In VJSTE Research Articles and Reports, the Materials and Methods section is published online so that sufficient detail can be provided to allow replication of the study.  Study design should be described in detail and reagent description should facilitate replication (for example source and purity should be specified, there should be evidence that antibodies have been validated, and cell lines should be authenticated). Statistics must also be comprehensively described as outlined below. VJSTE follows the principles and guidelines for reporting preclinical research available at http://www.nih.gov/about/reporting-preclinical-research.htm. Data must be available either in the main text or Supplementary Material, archived in an approved database (with accession number included in the acknowledgements) (see [data deposition] (data deposition#)). Any concerns about your ability to meet VJSTE 's requirements must be disclosed and discussed with an editor.

 

Statistical Analysis

Generally, authors should describe statistical methods with enough detail to enable a knowledgeable reader with access to the original data to verify the results.

• Data pre-processing steps such as transformations, re-coding, re-scaling, normalization, truncation, and handling of below detectable level readings and outliers should be fully described; any removal or modification of data values must be fully acknowledged and justified.
• Descriptive statistics should be presented for variables that are integral to subsequent analyses and interpretation of the study findings.
• The number of sampled units, N, upon which each reported statistic is based must be stated.
• For continuous variables, distributions should be described using graphical displays such as scatterplots, boxplots, or histograms or by reporting measures of central tendency (e.g., mean or median) and dispersion (e.g., SD, interquartile range).
• For continuous variables that are approximately normally distributed, mean and SD are suitable measures for center and dispersion, respectively.
• For continuous variables with asymmetrical distributions, median and range (or interquartile range) are preferred to mean and SD.
• All measures of central tendency or dispersion that are used should be identified.
• For very small samples sizes (e.g., N < 20), presentation of all data values in tabular format is desirable unless presentation would violate restrictions for privacy or confidentiality for human subjects.
• Units should be supplied for all measurements.
• Methods used for conducting statistical tests (e.g., t-test, Wilcoxon signed rank test, Wald test of regression coefficient) and for constructing confidence intervals (e.g., normal-based 95% CI: mean ± 2SD, likelihood ratio-based interval) should be clearly stated. Mention methods used in the Materials and Methods and then provide the individual test name in the figure legend for each experiment.
• The testing level (alpha) and whether one-sided or two-sided testing was used should be reported for each statistical test; typically two-sided testing is appropriate, but if one-sided testing is used its use should be justified.
• Adjustments made to alpha levels (e.g., Bonferroni correction) or other procedure used to account for multiple testing (e.g., false discovery rate control) should be reported.
• When Bayesian analyses are conducted, any assumptions made for prior distributions must be fully described.
• Sufficient information should be supplied to allow readers to judge whether any assumptions necessary for the validity of statistical approaches (e.g., data are normally distributed, survival data are consistent with proportional hazards in a Cox regression model) have been verified.
• An accounting of missing data values should be provided; if imputed data values are used in statistical analyses, the methods used for imputation should be fully described.
• Novel or highly complex statistical methods or computational algorithms should be adequately described with references supplied to allow readers the opportunity to recreate the calculations; at its discretion, the Journal may require that computer code and data be made available as supplementary information as a condition of publication.

Authors should present results in complete and transparent fashion so that stated conclusions are backed by appropriate statistical evaluation and limitations of the study are frankly discussed.

• Point estimates of population parameters (e.g., mean, correlation coefficient, slope) or comparative measures (e.g., mean difference, odds ratio, hazard ratio) should be accompanied by a measure of uncertainty such as a standard error or a confidence interval.
• Results of each statistical test should be reported in full with the value of the test statistic and p-value, and not simply reported as significant or non-significant; more than two significant digits on p-values are usually not needed except in situations of extreme multiple testing such as in genetic association studies where stringent corrections for multiple testing might be used.
• Any results that are reported to constitute a blinded, independent validation of a statistical model (or mathematical classifier or predictor) must be accompanied by a detailed explanation that includes: 1) specification of the exact “locked down” form of the model, including all data processing steps, algorithm for calculating the model output, and any cutpoints that might be applied to the model output for final classification, 2) date on which the model or predictor was fully locked down in exactly the form described, 3) name of the individual(s) who maintained the blinded data and oversaw the evaluation (e.g., honest broker), 4) statement of assurance that no modifications, additions, or exclusion were made to the validation data set from the point at which the model was locked down and that neither the validation data nor any subset of it had ever been used to assess or refine the model being tested.

 

Reporting Guidelines

Authors are encouraged to follow published standard reporting guidelines for the study discipline. A chart providing links to major biomedical research reporting guidelines is available at the [U.S. National Library of Medicine] (http://www.nlm.nih.gov/services/research_report_guide.html). Other guidelines may be found at the relevant society website, for example the American Chemical Society gives standards for the characterization of organic and inorganic molecular compounds http://pubs.acs.org/page/jacsat/submission/org_character.html.

 

Guidelines for Specific Types of Studies

Human subjects research: Informed consent must be obtained for studies on humans after the nature and possible consequences of the studies are explained. A statement that informed consent was obtained must also appear in the manuscript. All research on humans must have approval from the institutional IRB (Institutional Review Board) or an equivalent body. The editors reserve the right to request IRB documents associated with a particular paper.

Clinical trials:

A CONSORT Statement. [CONSORT] (http://www.consort-statement.org/consort-2010) includes recommendations, a checklist of items that should be included in a comprehensive report, and a participant flow diagram. The recommended checklist should be completed and provided at the time of manuscript submission. The recommended trial flow diagram may be presented as a figure (usually Fig. 1). Reports of randomized controlled trials that do not conform to the CONSORT guidelines may be returned to authors for revision prior to formal review.
Registration of clinical trials. Clinical trials should generally be registered in accordance with the criteria outlined by the [International Committee of Medical Journal Editors ] (http://www.icmje.org/), including the June 2007 update. Authors should provide the trial registration number in the Acknowledgements section and provide a link to the trial registration, to be cited as a reference.

Biomarker studies: Putative biomarkers must be evaluated with an independent validation set. Reports of unvalidated biomarkers will only be considered in the context of a clear experimental, mechanistic connection to disease or other unique contribution to understanding of disease or clinical practice. A statement should be included in all biomarker papers describing how overfitting (training models on large numbers of variables measured on small numbers of subjects) and other forms of bias were avoided. We strongly recommend all papers reporting potential new biomarkers be evaluated by an independent statistician before submission.

Modeling studies: Computational models should be validated either experimentally or through a dataset independent of the training set. All assumptions should be clearly stated with sources provided in the references and notes section. The code/algorithm used for the study must be included as a file in the Supplementary Materials to allow replication of the results by interested readers.

Animal studies: For all animal experimentation described in the manuscript, VJSTE requires that authors state in the Methods section their adherence to the [NIH Guide for the Care and Use of Laboratory Animals] (http://oacu.od.nih.gov/regs/guide/guide.pdf), or the equivalent.

Genetically modified animals. To avoid confounding effects of inbred strain background, littermate controls should generally be used, although exceptions may be allowed. Justification for other control animals should be included. Authors should fully describe the source of their animals and number of times backcrosses were performed.

 

Describing new taxa

Algal, Fungal, and Botanical Names: Since January 2012, electronic publication of algal, fungal, and botanical names has been a valid form of publication. Manuscripts containing new taxon names or other nomenclatural acts must follow the guidelines set by the International Code of Nomenclature for algae, fungi, and plants. Further helpful information by Sandra Knapp et al. is available here.

Authors describing new fungal taxa should register the names with a recognized repository, such as Mycobank, and request a unique digital identifier which should be included in the published article.

Zoological Names: Since January 2012, electronic publication of zoological names has been a valid form of publication if certain conditions are met. Manuscripts containing new taxon names or other nomenclatural acts must follow the guidelines set by the International Commission on Zoological Nomenclature. We require the new taxon name and the article it is published in to be registered with ZooBank. The unique identifier provided by ZooBank should be included in the published article. Authors will be able to update ZooBank with the final citation following publication. Further helpful information by Frank-T. Krell is available here.

Bacterial Names: In accordance with the International Code of Nomenclature of Prokaryotes (ICNP) effective publication of new prokaryotic names in electronic journals is possible. In order to comply with rules of the International Committee on Systematics of Prokaryotes (ICSP) for valid publication authors must submit a copy of the published article in its final form, together with certificates of deposition of the type strain (for unrestricted distribution), in at least two internationally recognized, publicly accessible culture collections located in different countries, to the International Journal of Systematic and Evolutionary Microbiology (IJSEM) editorial office. Following review by the List Editor, effectively published names that conform to all of the rules of the ICNP will appear on a subsequent Validation List, in the order received, thereby becoming validly published.

Virus Names: The proposal of new virus names must follow the guidelines established by the International Committee on Taxonomy of Viruses (ICTV) in the International Code of Virus Classification and Nomenclature. Proposals for new virus taxa should be forwarded to the relevant Study Group of the ICTV for consideration.