Instructions for Authors (sample)

 

Shortcuts

• Submission Checklist
• Manuscript Submission Overview
• Manuscript Preparation
• Preparing Figures, Schemes and Tables
• Original Images Requirements
• Supplementary Materials, Data Deposit and Software Source Code
• Research and Publication Ethics
• Authorship
• Editorial Independence
• Editorial Procedures and Peer Review

 

Submission Checklist

Please ensure the following before submitting your manuscript:

1. Read the Aims & Scope to gain an overview and assess if your manuscript is suitable for this journal.
2. Use the Microsoft Word Template to prepare your manuscript.
3. Make sure that issues about publication ethics, research ethics, copyright, authorship, figure formats and references format have been appropriately considered (all information are available on this page).
4. Ensure that all authors have approved the content of the submitted manuscript and confirm that they read the Instructions for Authors.

Manuscript Submission Overview

Types of Publications

AlYarmouk Journal welcomes submissions that are well-structured and cover the subject matter thoroughly, without imposing a maximum length restriction. To facilitate replication of research findings, detailed descriptions of the experiments are mandatory. Authors are expected to ensure their manuscripts are original and not currently under consideration by another publication. A list of acceptable article types is available [here].

Submission Process

Manuscripts can be submitted online by clicking on (Make a Submission). The submitting author i.e. The corresponding author assumes primary responsibility for the manuscript throughout the submission and peer review stages. This includes ensuring the author list is complete with all eligible co-authors, who must have reviewed and approved the submitted manuscript version.

Accepted File Formats

In order to streamline the copy-editing and publication timeline for accepted manuscripts, we highly recommend that authors leverage the provided Microsoft Word template for manuscript preparation.

Cover Letter

A concise cover letter is mandatory for all submissions.  It should highlight the manuscript's significance by explaining its findings in relation to existing research and demonstrating its alignment with the journal's scope. To ensure compliance, all cover letters must include the following confirmations:

• We confirm that neither the manuscript nor any parts of its content are currently under consideration for publication with or published in another journal.
• All authors have approved the manuscript and agree with its submission to AlYarmouk Journal.

Author Affiliation

Authors must provide both their current institutional affiliation and the primary affiliation where the bulk of the research for the manuscript was conducted.  We recommend prioritizing the affiliation that provided the most significant research support, but authors should verify any contractual obligations with their institutions.

Accurate author names and affiliations are crucial. Errors can lead to problems with attribution, citation, and potentially hinder career progression or funding opportunities.  Be aware that updates to the author’s affiliation may not be permitted after publication.

If one or all the authors are not currently affiliated with a university, institution or company, or have not been during the development of the manuscript, they should list themselves as an “Independent Researcher”.

Manuscript Preparation

General Considerations

• Research manuscripts should comprise:
• Front matter: Title, Author list, Affiliations, Abstract, Keywords.
• Research manuscript sections: Introduction, Materials and Methods, Results, Discussion, Conclusions (optional).
• Back matter: Supplementary Materials, Acknowledgments, Author Contributions, Conflicts of Interest, References.
• Review manuscripts should comprise:
• Front matter: Title, Author list, Affiliations, Abstract, Keywords.
• Review sections: a literature review organized logically within specific sections and subsections (optional).
• Back matter: Acknowledgments, Author Contributions, Conflicts of Interest, References.
• Acronyms/Abbreviations/Initialisms should be defined the first time they appear in each of three sections: the abstract; the main text; the first figure or table. When defined for the first time, the acronym/abbreviation/initialism should be added in parentheses after the written-out form.
• SI Units (International System of Units) should be used. Imperial, US customary and other units should be converted to SI units whenever possible.
• Equations: If you are using Word, please use either the Microsoft Equation Editor or the MathType add-on. Equations should be editable by the editorial office and not appear in a picture format.
• Research Data and supplementary materials: Acceptance of your manuscript for publication signifies your commitment to making all materials, data, and protocols underpinning the research readily accessible to readers. Any limitations on the availability of these resources should be clearly disclosed at the time of submission.

Front Matter

The following sections should appear in all manuscript types:

 

• Title: For optimal clarity, your manuscript title should be concise, specific, and directly relevant to the research presented. Indicate if the study reports on human or animal trial data, or if it falls under the category of a systematic review, meta-analysis, or replication study.  Please avoid using abbreviations or shortened forms in the title, as these will be removed during editorial processing.
• Author List and Affiliations: Authors' full names are required, including first and last names with optional middle name initials. Affiliation details should adhere to the PubMed/MEDLINE standard, encompassing the complete address with city, zip code, state/province, and country. Designate at least one author as the corresponding contact, whose responsibility it is to ensure all authors consent to displaying their email addresses in the published article. If any author (excluding the corresponding author) prefers not to have their email displayed, the corresponding author must notify the journal during proofreading.  Please be aware that changes to author details after acceptance may not be accommodated.

For authors with equal contributions, a superscript symbol (†) should be placed below the affiliations, accompanied by the sentence "These authors contributed equally to this work."  Equivalent author contributions should also be clearly reflected in the author contributions statement. Please read the criteria to qualify for authorship.

• Abstract: Abstracts should be concise, single paragraphs, and adhere to a structured format (approximately 250-300 words). This structure should encompass the following key points without explicit headings:1) Background: Briefly introduce the research question within its broader context and the study's rationale.2)Methods: Summarize the primary methodologies or treatments employed, including any relevant preregistration numbers and details regarding animal species and strains (if applicable).3) Results: Provide a succinct overview of the article's key findings.4)Conclusion: Briefly state the principal conclusions or interpretations drawn from the research.

The abstract should offer an objective reflection of the manuscript, avoiding inclusion of results not presented within the main text or overexaggerating the main conclusions.

• Keywords: Three to ten pertinent keywords need to be added after the abstract. We recommend that the keywords are specific to the article, yet reasonably common within the subject discipline.

Research Manuscript Sections

• Introduction: The introduction should succinctly establish the research within its broader context, emphasizing its significance. Clearly define the study's purpose and its contribution to the field, including any specific hypotheses under investigation.  Provide a concise review of current research in the area, incorporating relevant citations.  When applicable, highlight any areas of controversy or diverging viewpoints within the field.  Conclude the introduction by outlining the primary objective of the work and foreshadowing the main conclusions.  Strive to maintain a level of clarity that is accessible to scientists outside the specific research topic.
• Materials and Methods: They should be described with sufficient detail to allow others to replicate and build on published results. New methods and protocols should be described in detail while well-established methods can be briefly described and appropriately cited. Give the name and version of any software used and make clear whether computer code used is available.
• Results: Provide a concise and precise description of the experimental results, their interpretation as well as the experimental conclusions that can be drawn.
• Discussion: The discussion section, which may be merged with the results section, should delve into the interpretation of the findings in relation to prior research and the initial hypotheses. It's crucial to discuss the broader implications of the results while acknowledging any limitations inherent to the study. This section also offers an opportunity to propose potential avenues for future research.
• Conclusions: This section is not mandatory but can be added to the manuscript if the discussion is unusually long or complex.
• Patents: This section is not mandatory but may be added if there are patents resulting from the work reported in this manuscript.

Back Matter

• Supplementary Materials: Describe any supplementary material published online alongside the manuscript (figure, tables, video, spreadsheets, etc.). Please indicate the name and title of each element as follows Figure S1: title, Table S1: title, etc.
• Author Contributions: Authorship recognition in this journal is reserved for individuals who have made significant contributions to the research project. These contributions can encompass various aspects, including:  formulating the study's concept or design, gathering, analyzing, or interpreting the data, or creating new software used in the research.  Additionally, authorship extends to those who have drafted the manuscript or substantially revised it.  All authors are expected to approve the submitted version, including revisions made by journal staff that are relevant to their specific contributions.  Furthermore, each author holds personal accountability for their own work and shares responsibility with the co-authors for ensuring any inquiries concerning the research's accuracy or integrity are appropriately investigated, addressed, and documented within the scientific literature, even for aspects where they may not have been directly involved.

For research articles with several authors, a short paragraph specifying their individual contributions must be provided. The following statements should be used "Conceptualization, X.X. and Y.Y.; Methodology, X.X.; Software, X.X.; Validation, X.X., Y.Y. and Z.Z.; Formal Analysis, X.X.; Investigation, X.X.; Resources, X.X.; Data Curation, X.X.; Writing – Original Draft Preparation, X.X.; Writing – Review & Editing, X.X.; Visualization, X.X.; Supervision, X.X.; Project Administration, X.X.; Funding Acquisition, Y.Y.”, please turn to the CRediT taxonomy for the term explanation. Please adhere to Authorship criteria listed on this page.

• Funding: All sources of funding of the study should be disclosed. Clearly indicate grants that you have received in support of your research work and if you received funds to cover publication costs.
• Acknowledgments: The acknowledgments section provides an opportunity to express gratitude for contributions that fall outside the scope of the author contributions or funding sections. This might include administrative or technical assistance, or in-kind donations such as materials essential to the experiments.
• Conflicts of Interest: Authors are required to disclose any personal circumstances or potential biases that could be perceived as influencing the presentation or interpretation of their research findings. If no such conflicts exist, a simple statement like "The authors declare no conflict of interest" is sufficient.
• References: Number references consecutively throughout the text, including those appearing in tables and figure captions. Compile these references into a separate list at the end of your manuscript. Using bibliographic software like EndNote, Mendeley, or Zotero is highly recommended to minimize typos and duplicate entries.
• Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list.

In the text, reference numbers should be placed in square brackets [ ], and placed before the punctuation; for example [1], [1–3] or [1,3]. For embedded citations in the text with pagination, use both parentheses and brackets to indicate the reference number and page numbers; for example [5] (p. 10). or [6] (pp. 101–105).

The reference list should include the full title, as recommended by the ACS style guide. Style files for Endnote and Zotero are available.

References should be described as follows, depending on the type of work:

• Journal Articles:
  Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal NameYear, Volume, page range.
• Books and Book Chapters:
  Author 1, A.; Author 2, B. Book Title, 3rd ed.; Publisher: Publisher Location, Country, Year; pp. 154–196.
  3. Author 1, A.; Author 2, B. Title of the chapter. In Book Title, 2nd ed.; Editor 1, A., Editor 2, B., Eds.; Publisher: Publisher Location, Country, Year; Volume 3, pp. 154–196.
• Unpublished materials intended for publication:
  Author 1, A.B.; Author 2, C. Title of Unpublished Work (optional). Correspondence Affiliation, City, State, Country. year, status(manuscript in preparation; to be submitted).
  5. Author 1, A.B.; Author 2, C. Title of Unpublished Work. Abbreviated Journal Name year, phrase indicating stage of publication (submitted; accepted; in press).
• Unpublished materials not intended for publication:
  Author 1, A.B. (Affiliation, City, State, Country); Author 2, C. (Affiliation, City, State, Country). Phase describing the material, year. (phase: Personal communication; Private communication; Unpublished work; etc.)
• Conference Proceedings:
  Author 1, A.B.; Author 2, C.D.; Author 3, E.F. Title of Presentation. In Title of the Collected Work(if available), Proceedings of the Name of the Conference, Location of Conference, Country, Date of Conference; Editor 1, Editor 2, Eds. (if available); Publisher: City, Country, Year (if available); Abstract Number (optional), Pagination (optional).
• Thesis:
  Author 1, A.B. Title of Thesis. Level of Thesis, Degree-Granting University, Location of University, Date of Completion.
• Websites:
  Title of Site. Available online: URL (accessed on Day Month Year).
  Unlike published works, websites may change over time or disappear, so we encourage you create an archive of the cited website using a service such as WebCite. Archived websites should be cited using the link provided as follows:
  10. Title of Site. URL (archived on Day Month Year).

Preparing Figures, Schemes and Tables

• All Figures, Schemes and Tables should be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Scheme 1, Figure 2, Scheme 2, Table 1, etc.).
• All Figures, Schemes and Tables should have a short explanatory title and caption.
• All table columns should have an explanatory heading. To facilitate the copy-editing of larger tables, smaller fonts may be used, but no less than 8 pt. in size. Authors should use the Table option of Microsoft Word to create tables.

Original Images Requirements

To ensure the authenticity of submitted images (blots, gels, microscopy), the journal may request access to the original, unedited versions. These high-resolution files (minimum 1000 pixels or 300 dpi) should be provided in a compressed archive (.zip format) or through a link to a repository where they are deposited. Acceptable file formats include TIFF, PNG, GIF, and EPS.

Images included within the manuscript itself should be minimally processed to maintain data accuracy and adhere to established scientific standards. Electron microscopy images, in particular, must be presented in their entirety, without cropping, to ensure all relevant details are clearly visible for reviewers and readers.

When cropped versions of images are used within figures, the complete, uncropped versions must be submitted as supplementary material alongside the manuscript. Additionally, the reuse of control images for illustrative purposes must be explicitly acknowledged within the corresponding figure legend to avoid any misinterpretation of the data.

If any legitimate form of image processing is necessary to facilitate data interpretation, the software and specific enhancement techniques employed must be clearly outlined within the manuscript's methods section. This transparency is crucial for ensuring reproducibility of research findings. Techniques such as image grouping or splicing, which involve combining elements from multiple images, require explicit disclosure within both the manuscript and the figure text to avoid any potential confusion.

The application of software filters solely for the purpose of enhancing image quality is generally discouraged, as it can raise concerns about data manipulation. Minor adjustments to parameters like contrast, brightness, intensity, and color are generally acceptable, provided these modifications are applied uniformly across the entire image to enhance readability without compromising data integrity. Excessive manipulation techniques that target specific image regions while neglecting others constitute unethical practices, as they misrepresent experimental data in relation to control groups.

The combination of images acquired at different time points or locations into a single composite image is only permissible if explicitly declared as a product of time-averaged data or a time-lapse sequence. When juxtaposing separate images from different sources is essential for presentation purposes, clear demarcations of the borders within the figure and a detailed explanation within the legend are mandatory to avoid misleading interpretations.

Electrophoretic gels and blots

Ensure that:

• All experimental samples and controls used for one comparative analysis are run on the same blot/gel. When sample processing controls are run on different gels, this must be indicated in the figure legend. Cropped gels in the paper must retain all important bands.
• Molecular weight markers are included or indicated on the raw image, and any lanes not included in the final figure are marked with an “X” above the lane label on the original blot/gel image. All labeling and annotation should be performed without obscuring any data or background bands.
• Image processing methods, such as adjusting the brightness or contrast, do not alter or distort the information in the figure and are applied to every pixel. High-contrast blots/gels are discouraged.
• Cropped blots/gels present in the main text retain all important information and bands.
• Each original image is annotated, and corresponds to the figure in the main article or supplementary materials, and each lane or loading order is labeled.
• You have checked figures for duplications and ensured the figure legends are clear and accurate. Please include all relevant information in the figure legends and clearly indicate any re-arrangement of lanes.

When combining lanes from the same gel image (splicing), a thin line must be inserted at the junction point to clearly mark the manipulation.  Removing an entire lane for splicing with the remaining lanes is acceptable, but only if the fragments all originate from the same original image.  Always clearly indicate spliced sections with a thin line (white or black) in the final image, and provide a detailed description of the modification within the figure legend.

It's important to maintain the image's original background noise. Avoid manipulating the background to appear as a uniform color, as this can raise concerns about data authenticity.

It is not acceptable practice to “clean up” the background of images with rubberstamps, “wipe” tools to improve the aesthetic appearance or over-adjust the brightness or contrast to remove the background.

To ensure the most reliable comparisons, whenever possible, analyze all experimental samples and controls used in the same analysis on a single blot or gel image. This minimizes potential variations that can arise from processing samples on separate gels.  For quantitative analyses, where precise measurements are crucial, please provide blots or gels for each independent biological replicate used in the study. This additional information strengthens the overall analysis and data integrity.

While directly comparing samples analyzed on different gels or blots is generally discouraged due to potential processing variations, there may be situations where it's necessary.  If this is the case, ensure the figure legend clearly states that the samples originate from the same experiment (or parallel experiments) and that the gels or blots were processed together. This transparency allows readers to understand the context of the comparison and assess any potential limitations associated with it.

We encourage the inclusion of the following with the final revised version of the manuscript for publication:

For optimal reproducibility of your findings, the Methods section should include detailed information about the equipment used to acquire your gel or blot images. This includes the specific type of microscopes, objective lenses, cameras, and detectors employed, along with the filter model and its batch number. Additionally, specify the acquisition software used and include the magnification or scale bar information directly in the figure caption. While some variation between instruments is expected, listing the equipment settings used for critical measurements is also highly encouraged. This comprehensive information allows other researchers to replicate your experiments more effectively.

Be transparent about your data processing! In the Methods section, disclose the software used for blot/gel image processing. Describe any image manipulations (deconvolution, filtering, etc.) in the corresponding figure legends. This allows readers to assess potential effects on the results.

Comprehensive guidelines on data management and the ethical handling of digital images can obtained from The Office of Research Integrity: http://ori.hhs.gov/ images/ddblock/data.pdf

Supplementary Materials, Data Deposit and Software Source Code

Al-Yarmouk Journal supports open science! We believe in fostering collaboration and best practices for data sharing. We strongly encourage authors to deposit their research data alongside published articles. This data can encompass various materials like protocols, analysis methods, raw and processed data, code, software, algorithms, and even study materials.

The key is FAIRness: Findability, Accessibility, Interoperability, and Reusability. By adhering to FAIR principles, your research data becomes a valuable resource, readily discoverable and useable by other researchers, ultimately accelerating scientific progress.

To promote research transparency and reproducibility, we highly recommend depositing your data and code in a trusted repository.  This allows for maximum reusability by other researchers (detailed information on repositories can be found in the Data Preservation section below).  If depositing data or code isn't feasible, please explain the specific reason within the Data Availability Statement.  Additionally, in the Materials and Methods section, clearly identify any research materials essential for replicating your experiments.  This commitment to data sharing fosters collaboration and accelerates scientific progress.

Data sharing is highly encouraged, but not at the expense of ethical or legal obligations. If there are concerns regarding privacy, ethics, or legal restrictions, data may not be publicly shared.  Authors should clarify any limitations on data availability within the Data Availability Statement upon manuscript submission.  This transparency is crucial. Additionally, when sharing data containing confidential information, ensure it aligns with participant consent and anonymizes data sufficiently to protect participant identities and comply with local data protection laws. This balance between openness and ethical responsibility is paramount.

For datasets containing confidential or proprietary information, restricted access may be necessary.  In these cases, authors will be required to provide a clear explanation of the limitations on data access within the Data Availability Statement.  However, to facilitate peer review, authors are still expected to make the data available upon request, with the understanding that access will be granted solely for the purpose of reviewing the manuscript.

The Al-Yarmouk Journal recognizes that some institutions and funding agencies may have specific data retention periods after a project's completion or publication. However, our Data Availability Policy goes beyond these limitations. To ensure the long-term accessibility of your research data for the scientific community, we encourage authors to consider two options.  First, depositing your research data in a reputable data repository is highly recommended. This promotes data sharing and allows for future reuse by other researchers.  Alternatively, if depositing data in a repository isn't feasible, you can include minimal datasets directly relevant to your manuscript within the supplementary materials section of your submission.

Data availability statements

To promote transparency and facilitate research reproducibility, our journal requires a data availability statement for all published articles. During the peer review and editorial decision process, authors may be asked to share existing datasets or the raw data analyzed in the manuscript. This ensures reviewers can verify the research and allows other researchers to potentially access the data following publication. Additionally, authors will be required to detail any existing datasets used in the analysis.

Below are the recommended Data Availability Statements:

Data availability status	Recommended Data Availability Statement
Data available in a publicly accessible repository	The original data presented in the study are openly available in [repository name, e.g., FigShare] at [DOI/URL] or [reference/accession number].
Data available on request due to restrictions (e.g., privacy, legal or ethical reasons)	The data presented in this study are available on request from the corresponding author due to (specify the reason for the restriction).
3rd Party Data	Restrictions apply to the availability of these data. Data were obtained from [third party] and are available [from the authors/at URL] with the permission of [third party].
Embargo on data due to commercial restrictions	The data that support the findings will be available in [repository name] at [URL / DOI link] following an embargo from the date of publication to allow for commercialization of research findings.
Restrictions apply to the datasets	The datasets presented in this article are not readily available because [include reason, e.g., the data are part of an ongoing study or due to technical/ time limitations]. Requests to access the datasets should be directed to [text input].
Data derived from public domain resources	The data presented in this study are available in [repository name] at [URL/DOI], reference number [reference number]. These data were derived from the following resources available in the public domain: [list resources and URLs]
Data sharing is not applicable (only appropriate if no new data is generated or the article describes entirely theoretical research	No new data were created or analyzed in this study. Data sharing is not applicable to this article
Data is contained within the article or supplementary material	The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s.
Dataset available on request from the authors	The raw data supporting the conclusions of this article will be made available by the authors on request.

Data preservation

Long-term data preservation is a collaborative effort! We acknowledge the shared responsibility between researchers, institutions, journals, and data repositories. To ensure your data remains accessible for future reference, we encourage authors to choose data repositories committed to long-term data storage.

While not a replacement for repository deposit, authors are also encouraged to retain their datasets on lab or institutional servers for at least five years after publication. This acts as a safeguard in case the original repository ceases operation or experiences data loss. In such cases, we may request authors to upload the data to a new repository and potentially publish a correction to the original article.

Finally, if authors need to remove data from the original public repository or change access restrictions, we kindly ask for prompt notification to the editorial office. This transparency helps maintain data accessibility for the scientific community.

Research and Publication Ethics

Research Ethics

Research Involving Human Subjects

When reporting on research that involves human subjects, human material, human tissues, or human data, authors must declare that the investigations were carried out following the rules of the Declaration of Helsinki of 1975 (https://www.wma.net/what-we-do/medical-ethics/declaration-of-helsinki/), revised in 2013. According to point 23 of this declaration, an approval from the local institutional review board (IRB) or other appropriate ethics committee must be obtained before undertaking the research to confirm the study meets national and international guidelines.
As a minimum, a statement including the project identification code, date of approval, and name of the ethics committee or institutional review board must be stated in Section ‘Institutional Review Board Statement’ of the article. Authors should sign the Ethics Approval and Consent for Authors Form and upload it during submission process.

Example of an ethical statement: "All subjects gave their informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of XXX (Project identification code)."

Even in non-invasive studies like surveys, questionnaires, and social media research, ethical considerations remain paramount.  To ensure informed consent, participants must be fully aware of whether their anonymity is guaranteed, the research purpose, how their data will be used, and any potential risks involved.  As with all human subjects research, prior ethical approval from a relevant ethics committee is mandatory. However, in situations where ethical approval is not required, authors must either provide an exemption from the ethics committee outlining the justification, or cite the local/national legislation that waives such requirements for this specific type of study.  If an exemption is granted, the "Institutional Review Board Statement" section of the manuscript should include both the name of the ethics committee granting the exemption and a clear explanation for why formal ethical approval was not necessary.

A written informed consent for publication must be obtained from participating patients. Data relating to individual participants must be described in detail, but private information identifying participants need not be included unless the identifiable materials are of relevance to the research (for example, photographs of participants’ faces that show a particular symptom). Patients’ initials or other personal identifiers must not appear in any images. For manuscripts that include any case details, personal information, and/or images of patients, authors must obtain signed informed consent for publication from patients (or their relatives/guardians) before submitting to our journal. Patient details must be anonymized as far as possible, e.g., do not mention specific age, ethnicity, or occupation where they are not relevant to the conclusions. A template permission form is available to download. A blank version of the form used to obtain permission (without the patient names or signature) must be uploaded with your submission. Editors reserve the right to reject any submission that does not meet these requirements.

The editorial office may conduct additional scrutiny for research involving vulnerable populations. This may involve requesting documentary evidence, such as blank consent forms and any discussion documents related to the ethics board approval process.  Furthermore, when studies categorize participants by demographics such as race, ethnicity, gender, disability, or disease, a clear explanation for the necessity of such categorization within the context of the research must be provided within the manuscript itself. This transparency ensures robust ethical considerations are upheld for vulnerable populations and justifies the use of potentially sensitive information.

Ethical Guidelines for the Use of Animals in Research

The editors will require that the benefits potentially derived from any research causing harm to animals are significant in relation to any cost endured by animals, and that procedures followed are unlikely to cause offense to the majority of readers. Authors should particularly ensure that their research complies with the commonly accepted '3Rs [1]':

• Replacement of animals by alternatives wherever possible,
• Reduction in number of animals used, and
• Refinement of experimental conditions and procedures to minimize the harm to animals.

Authors must include details on housing, husbandry and pain management in their manuscript.

For further guidance authors should refer to the Code of Practice for the Housing and Care of Animals Used in Scientific Procedures [2], American Association for Laboratory Animal Science [3] or European Animal Research Association [4].

National regulations often mandate ethics committee approval for research involving vertebrates or higher invertebrates.  Authors must, at minimum, include the project ID code, approval date, and ethics committee name in the "Institutional Review Board Statement" section.  All research procedures must strictly adhere to national and institutional guidelines. Statements on animal welfare should demonstrate compliance with relevant legislation.  The American Veterinary Medical Association requires ethics committee oversight for clinical animal studies and procedures exceeding routine care.  For studies involving client-owned animals, informed consent, documented within the manuscript, is mandatory. Owners must be fully apprised of potential risks, publication intentions, and, whenever possible, receive a high standard of veterinary care. The onus of ensuring accurate statements within the manuscript lies with the authors.

In cases where national regulations don't necessitate ethics committee approval, authors should provide an exemption from the ethics committee, if obtainable.  If an exemption was granted, the "Institutional Review Board Statement" section of the manuscript must specify the name of the ethics committee that provided it and offer a clear explanation for why formal ethical approval wasn't required.

Even if an animal ethics committee isn't available, the ethical implications of your research will be scrutinized by reviewers and editors. To address this, authors should proactively provide a justification for the study's ethics, employing the same utilitarian framework typically used by ethics committees. This statement may be required even if you obtained formal ethical approval.

The journal endorses the ARRIVE guidelines (arriveguidelines.org/) for reporting experiments using live animals. Authors and reviewers must use the ARRIVE guidelines as a checklist, which can be found at https://arriveguidelines.org/sites/arrive/files/documents/ARRIVE%20Compliance%20Questionnaire.pdf. Editors reserve the right to ask for the checklist and to reject submissions that do not adhere to these guidelines, to reject submissions based on ethical or animal welfare concerns or if the procedure described does not appear to be justified by the value of the work presented.

1. NSW Department of Primary Industries and Animal Research Review Panel. Three Rs. Available online: https://www.animalethics.org.au/three-rs
2. Home Office. Animals (Scientific Procedures) Act 1986. Code of Practice for the Housing and Care of Animals Bred, Supplied or Used for Scientific Purposes. Available online here.
3. American Association for Laboratory Animal Science. The Scientific Basis for Regulation of Animal Care and Use. Available online: https://www.aalas.org/about-aalas/position-papers/scientific-basis-for-regulation-of-animal-care-and-use
4. European Animal Research Association. EU regulations on animal research. Available online: https://www.eara.eu/animal-research-law

 

Research Involving Cell Lines

The Methods section of your manuscript should clearly state the origin of all cell lines used in your research.  For established cell lines, indicate their source and provide references to either a published paper or the commercial supplier.  If your study utilizes previously unpublished, newly developed cell lines (de novo), including those obtained from another lab, you must provide details regarding the institutional review board (IRB) or ethics committee approval process. Additionally, for human-derived cell lines, confirmation of written informed consent must be obtained.

An example of Ethical Statements:

The HCT116 cell line was obtained from XXXX. The MLH1+ cell line was provided by XXXXX, Ltd. The DLD-1 cell line was obtained from Dr. XXXX. The DR-GFP and SA-GFP reporter plasmids were obtained from Dr. XXX and the Rad51K133A expression vector was obtained from Dr. XXXX.

Research Involving Plants

Experimental research on plants (either cultivated or wild) including collection of plant material, must comply with institutional, national, or international guidelines. We recommend that authors comply with the Convention on Biological Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and Flora.

All manuscripts involving genetic information or plant materials require documentation of origin.  For research using rare or non-model plants (excluding common models like Arabidopsis thaliana or Oryza sativa), depositing voucher specimens in a recognized herbarium or museum is mandatory. These specimens serve as a reference point for future researchers to verify the plant species used in the study, especially if taxonomic classifications change. Voucher specimens should include details like collection location (GPS coordinates), date of collection, and the specific plant parts used in the study. While voucher deposition may be waived for rare, threatened, or endangered species, authors must explicitly explain this in their cover letter.

Editors reserve the rights to reject any submission that does not meet these requirements.

An example of Ethical Statements:

Torenia fournieri plants were used in this study. White-flowered Crown White (CrW) and violet-flowered Crown Violet (CrV) cultivars selected from ‘Crown Mix’ (XXX Company, City, Country) were kindly provided by Dr. XXX (XXX Institute, City, Country).

Arabidopis mutant lines (SALKxxxx, SAILxxxx,…) were kindly provided by Dr. XXX, institute, city, country).

 

Dual Use Research of Concern

The journal follows the practical framework defined in Guidance for Editors: Research, Audit and Service Evaluations and introduced by the Committee on Publication Ethics (COPE). Research that could pose a significant threat, with broad potential consequences to public health or national security, should be clearly indicated in the manuscript, and potential dual-use research of concern should be explained in the cover letter upon submission. Potential areas of concern include but are not limited to biosecurity, nuclear and chemical threats, and research with a military purpose or application, etc. For these manuscripts to be considered for peer review, the benefits to the general public or public health must outweigh the risks. The authors have a responsibility to comply with relevant national and international laws.

Borders and Territories

Potential disputes over borders and territories may have particular relevance for authors in describing their research or in an author or editor correspondence address, and should be respected. Content decisions are an editorial matter and where there is a potential or perceived dispute or complaint, the editorial team will attempt to find a resolution that satisfies parties involved.

The journal stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Publication Ethics Statement

AlYarmouk Journal is fully adhere to the Committee on Publication Ethics (COPE) and its Code of Conduct and to its Best Practice Guidelines.

The editors of this journal enforce a rigorous peer review process together with strict ethical policies and standards to ensure to add high quality scientific works to the field of scholarly publication. Unfortunately, cases of plagiarism, data falsification, image manipulation, inappropriate authorship credit, and the like, do arise. The editors take such publishing ethics issues very seriously and are trained to proceed in such cases with a zero tolerance policy.

Authors wishing to publish their papers in this journal must abide to the following:

• Any facts that might be perceived as a possible conflict of interest of the author(s) must be disclosed in the paper prior to submission.
• Authors should accurately present their research findings and include an objective discussion of the significance of their findings.
• Data and methods used in the research need to be presented in sufficient detail in the paper, so that other researchers can replicate the work.
• Raw data should preferably be publicly deposited by the authors before submission of their manuscript. Authors need to at least have the raw data readily available for presentation to the referees and the editors of the journal, if requested. Authors need to ensure appropriate measures are taken so that raw data is retained in full for a reasonable time after publication.
• Simultaneous submission of manuscripts to more than one journal is not tolerated.
• If errors and inaccuracies are found by the authors after publication of their paper, they need to be promptly communicated to the editors of this journal so that appropriate actions can be taken.
• Your manuscript should not contain any information that has already been published. If you include already published figures or images, please obtain the necessary permission from the copyright holder to publish under the CC-BY license.
• Plagiarism, data fabrication and image manipulation are not tolerated.
• Plagiarism is not acceptable.

Plagiarism includes copying text, ideas, images, or data from another source, even from your own publications, without giving any credit to the original source.

Reuse of text that is copied from another source must be between quotes and the original source must be cited. If a study's design or the manuscript's structure or language has been inspired by previous works, these works must be explicitly cited.

All submissions are checked for plagiarism using the industry standard software iThenticate. If plagiarism is detected during the peer review process, the manuscript may be rejected. If plagiarism is detected after publication, an investigation will take place and action taken in accordance with our policies.

• Image files must not be manipulated or adjusted in any way that could lead to misinterpretation of the information provided by the original image.

Irregular manipulation includes: 1) introduction, enhancement, moving, or removing features from the original image; 2) grouping of images that should obviously be presented separately (e.g., from different parts of the same gel, or from different gels); or 3) modifying the contrast, brightness or color balance to obscure, eliminate or enhance some information.

If irregular image manipulation is identified and confirmed during the peer review process, we may reject the manuscript. If irregular image manipulation is identified and confirmed after publication, we may correct or retract the paper.

Our in-house editors will investigate any allegations of publication misconduct and may contact the authors' institutions or funders if necessary. If evidence of misconduct is found, appropriate action will be taken to correct or retract the publication. Authors are expected to comply with the best ethical publication practices when publishing in our journal.

Citation Policy

Authors should ensure that where material is taken from other sources (including their own published writing) the source is clearly cited and that where appropriate permission is obtained.

Authors should not engage in excessive self-citation of their own work.

Authors should not copy references from other publications if they have not read the cited work.

Authors should not preferentially cite their own or their friends’, peers’, or institution’s publications.

Authors should not cite advertisements or advertorial material.

In accordance with COPE guidelines, we expect that “original wording taken directly from publications by other researchers should appear in quotation marks with the appropriate citations.” This condition also applies to an author’s own work. COPE have produced a discussion document on citation manipulation with recommendations for best practice.

Authorship

The journal follows the International Committee of Medical Journal Editors (ICMJE) guidelines which state that, in order to qualify for authorship of a manuscript, the following criteria should be observed:

• Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
• Drafting the work or reviewing it critically for important intellectual content; AND
• Final approval of the version to be published; AND
• Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Those who contributed to the work but do not qualify for authorship should be listed in the acknowledgments. More detailed guidance on authorship is given by the International Committee of Medical Journal Editors (ICMJE).

Any change to the author list should be approved by all authors including any who have been removed from the list. The corresponding author should act as a point of contact between the editor and the other authors and should keep co-authors informed and involve them in major decisions about the publication. We reserve the right to request confirmation that all authors meet the authorship conditions.

Editorial Independence

Lack of Interference with Editorial Decisions

Editorial independence is of utmost importance and AlYarmok University College does not interfere with editorial decisions. All articles published by the journal are peer reviewed and assessed by our independent editorial boards, and the journal staff are not involved in decisions to accept manuscripts. When making an editorial decision, we expect the academic editor to make their decision based only upon:

• The suitability of selected reviewers;
• Adequacy of reviewer comments and author response;
• Overall scientific quality of the paper.

Editors and Editorial Staff as Authors

Editorial staff or editors shall not be involved in processing their own academic work. Submissions authored by editorial staff/editors will be assigned to at least two independent outside reviewers. Decisions will be made by other Editorial Board Members who do not have a conflict of interest with the author. Journal staff are not involved in the processing of their own work submitted to this journal.

Conflicts of Interest

The International Committee of Medical Journal Editors (ICMJE) emphasizes the importance of safeguarding research integrity.  Their guidelines recommend that authors refrain from entering into agreements with study sponsors, regardless of their profit status, that restrict access to study data or impede the authors' ability to independently analyze, interpret, and publish the data.  Transparency is paramount, and all authors must disclose any potential conflicts of interest, whether financial or non-financial, that could exert undue influence on their work.  Financial conflicts of interest encompass a variety of situations, including employment with a sponsor, consulting arrangements, stock ownership, honoraria, grants, and patent licensing agreements.  Non-financial conflicts may involve personal or professional relationships, affiliations, or personal beliefs.

Examples of disclosures:

Conflicts of Interest: Author A has received research grants from Company A. Author B has received a speaker honorarium from Company X and owns stocks in Company Y. Author C has been involved as a consultant and expert witness in Company Z. Author D is the inventor of patent X.

If no conflicts exist, the authors should state:

Conflicts of Interest: The authors declare no conflicts of interest.

Editorial Procedures and Peer Review

Pre-check

Immediately after submission, the journal’s Managing Editor will perform the technical pre-check to assess:

• Overall suitability of the manuscript to the journal/section/Special Issue;
• Manuscript adherence to high-quality research and ethical standards;
• Standards of rigor to qualify for further review.

Following submission, a designated editorial decision-maker (Editor-in-Chief for regular submissions, Guest Editor for special issues, or an Editorial Board member for conflict-of-interest cases and Editor-in-Chief approval) conducts an initial editorial assessment.  This pre-check evaluates the manuscript's alignment with the journal's scope, overall scientific merit, reference relevance, and methodological rigor. Based on this evaluation, the editor may render one of three decisions: manuscript rejection, request for revisions prior to peer review, or progression to the formal peer review process with selection of suitable reviewers.

Peer Review

Manuscripts meeting initial editorial criteria are assigned to at least two independent reviewers with relevant expertise.  A single-blind review process is employed, meaning reviewers are aware of the authors' identities.  Reviewer comments are strictly confidential and will only be disclosed with explicit reviewer consent.  For regular submissions, in-house editorial staff identify and invite reviewers, incorporating recommendations from the academic editor and potentially considering Editorial Board members, Guest Editors, or author suggestions.  To ensure impartiality, reviewers are excluded if they have co-authored publications with any co-author within the past three years or hold current professional affiliations with the co-authors' institutions.

Editorial Decision and Revision

All the articles, reviews and communications published in our journals go through the peer review process and receive at least two reviews. The in-house editor will communicate the decision of the academic editor, which will be one of the following:

• Accept after Minor Revisions:
  The paper is in principle accepted after revision based on the reviewer’s comments. Authors are given five days for minor revisions.
• Reconsider after Major Revisions:

The acceptance of the manuscript would depend on the revisions. The author needs to provide a point by point response or provide a rebuttal if some of the reviewer’s comments cannot be revised. A maximum of two rounds of major revision per manuscript is normally provided. Authors will be asked to resubmit the revised paper within a suitable time frame, and the revised version will be returned to the reviewer for further comments. If the required revision time is estimated to be longer than 2 months, we will recommend that authors withdraw their manuscript before resubmitting so as to avoid unnecessary time pressure and to ensure that all manuscripts are sufficiently revised.

• Reject and Encourage Resubmission:
  If additional experiments are needed to support the conclusions, the manuscript will be rejected and the authors will be encouraged to re-submit the paper once further experiments have been conducted.
• Reject:
  The article has serious flaws, and/or makes no original significant contribution. No offer of resubmission to the journal is provided.

All reviewer comments should be responded to in a point-by-point fashion. Where the authors disagree with a reviewer, they must provide a clear response.

Author Appeals

Following an editorial decision to "reject and decline resubmission," authors may initiate an appeal within a three-month timeframe. Appeals submitted via email to the journal's Editorial Office must provide a comprehensive justification that addresses, in a point-by-point manner, the feedback provided by reviewers and/or the Editor. Failure to adhere to these established criteria will result in the automatic dismissal of the appeal.  The Managing Editor will then forward the manuscript, along with the identities of the reviewers and any pertinent information, to a designated member of the Editorial Board. This Academic Editor will then offer a consultative recommendation on the manuscript, potentially advocating for acceptance, further peer review, or upholding the initial rejection decision.  The Editor-in-Chief holds the final authority to validate this recommendation.  A rejection decision rendered at this stage is definitive and cannot be overturned.

Production and Publication

Once accepted, the manuscript will undergo professional copy-editing, English editing, proofreading by the authors, final corrections, pagination, and, publication.