately measured using the proposed methodology. The limitations regarding cost calculations were addressed. We think it is unnecessary to further discuss this issue in the paper. On the data source can you describe the time frame of your data collection. Response: The data frame is described in the subsection “Study design and settings” and corresponded to July 1, 2016, through June 30, 2017. Reviewer #2: Minor Comment -English editing is required. Coherence and readability of the manuscript need an improvement. Response: The final version of the manuscript was edited by American Journal Experts. We hope this editing addresses this comment. We add the certificate. The authors Attachments Attachment Submitted filename: Response to Reviewers 18-10-22.docx https://doi.org/10.1371/journal.pone.0285889.r004
9 Feb 2023 Decision Letter - Nasser Hadal Alotaibi, Editor PONE-D-22-14695R2Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective studyPLOS ONE Dear Dr. Machado-Alba, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Mar 26 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Nasser Hadal Alotaibi Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: (No Response) Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Review for : Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective study The authors have addressed all comments given last time and has revised the manuscript. Just minor comments. Abstract I wouldn’t advise use of abbreviation on the abstract section of manuscript Methods Does the outcome of SLE not different according to age? How did you take account of that during your analysis? Since you included all age? But on the result it says 18-86..so you should either say we included all ages that are 18 and above Your sample size is totally not clear? It needs reference, show the formula you used, what does expect frequency 50% mean??? For retrospective cohort study there is a formula .. On the ethical declaration section good to include reference for Colombian regulations (Decree 8430 of 1993) Result Either report the age result in mean and SD or with the category mentioning both at the same time is not necessary. What I understood is this is observation retrospective study or retrospective cohort study do please report the incidence of SLE don’t talk about prevalence Limitation How does excluding incomplete data such as clinometric cases affected or limited your study in any way? How many cards did you initially find? And how many of them were incomplete? Mention this in the result first section I think this information is relevant to mention as limitation too…you said some variables are incomplete so what is that implication on your finding.. what were the variables Reviewer #2: I would like to appreciate the authors for taking their time to correctly address the issues raised during peer-review process. All the comments are satisfactorily addressed. This paper is a candidate for publication. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: Nuru Abdu ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: Plos review.docx https://doi.org/10.1371/journal.pone.0285889.r005
Revision 3
24 Mar 2023 Author Response Response to reviewers Dear Editor Journal: PLOS ONE Manuscript ID number: PONE-D-22-14695R2 Title: Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective study We have reviewed the manuscript and responded to each concern. Comments to the Author Reviewer #1: The authors have addressed all comments given last time and has revised the manuscript. Just minor comments. Abstract I wouldn’t advise use of abbreviation on the abstract section of manuscript R/ We have avoided the use of systemic lupus erythematosus (SLE) abbreviation. we can remove the acronym and leave the full words. Methods Does the outcome of SLE not different according to age? How did you take account of that during your analysis? R/ We have now included the results of the SLEDAI in table 1 according to the age categories in order to show the differences according to age. Since you included all age? But on the result it says 18-86..so you should either say we included all ages that are 18 and above R/ Corrected, thank you Your sample size is totally not clear? It needs reference, show the formula you used, what does expect frequency 50% mean??? For retrospective cohort study there is a formula .. R/ This is an observational, retrospective study. We used data from a cohort of patients with SLE, but the study design was not an analytical cohort study (we did not have an exposed and unexposed group comparison). An expected frequency of 50% was used to reach the highest sample size. We have now included the formula and references (17 and 18). We changed the term “expect frequency” for “estimated proportion”. On the ethical declaration section good to include reference for Colombian regulations (Decree 8430 of 1993) R/ Included (reference 19) Result Either report the age result in mean and SD or with the category mentioning both at the same time is not necessary. R/ We have eliminated the age groups from the text. What I understood is this is an observation retrospective study or retrospective cohort study do please report the incidence of SLE don’t talk about the prevalence R/ We did not consider the new cases of SLE during the time. We had a database of patients already diagnosed with SLE. Thus, the incidence of SLE can not be calculated. However, we did show the incidence of certain SLE manifestations during the follow-up year, such as lupus nephritis. Limitation How does excluding incomplete data such as clinometric cases affected or limited your study in any way? R/ Only patients with an initial SLEDAI were included in the sample, and thus the results showed in the manuscript for the 413 patients include this clinimetric information. The limitation is for the final SLEDAI results, which were available in only 227 patients. This is already explicitly stated in the second paragraph of the results section and in the limitations (in the discussion section). How many cards did you initially find? And how many of them were incomplete? Mention this in the result’s first section I think this information is relevant to mention as a limitation too…you said some variables are incomplete so what is that implication on your finding.. what were the variables R/ We do not have the data of initial registries that were incomplete. For the variables included in the study, only the last SLEDAI and the exact date of diagnosis had missing values. This is now included in the limitations. When we say that some variables were not complete due to the origin of the data, we also intend to mention that some other variables were not available (data was retrospective). We have now added this in the limitations. Reviewer #2 I would like to appreciate the authors for taking their time to correctly address the issues raised during peer-review process. All the comments are satisfactorily addressed. This paper is a candidate for publication. R/ thank you The authors Attachments Attachment Submitted filename: Response to Reviewers 24-03-23.docx https://doi.org/10.1371/journal.pone.0285889.r006
4 May 2023 Decision Letter - Nasser Hadal Alotaibi, Editor Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective study PONE-D-22-14695R3 Dear Dr. Machado-Alba, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Nasser Hadal Alotaibi Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0285889.r007
Formally Accepted
10 May 2023 Acceptance Letter - Nasser Hadal Alotaibi, Editor PONE-D-22-14695R3 Clinical characterization of a cohort of patients treated for systemic lupus erythematosus in Colombia: a retrospective study Dear Dr. Machado-Alba: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Nasser Hadal Alotaibi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0285889.r008

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