Production Guidelines

October 2008
A. When an article is accepted

1. Pre-production files
1.1 Messages received by Production Office:
As soon as an article is accepted, 3 different messages are sent to the Frontiers Production Office
- production.ofice@frontiersin.org
- password: frontiers08

1.1.1 Frontiers Article Accepted

This is the copy of the message received by the author:

Dear Prof. Paul Manger,

I am very pleased to inform you that your article was accepted for publication.
Title: Is 21st Century Neuroscience too Focussed on the Rat/Mouse Model of Brain Function and
Dysfunction?
Authors: Paul Manger, Jessica Cort, Naseem Ebrahim, Adelaya Goodman, Justine Henning,
Mohamed Karolia, Stacey-Lee Rodrigues, Goran Strkalj
Edited by: Patrick R. Hof
Submitted on: Tue, Aug-19-2008
Interactive Review Started on: Sep 02, 2008
Article Accepted on: Mon, Oct-06-2008
Please proceed with the payment of the publication fee by entering the Review Forum of your article
and clicking on «Pay Publication Fee». As soon as this is completed, your article will be forwarded
to the Publication Team.
Please login to your Frontiers account and select «For Authors => Accepted Articles.
Alternatively, you may also click the url as provided below to directly access the review forum for
your article and view/download a PDF invoice.
http://admin.frontiersin.org/neuroscience/directURL.do?directURLId=KWjfBiOuJUaR6avB9O0X6
EkYuEVwSuGfKLUQtd7sygXQ5ZUoMe
Website: www.frontiersin.org/neuroscience
Your username: paul.manger@wits.ac.
Your password: OpOC2dm8sP
With best regards,

Dr. Patrick R. Hof

Associate Editor, Frontiers in Neuroanatomy
www.frontiersin.org/neuroscience
*********************************
Where do I submit the publishing fees?
1. Log into your Frontiers account.
2. Select «For Authors» => «Accepted Articles» => «Enter Review Forum»
3. Select «Pay Publication Fees»

2 | Production Instruction | Oct 2008

 4. Proceed with the Paypal Instructions.
You will receive an automatic notification of the successful transfer. If you encounter problems,
please contact support@frontiersin.org.

Important information to take from this e-mail are:

• Name of the corresponding author
• List of authors
• Title of the article
• username and password of the corresponding author

1.1.2 [Paper Accepted Alert] Files status on FTP server

Dear,
An article has been accepted.
Journal :
Frontiers in Neuroanatomy
Article Title :
Is 21st Century Neuroscience too Focussed on the Rat/Mouse Model of Brain Function and
Dysfunction?
Authors :
Paul Manger,Jessica Cort,Naseem Ebrahim,Adelaya Goodman,Justine Henning,Mohamed
Karolia,Stacey-Lee Rodrigues,Goran Strkalj
Files upload status :
Number of files uploaded :
5 including one zip file.
Number of files the Zip File contains :
7
which includs Meta, PDF, Source, Figures and Data Files file.
Files uploaded at :
0_AcceptedArticles/10.3389_neuro.05_005.2008_Manger
Regards,
Frontiers Team

This functionnality is not available yet.

Please do not take this e-mail into account

1.1.3 <no subject>

“ <production.office@frontiersin.org>
Subject: Frontiers Article for Publication
Mime-Version: 1.0
Content-Type: multipart/mixed;
boundary=”----=_Part_5120_22876900.1223304379578”

www.frontiersin.org 3
 ------=_Part_5120_22876900.1223304379578
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

The following article has been accepted for publication. Please start the p=
reparation of the metafiles. Please note that only after you receive the pa=
yment notification for this article, it should be sent out for production.

You can download source, PDF files and high resolution images for the artic=
le from ftp://ftp.frontiersin.org/.

Title: Is 21st Century Neuroscience too Focussed on the Rat/Mouse Model of =

Brain Function and Dysfunction?=20
Authors: Paul Manger, Jessica Cort, Naseem Ebrahim, Adelaya Goodman, Justin=
e Henning, Mohamed Karolia, Stacey-Lee Rodrigues, Goran Strkalj
Submitted on: Tue, Aug-19-2008
Submitted to: Frontiers in Neuroanatomy=20
Edited by: Patrick R. Hof

This e-mail contains also the 2 review reports.

Please note that this e-mail contains a lot of bugs and is not useful for production..
Furthermore, for the moment, we do send the articles for production even before payment.

1.2 Collecting the production files

Here is the list of documents needed for the production of articles:

The .pdf of the manuscript

Please check that the figures are inserted in the text and that no part of the text is bold, underlined or
highlighted.

The source file

.doc file (exceptionally .tex: LaTex files) of the manuscript from which the pdf was made
Please remove all style in the text if necessary (bold, highlight, color, underline, etc...) and accept track
changes if they still appear.
If such changes had to be done, then please remake the pdf from the corrected source file.

Figures
All figures must be named properly (Figure 1, Figure 2, etc...).
Please open each figure with Adobe Photoshop and check the fgure resolution.
(Image > Image size)
Pay attention to the text in figures. It should be arial regular and should not be smaller than 8 pt text.
The letters should not be stair-stepped or blurred.
All figures must conform to the Frontiers Guidelines. Please refer to the table below.

4 | Production Instruction | Oct 2008

 Frontiers Image Specifications
All Images Must be Submitted At or Above Intended Display Size
Color Minimum
Image Type Description Example Format
Mode Resolution

An image composed
of lines and text, eps
900 - 1200
Line Art: which does not tif RGB
contain tonal or
dpi
jpg
shaded areas

A continuous tone eps

Halftone: photograph, which tif RGB 300 dpi
contains no text jpg

Image contains eps

500 – 900
Combination: halftone + text or line tif RGB
art elements
dpi
jpg

If any of these requirement is not met, then please contact the corresponding author and ask him for higher
quality figures. Please refer to the following section for author correspondence.

Tables
All tables must be named properly (Table 1, Table 2, etc...).
Figure can either be sent in .doc or as an image. They will be redrawn by the Typesetter so they just need to be
readable by these people.

Metafiles
• Please go to http://db.frontiersin.org/phpMyAdmin/
- login: metafiles
- password: metafiles
• go to finsDB (on the left menu)
• select the tab SQL
a) Paper ID
• copy the following request:
set @title = ‘%Copy the title of the paper here%’;
select p.paperId, p.title, concat(u.firstName, ‘ ‘,u.lastName) Author, dateAccepted, j.name Journal
from Paper p, Scientist s, Journal j, Users u where p.title like @title and p.correspondenceAuthor =
s.scientistId and s.userId = u.userId and p.journalId= j.journalId
• Copy the title of the article where it is mentionned

www.frontiersin.org 5
• click Go
This query will provide you the ID number of the article.
a) Metafile
• copy the following query
select distinct j.ISSN “Journal ISSN”,j.name “Journal Name”, j.shortName “Journal short name” ,
j.journalAbbreviation “4-5 letter Journal name abbreviation”,
SUBSTRING_INDEX(j.DOI,’.’,-1) “Journal Number”, p.DOI DOI, 2 Volume ,
if(p.journalId = 1, SUBSTRING(SUBSTRING_INDEX(p.DOI,’.’,-2),1,3),
SUBSTRING(SUBSTRING_INDEX(p.DOI,’/’,-1),1,3)) “Article Sequence Number”,
if(p.journalId = 1, ‘ continuous, determined by DOI sequence’,’ Always start with page 1.’)
Pagination,
‘Frontiers Research Foundation’ as “Journal Publisher”, ‘Neuroscience’ Subject,
case(p.submissionType) when 1 then ‘Original Research Article’
when 2 then ‘Perspective Article’
when 3 then ‘Hypothesis and Theory Article’
when 4 then ‘Focused Review Article’ end “Article Type”,
concat(p.title, ‘\n\n In case of doubt always use the title from the Manuscript.’) Title,
p.runningTitle “Running Title”,
Trim(Group_Concat(Distinct Concat(pa.firstName, ‘ ‘, IfNull(Concat(pa.middleName, ‘. ‘), ‘’),
pa.lastName, ‘\n’)
Order By pa.paperAuthorId Separator ‘\n ‘)) “Author List (remove all street addresses and zip code
information from the affiliation information)”,
concat(u2.firstName, ‘ ‘,IfNull(concat(u2.middleName, ‘. ‘),’’), u2.lastName, ‘, ‘,
Group_Concat(distinct af.institute,’, ‘,af.country separator ‘; ‘))
“Edited By (entire name, university, country)”,
if(editorIsReferee = ‘Y’, concat(Trim(Group_Concat(Distinct concat(u.firstName, ‘ ‘,
IfNull(concat(u.middleName , ‘. ‘),’’), u.lastName,
‘, ‘, refAff.institute, ‘, ‘,refAff.country, ‘; ‘)
Order by pr.paperRefereeId Separator ‘\n\n’ )),concat(u2.firstName, ‘ ‘,IfNull(concat(u2.
middleName, ‘. ‘),’’), u2.lastName, ‘, ‘,
Group_Concat(distinct af.institute,’, ‘,af.country separator ‘; ‘))), Trim(Group_Concat(Distinct
concat(u.firstName, ‘ ‘, IfNull(concat(u.middleName , ‘. ‘),’’), u.lastName,
‘, ‘, refAff.institute, ‘, ‘,refAff.country, ‘; ‘)
Order by pr.paperRefereeId Separator ‘\n\n’ ))) “Reviewed by (entire name, universtiy, country)”,
date_format(p.dateSubmitted,’%d/%m/%Y’) Received, date_format(ps.dateOpenReviewStarted,’%
d/%m/%Y’) “Paper Pending Published”,
date_format(p.dateAccepted,’%d/%m/%Y’) Accepted, IfNull(date_format(p.
datePublished,’%d/%m/%Y’) ,’ Please insert date of final proof.’) Published,
p.correspondenceString Correspondence
from Paper p left outer join PaperReferee pr on p.paperId = pr.paperId and pr.status = ‘A’ and
pr.assignmentAcceptance = ‘Y’
left outer join Scientist s on pr.scientistId = s.scientistId
left outer join Users u on u.userId = s.userId

6 | Production Instruction | Oct 2008

 left outer join PaperAuthor pa on pa.paperId=p.paperId
left outer join Scientist s1 on pa.scientistId = s1.scientistId
left outer join Users u1 on s1.userId = u1.userId
left outer join Affiliation refAff on refAff.scientistId = pr.scientistId,
Scientist s2, Users u2, Journal j, Affiliation af, PaperStatus ps, Users cor, Users sub, Scientist scor,
Scientist ssub
where p.editorId = s2.scientistId
and s2.userId = u2.userId
and p.journalId = j.journalId
and s2.scientistId = af.scientistId
and p.paperId = ps.paperId
and sub.userId = ssub.userId
and ssub.scientistId = p.submittedBy
and cor.userId = scor.userId
and scor.scientistId = p.correspondenceAuthor

and p.paperId in (Insert paper ID)

group by p.paperId
order by p.journalId, p.DOI;
• Insert the paper ID where it is mentionned
• click Go
• Then click Export
• Select “Microsoft Excel 2000”, “Put fields names in the first row”
• Select “Save as file” and use the last name of the corresponding author for file naming
• For compression, select “None”
• click Go
This document needs to be formatted.
Please select the «Wrap text» option, draw borders to the cells and shade the title row in blue.
All information need to be checked and sometimes corrected:
• Insure that all information about the journal are coherent (ISSN, Full Name, Short Name, Abbre-
viation and Journal Number
• The DOI needs to be written as following:
- 10.3389/neuro.AA.BBB.YYYY
- AA is the Journal Number
- BBB is the article sequence number
- YYYY is the year of publication
- Please replace the second slash “/” (between AA and BBB) by a dot ”.” like in the example
• The volume number depends on the year of publication.
Volume 1 = 2007; Volume 2 = 2008; etc... for all journals except for Frontiers in Molecular
Neuroscience, Frontiers in Neuroenergetics and Frontiers in Neuroengineering, for which
Volume 1 = 2008

www.frontiersin.org 7
 • Then Volume and Article sequence number must be consistent with the DOI number.
• The pagination is “Always starts with page 1” for Tier 1 articles and “continuous, determined by
DOI sequence” for Tier 2 articles
• The publisher is Frontiers Research Foundation
• The subjct and article type are specified
• Title and Running Title must be cross-checked with the manuscript. In case of doubt, please al-
ways conform to the final manuscript.
• Author list must be cross-checked with the final manuscript. After each name, please insert affilia-
tion given in the manuscript. Please spare street names and zip codes:
i.e. Institute, University, City, Country
• Please check Editor and Reviewers names and affiliations. If any name is missing, please ask the
editorial office to provide the name and find the affiliation on the internet.
• The corresponding address should contain the name of the corresponding author, detailed address
and an e-mail address. Please conform with the address provided in the final manuscipt

1.3 Sending the production files

All the files must be stored in a folder with a proper name, based on the DOI number and the corresponding
author name: neuro.AA_BBB.YYYY_Name
example: neuro.09_005.2008_Olsson
This folder must be compressed and put on the ftp server in the folder 2_Production.
Please create a new folder, using the date for naming: YYMMDD (081203 on the 3rd of December 2008)
Please send an e-mail to Murali from Scope at murali@scopeknowledge.com in order to tell him that a new
article entered the production pipeline.

New article(s) for production

Dear Murali,

Please find the production files of (Name)’s article at the following location:
ftp://ftp.frontiersin.org/Alfresco/FTP/2_Production/YYMMDD/10.3389_neuro.AA_BBB.YYYY_
Name.zip

(Here you can detail the problems that Scope could encounter during the production process, such as
quality of the figure, order of the figures, figure missing that the author will soon provide, etc...)

With best regards

(Signature)

2. Provisional PDF
Please make the provisional PDF of the article by combining the Provisional PDF front page of the
particular journal in which the article was submitted and the PDF of the manuscript downloaded on
the Review Forum.
Please name this file as following: Provisional_neuro.AA_BBB.YYYY_Name
Please see the section 5 below for uploading the Provisional PDF on the website.

8 | Production Instruction | Oct 2008

3. Author Proof
Scope processes the production files and sends the author proof to both Frontiers Production Office and
corresponding author. Please write the batch number (e.g. 081203), the date of reception and the size of the
file on the printed proof.
All lines are numbered and they write queries to Author and/or Publisher at the end of the article.
There are several things to check on this proof, please refer to the list below:
• Title, running title, author names and affiliations must be consistent with the fnal manuscript
• Affiliations of the editor and reviewer must be listed as te following:
Name, University, city, Country.
• The name of the journal is consistent throughout the article (logo, citation, footers)
• The dates must be consistent throughout the article (accepted, citation, copyright, footers)
• The dates, corresponding address are consistent with the metafile and/or the manuscript
• The date (Month Year, volume and article sequence numbers) are correct
• Only the first letter of the title and the running title are capitalized (except for special names or abbrevia-
tions)
• All keywords are low case (except for special names or abbreviations)
• For Original Research Articles, first level headings are the following:
Introduction
Materials and Methods
Results
Discussion
Conflict of Interest Statement
Acknowledgements
References
• First sentence of figures and tables captions is bold. Maths formulas are in serif font in captions.
• Figure panels labels are capital letters bold, italic and in brackets in the caption; They are capital letters,
arial and bold with a consistent size in the figure.
Please also check the sequencing of the figures. Figure must appear in the same order as they are cited in the
text.
You can also make some suggestion about the figure size and position of the figures.

Please write your comments in a word document as the following example and send them as an attached
document to an e-mail to Murali.

www.frontiersin.org 9
Batch-YYMMDD_FrontiersComments.doc

Frontiers Feedback

General Comment:

1) Name: Mel Slater

File Name: fnhum-02-006
DOI: 10.3389/neuro.09.006.2008

Comments:
a) Comment 1
b) Comment 2
etc...

2) Name: Jonathan Nissanov

File Name: fninf-02-003
DOI: 10.3389/neuro.11.003.2008

Comments:
a) Comment 1
b) Comment 2
etc...

3) etc...

4. Publisher Proof
Scope incorporates Frontiers Comments and Author comments and corrections to the Author Proof. THen
they send the Publisher Proof to Frontiers Production Office.
Please write the batch number (e.g. 081203), the date of reception and the size of the file on the printed proof.
Then check if all the corrections were made.
If everything is fine, please send an e-mail to Murali at Scope for them to start the production of HTML and
XML files for this article.

5. HTML files
HTML files are sent in a zip file. Please unzip it and check that all figures, and HTML file are present.
and must be uploaded in a zip file

6. XML for PubMed

7. Uploading the files on the website

• Go to http://www.frontiersin.org/my/

10 | Production Instruction | Oct 2008

 - login: author
- password: author
• Select PAPERS > Edit Paper Links
• Select the Journal
• Select the article for which you want to upload the file
• Select the file on your computer
• Selcect the type of document you are uploading
• Click Upload Files
• Check on the main website if the correct file has been uploaded

8. Abstract Management Screen (AMS)

This screen allows you to make the correction needed on the Abstract pages.
• Go to http://www.frontiersin.org/my/
- login: author
- password: author
• Select PAPERS > Search/Edit Article
• Search the paper you want to make correct
• Edit the article
• Then Edit the fields you want to correct and click save for each
• Add the volume number and the publication date
• NEVER CHANGE THE DOI NUMBER, in case of need, please contact IT team.
• Please note that DOI number is written with a slash instead of a dot (e.g. 0.3389/neuro.09/014.2008) but it
will be displayed properly o the abstract page
• Click Preview and Save
• Click Save Changes
• Check on the main website if the abstract page has been corrected
• If you encounter any problems, please contact Adil on JIRA by writing a new Issue in Frontier Public
Portal

9. DOI number and CrossRef

Each publication is referenced by a DOI number (please see the metafile section above). It allows anyone to
reach the abstract page of an article by knowing only this number.
Each DOI number must be registered at CrossRef following the instructions below.
• Go to http://www.crossref.org/webDeposit/
• Fill the form properly, the following fields have to be filled:
-- Name of the Journal
-- Abbreviated name of the Journal
-- Electronic ISSN number (and both print and electronic one for fnins)

www.frontiersin.org 11
 -- Volume number (and Issue numner for fnins)
-- Year
• Click Add Articles and continue to fill the form:
-- Title of the article
-- First name and last name of the first author (often different from the corresponding
author)
-- DOI number
-- URL
-- Page numbers for fnins
• If you need to register DOI numbers for the same journal, please click “Add Another Article”
• When all DOI numbers have been registered, please click “Finish”
-- Username: fron
-- Password: fron905
-- select “send XML”
-- enter production.office@frontiersin.org

12 | Production Instruction | Oct 2008