Basic instructions

Please follow the instructions in the below order:

1. To start, click [Proceed] to go to the proof page.
2. In the proof page, a Tracker window listing all the Edits made by the Copy-Editor will be displayed. Click on each Edit to get a [Click For Details] button. Accept/Reject options (as a tool-tip) will be available under this view. In case you do not agree with a change, press [Reject the change] button. This will revert the change to the author’s version. Additionally, if you need to hide the tracker window, you may do so by disabling the [Tracking Changes] button available at the top panel.
3. Click [Compile] to compile your TEX file once to sync the TEX and PDF.
4. The queries added by the Typesetter/Copy-Editor is listed under the [Queries to Author] tab in the bottom panel. You need to go through each of the queries and add your comments/responses in the [Reply] field.
5. Your document will be saved everytime you press [Save] button or as and when you compile the document.
6. In case of any comments, use [F7] or click on the specific line number to insert inline comments within the TEX source itself. If there are generic comments, please use [Additional Comments] tab.
7. Changes made by you in the document can be seen in the tracker available under [Source Comparison] tab. It is always recommended that you go through it once before submitting the corrections. Use [Upload] tab to upload any additional documents.
8. After all the corrections are made, click [Submit] for final submission. Before submitting the changed document, make sure all queries under [Queries to Author] tab are responded to.
9. Note that once your corrections have been submitted, your article is finalized and any further correction is no longer possible.
10. Another important point to be noted is that the author should restrict from editing certain fields in the document. These include:

         \documentclass[fleqn,s1,tex,nogcns]{neptune}
         \usepackage[5.5]{neptune-els-dtd}
         \stmchangemodel{stmjnl}{5GeSdc}
         \bookindate{2018-12-01}
         \proofdate{2018-12-01}
         \usepackage[cas]{neptune-els}
    

    Also, care should be taken to ensure that the query commands in the document are not deleted even if the particular queries have been responded to. Such commands will be in the format, for example:

         \QUERY[1][a]{}
         \QUERY[4][no={71}]{}
    

Features

Menu

The editor menu

The following explanation corresponds to each tab or item or button from left to right and on a row by row basis.

• Article: Clicking this tab will load the copy-edited author source on the left side and the corresponding PDF on the right side. This is the default state when a user lands at NEPTUNE (Screenshot).
• Source Comparison: Click this tab (middle) to load pre-author-edited version, post-author-edited version (right) and a tracker window (left) listing only author made changes which are hyperlinked to the edited source document (Screenshot).
• PDF Comparison: Click this tab to load the PDF generated from copy-edited sources on the left and the PDF generated from author edited sources on the right. This would provide the authors a chance to compare the changes made by them (Screenshot).
• Track Changes: This button (ON by default) when turned off, will hide the tracker window.
• Undo: Undo a change.
• Redo: Redo a change.
• Find & Replace: Find/Replace a string.
• Go to line: By providing the line number in the adjacent box and clicking this button, you will be taken to the corresponding line number in the text editor.
• Save: As the name indicates, click to save the edited document. Changes will be auto-saved on compilation.
• Compile: Click to compile the edited document to generate PDF.

Output viewer menu

• Version History: Clicking on this item provides the author the option to save the active file to a version control system and reload it at will.
• Help: By clicking on this item, the author can choose between a help document or a video tutorial explaining all menu items and elaborating on the features and editing procedures of NEPTUNE.
• Submit: Submit the edited document once all the edits are done. All the queries should be resolved before submitting. If not, NEPTUNE will not allow this task. Upon submission, no further changes will be allowed on the document.
• Sign Out: Leave NEPTUNE.
• Buttons (white row): The buttons are standard and are explained in sequential order from left to right: bookmarks; search string in PDF; previous page; next page; go to page; zoom out; zoom in; view menu; fullscreen; print; download; current view; tools menu. All buttons have tooltip explaining functionality.

Screenshot of cursor location in PDF

In the PDF window, you can see a red bullet blinking which corresponds to the cursor location in the source document. The red circle will remain in the PDF window for five seconds and will disappear.

For navigating from PDF to source, click on the desired line in the PDF for the corresponding line in the text editor window to be highlighted.

This screenshot shows the tracker window at left, source file in the middle and PDF output in the right.

Author notes, requests, comments, etc.

NEPTUNE provides the facility to add a note, instruction, request, comment or anything of that sort to any location in the document. The user can insert a note or a similar object simply by clicking the line number in the left margin of the document source. A small text-area window will pop up, where the user can enter text. Click the [Comment] button once done.

Here is the screenshot of notes in action:

Log

Clicking Log button in the bottom menu, the user can launch log window which provides a variety of logs generated during TEX’s compilation process. The log window has five buttons that are explained below:

• Ignore Compilation Errors: Switch this button on to ignore compilation errors so that TEX will enter non-stop compilation mode.
• Summary: A quick summary in an easy format. This is the default.
• Detailed: A full and detailed log of a LATEX run for exhaustive debugging.
• Aux: Click this to view the .aux created during compilation. This .aux file has ref/citation info.
• Safe Clean: Click this to remove all temporary files generated in previous run of TEX.
• Hide: Click to hide the expanded log window to its original state.

Screenshot of Log window expanded

Query

Queries to Author window provides a list of queries directed towards the author that needs to be resolved before finishing the editing job. The number of queries that the author has responded to against the total number of queries is displayed alongside the [Queries to Author] tab. Clicking on the query will take you to the corresponding location in the document source. Additional space is provided in the Reply field where you can enter your comments pertaining to each query.

Some of the queries addressed to the author will be boolean queries where the author has to provide his response from Yes or No options. Below is a screenshot of a highlighted boolean query.

File upload

By selecting the [Upload Files] tab from the bottom panel and clicking on the [Select Files to Upload] button, the user can upload input TEX files, graphic materials, zip files etc. to NEPTUNE.

With appropriate edits or changes in the author source, these files can be accessed immediately and the results introduced in the output for instant verification. In case a biography photo is uploaded, it will be automatically resized to the appropriate specifications.

Screenshot of Pre/Post-edited Sources

Screenshot of Pre-/post-edited PDFs

General editing

There is nothing special to say about general editing of text. The usual text attributes like bold (\textbf{...}), italics (\emph{...} or \textit{...}) and small-caps (\textsc{...}); font attributes like sans serif (\textsf{...}), fixed width font (\texttt{...}); size changing commands like \large, \small, \footnotesize, and the like will work as one would expect. A blank line will insert a para token.

In short, all standard commands in general text manipulations work fine without any surprises.

Frontmatter

If the given name and surname has one name each, then, you can straight away enter the names as given below. Firstname will be treated as Firstname and Surname will be treated as Surname.

  \author[1]{Firstname Surname}
  \author[1]{John Hopper} %% Surname is ‘Hopper’

However if Surname has two or more names in it, you have to group the Surname as given in the below example:

  \author[1]{Firstname {Surname1 Surname2}}
  \author[1]{John {Riley Hopper}} %% Surname is ‘Riley Hopper’

Edit heading levels

For inserting a new section or any other sectional heading, standard LATEX commands can be used. An example of the code is provided in the below verbatim:

\section{A New Section}
 \xlabel{sec30}
 Using standard \LaTeX{} commands, one can create a
 new section while editing a document in Neptune.
\subsection{A subsection heading}
 \xlabel{sec30a}
 Look at this new subsection. It’s counter is auto-generated.
 You might refer the previous section like this. See \xref{sec30}.

By clicking on the tab PDF Comparison in the main menu bar, the author can load both the PDFs from pre- and post-edited LATEX sources in the left and right sides of NEPTUNE window. Authors can check if their changes have correctly been reflected in the final versions.

Slightly modified \xlabel{...} is used in place of \label{...} with the same functionality. In the same vein, \xref{...} takes the role of \ref{...}. The cross-ref command, \xref{...} accepts more than one label as its argument and the output will be sorted and compressed if needed.

As you’re aware, two TEX runs are needed to fix cross-references to newly inserted objects correctly. You might see the output below:

Screenshot of inserted headings.

Lists

enumitem package is loaded by default, hence all options of enumitem work fine with NEPTUNE.

 \begin{enumerate}[<options>]
   \item ...
   \item ...
   \item ...
 \end{enumerate}

is an example of how an enumerated list will look like. Similarly, itemize and description lists can be used.

The most useful option in an enumerate list is to change the list label to suit one’s requirement. Following enumerated list label options are supported:

• label={<label choice>} ⟹ Add custom label. The possible labels are:
  • \arabic* ⟹ provides arabic number.
  • \alph* ⟹ provides lower alpha label.
  • \Alph* ⟹ provides upper alpha label.
  • \roman* ⟹ provides lower Roman numeral.
  • \Roman* ⟹ provides upper Roman numeral.
• l={<label>} ⟹ is a shortcut for the above options with possible label values:
  • 1 or 1. or 1) or (1) ⟹ arabic numeral.
  • a or a. or a) or (a) ⟹ lower alpha labels.
  • A or A. or A) or (A) ⟹ upper alpha labels.
  • i or i. or i) or (i) ⟹ lower Roman numeral.
  • I or I. or I) or (I) ⟹ upper Roman numeral.

Example

\begin{enumerate}[label={(\alph*)}]  or [l={(a)}]
  \item Case of a complex root ...
  \para Next para ....
  \item Convergence but not complex root ...
\end{enumerate}

Output

(a) Case of a complex root ...
    Next para ....
(b) Convergence but not complex root ...

Theorems and similar environments

All the theorem creating commands in LATEX will work correctly and can be used in NEPTUNE.

However, there are three more commands to create theorem like environments:

• \newdefinition: creates a theorem like environment; the key difference is that the statement font is upright, unlike italic in the standard theorem. All the options in the theorem will work here too.
• \newproof: creates a Proof environment with no counters and with upright font.
• \newitproof: is similar to \newproof, the only difference being the font is in italic shape.

Math

All the standard math commands in LATEX will work fine and can be used in NEPTUNE. Inline math commands ($ and \(/\)) have the very same functionality without any differences.

The displayed equation environments of $$, \[/\], {equation}, {eqnarray}, {align}, {gather}, {aligned}, {gathered}, {alignat}, {multline}, and all their starred variants have the very same functionality. Various kinds of fractions, square roots, matrices and commutative diagrams of amsmath can also be used without any fear of misfiring.

The functionality associated with complex math commands derived from xypic, tikz, and the like will also work fine, provided the packages are loaded in the preamble of the document if not done previously.

However, a small change that has been introduced to augment XML generation from newly inserted author code is the change of \label{...} to \xlabel{...}. A few examples are given hereunder:

For single line displayed equation, the syntax is:

    \begin{equation}\xlabel{eqn1a}
     (a+b)^2 = a^2 + 2ab + b^2
    \end{equation}

On the contrary, if the displayed equation is multi-lined, the syntax takes the following forms:

  \begin{align}
     (a+b)^2 & = a^2 + 2ab + b^2\\
     (a-b)^2 & = a^2 - 2ab + b^2
   \end{align}

Or

  \begin{align}
     \nf& (a+b)^2  = a^2 + 2ab + b^2\\
     \nf& (a-b)^2  = a^2 - 2ab + b^2
   \end{align}

Note: Please do not remove the \nf command unnecessarily.

If an equation with a custom equation number like $x_1^2$ is to be inserted, here is the way:

    \begin{equation}\tag{$x_1^2$}
     (a+b)^2 = a^2 + 2ab + b^2
    \end{equation}

Figures, display figures and inline figures

The default figure inclusion command in LATEX, \includegraphics shall be used for inclusion of graphic material. All options like width, height, rotation to arbitrary angles, trim, clip, scale (down or up), and all other options will work as one would expect. New figures can be uploaded using the upload tab. For more information check the File Upload section of the user guide.

The default {figure} environment in LATEX with all options will work correctly and can be used in NEPTUNE. E.g.,

  \begin{figure}[<options>]
   \caption{ ... }
   \xlabel{<label>}
   \includegraphics[<options>]{<figure file name>}
  \end{figure}

Various options to \includegraphics can be added as

   \includegraphics[width=\textwidth,scale=0.5,angle=90]{gr1}

The starred variant ({figure*}) shall be used when large-sized graphic materials have to be included in a two-column page layout.

Sub-figures shall be tagged with the command \subfloat. A typical example with usage explanation is provided below:

  \begin{figure}[t]%4
  \caption{Result of the measurement of channels 1--8.\xlabel{fig:DNL}}
    \subfloat[Channel 1.]{\includegraphics{gr4a}\xlabel{fig:DNLa}}
    \subfloat[Channel 2.]{\includegraphics{gr4b}\xlabel{fig:DNLb}}
   \break
    \subfloat[Channel 3.]{\includegraphics{gr4c}\xlabel{fig:DNLc}}
    \subfloat[Channel 4.]{\includegraphics{gr4d}\xlabel{fig:DNLd}}
   \break
    \subfloat[Channel 5.]{\includegraphics{gr4e}\xlabel{fig:DNLe}}
    \subfloat[Channel 6.]{\includegraphics{gr4f}\xlabel{fig:DNLf}}
   \break
    \subfloat[Channel 7.]{\includegraphics{gr4g}\xlabel{fig:DNLg}}
    \subfloat[Channel 8.]{\includegraphics{gr4h}\xlabel{fig:DNLh}}
  \end{figure}

The syntax of \subfloat command is:

  \subfloat[<optional sub caption>]{<fig inclusion command>}

The sub-figures will be arranged horizontally and \break command shall be used to break the line to arrange remaining figures in another line.

If new subfloats are to be added then please upload each subfloat individually and move the \nosubfloat command present in TeX code after the newly added subfloats.

The {figure} environment shall be used to wrap up all sub-figures. The starred variant ({figure*}) shall be used in a two-column page.

Additionally, there are two more types of figures used: (1) display figures and (2) inline figures.

• Display figure: A non-floating figure without caption shall be provided as:

       \begin{dfigure}
           \includegraphics[<options>]{<figure file name>}
       \end{dfigure}
  

• Inline figure: \infig with file name shall be used to insert inline graphic material.

       \infig{<figure file name>}
  

Floating and display tables

The default {table} environment in LATEX with all options will work correctly and can be used in NEPTUNE. E.g.,

 \begin{table}
  \caption{Relation between the calculated and measured bin sizes
           \xlabel{tab:DNL_bin_110MHz}}
  \begin{tabular*}
    {\columnwidth}
    {@{\hspace*{6pt}}@{\extracolsep{\fill}}*{4}{l}@{\hspace*{6pt}}}
    \beginthead
    Phase $j$ & Input signal & Calculated & Measured\\
    \endthead
    % \hline
    0 & 4.62 & 0.20 & 0.21 \\
    1 & 4.70 & 0.20 & 0.20 \\
    2 & 4.79 & 0.34 & 0.36 \\
    3 & 4.73 & 0.39 & 0.37 \\
    \bottomrule
  \end{tabular*}
 \end{table}

The starred variant ({table*}) shall be used when large-sized tables have to be included in a two-column page layout.

The {tabular*} needs to be used always as we need to control the width of the tabular, often we have to span the tabular to the width of the column depending on the number and size of columns.

The commands \beginthead and \endthead are extra structuring additions to augment XML generation. Those will further add horizontal rules above and below tabular heading row(s).

\bottomrule has to be added before the tabular ending command \end{tabular*}, to insert a rule at the bottom of the tabular.

Display table: A non-floating table without caption shall be provided as:

 \begin{informaltable}
  \begin{tabular}{<column specs>}
    ... ... ... \\
    ... ... ... \\
    ... ... ... \\
    ... ... ...
  \end{tabular}
 \end{informaltable}

Bibliography

The bibliographic items have to be heavily structured to generate the right kind of XML from the LATEX documents. As a standard, popular, user friendly and optimal tagging scheme that meets the technical requirements of both typesetting and XML generation with least effort on the part of the authors, we have adopted BibTEX format for bibliography which TEX authors are familiar with its usage and functionality. BibTEX helps to re-order the listing as per the order of citations in the body of the document in numbered citation style and sorting of bib items in author-year scheme painlessly even after several bib items have been added or removed during author proofing.

However, to save the drudgery of keying the BibTEX record when an author needs to insert a \bibitem afresh, a simpler type, namely, @others is adopted in which authors need to insert the whole bibliographic item text as an argument of the field, commn. Here is a typical example of new coding:

   @others{bibkey,
    commn={Welch, Ivo. (2010) A comprehensive look at the empirical
     performance of equity premium prediction. Rev. Financ. Stud.
     123 (1), 121-133.}
   }

A few BibTEX record examples are given below.

Journal

@ARTICLE{submonorev,
 serialno={43},
 author={Oliveira, T.J. and Aarao Reis, F.D.A.},
 title={Scaling in reversible submonolayer deposition},
 journal={Phys. Rev. B},
 volume={87},
 year={2013},
 artnum={235430},
 doi={10.1103/PhysRevB.87.235430},
}

Book

@BOOK{zhao,
 serialno={26},
 author={Zhao, Y. and Wang, G.-C. and Lu, T.-M.},
 year={2001},
 booktitle={Characterization of Amorphous and Crystalline
            Rough Surface: Principles and Applications},
 publisher={Academic Press},
 city={San Diego, CA, USA},
}

Inbook

@INBOOK{Huang,
 serialno={3},
 author={Huang, D. and Li, Shuliang},
 pages={42-52},
 year={2018},
 title={A Survey of the Current Status of Research
        on Quantum Games},
 booktitle={Proc. of the 2018 4th Int. Conference on
            Information Management, ICIM2018},
 orgname={IEEE, The University of Oxford},
 city={UK},
}

Others/Miscellaneous

@OTHERS{Khan2018,
 serialno={6},
 commn={Khan, F.S. and Solmeyer, N. and Balu, R. and Humble, T.,
         Quantum games: a review of the history, current state,
         and interpretation, 2018. ArXiv preprint
         \myehost{arXiv:1803.07919}},
}

Biography

Following is the default biography coding. In this case the biography photos will be named as pic1.pdf, pic2.pdf etc.

 \begin{biography}
%  \includepic
  \textbf{<author name>} <biography text>
 \end{biography}

An example is given here:

 \begin{biography}
%  \includepic
  \textbf{John Hopper} This is the biography text. This is the
    biography text. This is the biography text. This is the
    biography text.
 \end{biography}

You may even upload a new photograph for a newly provided biography or as a replacement to the existing one. In that case, you have to mention the filename of the photograph as given below. .pdf, .png and .jpg are accepted.

 \begin{biography}
  \includepic[john_hopper.jpg]
  \textbf{John Hopper} This is the biography text. This is the
    biography text. This is the biography text. This is the
    biography text.
 \end{biography}

Conflict of interest

If the proof is missing conflict of interest section and you were requested to provide one, then please provide the same after the last section but before or after acknowledgement. An example is given below:

\conflictofinterest
No author associated with this paper has disclosed any potential or
pertinent conflicts which may be perceived to have impending conflict
with this work.

Labels and Cross-references

Slightly modified \xlabel{...} is used in place of \label{...} with the same functionality. In the same vein, \xref{...} takes the role of \ref{...}. The cross-ref command, \xref{...} accepts more than one label as its argument and the output will be sorted and compressed if needed.

As you’re aware, two TEX runs are needed to fix cross-references to newly inserted objects correctly.

Cross-ref commands

• \xref{clm1} ⟹ Claim 3.2 [Default string + counter]
• \xref{clm1,clm2} ⟹ Claims 3.2 and 3.3 [Default string + counters]
• \xref{clm3,clm2,clm4} ⟹ Claims 3.2---3.4 [Default string + counters, sorted and compressed]
• \nxref{clm1} ⟹ 3.2 [Only counter]
• \xref[env=Postulate]{clm1} ⟹ Postulate 3.2 [Custom string + counter]

• \xref[nosort]{label1,label2}

• \norefsort ⟹ Do not sort the ref values in the document.
• \refsort ⟹ Sort the ref values in the document (default).

Cross-ref Options

• id=<id> ⟹ Add custom id (applicable only during XML generation).
• num=<number> ⟹ Add custom number instead of default counter.
• env=<env string> ⟹ Add custom environment string.
• nolink ⟹ Remove link.
• noenv ⟹ Remove string.
• noctr ⟹ Remove counter.
• sort ⟹ Sort the values in current xref command alone (in a non-sorted surrounding).
• nosort ⟹ Do not sort the values in current xref command alone (in a sorted surrounding).
• sfx ⟹ Add suffix to the counter.
• pfx ⟹ Add prefix to the counter.
• linkstr={<link string>} ⟹ Change default string in a multi-label \xref{...} command. Default is and, at times, users might need to change it to through and the like.
• range ⟹ Provides range of references if labels for begin and end refs are provided, separated by comma.

Examples for ranged xref

• \xref[range]{fig1,fig4} ⟹ Figs. 1---4
• \xref[range]{eqn1,eqn5} ⟹ Eqs. (1)---(5)
• \nxref[range]{eqn1,eqn5} ⟹ (1)---(5) [without the string Eqs.]
• \xref[range,linkstr={ through }]{fig1,fig8} ⟹ Figs. 1 through 8
• \nxref[linkstr={ through }]{eqn1,eqn2,eqn3,eqn4} ⟹ (1) through (4) [no range option used, hence need to provide all labels.]
• \nxref[range,linkstr={ through }]{eqn1,eqn4} ⟹ (1) through (4) [ range option used, hence need to provide only begin and end labels alone, linkstr changed.]

Citations

• The bibliographic model as specified by the journal will be chosen by NEPTUNE automatically and authors need not be bothered about it.
• Irrespective of authors’ coding of bibliographic items (i.e., author-year or numbered schemes), NEPTUNE will take care of citations depending on the journal style.
• NEPTUNE loads natbib.sty by default.
• All the commands provided by natbib will work fine.

Line number

Line numbers are disabled in the PDF. However if authors want to enable line numbers, add the command \stmlinenumbers after \begin{document}.