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- Author Choice Option
- Copyright Transfer
- Editorial Policies
- Funding Body Public Access Policy FAQs
- ORCID Numbers
- Peer Review Information
- Public Access
- Publication Fees
- The JI Editorial Board
- Contact Information
All manuscripts are considered to be the property of AAI from the time of submission. Should AAI not publish the paper, AAI releases its rights therein at the time the manuscript is returned to the corresponding author.
Manuscripts published in The Journal of Immunology become the sole property of, with all rights in copyright reserved to, The American Association of Immunologists, Inc. (AAI).
The corresponding author, on behalf of all authors, signs a copyright transfer form. When all authors of an article have written it as part of their official duties as employees of the U.S. government, the article is exempt from this requirement for transfer of copyright.
Authors retain the following permissions as long as proper attribution (Originally published in The Journal of Immunology. Author(s). Year. Title. J. Immunol. Vol: pp-pp. Copyright © [year] The American Association of Immunologists, Inc.) is included:
- If mandated by the funder of the research, authors may deposit the accepted, uncopyedited version of the manuscript into PubMed Central, with an embargo period (time at which the manuscript is available to the public) of 12 months after publication. This right applies solely to deposition into PubMed Central; the authors agree not to deposit the manuscript to any other repository (except a thesis repository if required - see item 3), agency, or entity. Authors whose funder mandates a PubMed Central embargo of 6 months have permission to make the manuscript available at 6 months after publication. This right applies only to articles under a funder mandate to submit to PubMed Central (for research funded by NIH, this means articles accepted for publication on or after April 7, 2008).
- To reuse original figures or tables in the author's own work. This permission extends to the author only, not to the institution. The author may not permit others to reproduce their figures or tables in works not written by the author.
- To include the final, published version of the article in a thesis and/or dissertation in print. If required by the degree-conferring institution, an electronic version of the final, published version may be deposited into a thesis repository as long as a link to the article on The Journal of Immunology website is included.
- To reprint the article in print collections composed solely of the author's own writings. Permission must be obtained from AAI to reprint the article in any publication that includes the work of others.
- To post a copy of the accepted, uncopyedited version on the author's personal website with a notice that "This is the accepted, uncopyedited version of the manuscript. The definitive version was published in The Journal of Immunology Vol: pp-pp. DOI." A hyperlink to the published article on The Journal of Immunologywebsite must be included; the published PDF may not be displayed. For posting on any other website, including any social media, corporate or government (other than PubMed Central according to the terms in item 1 above) website, permission must be requested from AAI. POSTING TO INSTITUTIONAL REPOSITORIES IS NOT PERMITTED.
- To present the work orally in part or in its entirety.
- If the work was prepared as a work-for-hire, the author's employer may print out PDFs or make photocopies for internal use only. Distribution of the article by the author's employer in other formats or for any other purpose requires permission from AAI.
Authors reusing their own material as described in items 1-7 do not need to contact AAI for permission, except where noted. For all other reuse, the authors should contact AAI.
The American Association of Immunologists, Inc. allows free public access to full-text articles published in The Journal of Immunology from 1998 to one year prior to the current issue date. Tables of content and abstracts of all online articles are accessible to the public free of charge, immediately upon publication. Use of material posted on The Journal of Immunologywebsite is subject to certain terms and conditions. Please see Content Available for Public Access for details.
Archiving in PMC/Europe PMC (see also NIH Public Access Policy and FAQ)
In March 2011, The American Association of Immunologists (AAI) began a new, free service to authors, to deposit selected manuscripts to PubMed Central (PMC).
Several funding bodies, including the National Institutes of Health (NIH), Howard Hughes Medical Institute (HHMI), Wellcome Trust and Research Councils UK (RCUK), mandate that authors deposit published articles into PMC or Europe PMC. While these mandates apply to authors, not publishers, the new AAI service will help authors comply with these mandates. On behalf of authors who are funded by NIH, HHMI, Wellcome Trust and RCUK, AAI will deposit to NIHMS or Europe PMC, as applicable, for display in PMC or Europe PMC, all manuscripts that begin submission to The Journal of Immunology after 10AM (EDT) March 29, 2011 and are ultimately accepted for publication; the author must select this option on the online submission form in order for AAI to do so. AAI will deposit the version of the manuscript that has undergone peer review and has been accepted for publication, before copyediting and formatting.
Most funders mandate that articles be made available to the public in PMC at either 6 or 12 months after publication; manuscripts deposited by AAI will comply with these embargo periods. Authors will receive at least two email notifications from PMC about their manuscripts. Authors must respond to both emails in order for the process to be completed.
This free service is not applicable to work that is funded by bodies other than NIH, HHMI, Wellcome Trust and RCUK. Authors funded by other entities which mandate deposition into PMC/Europe PMC must deposit the accepted version of the manuscript themselves.
How this service works:
- As part of the online submission process, authors select whether or not this service applies to them
- If the manuscript is accepted for publication, AAI will send all files, including Supplemental Data and video files, to NIHMS or Europe PMC for display in PMC or Europe PMC
- Authors will receive an email from PMC (NIH/NLM/NCBI) or Europe PMC to approve the submitted files
- Authors will receive an email from PMC (NIH/NLM/NCBI) or Europe PMC to approve the XML format
- After final approval by the author, PMC or Europe PMC will make the manuscript publically available after the embargo period
Further information is available at http://www.nihms.nih.gov/help/publishers.shtml
- General Guidelines
For the initial submission of Full-Length manuscripts:
A format-neutral manuscript may be submitted for the first round of review. Manuscripts do not need to be formatted according to The JI guidelines for the initial submission, except that all authors must be listed for each reference.
NOTE: Numbering of lines and pages, and easy-to-read figures will make the task of the reviewers and editors easier.
Please see specifications for Cutting-Edge Manuscripts.
For revised submissions, please follow the guidelines below:
- A 12-point serif font, preferably Times New Roman, is required for all text, except within the figures. Do not use compressed type format. Double-space entire manuscript; number each line and each page. Each of the following components should begin on a separate page:
The Title Page must include the full title; a running title (not to exceed 60 characters); each author's full name as it should be published (first name, middle initial, last name) and the affiliations of all authors and their institutions, departments, or organizations (use the following symbols in this order to designate authors' affiliations: *, †, ‡, §, ¶, ||, #, **, ††, ‡‡, §§, ¶¶, || ||, ##). List the phone number, fax number, and e-mail address of the corresponding author on the title page. (See the Submit Online section for information about the corresponding author designation during submission and peer review.)
- The Abstract must be 250 words or less for Full-Length type manuscripts. Reference citations should not be included in the Abstract. The species of animals or species of origin of cells used in the manuscript must be clearly stated in the Abstract. Please ensure that the final few sentences (50 words or less) of the Abstract provide a succinct summary of the main point of the paper.
- The Introduction, Materials and Methods, Results, and Discussion sections should begin on separate pages in that order. Do not combine the Results and Discussion sections for Full-Length papers.
- For flow cytometry experiments, authors should specify the gating strategies in the Materials and Methods or in the figure legend.
- Authors are encouraged to include the Minimal Information About T cell Assays (MIATA) in the Materials and Methods, the figure legend or elsewhere as appropriate.
- Acknowledgments appear immediately after the Discussion and before References.
- Grant support must NOT be included in the Acknowledgments but should be cited as a footnote to the title. All funding sources must be disclosed and will be published as a footnote to the title; anonymous or pseudonymous funders are not permitted.
- References must be numbered as they appear in the text and should refer to primary literature rather than review articles wherever possible. All authors must be listed for each reference. If citations are included in tables or in figure legends, they must be numbered according to the position of citation of the table or figure in the text. Only published papers and papers in press may be included in the References. In press articles, i.e., papers not yet published, must be submitted as online attachments in PDF format at the time of article submission. NOTE: Do NOT submit as attachment papers that are already published, e.g., manuscripts published ahead of print. Such papers must be incorporated into the References and cited with their DOI numbers and year of publication. Citations of "manuscripts in preparation," "unpublished observations," "manuscripts posted on preprint servers," and "personal communications" must appear parenthetically in the text. Manuscripts "submitted for publication" (i.e., not yet accepted) also are mentioned parenthetically in the text. Written approval by the persons cited in personal communications must accompany the manuscript unless they are also authors of the manuscript submitted to The JI.
Format for references:
- Periodicals: Wells, A. D., M. C. Walsh, D. Sankaran, and L. A. Turka. 2000. T cell effector function and anergy avoidance are quantitatively linked to cell division. J. Immunol. 165: 2432–2443.
- Books: McIntyre, T. M., and W. Strober. 1999. Gut-associated lymphoid tissue: regulation of IgA B-cell development. In Mucosal Immunology, 2nd ed. P. L. Ogra, J. Mestecky, E. Lamm, W. Strober, J. Bienenstock, and J. R. McGhee, eds. Academic Press, San Diego, CA. p. 319–356.
- Articles published ahead of print: Fraser, D.A., A. K. Laust, E. L. Nelson, and A. J. Tenner. 2009. C1q differentially modulates phagocytosis and cytokine responses during ingestion of apoptotic cells by human monocytes, macrophages, and dendritic cells . J. Immunol. doi:10.4049/jimmunol.0902232.
- Footnotes should be used to designate the source of support, new or special abbreviations used, correspondence address, current address, etc. Footnotes should be numbered consecutively and will appear on the title page, but for submission are grouped together and placed on a separate page between the References and the Figure Legends.
- Abbreviations that may be used without definition are provided below. Spell out nonstandard abbreviations used less than three times. Nonstandard abbreviations used three or more times must be defined in a footnote. Abbreviations and their definitions must be consistent throughout the text.
- The abbreviations listed below are used without definition in articles published in The JI. The form may be used for both singular and plural, or made plural with "s" at the author's option. The list of standard abbreviations is published in the first issue of each volume.
|Å, angstrom||kb, kilobase (only with numbers)|
|aa, amino acid (only with numbers)||kbp, kilobase pair (only with numbers)|
|Ab, antibody||Ka, association constant|
|ABTS, 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid)||Kd, distribution coefficient; dissociation constant|
|ADP, adenosine 5'-diphosphate||KD, affinity constant|
|Ag, antigen||kDa, kilodalton (only with numbers)|
|AIDS, acquired immunodeficiency syndrome||L chain, light chain|
|AMP, adenosine 5'-monophosphate||LD50, 50% lethal dose|
|ANOVA, analysis of variance||LFA, leukocyte (lymphocyte) function-associated Ag|
|AP-1, activator protein 1||LIF, leukemia inhibitory factor|
|APC, Ag-presenting cell||LPS, lipopolysaccharide|
|ATP, adenosine triphosphate||LU, lytic unit|
|BALB/c, a mouse strain||2-ME, 2-mercaptoethanol|
|BALT, bronchus-associated lymphoid tissue||mAb, monoclonal Ab|
|BAPTA-AM, 1,2-bis(2-aminophenoxy)ethane-N,N,N',N' -tetraacetic acid acetoxymethyl ester||MACS, magnetic-activated cell sorting|
|BCR, B cell receptor||MALDI, matrix-assisted laser desorption ionization|
|bp, base pair (only with numbers)||MALDI-TOF, matrix-assisted laser desorption ionization-time of flight|
|BrdU, 5-bromo-2'-deoxyuridine||MALT, mucosa-associated lymphoid tissue|
|BSA, bovine serum albumin||MAPK, mitogen-activated protein kinase|
|C, complement||MCP, monocyte chemoattractant protein|
|C region, constant region of Ig||M-CSF, macrophage CSF|
|cAMP, cyclic AMP||MEK, mitogen-activated protein kinase kinase|
|C-terminal, carboxyl-terminal or COOH-terminal||MEM, minimum essential medium|
|Cterminus, carboxyl or COOH terminus||MES, 2-(N-morpholino)ethanesulfonic acid|
|CCL, CC chemokine ligand||mg, milligram (only with numbers)|
|CCR, CC chemokine receptor||MHC, major histocompatibility complex|
|CD40L, CD40 ligand||min, minute (only with numbers)|
|cDNA, complementary DNA||MIP, macrophage-inflammatory protein|
|CDP, cytidine 5'-diphosphate||ml, milliliter (only with numbers)|
|CDR, complementarity determining region||MLC, mixed lymphocyte culture|
|C/EBP, CCAAT/enhancer-binding protein||MLR, mixed leukocyte reaction|
|CFA, complete Freund's adjuvant||mo, month(s) (only with numbers)|
|CFSE, 5- (and 6-)carboxyfluorescein diacetate succinimidyl ester||Mr, relative molecular mass|
|CFU, colony-forming unit||mRNA, messenger RNA|
|cGMP, guanosine 3',5'-cyclic monophosphate||MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-dimethyltetrazolium bromide|
|CHAPS, 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate||μg, microgram (only with numbers)|
|Ci, curie||μl, microliter (only with numbers)|
|CIITA, class II transactivator||m.w., molecular weight|
|CLIP, class II-associated invariant-chain peptide||MyD88, myeloid differentiating factor 88|
|cM, centiMorgan(s)||n, number in study or group|
|CMP, cytidine 5'-monophosphate||NAD, nicotinamide adenine dinucleotide|
|CMV, cytomegalovirus||NADH, reduced NAD|
|CNS, central nervous system||NaDodSO4, sodium dodecyl sulfate|
|CoA, coenzyme A||NADP, NAD phosphate|
|Con A, concanavalin A||NADPH, NAD phosphate (reduced)|
|CpG, cytosine guanine dinucleotide||NBT, nitroblue tetrazolium|
|cpm, counts per minute||ND, not determined|
|CREB, cAMP response element binding protein||NDP, nucleoside 5'-diphosphate|
|cRNA, complementary RNA||NF, nuclear factor|
|CSF, colony-stimulating factor||NFAT or NF-AT, nuclear factor of activated T cells|
|CTL, cytotoxic T lymphocyte||NF-κB, nuclear factor κB|
|CTLA, cytolytic T lymphocyte-associated Ag||Ni-NTA, nickel-nitrilotriacetic acid|
|CTP, cytidine 5'-triphosphate||NK cell, natural killer cell|
|CXCL, CXC chemokine ligand||NMP, nucleoside 5'-monophosphate|
|CXCR, CXC chemokine receptor||NO, nitric oxide|
|d, day(s); deoxy; distilled (as in dH2O)||NOD, nonobese diabetic|
|D region, diversity region of Ig or T cell receptor for Ag||NS, not significant|
|Da, dalton (only with numbers)||nt, nucleotide (only with numbers)|
|DAPI, 4',6'-diamidino-2-phenylindole||N-terminal, amino-terminal or NH2-terminal|
|DEAE, diethylaminoethyl||N terminus, amino terminus or NH2-terminus|
|df, degrees of freedom||NTP, nucleoside 5'-triphosphate|
|DMEM, Dulbecco's modified Eagle's medium||OCT, octamer-binding factor|
|DMSO, dimethylsulfoxide||OD, optical density|
|DNA, deoxyribonucleic acid||OVA, ovalbumin|
|DNase, deoxyribonuclease||p, probability|
|DNP, dinitrophenyl||PAGE, polyacrylamide gel electrophoresis|
|dpm, disintegrations per minute||PBL, peripheral blood lymphocyte|
|ds, double-stranded (as dsDNA)||PBMC, peripheral blood mononuclear cell|
|DTT, dithiothreitol||PBS, phosphate-buffered saline|
|E, erythrocyte||PCR, polymerase chain reaction|
|EBV, Epstein-Barr virus||PE, phycoerythrin|
|EC50, 50% effective concentration||PECAM-1, platelet endothelial cell adhesion molecule-1|
|ECL, enhanced chemiluminescence||PerCP, peridinin chlorophyll protein|
|ED50, 50% effective dose||PFU, plaque-forming unit|
|EDTA, ethylenediaminetetraacetic acid||PG, prostaglandin|
|EGTA, ethylene glycol-bis(b-aminoethyl ester)-N,N,N',N'- tetraacetic acid||PHA, phytohemagglutinin|
|ELISA, enzyme-linked immunosorbent assay||PI3K, phosphatidylinositol 3-kinase|
|ELISPOT, enzyme-linked immunospot||PIPES, piperazine-N,N'-bis(2-ethane sulfonic acid)|
|EMSA, electrophoretic mobility shift assay||PMA, phorbol myristate acetate|
|ERK, extracellular signal-regulated kinase||PMSF, phenylmethylsulfonyl fluoride|
|E:T ratio, effector to target ratio||PWM, pokeweed mitogen|
|Fab, Ag-binding fragment||r, recombinant, (e.g., rIFN-γ)|
|F-actin, filamentous actin||R, receptor (e.g., IL-2R)|
|FACS, fluorescence-activated cell sorter||RACE, rapid amplification of cDNA end|
|FAM, 6-carboxyfluorescein||RAG, recombination-activating gene|
|FBS, fetal bovine serum||RANTES, regulated upon activation, normal T cell expressed and secreted|
|FcR, Fc receptors (e.g., FcgRI)||RBC, red blood cell|
|FCS, fetal calf serum||RFLP, restriction fragment length polymorphism|
|FITC, fluorescein isothiocyanate||RIA, radioimmunoassay|
|FLICE, Fas-associated death domain-like IL-1Β-converting enzyme||RNA, ribonucleic acid|
|FLIP, FLICE inhibitory protein||RNase, ribonuclease|
|FLT3, fms-related tyrosine kinase 3||rpm, revolutions per minute|
|fMLF, formyl-methionyl-leucyl-phenylalanine||RPMI (usually RPMI 1640)|
|fura 2-AM, fura 2-acetoxymethyl ester||rRNA, ribosomal RNA|
|g, gram (only with numbers)||RT-PCR, reverse transcriptase polymerase chain reaction|
|GALT, gut-associated lymphoid tissue||s, second (use only with numbers)|
|GAPDH or G3PDH, glyceraldehyde-3-phosphate dehydrogenase||s.c., subcutaneous|
|G-CSF, granulocyte CSF||SCID, severe combined immunodeficiency|
|GDP, guanosine 5'-diphosphate||SD, standard deviation|
|GFP, green fluorescent protein||SDS, sodium dodecyl sulfate|
|GM-CSF, granulocyte-macrophage CSF||SE, standard error|
|GMP, guanosine 5'-monophosphate||SEM, standard error of the mean|
|gp, glycoprotein (e.g., gp100)||SHIP, src homology 2-containing inositol 5' phosphatase|
|GPI, glycosylphosphatidylinositol||SIV, simian immunodeficiency virus|
|GST, glutathione S-transferase||sp. act., specific activity|
|GTP, guanosine 5'-triphosphate||SRBC, sheep red blood cell|
|h, hour (only with numbers)||ss, single-stranded (e.g., ssDNA)|
|H chain, heavy chain||SSC, standard saline citrate|
|H&E, hematoxylin and eosin||STAT, signal transducer and activator of transcription|
|HBSS, Hanks' balanced salt solution||SV40, simian virus 40|
|HEPES, N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid||t1/2, half-life, half-time|
|HIV, human immunodeficiency virus||TAMRA, 5-(and 6)-carboxytetramethylrhodamine|
|HLA, human histocompatibility leukocyte Ag||TAP, transporter associated with Ag processing|
|HPLC, high performance liquid chromatography||TBS, Tris-buffered saline|
|HRP, horseradish peroxidase||TBST, TBS with Tween 20|
|HSV, herpes simplex virus||TCA, trichloroacetic acid|
|HUVEC, human umbilical vein endothelial cell||TCR, T cell receptor for Ag|
|IC50, 50% inhibition/inhibitory concentration||TDP, thymidine 5'-diphosphate|
|ICAM, intercellular adhesion molecule||TdT, terminal deoxynucleotidyltransferase|
|ICOS, inducible costimulator||TGF, transforming growth factor|
|Id, idiotype; idiotypic determinant||Th cell, T helper cell|
|ID50, 50% infective dose or 50% inhibiting dose||TLC, thin layer chromatography|
|IDO, indoleamine 2,3-dioxygenase||TLR, Toll-like receptor|
|IFA, incomplete Freund's adjuvant||TMP, thymidine 5'-monophosphate|
|IFN, interferon (e.g., IFN-γ)||TNF, tumor necrosis factor|
|Ig, immunoglobulin (also IgA, IgD, IgE, IgG, IgM)||TRAIL, TNF-related apoptosis-inducing ligand|
|IgH, Ig heavy chain||Tris, tris(hydroxymethyl)aminomethane|
|IκB or I-κB, inhibitory NF-κB||tRNA, transfer RNA|
|IL, interleukin (e.g., IL-2)||TTP, thymidine 5'-triphosphate|
|i.m., intramuscular||TUNEL, TdT-mediated dUTP nick end labeling|
|IMDM, Iscove's modified Dulbecco's medium||U, unit (only with numbers)|
|IMEM, Iscove's minimal essential medium||UDP, uridine 5'-diphosphate|
|i.p., intraperitoneal||UMP, uridine 5'-monophosphate|
|ITAM, immunoreceptor tyrosine-based activation motif||UTP, uridine 5'-triphosphate|
|ITIM, immunoreceptor tyrosine-based inhibitory motif||UV, ultraviolet|
|IU, international unit||v/v, volume to volume ratio (%)|
|i.v., intravenous||v/w, volume to weight ratio (%)|
|J region, joining region of Ig or T cell receptor for Ag||V region, variable region of Ig|
|JAK or Jak, Janus kinase||VCAM, vascular cell adhesion molecule|
|JNK, c-Jun N-terminal kinase||V(D)J or VDJ, variable diversity joining|
|VLA, very late activation Ag|
|W, watt (only with numbers)|
|WBC, white blood cell|
|wk, week (only with numbers)|
|xid, X-linked immunodeficiency|
|ZAP70, ζ-associated protein 70 (or ζ-chain-associated protein 70)|
- Tables must be numbered with Roman numerals in order of appearance in the text. All tables must have a title. Table legends are prepared as footnotes to the table and are included with the table. Tables must be in DOC file format. Each table should be submitted as a separate file.
- Figure legends must be numbered with Arabic numerals in order of appearance in the text and should include a short title after the figure number. Where possible, symbols and patterns used to distinguish data should be defined in a key placed within the graphic rather than in the figure legend. All figure legends must specify the number of times each experiment was independently performed, as well as the number of animals or replicates in each experimental group. For flow cytometry experiments, authors should specify the gating strategies in the Methods or in the figure legend.
- Figures: At initial submission, please submit low resolution files of the smallest possible file size that will convey the needed information. Smaller files can be downloaded more quickly by reviewers and will hasten the review process. Alternately, single PDF of text plus figures may be submitted at initial submission.
- Color: Color figures must be in the RGB color space.
- File Sizes: Figure files should not exceed 10 MB (average size is about 2 MB).
- Image Sizes: Figures should be submitted in final print publication size (printed 1:1). Figures may be published in print as:
- 1-column wide: 20 picas/ 3.3"/ 8.5 cm
- 1.5 column wide: 30 picas/ 5"/ 12.7 cm
- 2 columns wide: 41.5 picas/ 6.9"/ 17.5 cm.
- The single-column format is preferred. Unless the file size is too large, multi-panel figures should be submitted as a single file.
- Text and Lines: Text within figures must be 6-8 points in size, except for single letter markers, which may be 12 points. Helvetica or Arial should be used for all figure text (except for the use of symbols). Line widths must be greater than one point thick or they will not be visible on the PDF version of the article.
- Numbering: Figures must be numbered to enable reviewers to know the figure number for each figure.
- File Format: Figures should be in TIFF (better for halftone art e.g., blots, photographs) EPS(better for line art or monochrome art, i.e., anything that involves sharply delineated lines), or PDF format. PowerPoint files are not suitable quality, as their resolution is too low for print. Please click here for detailed instructions on converting PowerPoint files to TIFF files.
- Digital Images: All images submitted to The Journal of Immunology must accurately represent the original data. Original data (digital files, autoradiographs, films, etc.) for all experiments should be fully annotated, secured, and retrievable. The original image file (raw data file) should be kept in an unprocessed and non-compressed file format. For figures that are compiled into multi-figure panels, the individual image files should be kept. For additional information, see:
- Digital Images Dos and Don'ts
Although manipulation of images should be kept to an absolute minimum, there are some circumstances when manipulations are necessary. If, however, the quality of an image is too poor to clearly convey the conclusion, the experiment should be repeated.
Figures in manuscripts considered for acceptance will be screened for evidence of inappropriate manipulation. Manuscript acceptance is contingent upon a satisfactory outcome of the screening process. Please adhere to the following guidelines in preparing figures for manuscripts:
- Collecting images: If multiple images are compared to one another, collect each image in the same manner. Any post-collection processing should be applied in a uniform manner to all images. If differences in collection/post-collection are necessary, these need to be described in the legend or in the Materials and Methods section.
- Brightness and Contrast: Adjustments in brightness and contrast should be avoided if possible. If the brightness or contrast of an image needs minor adjustment, the adjustments must not obscure or eliminate any information and must be applied to the entire image. Significant adjustments should not be made. Do not use excessive contrast that removes background. Always note any adjustment in the legend or in the Materials and Methods section.
- Cloning Tools: Images should not be “airbrushed” (with Clone Stamp Tool/Clone Brush) to remove “blemishes”. Do not use cloning tools to insert something into an image from elsewhere.
- Gels/Blots: All gels should contain a positive and a negative control, and a set of molecular weight markers. For Western blots, control panels (actin, GAPDH, etc.) should come from a stripped and re-probed membrane of the experimental blot shown. If this is not possible, the control blots should be derived from the same samples and this should be indicated in the figure legend.
- Cropping: Conservative cropping of gels and blots to improve clarity and conciseness may be permitted if the following points are observed:
- important bands must be retained
- at least several band widths should be retained above and below the cropped band
- cropping must be noted in the legend
- band(s) of interest must be clearly labeled
- molecular weight marker positions should be shown in all gels/blots
- Splicing: Occasionally, images are spliced to rearrange the order of samples for the sake of presentation, such as those in a Western blot. If splicing of data from a single experiment is necessary, draw contrasting (black or white) vertical lines to indicate where the images were joined and state the manipulation in the legend. It would be preferable to re-run the gel so that the order is correct. Images from different experiments should not be spliced to form a new single image.
Cover Art: Cover art is selected from images in accepted articles and changes with each issue of The JI. Authors are encouraged to submit color figures with their manuscripts for possible use as cover illustrations. If an image is selected as cover art, the file must have a resolution of at least 300 dpi at a size of 8.5" x 11".
High-resolution structural data: Any paper submitted to The JI that contains new high-resolution structural data requires an accession number from the Protein Data Bank and assurance that unrestricted release will occur at or before the time of publication. The accession number should be accompanied by the Website address of the databank.
Nucleotide sequences: Sequences of nucleotides or amino acids longer than 50 bases/residues should not be presented in the text or in table form, but rather submitted as a publication-quality figure. Original nucleotide sequences, determined nucleotide sequences encoding reported amino acid sequences, and files of nucleotide sequences derived from high throughput/deep sequencing (RNA-seq, ChIP-seq, MeDIP-seq, etc.) described in the manuscript must be submitted to the appropriate public database (e.g., GenBank, or European Nucleotide Archive) at the time of manuscript submission. Trace and short read sequencing data should be deposited at the NCBI Trace Archives, NCBI SRA or ENA's Sequence Read Archive. An accession number and sequence availability are required at the time of publication. The accession number should be accompanied by the Website address of the databank.
Microarray Data:The JI will not publish descriptive manuscripts that report microarray data, unless such information can be considered of unusual immunological significance and/or include functional experiments that provide novel insight into mechanism. As with other scientific approaches, current experimental, quantitation, verification, and statistical analyses are expected. Microarray experiments should be Minimum Information About a Microarray Experiment (MIAME) compliant. Whereas limited online space may be available for supplemental tables associated with the manuscript, complete microarray data must be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX), and must be accessible without restriction from the date of publication. An entry name or accession number must be included in the paper before publication. The accession number should be accompanied by the Website address of the databank.
Estimating Manuscript Length: One printed page in The JI contains approximately 8,000 characters, including spaces. Thus, an 8 page, Full-Length article would contain approximately 64,000 characters. Each line in a table occupies about 60 characters for a single-column table (120 characters for a double-column table). Figures occupy about 180 characters per centimeter height for single-column figures (360 characters for double-column figures). Determine the total character count for the text of your manuscript and add the character-equivalents for the tables and figures. This will provide a reasonable estimate for the printed length of a manuscript.
Human And Animal Use: All studies involving human subjects must be conducted in accordance with the guidelines of the World Medical Association's Declaration of Helsinki (most recent revision). All animal studies must be performed in compliance with the U.S. Department of Health and Human Services Guide for the Care and Use of Laboratory Animals (or otherwise equivalent guidelines). A statement that human and/or animal studies have been reviewed and approved by an appropriate institutional review committee must be included in the Materials and Methods section of the manuscript.
|CELLS||B Cells||Dendritic Cells||Endothelial Cells|
|Natural Killer Cells||Neutrophils||Stem Cells|
|Stromal Cells||T Cells||T Cells, Cytotoxic|
|Endotoxin Shock||Graft Versus Host Disease||Immunodeficiency Diseases|
|Rheumatoid Arthritis||Systemic Lupus Erythematosus|
|MOLECULES||Acute Phase Reactants||Adhesion Molecules||Antibodies|
|Antigens/Peptides/Epitopes||Autoantibodies||Cell Surface Molecules|
|Cytokines||Fc Receptors||Lipid Mediators|
|Protein Kinases/Phosphatases||Superantigens||T Cell Receptors|
|Cell Activation||Cell Differentiation||Cell Proliferation|
|Cell Trafficking||Chemotaxis||Comparative Immunology/Evolution|
|Repertoire Development||Reproductive Immunology||Signal Transduction|
|Tolerance/Suppression/ Anergy||Transplantation||Tumor Immunity|
|Gene Therapy||Molecular Biology||Transgenic/Knockout Mice|
|Spleen and Lymph Nodes||Thymus|
Style Guide General style conventions: In general, The JI follows Scientific Style and Format: The CSE Manual for Authors, Editors, and Publishers, seventh edition, published by the Council of Science Editors, Inc., in instances where style issues are not directly addressed.
Abbreviations for references:PubMed is the primary source for journal name abbreviations.
- Allergen nomenclature: Nomenclature for allergens should be assigned in cooperation with the IUIS Allergen Sub-Committee. Authors of accepted manuscripts that describe novel allergens will be requested to complete a brief standard form available at IUIS Allergen Nomenclature.
- CD nomenclature: For the purpose of consistency, The JI will follow CD nomenclature. For murine molecules, The JI will follow the nomenclature previously published (J. Immunol. 160: 3861-3868, 1998). For human molecules, standard CD nomenclature will be followed as updated (J. Immunol. 168: 2083-2086, 2002). See also HCDM
- Chemical names: Follow the IUPAC-IUB Commission on Biochemical Nomenclature-Chemical Abstracts or the Chemical Abstracts Guide to Naming and Indexing of Chemical Substances for proper spelling and style of chemical names.
- Chemokine/chemokine receptor nomenclature: The systematic name for chemokines and chemokine receptors should be used. The original name may be given in parenthesis if desired. See Cytokine 21:48-9, 2003.
- Enzyme Nomenclature is The JI source for style and spelling of enzyme names.
- Gene nomenclature for humans: The HUGO guidelines for gene symbols and nomenclature should be used for naming human genes; nomenclature of genome sequence variants should use the Human Genome Variation Society (HGVS) nomenclature, summarized at http://www.hgvs.org/mutnomen/. If commonly found in the literature, alternative nomenclature may be used in addition to HGVS nomenclature. Authors should submit all variants included in a manuscript to the relevant database (e.g. dbVar) for public release if the manuscript is published; the accession number and database URL should be included in the manuscript.
- Gene and strain nomenclature for mice: Mouse Genome Informatics is a reference source for naming mouse genes. A current listing of inbred strains of mice and rats is also available at Mouse Genome Informatics. Authors are also encouraged to deposit their mapping data with the Mouse Genome Database (MGD) before publication and to include the assigned MGD accession numbers in their manuscripts. Information about electronic submission of datasets can be obtained at the Data and Nomenclature Submissions page. Gene symbols should be reserved with MGD in advance of publication.
- HLA nomenclature: HLA nomenclature is updated periodically by the WHO Nomenclature Committee for Factors of the HLA System. Annual comprehensive revisions are published in Human Immunology. See also:EMBL-EBI
- Supporting data that are not essential to understanding the material presented in the manuscript may be submitted with the original paper for peer review; however, the print version of the paper must stand on its own without the supplemental material.
- Supplemental material is primarily intended for short videos, large tables, large sequence alignments, or large data sets. Additional supplemental figures and tables that support the interpretation and conclusions drawn in the manuscript may, however, also be submitted for review with the manuscript.
- Supplemental material must be submitted as separate files from the rest of the manuscript during the online submission; select "Supplemental Data" as the "File Type" when uploading the files.
- Apart from videos, all files must be either PDF or Excel file format; multiple PDF files should be combined into a single PDF file.
- For Cutting Edge manuscripts, no more than two supplemental figures and/or tables may be submitted. One of the two allowable Cutting Edge supplemental items can be a description, no more than one page in length, of computational or bioinformatics methods. Methods that are normally found in the body of the article may not be included in this Cutting Edge supplemental item.
- For Full-Length manuscripts, no more than four supplemental figures and/or tables may be submitted.
- Each supplemental figure should comprise no more than a single 8.5”x11” PDF page, and be large enough to be legible when that page is opened.
- Legends or short explanations must accompany all supplemental figures and videos; no other supplementary text is permitted in full-length manuscripts. Legends should be placed below the corresponding figure in the PDF. Legends for videos should be submitted as a single PDF. Table legends must be prepared as footnotes to the table; all tables must have a title.
*Note: Excel files will be converted to PDFs for the review process only. At publication, the file(s) will be uploaded in the original Excel format.
Videos must be 320 x 480 pixels or smaller for best viewing within a browser. Videos must be no longer than 30 seconds and under 10 MB, with no sound or voice-over. Submit videos in MPG or QuickTime format. Change QuickTime file extensions to ".mov" so that Web browsers will recognize the file type and play the movie. Compress videos as much as possible to help control file size. Name videos by order of citation appearance (e.g., video1.mov). Select "Video" as the "File Type" when uploading the files during online submission. Authors will be notified if problems exist with videos as submitted and will be asked to take responsibility for modifications. No editing will be done to videos at the Editorial Office.
Links to the Supplemental Material will appear in two places in the online journal: in the Table of Contents and in the information box associated with the first page of the full-text article. There will not be any links in the body of the article. In the printed paper, supplemental material will be footnoted the first time mentioned: "The online version of this article contains supplemental material."
Supplemental Materials are posted online as provided by the author.
There is a publication charge of $75 per supplemental figure or table.
Web Links in Submitted Manuscripts: Links to Websites are permitted only if the information contained on the Website is not essential to the understanding and assessment of the manuscript or to the ability to repeat the experiments described in the paper. Web links will not be checked after submission for correctness or functionality; it is the responsibility of the authors to ensure that the web link is correct.
Cutting Edge Manuscripts: Manuscripts submitted to the Cutting Edge section should conform to the General Guidelines for the revised version of Full-Length manuscripts as well as the additional guidelines below:
- Cutting Edge articles, including figures and references, must fit within 5 journal pages. See Estimating Manuscript Length for how to estimate the size of figures and tables and limit the text accordingly. One printed page in The JI contains approximately 8,000 characters, including spaces. Thus, a 5-page Cutting Edge article would contain approximately 40,000 characters.
- The Abstract is limited to 150 words.
- The Materials and Methods section may be sharply limited but should be sufficient to allow the evaluation of results and conclusions.
- Authors may combine the Results and Discussion sections.
Preparation of the Revised Manuscript:
Submit online at ji.msubmit.net. Follow The JI Editorial Office instructions contained in the previous decision letter carefully and thoroughly. A revised manuscript not returned within nine months of the date of the decision letter will be considered a new manuscript and subject to a new, complete review.
Individual manuscript files, files for each figure and table (even if they are unchanged from the previous submission), and a point-by-point reply to all referee comments, must be uploaded to the system. The revised manuscript text must be marked to show changes using yellow highlighting (Microsoft Word files preferred). Do not show deletions, because if the manuscript is accepted, this version will be immediately sent for publication. High-resolution figure files must be submitted. Figures must be in TIFF, EPS, or PDF format and prepared as described under Figures. Authors should retain for themselves copies of all the files in their original formats.
After the manuscript has been checked by journal staff, the Corresponding Author will receive an email acknowledging receipt of the revised manuscript. Please contact [email protected] if you do not receive the acknowledgment email.
Submit online at ji.msubmit.net.
- For the initial submission of Full-Length manuscripts:
- A format-neutral manuscript may be submitted for the first round of review. Manuscripts do not need to be formatted according to The JI guidelines for the initial submission, except that all authors must be listed for each reference. NOTE: Numbering of lines and pages, and easy-to-read figures will make the task of the reviewers and editors easier.
- Either a PDF of the entire manuscript (text, figures and tables), or individual manuscript, figure, and table files may be uploaded to the system. If individual files are uploaded, the system then creates a single PDF for review purposes.
- For Cutting Edge submissions and all revised manuscripts:
- Individual manuscript, high resolution figure, and table files must be uploaded to the system. Authors should save copies for themselves of all the files in their original formats.
- See Author Instructions for online submission requirements.
- See the Figures section for help with preparing digital art.
- The system will ask submitters to designate the Corresponding Author.
- Authors will be offered the option to include their ORCID number.
- Corresponding Authors may utilize this option during submission.
- Contributing Authors should update their "Profile" (at bottom of the home screen, under "General Tasks") with their ORCID number. Then, during submission, the "Find Person" button should be used to enter the Contributing Author (enter "Last Name," then click "Find Person," and select the correct person from the drop down menu); this will pull in the ORCID for the Contributing Author.
- If authors wish to include their ORCID numbers, these must be submitted via the submission system; they CANNOT be added at page proofs.
The Corresponding Author must be the person who has the authority to take responsibility for all obligations related to the manuscript and its submission. These responsibilities include but are not limited to:
- Ensuring the scientific integrity of the submission;
- Confirming that all authors have read and concur with the submission of the manuscript;
- Resolving any authorship disputes;
- Ensuring that all funding sources are listed in a footnote to the title;
- Making unique materials available to qualified investigators;
- Complying with requirements to deposit microarray and other similar datasets in public venues.
- Confirming that any human and/or animal studies have been approved by an appropriate institutional review committee;
- Ensuring that all conflicts of interest or financial interests are listed;
- Confirming that the manuscript is original;
- Confirming that no part of the manuscript has been previously published, submitted elsewhere, or posted on the Internet;
- Ensuring that the manuscript contains no fabrications, fraud, or plagiarism;
- Transferring the copyright interest in the manuscript and all Supplemental Materials to AAI;
- Maintaining/archiving all data related to the manuscript;
- Signing the Submission form and the Publication Charges forms.
Someone other than the Corresponding Author may begin online submission of the manuscript (this person can upload the files and enter all required information). However, the Submission and Publication Charges forms MUST be completed by the Corresponding Author. If the Submitter is not the Corresponding Author, the submission will move from the Submitter's account to the Corresponding Author's account when the Submitter has completed all parts of the submission except the forms, to enable the Corresponding Author to complete the forms.
Please note that the Corresponding Author is the person who receives and responds to communication from the Editor-in-Chief and Editorial Office during the peer-review process. The designation of Corresponding Author does not refer to the person with whom readers may correspond after an article is published.
After the manuscript has been checked by journal staff, the Corresponding Author will receive an email acknowledging receipt of the manuscript. Please contact [email protected] if you do not receive the acknowledgment e-mail.
Submission fees are waived and certain publication fees are reduced for Regular, Associate, Emeritus or Honorary AAI members in good standing at the time of submission and manuscript acceptance, respectively. To review membership qualifications or to join AAI now, click here.
All publication fees are payable in U.S. dollars. Accepted manuscripts are published only upon commitment by the author(s) or institutional financial officer to pay these charges.
Submission Fee: If the corresponding author is not an AAI member*, a nonrefundable fee of $50 per manuscript must be paid by credit card (American Express, MasterCard, or Visa) during the submission process. If payment by credit card is impossible, please contact [email protected] to arrange payment by check (drawn on a U.S. bank). We do not accept cash or purchase orders.
* There is no processing fee for Regular, Associate, Emeritus or Honorary AAI members in good standing.
- $70 per page for up to 8 printed pages in the article
- $175 for each additional page from 9 to 12 pages
- $225 for each additional page over 12 pages
Color Charges: Color figures may include multiple color panels. Within 24 hours of receiving page proofs, authors will be notified of the cost of color reproduction via a link in an email from [email protected] Authors must confirm acceptance of the charges in writing. Authors should expect that color figures in the accepted paper will be reproduced in color and will incur color charges.
Note that AAI members receive a significant discount on color charges.
Non-AAI Members: $600 for each color figure
AAI Members: $300 for each color figure for corresponding authors who are Regular, Associate, Emeritus, or Honorary AAI members in good standing on the date of manuscript acceptance
- $75 per supplemental figure or table
Online Posting Fee: $150 per published article.
Author Choice Option: is available for $2,500 to Corresponding Authors who are Regular, Associate, Emeritus or Honorary AAI members at the time of manuscript acceptance. The Author Choice fee for Corresponding Authors who are not members of AAI is $3,000. The Author Choice fee is in addition to other Publication Fees (such as page charges, color charges, and Supplemental Data charges). More information at Author Choice.
Reprints must be ordered in advance of publication. Within 24 hours of receiving page proofs, authors will receive an email directing them to the author billing system. From this site you will be able to order reprints, view the estimated charges for your upcoming article, and make payments electronically. Reprint orders from noncontributors must be directed to the Editorial Office.
- The Process
- Communication With Authors
- Manuscripts Submitted From The Institution Of An Editor
The Process: By submitting a manuscript to The JI, the authors agree to subject it to the confidential peer-review process. Editors and reviewers are informed that the manuscript must be considered confidential. After a manuscript is received, it is assigned by PhD scientists on staff to a specific Deputy Editor and a Section Editor, whose expertise is considered to be appropriate. The Section Editor prepares a list of expert reviewers, which may include some suggested by the PhD scientists. Authors can indicate specific individuals whom they would like to have excluded as reviewers. Generally, requests to exclude certain potential reviewers will be honored except in fields with a limited number of experts.
All potential reviewers are contacted individually to determine availability. Manuscript files are sent to at least two expert reviewers. Reviewers are asked to complete the review of the manuscript within two weeks and to return a short review form. Based on the reviewers' comments, the Section Editor recommends a course of action and communicates the reviews and recommendations to the Deputy Editor for a final decision.
The Deputy Editor considers the comments made by the reviewers and the recommendation of the Section Editor, selects those comments to be shared with the authors, makes a final decision concerning the manuscript, and prepares the decision letter for signature by the Editor-in-Chief. If revisions of the manuscript are suggested, the Deputy Editor also recommends who should review the revised paper when resubmitted. Authors are informed of the decision by e-mail; appropriate comments from reviewers and editors are appended.
Decisions: There are four categories for initial decisions: accept, accept with minor revision, return for revision, and reject. Some manuscripts are accepted provisionally, pending relatively minor revisions. In this case, the Deputy Editor may conduct the re-review. For many manuscripts, authors are invited to resubmit if revision or additional experimentation can address major criticisms. Typically, one or more reviewers will then be asked to consider the adequacy of the revisions. Cutting Edge papers are allowed only minor revisions because of time constraints. All revised manuscripts are carefully reexamined, and ultimate acceptability is not guaranteed. The JI does not provide for an advance determination of the acceptability of a particular manuscript for publication, nor does it promise expedited review of selected manuscripts.
Communication With Authors: To minimize the possibility of misinterpretation or errors in verbal communication, the Editorial Office will provide information, in writing, only to the corresponding author and will not provide extensive details (e.g., exact status of a review or a predicted time to final decision). Deputy Editors do not take calls from authors concerning decisions or other related matters. All such inquiries should be addressed in writing to the Editor-in-Chief, who will discuss concerns with the Deputy Editor. This policy has been established to provide for uniformity and fairness in addressing concerns about the review process.
Manuscripts Submitted from the Institution of an Editor: Manuscripts submitted from the institution of any Section or Deputy Editor or the Editor-in-Chief are reviewed by other editors from outside that institution. The Editorial Office ensures confidentiality and equity in reviewing all manuscripts.
Rebuttals: If the authors believe that a serious scientific error occurred during the review, a letter of rebuttal may be sent to the Editor-in-Chief, explaining the reasons why the decision should be reconsidered. Letters of rebuttal must be received by the Editor-in-Chief within six weeks of the date the decision letter was sent. When appropriate, the matter will be taken up with the initial Deputy Editor, Section Editor, or additional reviewers. Rebuttals that challenge rejections that were based on priority alone are rarely successful, since the assignment of priority is necessarily a matter of opinion. If the authors of a rejected manuscript are able to make new advances that go far beyond the original submission, they will often expedite consideration of their paper through the submission of a completely new manuscript.
Selection: Selection of reviewers is the responsibility of the Section Editor, although the PhD scientists on staff make recommendations to the Section Editor from a database of individuals who have reviewed manuscripts previously. This database includes self-identified areas of expertise as well as information about the perceived usefulness and timeliness of past reviews. Individuals who consistently have provided tardy or unhelpful reviews are removed from the database. Every effort is made to avoid both real and apparent conflicts of interest with respect to research activities or collaborative or personal interactions. Reviewers are asked to withdraw from considering any manuscript in which they identify a conflict that has escaped the attention of the Section Editor.
Scientific Integrity: Information contained in manuscripts is considered confidential and should not be shared or distributed. If necessary, a reviewer can consult with others for an adequate evaluation of the research findings if all individuals involved maintain confidentiality, objectivity, and avoid conflict of interest. AAI is not responsible for acts and conduct by reviewers that are not in accordance with accepted professional standards. Reviewers are asked to be objective in their evaluations and to judge primarily the novelty and soundness of the information presented.
Anonymity: Although reviews are anonymous, all comments should be capable of withstanding public scrutiny. Except in very unusual circumstances, the identity of the reviewers and Section and Deputy Editors involved in the review of any given manuscript is kept confidential.
The AAI Council, upon recommendation of the Publications Committee, appoints the Editor-in-Chief for a term of five years.Deputy Editors, Section Editors, and Associate Editors are nominated by the Editor-in-Chief and appointed by the Publications Committee. The Editor-in-Chief, the Deputy Editors, and the Section Editors constitute the Editorial Board. Deputy Editors are appointed for variable terms. Section Editors and Associate Editors are appointed for one renewable term of two years in most circumstances. Deputy Editors, Section Editors, and Associate Editors are required to be members of AAI. The Editor-in-Chief is responsible for the specific editorial conduct of The JI. The AAI Publications Committee is responsible for the management and evaluation of The JI and any other official publications of AAI, subject to the general supervision of the AAI Council.
The Journal Of Immunology
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Last Updated 1/10/2017