Submissions

Author Guidelines

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.