Instructions for AIDS Research and Therapy authors

General information

Submission process

Manuscripts must be submitted by one of the authors of the manuscript, and should not be submitted by anyone on their behalf. The submitting author takes responsibility for the article during submission and peer review.

To facilitate rapid publication and to minimize administrative costs, AIDS Research and Therapy accepts only online submission. The submission process is compatible with version 3.0 or later of Internet Explorer and Netscape Navigator, and with most other modern web browsers. It can be used from PC, Mac, or Unix platforms.

Files can be submitted as a batch, or one by one. The submission process can be interrupted at any time - when users return to the site, they can carry on where they left off.

See below for examples of acceptable word processor and graphics file formats. Additional files of any type, such as movies, animations, or original data files, can also be submitted as part of the publication.

During submission you will be asked to provide a cover letter. Please use this to explain why your manuscript should be published in the journal and to elaborate on any issues relating to our editorial policies detailed in the instructions for authors.

Assistance with the process of manuscript preparation and submission is available from the customer support team (info@biomedcentral.com).

We also provide a collection of links to useful tools and resources for scientific authors, on our Tools for Authors page.

Publication and peer review processes

AIDS Research and Therapy uses online peer review to speed up the publication process. The time taken to reach a final decision depends on whether reviewers request revisions, and how quickly authors are able to respond.

Once an article is accepted, it is published in AIDS Research and Therapy immediately as a provisional PDF file. The paper will subsequently be published in both fully browseable web form, and as a formatted PDF; the article will then be available through AIDS Research and Therapy, BioMed Central and PubMed Central, and will also be included in PubMed.

The ultimate responsibility for any decision lies with the Editor-in-Chief, to whom any appeals against rejection should be addressed.

Article-processing charges

AIDS Research and Therapy levies an article-processing charge for every accepted article, to cover the costs incurred by open access publication. In 2008 the article-processing charge is £850 (€1070, US$1660). Generally, if the submitting author's institution is a BioMed Central member the cost of the article processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are supporter members of BioMed Central, however, a discounted article processing charge is payable by the author. Please click here to check if your institution is a BioMed Central member. We offer a £30 discount for manuscripts formatted with EndNote 5 (or later versions) or Reference Manager 10 or created using Publicon. Waivers may be granted, particularly for authors from developing countries. For further details, see more information about article-processing charges.

Editorial policies

Any manuscript submitted to the journal must not already have been published in another journal or be under consideration by any other journal, although it may have been deposited on a preprint server. Manuscripts must not have already been published in any journal or other citable form, with the exception that the journal is willing to consider peer-reviewing manuscripts that are translations of articles originally published in another language. In this case, the consent of the journal in which the article was originally published must be obtained and the fact that the article has already been published must be made clear on submission and stated in the abstract. Manuscripts that are derived from papers presented at conferences can be submitted unless they have been published as part of the conference proceedings in a peer reviewed journal. Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party. Authors who publish in AIDS Research and Therapy retain copyright to their work (more information). Correspondence concerning articles published in AIDS Research and Therapy is encouraged .

Submission of a manuscript to AIDS Research and Therapy implies that all authors have read and agreed to its content, and that any experimental research that is reported in the manuscript has been performed with the approval of an appropriate ethics committee. Research carried out on humans must be in compliance with the Helsinki Declaration, and any experimental research on animals must follow internationally recognized guidelines. A statement to this effect must appear in the Methods section of the manuscript, including the name of the body which gave approval, with a reference number where appropriate. Informed consent must also be documented. Manuscripts may be rejected if the editorial office considers that the research has not been carried out within an ethical framework, e.g. if the severity of the experimental procedure is not justified by the value of the knowledge gained.

Generic drug names should generally be used. When proprietary brands are used in research, include the brand names in parentheses in the Methods section.

We ask authors of AIDS Research and Therapy papers to complete a declaration of competing interests, which should be provided as a separate section of the manuscript, to follow the Acknowledgements. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'. Much has been written about competing interests (or conflict of interest, as other journals call it) within scientific research, but the following articles provide some background:

R Smith: Beyond conflict of interest. BMJ 1998, 317 :291-292

R Smith: Making progress with competing interests. BMJ 2002, 325 :1375-1376

CD DeAngelis, PB Fontanarosa, A Flanagin: Reporting financial conflicts of interest and relationships between investigators and research sponsors. JAMA 2001, 286 :89-9

K Morin, H Rakatansky, FA Riddick Jr, LJ Morse, JM O'Bannon 3rd, MS Goldrich, P Ray, M Weiss, RM Sade, MA Spillman: Managing conflicts of interest in the conduct of clinical trials. JAMA 2002, 287 :78-84

For all articles that include information or clinical photographs relating to individual patients, written and signed consent from each patient to publish must also be mailed or faxed to the editorial staff. The manuscript should also include a statement to this effect in the Acknowledgements section, as follows: "Written consent for publication was obtained from the patient or their relative."

AIDS Research and Therapy supports initiatives to improve the performance and reporting of clinical trials, part of which includes prospective registering and numbering of trials. While there are initiatives to ensure that all clinical trials are registered (most notably the recent statement from the International Committee of Medical Journal Editors - see http://www.icmje.org/clin_trialup.htm), we are focussing on controlled trials of healthcare interventions, for now. Authors of protocols or reports of controlled trials of health care interventions must register their trial prior to submission in a suitable publicly accessible registry. The trial registers that currently meet all of the ICMJE guidelines can be found at http://www.icmje.org/faq.pdf.

The trial registration number should be included as the last line of the abstract of the manuscript.

AIDS Research and Therapy also supports initiatives aimed at improving the reporting of biomedical research. Checklists have been developed for randomized controlled trials (CONSORT), systematic reviews (QUOROM), meta-analyses of observational studies (MOOSE), diagnostic accuracy studies (STARD) and qualitative studies (RATS). Authors are requested to make use of these when drafting their manuscript and peer reviewers will also be asked to refer to these checklists when evaluating these studies. For authors of systematic reviews, a supplementary file, linked from the Methods section, should reproduce all details concerning the search strategy. For an example of how a search strategy should be presented, see the Cochrane Reviewers' Handbook.

Authors from pharmaceutical companies, or other commercial organizations that sponsor clinical trials, should adhere to the Good Publication Practice guidelines for pharmaceutical companies, which are designed to ensure that publications are produced in a responsible and ethical manner. The guidelines also apply to any companies or individuals that work on industry-sponsored publications, such as freelance writers, contract research organizations and communications companies.

The involvement of medical writers or anyone else who assisted with the preparation of the manuscript content should be acknowledged, along with their source of funding, as described in the European Medical Writers Association (EMWA) guidelines on the role of medical writers in developing peer-reviewed publications. If medical writers are not listed among the authors, it is important that their role be acknowledged explicitly. We suggest wording such as 'We thank Jane Doe who provided medical writing services on behalf of XYZ Pharmaceuticals Ltd.'.

Submission of a manuscript to AIDS Research and Therapy implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article.

Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

Structures

Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

Chemical structures and assays

Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

Microarray data

Where appropriate, authors should adhere to the standards proposed by the Microarray Gene Expression Data Society and must deposit microarray data in one of the public repositories, such as ArrayExpress, Gene Expression Omnibus (GEO) or the Center for Information Biology Gene Expression Database (CIBEX).

Computional modeling

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.

Plasmids

We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.

BioMed Central is a member of the Committee on Publication Ethics (COPE). Authors who have appealed against a rejection but remain concerned about the editorial process can refer their case to COPE. For more information, visit www.publicationethics.org.uk.

BioMed Central endorses the World Association of Medical Editors (WAME) Policy Statement on Geopolitical Intrusion on Editorial Decisions.

Preparing main manuscript text

File formats

The following word processor file formats are acceptable for the main manuscript document:

• Microsoft Word (version 2 and above)
• WordPerfect (version 5 and above)
• Rich text format (RTF)
• Portable document format (PDF)
• TeX/LaTeX (use BioMed Central's TeX template)
• DeVice Independent format (DVI)
• Publicon Document (NB)

Users of other word processing packages should save or convert their files to RTF before uploading. Many free tools are available which ease this process.

TeX/LaTeX users: We recommend using BioMed Central's TeX template and BibTeX stylefile. If you use this standard format, you can submit your manuscript in TeX format (after you submit your TEX file, you will be prompted to submit your BBL file). If you have used another template for your manuscript, or if you do not wish to use BibTeX, then please submit your manuscript as a DVI file. We do not recommend converting to RTF.

Publicon users: Information about Publicon and instructions for authoring in Publicon are available.

Note that figures must be submitted as separate image files, not as part of the submitted DOC/ PDF/TEX/DVI file.

Article types

When submitting your manuscript, you will be asked to assign one of the following types to your article:

Please read the descriptions of each of the article types, choose which is appropriate for your article and structure it accordingly. If in doubt, your manuscript should be classified as Research, the structure for which is described below.

Preparing illustrations and figures

Figures should be provided as separate files and should not be included in the main text of the submitted manuscript. Each figure should comprise only a single file. There is no charge for the use of color.

Please read our figure preparation guidelines for detailed instructions on maximising the quality of your figures.

Formats

The following file formats can be accepted:

• EPS (preferred format for diagrams)
• PDF (also especially suitable for diagrams)
• PNG (preferred format for photos or images)
• Microsoft Word (version 5 and above; figures must be a single page)
• PowerPoint (figures must be a single page)
• TIFF
• JPEG
• BMP
• CDX (ChemDraw)
• TGF (ISIS/Draw)

Figure legends

The legends should be included in the main manuscript text file immediately following the references, rather than being a part of the figure file. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals - i.e. Figure 1, 2, 3 etc); short title of figure (maximum 15 words); detailed legend, up to 300 words.

Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.

Preparing tables

Each table should be numbered in sequence using Arabic numerals (i.e. Table 1, 2, 3 etc.). Tables should also have a title that summarizes the whole table, maximum 15 words. Detailed legends may then follow, but should be concise.

Smaller tables considered to be integral to the manuscript can be pasted into the end of the document text file, in portrait format (note that tables on a landscape page must be reformatted onto a portrait page or submitted as additional files). These will be typeset and displayed in the final published form of the article. Such tables should be formatted using the 'Table object' in a word processing program to ensure that columns of data are kept aligned when the file is sent electronically for review; this will not always be the case if columns are generated by simply using tabs to separate text. Columns and rows of data should be made visibly distinct by ensuring the borders of each cell display as black lines. Commas should not be used to indicate numerical values. Color and shading should not be used.

Larger datasets can be uploaded separately as additional files. Additional files will not be displayed in the final, published form of the article, but a link will be provided to the files as supplied by the author.

Tabular data provided as additional files can be uploaded as an Excel spreadsheet (.xls) or comma separated values (.csv). As with all files, please use the standard file extensions.

Preparing additional files

Although AIDS Research and Therapy does not restrict the length and quantity of data in a paper, there may still be occasions where an author wishes to provide data sets, tables, movie files, or other information as additional information. These files can be uploaded using the 'Additional Material files' button in the manuscript submission process.

The maximum file size for additional files is 20 MB each, and files will be virus-scanned on submission.

Any additional files will be linked into the final published article in the form supplied by the author, but will not be displayed within the paper. They will be made available in exactly the same form as originally provided.

If additional material is provided, please list the following information in a separate section of the manuscript text, immediately following the tables (if any):

• File name
• File format (including name and a URL of an appropriate viewer if format is unusual)
• Title of data
• Description of data

Additional datafiles should be referenced explicitly by file name within the body of the article, e.g. 'See additional file 1: Movie1 for the original data used to perform this analysis'.

Formats and uploading

Ideally, file formats for additional files should not be platform-specific, and should be viewable using free or widely available tools. The following are examples of suitable formats.

• Additional documentation
• PDF (Adobe Acrobat)
• Animations
• SWF (Shockwave Flash)
• Movies
• MOV (QuickTime)
• MPG (MPEG)
• Tabular data
• XLS (Excel spreadsheet)
• CSV (Comma separated values)

As with figure files, files should be given the standard file extensions. This is especially important for Macintosh users, since the Mac OS does not enforce the use of standard extensions. Please also make sure that each additional file is a single table, figure or movie (please do not upload linked worksheets or PDF files larger than one sheet).

Mini-websites

Small self-contained websites can be submitted as additional files, in such a way that they will be browsable from within the full text HTML version of the article. In order to do this, please follow these instructions:

1. Create a folder containing a starting file called index.html (or index.htm) in the root
2. Put all files necessary for viewing the mini-website within the folder, or sub-folders
3. Ensure that all links are relative (ie "images/picture.jpg" rather than "/images/picture.jpg" or "http://yourdomain.net/images/picture.jpg" or "C:\Documents and Settings\username\My Documents\mini-website\images\picture.jpg") and no link is longer than 255 characters
4. Access the index.html file and browse around the mini-website, to ensure that the most commonly used browsers (Internet Explorer and Firefox) are able to view all parts of the mini-website without problems, it is ideal to check this on a different machine
5. Compress the folder into a ZIP, check the file size is under 20 MB, ensure that index.html is in the root of the ZIP, and that the file has .zip extension, then submit as an additional file with your article

Style and language

General

Currently, AIDS Research and Therapy can only accept manuscripts written in English. Spelling should be US English or British English, but not a mixture.

Gene names should be in italic, but protein products should be in plain type.

There is no explicit limit on the length of articles submitted, but authors are encouraged to be concise. There is no restriction on the number of figures, tables or additional files that can be included with each article online. Figures and tables should be sequentially referenced. Authors should include all relevant supporting data with each article.

AIDS Research and Therapy will not edit submitted manuscripts for style or language; reviewers may advise rejection of a manuscript if it is compromised by grammatical errors. Authors are advised to write clearly and simply, and to have their article checked by colleagues before submission. In-house copyediting will be minimal. Non-native speakers of English may choose to make use of a copyediting service.

Help and advice on scientific writing

The abstract is one of the most important parts of a manuscript. For guidance, please visit our page on "Writing titles and abstracts for scientific articles".

Tim Albert has produced for BioMed Central a list of tips for writing a scientific manuscript. MedBioWorld also provides a list of resources for science writing.

Abbreviations

Abbreviations should be used as sparingly as possible. They can be defined when first used or a list of abbreviations can be provided preceding the acknowledgements and references.

• Please use double line spacing.
• Type the text unjustified, without hyphenating words at line breaks.
• Use hard returns only to end headings and paragraphs, not to rearrange lines.
• Capitalize only the first word, and proper nouns, in the title.
• All pages should be numbered.
• Use the AIDS Research and Therapy reference format.
• Footnotes to text should not be used.
• Greek and other special characters may be included. If you are unable to reproduce a particular special character, please type out the name of the symbol in full.
  
  Please ensure that all special characters used are embedded in the text, otherwise they will be lost during conversion to PDF.

Units

SI Units should be used throughout (liter and molar are permitted, however).

Last revised: 3 October 2005