Factors affecting calving to conception interval (days open) in dairy cows located at Dessie and Kombolcha towns, Ethiopia

Migbnesh Yekoye Temesgen; Alula Alemayehu Assen; Tarekegn Tintagu Gizaw; Bethelehem Alemu Minalu; Anteneh Yenehun Mersha

doi:10.1371/journal.pone.0264029

Peer Review History

Original SubmissionOctober 7, 2021
29 Nov 2021 Decision Letter - Dawit Tesfaye, Editor PONE-D-21-31364Survival analysis of calving to conception interval in dairy cows located at Dessie and Kombolcha towns, EthiopiaPLOS ONE Dear Dr. Assen, 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 Jan 13 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, Dawit Tesfaye 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. In your Methods section, please provide additional location information, including geographic coordinates of your field collection site if available. 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. 4. 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. 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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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: No 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: Yes ****** 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: Dear Authors Many thanks for your interesting work. In general you have applied appropriate statistical methods and models to your data in a clear way and understandable way. Although these statistical approaches are not new, in my opinion your results are important for countries with similar climate and production conditions like Ethiopia. However, I need more information about the conditions (production system, climate …) of your study. Regarding these aspects, I have ranked your work into the category “Major revisions”. Details, which needs further clarifications: L54: You have postulated that an acceptable CI is about 85 days. Why did you use a threshold of 80 days in your analysis? L65: Please provide the literature source. L98: Although it might be difficult to answer but important: What are the breeds used in the crossbred scheme? Where are the herds located? How many herds were in one town? ... L102ff: How many herds are within the dataset? Please give more information about the production system and herd sizes. L113: I have problem to understand what you mean by “censored”. a) Did you integrate only cows, which have the chance to become pregnant? In other words, cows with a calving date close to the final (max) date of your dataset were discarded? b) If a cow was culled within the 210 day period because of low milk yield is also coded as 0? Do you have reliable information about this? It might be that you have answered these questions in the lines L121ff. However, I have problems to understand. Please clarify. L147: Your initial model should include interaction terms, but I could no find any information about this in the rest of your paper. L157: I am wondering that you integrate two seasonal factors (insemination, calving season) into your model which might be confounded. I mean, if you look at the distribution (4 x 4 table) of your data, most information should be on the diagonal. If this is true, you should skip one of the effects from your model. L179: “This classification … genetic level …” I do not understand this sentence. Needs some clarification. L181: Please provide some information about the threshold in units of milk yield within 100d. L256: Please check the numbering of you figures. L296: “The variation in days … or lactation level”. I do not understand this sentence. Needs some clarification. L300: It would be useful if you could provide some information about temperature and humidity of the seasons. This would help to understand your results. Reviewer #2: 1. Keywords in the abstract part should be put in alphabetical order and contain key words 2. The introductory part should review variable under study and also should have gap that lead the researcher to conduct this work. 3. The research topic (title) and the objective (s) should match!! 4. In the methodology part the following questions should be answered! a. Why only the two towns from South Wollo? b. The number of dairy farms from each town & how these farms were selected? c. The number of animals from each town & how these animals were selected? d. How sample size was determined? e. Sources of data and method of data collection were poorly indicated!!! f. Variables to be measured should be clearly put g. Production system should get due attention!!!!!!!!!! 5. Tables in the result part should be clearly put and justified. 6. The major points from this findings in each table should be well discussed. Few points from the table were put in the form of conclusion!!! 7. The figures are not witnessing the discussed points in the body part. 8. The discussion part seems well written 9. The manuscript lacks recommendation 10, References should be listed in alphabetical order! 11. Generally it is advisable to follow the article writing manual ****** 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: No 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. Attachments Attachment Submitted filename: PONE-D-21-31364 Article 1.pdf https://doi.org/10.1371/journal.pone.0264029.r001
Revision 1
25 Jan 2022 Author Response 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. - File naming was edited to comply with the style requirements. We hopefully have no divergences from the PLOS ONE’s style requirements now. 2. In your Methods section, please provide additional location information, including geographic coordinates of your field collection site if available. - Thank you for the comment. The suggestions made by the editor were included in the revised manuscript from L102 to L108. 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. - The dataset and R script are provided as part of the manuscript supporting information. In addition, the dataset and R script used for analysis are available at the figshare repository via the following link https://doi.org/10.6084/m9.figshare.19062554.v1 4. 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. - Thank you for the suggestions given we have reviewed the references used in the body of text and the lists of references thoroughly and ensured that it is complete and correct. We haven’t cited a retracted paper. However, in the revised manuscript we have included new reference lists to substantiate newly included pieces of information and removed references for literature that are omitted in the revised manuscript. Reviewers comments Reviewer 1: Reviewer #1: Dear Authors Many thanks for your interesting work. In general you have applied appropriate statistical methods and models to your data in a clear way and understandable way. Although these statistical approaches are not new, in my opinion your results are important for countries with similar climate and production conditions like Ethiopia. However, I need more information about the conditions (production system, climate …) of your study. Regarding these aspects, I have ranked your work into the category “Major revisions”. - We thank you very much for the positive compliment about the work and its importance for countries like Ethiopia. We agreed that we have missed information on the climate and production system of the area from the manuscript. Hence, we have included this information in the revised manuscript from L108 to L110 and L130 to L134, respectively. Details, which needs further clarifications: L54: You have postulated that an acceptable CI is about 85 days. Why did you use a threshold of 80 days in your analysis? - Thank you for your suggestions and comments forwarded. We are sorry for the discrepancies created and we admitted that the threshold value used in our analysis and introduction should be inline. Hence, we have done the analysis again considering 85 days as a threshold cutoff value for calving to insemination interval. Thus, we stratified the calving to insemination interval (CI) variable which is continuous data type into two classes (less than or equal to 85 days vs greater than 85 days) to look at possible nonlinear effects. L65: Please provide the literature source. - Thank you for the comment and we amend the statement to some extent and included the literature source in L74. L98: Although it might be difficult to answer but important: What are the breeds used in the crossbred scheme? Where are the herds located? How many herds were in one town? ... - Thank you very much for the concern and suggestions. All the information missed from the previous manuscript was included from L117 to L126. L102ff: How many herds are within the dataset? Please give more information about the production system and herd sizes. - We are grateful for the comments forwarded. The number of dairy herds included in the dataset, herd sizes and production system of the herds were included in the revised manuscript from L124 to L125. L113: I have problem to understand what you mean by “censored”. - We have elaborated what censored observation meaning in the revised manuscript from L64 to L167. a) Did you integrate only cows, which have the chance to become pregnant? In other words, cows with a calving date close to the final (max) date of your dataset were discarded? - Cows with known last calving date and which are not yet pregnant will be included in the follow up (retrospectively or prospectively). Then, during the follow up period, the cow may show the event of interest (i.e. conception) considered as an event and other cows may not show the event of interest due to death, culling or sold and end of the study period are considered as censored observation. Therefore, the result of the follow up study was either conception (event) or not (censored). Thus, every cow has a chance to be included in the follow-up although the study period was close to the final date of your dataset. As a result, we haven’t discard cows with a calving date close to the final date of follow-up period. b) If a cow was culled within the 210 day period because of low milk yield is also coded as 0? Do you have reliable information about this? It might be that you have answered these questions in the lines L121ff. However, I have problems to understand. Please clarify. - Yes, if a cow under study is culled from the herd due to poor characteristics such as low milk yield is considered as censored observation (coded as 0). We can have reliable information on each and every cow under follow-up since we made a regular herd visit on their pregnancy status every 2 weeks and collect the required information. L147: Your initial model should include interaction terms, but I could no find any information about this in the rest of your paper. - Thank you for the comments. Since we didn’t include and compute the interaction term in the full model we have removed these ststistics in the revised manuscript. L157: I am wondering that you integrate two seasonal factors (insemination, calving season) into your model which might be confounded. I mean, if you look at the distribution (4 x 4 table) of your data, most information should be on the diagonal. If this is true, you should skip one of the effects from your model. - Thank you for the concern and suggestions. We have removed one of the possible confounding variables (calving season), which have a relationship with insemination season and event of interest (i.e. conception). L179: “This classification … genetic level …” I do not understand this sentence. Needs some clarification. - We are sorry for the lack of clarity we produced and made improvements to elaborate further in the revised version of the manuscript from L207 to L209 and hopefully this wording clarify better than the previous one. L181: Please provide some information about the threshold in units of milk yield within 100d. - Thank you for the suggestions and comments. We have made the improvement on the comments from L211 to L215. L256: Please check the numbering of you figures. - Thank you for the comments and we have checked and corrected. L296: “The variation in days … or lactation level”. I do not understand this sentence. Needs some clarification. - Edited in the revised manuscript L300: It would be useful if you could provide some information about temperature and humidity of the seasons. This would help to understand your results. - Thank you for the suggestions and we have included the required information from L108 to L110 Reviewer #2: 1. Keywords in the abstract part should be put in alphabetical order and contain key words - Thank you for the suggestion. We put the keywords in alphabetical order in the revised manuscript and included keywords in L43. 2. The introductory part should review variable under study and also should have gap that lead the researcher to conduct this work. - We have included additional literature on the variable in introduction section from L54 to L64 3. The research topic (title) and the objective (s) should match!! - We thank you for the suggestions and amend the title of the manuscript as “Factors affecting calving to conception interval (Days open) in dairy cows located at Dessie and Kombolcha Towns, Ethiopia” in the revised manuscript in L1 to L3. Therefore, we amended the title of the manuscript from the electronic submission form. 4. In the methodology part the following questions should be answered! a. Why only the two towns from South Wollo? - The reason why only the two towns selected from south wollo zone were included in the revised manuscript from L110 to L115. b. The number of dairy farms from each town & how these farms were selected? - The information lacked on the number of dairy farms from each town and how they are selected is included in the revised manuscript from L121 to L126. c. The number of animals from each town & how these animals were selected? - Thank you very much for the suggestions and we have included the required information in the revised manuscript from L126 to L130. d. How sample size was determined? - Thank you for the question and concern. We couldn’t calculate the sample size of this study because there is no formula for setting the sample size for the purposive sampling technique employed in this study. There is no need for a statistical representative sample. Any number of sample (sample size) can be selected, which can serve the purpose of the researcher. Instead, judgments must be made, based on the expected heterogeneity of areas, population groups, locations, households and individuals. e. Sources of data and method of data collection were poorly indicated!!! - We thank you for the suggestions and we are sorry for the lack of clarity created. The data source and data collection employed were included in the revised manuscript from L142 to L184. f. Variables to be measured should be clearly put - the variables measured and recorded in the study were presented under the variable definition subtopic in the revised manuscript from L187 to L234. g. Production system should get due attention!!!!!!!!!! - Thank you for the suggestion and we have incorporated the dairy production system in the revised manuscript from L131 to L134. 5. Tables in the result part should be clearly put and justified. We thank you for the suggestions and improved the tables in the revised manuscript. 6. The major points from this findings in each table should be well discussed. Few points from the table were put in the form of conclusion!!! We have described the tables better in the revised manuscript. 7. The figures are not witnessing the discussed points in the body part. We agreed on the comment and included the description of each figure in the revised manuscript. 8. The discussion part seems well written We are thankful for the positive compliment. 9. The manuscript lacks recommendation Thank you for the suggestions. We have included the recommendation in the revised manuscript from L457 to L459. 10, References should be listed in alphabetical order! Thank you for the suggestions and we have arranged the references as per the PLOS ONE journal guideline. It says the reference list should be put as per the order of the reference in the body of the text. As a result, I listed the reference accordingly. 11. Generally it is advisable to follow the article writing manual We have admitted the concern and suggestions from the reviewer and the corresponding author and co-authors believed that the revised manuscript is prepared in accordance with the PLOS ONE journal. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0264029.r002
2 Feb 2022 Decision Letter - Dawit Tesfaye, Editor Factors affecting calving to conception interval (days open) in dairy cows located at Dessie and Kombolcha towns, Ethiopia PONE-D-21-31364R1 Dear Dr. Assen, 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, Dawit Tesfaye Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: None https://doi.org/10.1371/journal.pone.0264029.r003
Formally Accepted
8 Feb 2022 Acceptance Letter - Dawit Tesfaye, Editor PONE-D-21-31364R1 Factors affecting calving to conception interval (days open) in dairy cows located at Dessie and Kombolcha towns, Ethiopia Dear Dr. Assen: 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. Dawit Tesfaye Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0264029.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .