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Prospects with a Computational Social Science degree
During college, I decided to use my free electives to pursue a second major I had an interest in (Sociology) besides my main focus on computer science.
I am contemplating applying to some phD programs that intersect both of these fields. However, I know these are new programs.
I have e-mailed a few departments but I get the vibe that they are more focused in getting people to apply to these new programs rather than necessarily being honest about prospects.
So my question is essentially, are there tenure track professorships that are interested in applicants with these kinds of backgrounds? And if so is it only a very small group of institutions?
Example of one of the programs I am referring to: Ph.D Program in Computational Social Sciences

The digression about the Sante Fe Institute's MOOCs doesn't really address the question about job prospects in the wider market. Can you expand this to be more than "doesn't look good to me"? You say you are at GMU as well, maybe you know something specific about that program and where people end up from it?

Generally, if this is a relatively new cross-disciplinary area, this will start as a very small group of institutions. If it's a fruitful area, that number will grow quickly, and among  the early adopters might well be some of the best universities.
And yes, to set up these programmes in the first place, does indeed require buy-in from professors and top-level university administrators, so there are tenure-track professorships interested in applicants with those sort of cross-disciplinary backgrounds
What is it like to study in a new cross-disciplinary area?
There are a few things that make it different.
You might find yourself building the foundations. A lot of the work might be much more exploratory. It can be the wild west, with few established paths and no signposts; and you may end up making up the rules as you go along.
That is to say, established fields tend to have well-defined protocols for things like data collection; and a proven set of tools to work with. Whereas in a new cross-disciplinary area, you're more likely to be building the basic toolkit from scratch: writing your own protocols starting from bare bones.  There will be things you can take from each of the disciplines that you span, but combining them will be untested ground.
Some of the papers you write may end up being foundational for the new cross-disciplinary area, and highly-cited for years to come. Even though the work they contain, might seem fairly basic to you.
It can be lonelier. Scarier. More exciting. Harder to get funding. Or easier to get funding. Your reading will be broader, as it will span journals across more than one discipline, and you won't find enough journals or conferences that are closely-enough targeted at your field. You might end up starting your own conference, just to help build the platform.
disclaimer: I do work in a new cross-disciplinary institute, but I do not work in computational social sciences (though one or two of my colleagues are indeed computational social scientists)

Pardon me if you don't feel comfortable answering, but what institutions did your colleagues attend for their doctorate before they arrived at your institute? As these programs are rare and I'm always interested in finding more.

I lead the semantic technologies and cultural heritage research line at Incipit CSIC (www.incipit.csic.es) in Spain. We are right in the cross between software engineering, philosophy of language and cultural heritage.
To answer your question, we desperately seek people with a profile like yours. We just had a vacancy for a PhD position and it was (as usually is) extremely difficult to find suitable candidates. When we find them, we treat them with much care and respect, and our aim is to have tenured positions in the future for these people.
Having said that, I must admit that this is a quite uncommon situation. Most research institutes in Spainand Europe tend to align their research lines along more conventional paths, and recruit people with more conventional backgrounds.
I guess your will need to work hard to find a place that needs people with your hybrid profile. There are few, but you will be gold to them.

I'm in the CSS department at George Mason University, just starting my dissertation.  Though I'm not primarily aimed at tenure-track academic jobs after graduating, I have some insights regarding the questions you have asked.
First, you should know that CSS at GMU (and most other places similar to it) are not solely focused on placing their graduates into academic jobs.  There's a wide diversity of career paths, both prior to entering and after graduating.  To me, that creates a looseness and openness among the students.  This is in contrast to discipline-focused departments where everyone is expected to prepare for and compete for top academic jobs.  In those situations, there seems to be a strong emphasis on things other than just learning and doing good research (competition, prizes/awards, getting into the 'in crowd', elitism, etc.)
Second, CSS would be a poor fit for many academic jobs (research or teaching) that really want depth and credentials in a single discipline -- Economics, Sociology, Business, or Computer Science.
Finally, there is significant growth in the number of departments and jobs (internationally and in the US) that specifically call for Computational Social Science or similar interdisciplinary degree.  This is driven in part by funding agencies who have become very enthusiastic for CSS and similar types of programs and projects.  It's also driven by market demand -- especially for social network analysis, Big Data in social science, and programmatic research (e.g. public health, international development, conflict studies, cyber security). While the number of these jobs may not be large in absolute terms,  CSS graduates could be extremely well-qualified to fill them, compared to single-discipline graduates.


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Is reviewing papers mandatory?
I am baffled by this question. Elsevier boycott aside, is one supposed to review a paper every time he/she is asked? And somebody will be upset if he/she declines the request to review? Or is this only maths thing?
Reviewing paper is unpaid, while it takes a lot of time and effort (at least for me). As such, I expect someone in editorial board to be thankful if one accepts to review a paper, and move on if his/her request for reviewing is declined.
To be angry with a (junior) researcher for not reviewing a paper is unacceptable behaviour for me. We are not slave.
Note: Until now, I am happy every time I am asked to review a paper.

See How many papers should I be reviewing as a referee?, When is it appropriate to decline a review request? & Do people say why they decline a paper review request?

No, reviewing is not mandatory, it's just good community service.
When I'm soliciting reviews, as an editor or program chair, I would actually much rather have people who don't want to review simply decline to review.  It does mean that I have to search for more reviewers, but it's much preferable to getting low-quality reviews or no review at all.
Moreover, there is always a limit to the amount of service that one should be expected to do.  If you're reviewing a good amount of papers (see discussion in this question about how much is enough), you should feel free to triage. Just be polite when you decline: even with things you don't want to deal with, it's usually better to simply say "I don't have time right now" (true enough) than to offend a person by completing the sentence with something like "... for your crappy journal" or "... for this horribly tedious-looking paper."
Of course, there is always the possibility of encountering an ego-centric jerk on a power-trip, but life is too short to spend all of fearing that you might encounter such.

Still, if you "hate Elsevier", it makes a perfect sense to state it: "Sorry, I won't do the review since I don't volunteer for Elsevier." Fair enough, in my opinion. After all, what would a boycott be good for if the target didn't know about it?

@yo' I agree.  However, you can still be polite about it.  There's a big difference between "Screw Elsevier, and screw you for working with them!" and "My apologies, but due to my disagreement with Elsevier's publishing practices, I have chosen not to submit to or review for Elsevier publications."

Ok, it seems we come to agreement, which is good :) To me it just appeared that this point is missing in the answer.

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PhD interview question when you don't know the answer
How should you handle a question in an interview for a PhD program when you don't know the answer ?
Should you try to just say something even if this is wrong or just tell the interviewer that you don't know the answer?

Honesty talks, BS walks.

@DanielR.Collins BS ?

I refer you to the canonical text by Harry G. Frankfurt, professor emeritus of philosophy at Princeton University: http://www.amazon.com/On-Bullshit-Harry-G-Frankfurt/dp/0691122946

What kind of question are we talking about here? It makes a huge difference.

"I don"t know."

Look like you care, look like you feel you ought to know, look like you want to work it out straight away and will do in front of them immediately given half the chance.  And don't forget to mention any closely related things you do know the answer to.

In most cases, the interviewer does not care about the "answer", but rather about how you answer. I would answer honestly with something like "I do not know, would you like me to try and work it out?"

I am not sure that the interviewer won't care about the answer, but this is still probably the optimal strategy.

@Bitwise it would be very strange for the interviewer to not already know the answer to a technical question (unless of course it is truly impossible to answer).

Perhaps I misunderstood - I agree that the interviewer would usually know the answer. I meant that the interviewer will care whether the candidate does or does not know that answer. However, I can also imagine scenarios in which the interviewer actually does not know the answer - for example if asking about the candidate's past research.

Yup. The idea is to find out whether you're curious and whether you are capable of learning. If you don't know outright, if they can lead a little bit and you can eventually figure it out, that's really good.

I don't recommend lying but there is a saying "Nice guys always finish last". It's sad but true that the modern world values bravado over honestly and sensitivity.

Honesty would be the best and tactical strategy. No one is expected to know everything. An ideal panel would only be interested in how much you know and how much of that pertains to your candidate position as a PhD scholar.
The time given for you in the interview process is gold -- you must try to expose your potential as much as you are able to within the period. If you spend too much time in an a question you cannot make out the answer, then you are probably losing time to express the answers for the future questions you might know. Hence it would be better to admit that you do not know the answer and try if you are confident (as suggested by @StringBad) or move to the next possible question if not.

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What is the standard way to include math equations in a CS research paper?
I am currently working on a research paper in Computer Science which involves quite a few math equations. I am using MS Word currently to write the paper. I haven't yet included the equations. I am planning to send it to a journal.
I have a previously published paper in IEEE Digital Xplore for which I used LibreOffice Writer in Ubuntu to specify the equations and the content. I thought it wouldn't matter what platform I used because I would later convert the document into PDF format. But in the actual paper available on the website, the equations all look pixelated and downright illegible.
http://ieeexplore.ieee.org/document/7518940/
My question is, what is the standard way of specifying equations for a research paper? Should I convert the whole document to LaTex and specify equations there? If so, should I look up on the particular journal format to use before including the content?

LaTeX is fairly standard in CS for typesetting conference and journal papers. You can try to find out a way to produce better looking equations in other software if you like, but that kind of software question would probably be out of the scope of this site.

Just to clarify: did you have to produce and send the final pdf file yourself (what journals often call a "camera-ready copy"), or did you just send them the .doc source files? Was there a style guide for authors? What did it say about equations?

Looking at the rest of the papers in that conference, it looks like yours emerged relatively unscathed. I suggest that before submitting a paper to a conference or journal, you read past issues of that publication and make sure that you would be proud to have your paper appear among them (both in terms of how professional it is, as well as the content of the papers.)

@FedericoPoloni I had to send the camera ready copy.

If you can write in latex, you should write on it versus word. The latex is specially designed to work with technical documents with a lot of mathematical equations.
Also, you can write math equations in word using built-in equation editor of Microsoft word or MathType as a better alternative than built-in ones.
See this link for word equation for equation writing in Word with better configuration.
Technically the MathType produces equations with higher equality than Word built-in and I recommend it to use as a macro on Word.
About writing in Latex and then revert to Word, it wouldn't be recommended and will be reduced the quality of equations (due to reversion complexities and equation editors' of Word difficulties).

[EDIT: this answer refers to contexts in which the publisher is responsible for the typesetting. In contexts in which the author is supposed to produce directly a "ready-to-upload" pdf file, what I write is inappropriate, as correctly noted in the comments.]
Your only responsibility is making sure the equations are readable and understandable to the referees. I assume that the equations looked better in the manuscript that you first submitted, so you are clear.
It's the typesetters'/copy editors' job to make sure that the final pdf looks good, and they should be professionals who know the functioning of the software tools they use and the basic things to check when they convert from one format to another. They should have caught this problem before the paper went online, and fixed it themselves or asked you for a copy of the equations in a different format. They completely failed at doing their job.
You should complain with the publisher and request a change. In addition, you should also let the scientific board of the conference know informally, possibly by contacting the editor you have interacted with. The panel deserves to know that the publisher they use did such a bad job, because they are the ones that can complain at a higher level and change things.

This answer is not accurate for many (most?) publications in CS. For conference publications and many journals in CS, the author does the typesetting themself, not the publisher, and is responsible for uploading the final camera ready paper in PDF format.

@ff524 You are correct. I have edited the answer to specify that it is inappropriate in this context, and I am considering deleting it since OP speaks about a conference. But if this is the case, then the question reduces to "how do I typeset equations (either with Openoffice or by switching to some other program) so that they look good when converted to pdf", and I am afraid that it is off-topic here.

It looks like for the conference the OP last published in, they ask for the paper in MS Word format. The whole conference looks like a rather haphazard operation (there seems to be only one week for "peer review"!), so... I would recommend complaining to IEEE about publishing these conference proceedings, rather than complaining to the conference about using IEEE as a publisher.

+1. I agree with @ff524. Such conferences are making fun of young researchers and the efforts they do put for the work. I saw the paper of the OP in the IEEE LIBRARY. The conference should be reported to IEEE.

If OP submitted only a .doc file, who did the faulty conversion to pdf then? Someone hired by the conference? The editors themselves? Typesetters at IEEE?  Unpaid volunteer phd students? Who does it usually for CS conferences?

@FedericoPoloni The conference is responsible for taking care of all of this, and delivering the final result to IEEE ready to be distributed on the website. Normal conferences have  "publication chair" who oversees the process. This particular conference did a really, really awful job (if you browse some other papers in the proceedings, you will see that many are much worse off than the OP...) and seems like a terribly unprofessional operation in general.


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How to make a software documentation "officially" citable?
We are currently finishing the implementation of a scientific software library. It's the first project of this type for me and I'm curious, how to make the software citable in a similar way to Molpro or R?
I was thinking about writing a short paper introducing the library, which could be subsequently cited. But I'm not sure, how to deal with the different versions? I don't think it's possible to write just some "changelog" paper once a year to summarize new released version.

I don't understand the question. Your software is already citable, by listing your name, the name of the library, and the URL.

@JeffE That's the truth, but it's not going to be indexed anywhere, not even Google Scholar, if I'll have just the name and URL...

@Eenoku Are you sure that Google Scholar won't index? If your software is consistently cited---e.g., Eenoku (2019) Library, http://url.com---then surely Google will index that.

You may be wrong. Google Scholar reports that a subset of my lecture notes, which is only published as PDFs on my web page, has 5 citations.

There are about as many approaches to citing software (and making software citable) as there are software packages.
One way is to create a DOI for your software via Zenodo. This DOI can then be updated for each version of the software. Another way is to write a paper about the design and features of your software and see that it gets published somewhere. There are numerous journals for this -- for example, SoftwareX or, for mathematical software, the ACM Transactions on Mathematical Software. (Disclaimer: I'm a co-Editor-in-Chief of the latter.)
There are numerous other projects that have guidelines of how to best do this. You may want to take a look at the Force11 project, for example, as well as the outcomes of the WSSSPE series of workshops.

Thank you very much for the very informative answer, Wolfgang! I'd like to ask about ACM Transactions on Mathematical Software specific topics - is it possible to publish there about machine-learning software, but with emphasis to 1) improved training methods and 2) involvement of ANNs in numerical methods used in Quantum Chemistry?

You will probably want to take a look here: https://toms.acm.org/authors.cfm

I'd have to see more of the paper to tell you whether what you want to do fits into TOMS. A single sentence is just not enough :-)

I'm afraid I don't have the paper yet, but we can discuss it before my first publication attempt :-)

Another important consideration is that the approach to use will also be influenced by the field the software is intended for. Conventions and details on how authors and journals like to handle software citations in field with heavy software usage (like statistics) are going to be different than a primarily non-computational field (like biochemistry).

Yes, that is most definitely true. That said, there has been growing realization over the past decade that many disciplines struggle with the same issues of how to cite software. And people from many different disciplines have been working together in the initiatives that have arisen to address these questions. There is definitely a convergence of approaches that were unconnected before.

Neither a DOI nor an explanatory research paper is actually necessary for something to be citable.

@JeffE: That might be true in a literal sense, but if you want to encourage people to actually cite you, it's useful to have a thing that follows the scheme people are used to. If you need to explain to people how to cite your software, you've already lost 3/4 of those who would otherwise be willing to do so.

@WolfgangBangerth It's not only true in a literal sense; it's true in a practical sense; the pattern "Author, title, year, URL" is pretty versatile. (I have lecture notes, blog posts, and even StackExchange questions with multiple citations.)  But fair point about meeting community expectations.  If your audience believes a DOI is necessary for citation, then you need a DOI to be cited; whether your audience's belief is correct is irrelevant.

Write a manual and release it as a technical report.

how to deal with the different versions?

Put the version number in the manual's title and have a different version of the manual for every release. (Alternatively, revise the manual every major release or ...)

I don't think it's possible to write just some "changelog"

You could have a CHANGELOG in the manual, which summarises what's new in the current version. Alternatively, a CHANGELOG could be distributed with the software.

Ok, I suppose, that this it the case for Molpro software... But where do you officially publish a technical report? Otherwise yes, I know, that you can have a CHANGELOG in your repository, but that's not the place to be cited from :-)

Just publish the manual alongside the software. You could publish on arXiv, but that's not strictly necessary and adds an additional burden. Regarding the CHANGELOG, I'm not sure whether it needs to be cited, perhaps it suffices to just have different versions of the manual, one for each release.

In addition to the above answers, you can publish a short article about the software at the Journal of open Source Software (JOSS). How this journal differs from other journals is described in its announcement post.
Your submitted article and the associated software are thoroughly peer reviewed. If the article is accepted, it will be assigned a volume number, official DOI, etc. In effect, you have a "real" article that can be cited just like a "regular" journal article. This is separate from obtaining a DOI just for your software through services such as Zenodo and figshare, which are mainly intended for archival storage of software and datasets.

Having published in JOSS, their review process is very interesting (based almost solely around the software itself, done publicly on github, meant to improve the software and ensure its ready for production with adequate documentation) and leads to very quick turnaround times depending on how quickly you address reviewer concerns. Submission to publication took 10 days for me. Their requirements for the manuscript itself are minimal.

Concerning the DOI / citable discussion, see DOI != citable
And if your using Zenodo to create a DOI, as @Wolfgang Bangerth mentioned, see Making Your Code Citable.
Basically here you have to decide how you will make your library publicly available. There are different ways to do it but the links describes how to connect Zenodo with GitHub. This may also depend on whether you want to allow citing different versions of your library or just "link to releases" on you institute's webpage.
Here you will find more input for the discussion How to cite and describe software.
They're showing recommendations from software providers, which is as simple as creating your own BibTeX entry with an url.
However, the next section shows different positions of "Software is not a citable output". Keep that in mind when providing a special way to cite your library.

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How do institutions evaluate requests for faculty startup funds if they have never hired in the subfield before?
Smaller departments typically want to hire someone with different expertise from the faculty they already have.  Suppose they have decided to advertise that they want to hire an experimentalist in an area of research with which the institution has no experience.  How do they evaluate applicants' requests for laboratory start-up funds?  Assume this is an experimental area where equipment costs are in the six figure range (USD).

We usually follow the following routine:
A) The department chair calls their friends at comparable rank and size schools who have hired in a comparable field and ask them what their new faculty member's startup packages are. The chair may also ask the candidate if they have any special equipment needs.
B) We assume the Provost (who is in charge of finances) is checking with their colleagues at other institutions as well as what the campus recruitment budget is.
C) The chair goes into a meeting with the provost and comes up with a third figure.
D) We then bring that to the candidate who may come back with a counteroffer either based on chutzpah or an actual figure based on what another or their current school is offfering.
E) We negotiate by going back to Step C or drop candidate #1 as too expensive and go to candidate #2.


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Is it appropriate to guess page numbers of a book from its translated version?
Short: It's easy to find bibliographical info, but how to guess page numbers?
I'm writing a paper in English. I want to cite certain book, originally published in French. It is translated to English and Russian. I own a Russian translation. I'd like to reference English translation. I don't have access to other language versions and I'm not going to purchase them.

I also think sould cite the version you have read. But maybe you can put a note that this is a translation and give the original French title.

how to guess page numbers? — Do not even try.

Cite only the version that you have access to and you are reading.

You don't need to buy a book just to give a quick look at it. If you work/study in a university, ask your library for the possibility of interlibrary loans.

Regarding your original question, if you have access to a Russian translation and you want to cite the English translation, but you do not have access to the English translation, then you really need to focus on citing what you have access to.
Now, I understand it turns out you do have access to the English version as stated in your answer but for future reference, you should not cite a version of a text you do not have acces to. The reasons are more than simply that you don't know the page numbers. It is possible that there is a problem in the Russian translation but the English version does not have that problem. Likewise the opposite could be true. Basically, the two versions could be slightly but meaningfully different. Because of this possibility, you should only cite what you have access to. Otherwise, cite through a third-party "Jones wrote in 2001 (cited in Simpson, 2005)."

You can even have bigger differences between the books.  Occasionally a translator makes substantial changes with the author or publisher's blessing (rearranging material, adding commentary or recent references, replacing background references with ones in the target language, etc.).

@AnonymousMathematician And occasionally, the authors make two versions: Czech and English for instance, the titles match, not so quite the contents. I know one such example where the two books are substantially different.

You should cite the version you have available, since section numbering, pagination etc. can get shifted. The proper way to do it is to simply cite both, for instance:

[Doe06] John Doe. Prostory. Nakladatelsví XYZ, Prague, 2010, 512 pp. Translation of: John Doe. Spaces. Publisher ABC, New York, 2006, 480 pp.

This way, the citation contains the necessary information, and this is completely acceptable. Second option is to make it two citations:

[Doe06] John Doe. Spaces. Publisher ABC, New York, 2006, 480 pp.
[Doe10] John Doe. Prostory. Nakladatelsví XYZ, Prague, 2010, 512 pp. Translation of [Doe06].

Sorry, I didn't notice it's 3 versions. Of course, you cite them as translations of the original (in this case French) one, preferably.

After expressing my question, I understood that I can find the English translation in Google Books and look into contents with page numbers. So I can have references like (1998, 36-67). Actually I can even search within a book, so I can find exact page numbers for the passages referenced.

@earthling 's answer is correct: if you don't have the book, don't cite it.  On the other hand, if you can verify that the (probably more accessible) English version says what you want to support with the citation, cite that, or even both.

Don't cite page numbers, cite chapter and section numbers. They won't change irrespective of the translation. Also they are less likely to change after small corrections in reprints.

Theoretically they shouldn't change in a sufficiently faithful translation, but they actually can and do change sometimes in practice (since faithfulness to the original is not the most important goal).  Sometimes the author suggests changes he/she thought of after the original book appeared, or the translator suggests adding, dropping, or moving something and the author or publisher agrees.

@AnonymousMathematician Exactly. Citing sections/chapter/theorem numbers need not be sufficient, since some publishers apply rules that the original work need not have followed. (For instance: no solitaire sections, introduction obligatorily numbered or obligatorily unnumbered, etc.).


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Are there many journals that do not accept TeX/LaTeX?
I have been told by our head of department, a veteran academic with a lot of publications behind his name, that I am not allowed to write my masters dissertation with TeX/LaTeX, as many journals do not accept TeX/LaTeX documents, and now I have to use Word. I work in thermoflow research.
I can almost not believe that journals would prefer Word over TeX/LaTeX, or is this in actual fact true?
I would appreciate answers from people actually working in academic publishing.

Also, when you say TeX, do you also mean LaTeX, etc.?

All journals I have come to contact with, one way or another, accept Word or (La)TeX documents. Either of these formats is an intermediary, as they likely generate a printer-native format like EPS, with the figures and tables in, and the correct layout etc.

How is the tool used to write your MSc thesis related to the file formats supported by journals? No matter which format you use, you cannot just take your MSc thesis and submit it to a journal...

In my field - Atmospheric pollution and boundary layer meteorology - you have to use Word for all conferences and it is preferred in most journals, but many will accept any PDF.

Yes, journals that only accept MS Word manuscripts do exist (sadly). However, for me this is more a reason to not submit there than to change the format of my text.

do not submit to journals that do not accept LaTex..  More strongly, I would hesitate writing a manuscript without an example Latex file.

@seteropere: It appears that in some fields, your advice reduces to "do not submit to journals."

Write it in LaTeX, convert individual pages to high-res images and include them in the Word file. Problem solved.

@seteropere this is not a good piece of advice. Choose journals for their relevance, high impact, reputation in your field, etc. not on anecdotical formatting criteria.

@JukkaSuomela In some places, a masters dissertation is pretty much a journal publication.  E.g., if you get a journal publication, then the school will accept that (perhaps with some formatting changes and an additional literature review) as the master's dissertation.  I still think the head's behavior is odd, but it could be in anticipation of "You need to be able chop these sections off and immediately submit it for publication."

@Raphael, using your proposed method, the text will not be editable.  Because of this, the journal might not accept the file even though it is in Word format.

just out of curiosity: how old is your head of department?

http://tex.stackexchange.com/questions/1319/showcase-of-beautiful-typography-done-in-tex-friends Not an answer but a rather long comment. LaTeX can replicated everything Word can do and way more. Of course some journals may not accept it but please show the awesome (in the literal sense) examples above to your head of department and see if he/she changes his/her mind.

@leonardo: No problem: we dump the unformatted text behind the images. But is that really my problem, anyway? ;) (This is, obviously, not an entirely serious proposal. It may be worth a shot in a field in which LaTeX has some traction, though, just to raise awareness at the journal.)

Funny, but my wife is in History and she recently submitted her PhD dissertation typeset in LaTeX (with my help). We decided it's just much easier to get the grad school required formatting (table of contents, footnotes etc) this way, from the templates. Plus, it just looks so much better this way!

When you work with LaTeX using lyx, it's almost as if you were using Word, but you don't need to worry about the details too much - at least until you get your style set up to match university/department regulations. I did most of my grad school homework in LyX/LaTeX.

@user479: It would be better to ask new question, also notice that tex.sx might be a better venue for this. I did a simultaneous Word and LaTeX output with markdown. (And I also necroposted, oops.)

I would just add that Word is the default in business, government, etc.  (IOW "civilian world".)  Even within Academia it is more normal in fields other than computer science, math and physics.  (But I don't see what the big deal is.  Just convert it to Word and fix the glitches.  Should take you less than a day.)

The answer is that in some fields (La)TeX dominate whereas in other fields (La)TeX is largely unknown. Obviously any field where equations are required is more likely to be using (La)TeX for writing and publishing. However, it is not uncommon that journals, or rather, type-setters of journals, use LaTeX for final production regardless of submitted format. The same applies to book publishers. But, the fact is that the use varies and one needs to check with the journal to which you wish to submit.
The fact that you are not "allowed" to write your thesis with (la)TeX is perhaps because your advisor does not use it. I am an avid LaTeX user and am struggling to convince both colleagues and students in my department to at least try using it so I know how difficult it can be. In the end, I need to use both to be able to communicate with my colleagues and peers. So although I do not see why you should not set the thesis in (La)TeX in the end, you probably need to use word for the manuscript so that your advisor can provide input on files you supply. But, check how many journals actually use LaTeX in your field and strike up a discussion with your fellow students and your advisor. I think it is worthwhile to be fairly fluent in using many tools.
Edit: I will just add that I was convinced by a friend to use TeX (not LaTeX, it was a long time ago) when I wrote my thesis (a monograph at a US university) while almost no-one in the department used TeX; but then my advisor always provided feedback from double-spaced printouts which were platform independent. Those were the days.

@Peter consider Org Mode if you use emacs. It exports to LaTeX and ODT (Word). Makes it easier to collaborate with others.

There are many journals that do not accept, or actively discourage LaTeX-based submissions. I've always found the assumption in LaTeX heavy fields that it's ubiquitous to be an interesting quirk.
For example, two journals that will accept LaTeX based submissions, but would rather you not:
American Journal of Epidemiology:

Prepare your manuscript, including tables, using a word processing
  program and save it as a .doc, .rtf or .ps file. All files in these
  formats will be converted to .pdf format upon submission. Please note:
  This journal does not accept Microsoft Word 2007 documents at this
  time. Please use Word's "Save As" option to save your document as an
  older (.doc) file type.

On LaTeX:

Prepare any other files that are to be submitted for review, including
  any supplementary material. The permitted formats for these files are
  the same as for manuscripts and figures. Other file types, such as
  Microsoft Excel spreadsheets and Powerpoint presentations may be
  uploaded and will be converted to .pdf format. It is also possible to
  upload LaTeX files but these will not be automatically converted to
  .pdf format (and are therefore discouraged). The journal staff,
  editors and reviewers will only be able to view these unconverted
  files if they have the appropriate software, which cannot be
  guaranteed.

Epidemiology:

Manuscripts should be in a standard word processing format. We prefer Microsoft Word but we can also use RTF, TXT, LaTeX2e, and AMSTex. Application software programs released before 2001 are not supported.

The New England Journal of Medicine actively doesn't accept them, at least not unless converted to a PDF:

All text, references, figure legends, and tables should be in one
  double-spaced electronic document (preferably a Word Doc). You may
  either insert figures in the text file or upload your figures
  separately. We prefer the former, but this may not work well for
  complicated graphics, which should be sent separately. It is
  permissible to send low-resolution images for peer review, although we
  may ask for high-resolution files at a later stage.
Legends for all figures should be included in the file with the text
  and should not appear on the figures.
Our preferred file type for new manuscript submissions is a Word or
  text document with all figures in the same document. We will also
  accept Adobe Acrobat portable document format (.pdf) , WordPerfect
  (.wpd), text (.txt) documents, or .rtf file format.

Clinical Infectious Diseases doesn't even want your PDFs:

The preferred format for submitting manuscripts online is Microsoft
  Word (.doc files). PDF files are not acceptable for submission.

These are all very good journals in my field - a happy, healty, high-impact, tenure friendly career could very easily be had never touching LaTeX.

While I agree with what you said, I’ve also always found it a very strange quirk that a lot of people assume everyone has access to (or would even consider using) Word. (Or that people think “TeX” meant Knuth’s macro package “plain TeX,” not just “anything from the plain TeX-LaTeX-ConTeXt-etc. family.” But that’s a different topic.)

Sometimes the statements on the website are actually inaccurate. I once submitted to a journal which (according) to the website only accepted .doc, but the submission system allowed me to upload .tex files and nobody complained.

Yes, journals that do not accept LaTeX do exist. If LaTeX is not widely used in your field you might have surprises even with those journals that claim to accept it, since they in fact almost never have to. I recently submitted a manuscript in LaTeX to a Taylor & Francis journal which stated it did accept LaTeX submissions, only to find my piece "unsubmitted" the next day with a request to re-submit in Word.

Weird. Every journal I've ever submitted to accepted only PDF (or back in the mists of time, paper).

Although I love LaTeX, I'm in a similar field to Fomite, so am very envious of you all in the equation sciences. If only they would accept pdf....

I am very much in the equation sciences and cannot use LaTeX. Very frustrating.

@Michael_K Have a look at the MathType add-on if you need to use Word.

@user11192: I'm sure most such people do use MathType. That doesn't make up for the fact that Word is a very unpleasant environment to use for creation of large and complicated technical documents, particularly those with lots of equations (and did I mention there's incompatibilities between Word/MathType for Windows and Word/MathType for Mac?).

Yes I know MathType and use it instead of Word's equations, but it still doesn't come close to LaTeX.

@aeismail Fair enough. Just wanted to mention it since I've not seen it mentioned on the Word bashing threads here. :)

I've worked in journal publishing (for a large STEM publisher, a large STEM printer, and now a scientific association) for almost 25 years, and LaTeX is always a problem. Typesetters have standardized around Word because there are literally millions of users, possibly a billion. But standardizing around Word means that there are going to be problems with any non-Word submissions. In most cases, TeX manuscripts will be converted to Word, either through some automated means or through double-keying (i.e., two poorly paid people in the Pacific rim will rekey the manuscript; the two versions are merged because it's unlikely—though not impossible—that they will make the same mistakes). Also keep in mind that there are more manuscripts that do not contain math than do, so the publisher, again, is not going to standardize around a niche.
However, in reading the above answers, I note the common expression of how beautiful and pleasing the final TeX product is. Here's the problem: if you want to be published, the manuscript is not the final product. Think about it from a journal publisher's point of view: They want their final product to be beautiful, too, subjective as that may be, and there is some beauty in uniformity.
Once your article has been accepted for publication, it is in many senses no longer your article. There are certain things over which you no longer have any say, such as typefaces, whether a serial (Oxford) comma is used, or whether hyphens are used in compound adjectives (which is a surprising point of contention for authors).
TL;DR: The publisher has found the easiest path to get to its desired result; even if you insist on deviating from the path, the product will be the same, and you and everyone else will be frustrated along the way.

I believe there are literally millions of LaTeX users as well, but I agree with your point that the number is likely dwarfed by the number of Word users. According to Microsoft, there's at least 1.2 billion MS Office users, so a billion Word users is probably not far off the mark actually.

I wonder how a typesetter fixes the fonts of all the equations in a word document. Latex is designed to be flexible. If a publisher wants to change how some font is to be used, they just need to use the right document class, that's it. I would say the publishers are foolishly clinging to a technology that is not designed to do the job.

user2833557: What do you mean by "fixes"? Also, it's highly likely that the publisher knows more about their processes than you (or I) do, so perhaps your suggestion just doesn't work as you think it will on the path from from the desktop to high-end printing presses.

As many mentioned already, yes, there are journals that would not take LaTeX submissions. Even if they take PDF submissions, they will sometimes redo the type-setting and create ugly final equations and texts (e.g. Journal of Neuroscience).
However, that should not be the reason to not use LaTeX. You can always convert it to RTF or DOC format. latex2rtf -M12 usually does the trick (there are other solutions, too). It converts equations to bitmap (png) images, so they can't edit the equations, but the text is editable. If your advisor wants to give you feedback using 'Track changes' in MS word, that's great. It's usually much better than directly getting the modified TeX file, actually. So you get the best of both worlds: beautiful typesetting of the final product, and easy to track text changes.
TL;DR: use LaTex and convert to other formats if needed.

Commenting / editing LaTeX can be greatly simplified and streamlined with the use of revision control tools. This is what any serious researcher need to learn and use, anyway.

@StasK Yes, of course. I use git these days. Using the right diff-tool is the key there. It also has the advantage of supporting simultaneous merging and log. Still, git is much more difficult to use than 'track changes'.

@Memming I tried latex2rtf but am not to impressed with the results. First it just cleared the .tex file I tested it on, at least I didn't need the contents anymore, and when I finally got it to work the results were average at best. I have to say I didn't really play with the settings of the program, maybe that is necessary to get good output?

@Michael_K it is just a script so the output often needs further clean up, and sometimes preprocessing. It does a pretty good job considering what it is trying to do. An alternative could be to use pandoc but I haven't tried it personally. The focus is to get good PDF and editability using Word if nessesary; not a perfect Word document.

Thank you @Memming, I agree. The final version of the document will be typeset with LaTeX anyway, the latex2rtf will basically just be to see 'track changes'. Thanks.

"It converts equations to bitmap (png) images, so they can't edit the equations"
The equations will probably be rekeyed in order to make them editable. The typesetter I work with can convert them to Word's equation format.

Out of my ~12 publications (spanning statistics, and applications of statistics in economics, psychology, sociology), I vividly recall at least two being rewritten in the publishing house from LaTeX into Word, with an innumerable typos, mistakes, etc. that I had to weed out comparing their proofs to my beautiful PDFs. There may have been more than two that were retyped into something else, actually, but these two were obvious downgrades.

This sounds like a minor miscommunication. Your mentor is correct in that many publications do not accept TeX documents, but you do not (usually) submit the latex version of your document in the first place. You compile it to produce a PDF which is what you submit. The publications that want to edit your PDF will normally have the tools to convert from PDF to word or whatever other format they work with.

Interesting fact is that I didnt even get this from my study leader ! But from the head of department, and he basically told me that I have to write up in Word!

"You compile it to produce a PDF which is what you submit." This varies by field. Submission of TeX source is routine in astronomy and physics. http://aas.org/authors/manuscript-preparation-aj-apj-author-instructions https://journals.aps.org/authors/tips-authors-physical-review-physical-review-letters

@coneslayer: Indeed, in my experience (math), journals that are typeset with LaTeX (in math, all of them) typically require that authors submit LaTeX source if possible.  If you were to submit only the PDF, the process of converting it back to LaTeX would be unnecessarily time-consuming and error-prone.

That is my point, any publication can accept PDF and convert to the format they prefer. It is often the second choice, but it is always possible.

@PaulSmith it may be possible, but that doesn't mean they will do it. There are plenty of publications out there that require sumissions in Word format, and plenty of others that require LaTeX.

In my experience on the publisher side, a Word file is preferred. In many cases, the subject matter of the journal is less the defining element than the publisher. Publishers contract out for typesetting and composition, and that's who dictates the file format.

I wrote some books in LaTeX and another one with Word. I lose plenty of time with Word and I don't like to renew this experience. In october I'll give a course about LaTeX for an association in amateur radio with Smith diagrams examples. I'm not sure I could draw them easily with Word. For the moment publications in this amateur radio association are made with Word; some people in this association know the LaTeX name and its potential but they haven't yet the level required to use it. In my experience some Editors don't like LaTeX because they haven't internal knowledges but undoubtly they are frightened with its tremendous potential.

authors: Vladimir F Героям слава

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Published and unpublished dissertation; DOI assignment
I have recently defended my Ph.D. dissertation and submitted it to my graduate school's e-repository of scholarly works as well as to the ProQuest database. I have not heard yet from ProQuest about the respective publication, but my work appeared blazingly fast in my school's repository, which is great, as I already can cite it in my CV and elsewhere, where appropriate.
As I understand the terminology in the area, dissertation or thesis, submitted to ProQuest (or another scholarly database, for that matter) is referred to as published. On the other hand, the same document, submitted to university's e-repository or similar archive, is referred to as unpublished. Also, while I expect the ProQuest to assign a DOI to my work, my university's e-repository doesn't seem to include this step. Considering all the above-mentioned information, I am curious about the following:

What is the optimal strategy for maintaining and citing both unpublished and published versions of my dissertation? Since the published (ProQuest) version will not be available to people, lacking access to ProQuest, does it make sense to maintain and cite both versions, so that other interested people will be able to access and cite the unpublished version?
What is the optimal strategy for assigning DOI to my dissertation report (either to both versions, or to the unpublished, if ProQuest will assign DOI to the published one)?

As I understand the terminology in the area, dissertation or thesis, submitted to ProQuest (or another scholarly database, for that matter) is referred to as published. — I've never heard this distinction before.  In its raw etymology, "published" merely means "made public".  Some people (and fields) would consider a thesis available only as a paper copy in your university library, or only as a PDF from your web page, to be "published".  Others would not consider a ProQuest version "published", because it hasn't been reviewed by an editor.

@JeffE: Thank you for your comment. I agree with it and, actually, I now cite my dissertation (i.e., in my CV) as an "unpublished doctoral dissertation" (which is what APA Style recommends).

I would (and do) omit the adjective "unpublished", and just list it as your PhD dissertation.  If you later publish it as a book, then you can list it as a book.  But the correct protocol probably depends on your field; ask your advisor.  (In my field, almost nobody reads PhD theses—and some people don't even list their PhD thesis in their CV—because thesis results are normally published in conference and journal papers, often before the thesis itself.)

@JeffE: I appreciate your latest comment - very useful information. I do not plan to publish my dissertation as is as a book. Instead, I plan to convert it into several research papers; plus an additional paper will cover my research software. In the longer term, I plan to create a more comprehensive coverage of the topic or, even, larger subject domain, both theoretically and experimentally, and publish all that material in a form of either a book (preferably), or, at least, a chapter. Does this plan makes sense to you?

You should avoid citing it twice, because it's the same work (think of it as a book published by two different publishers - you wouldn't cite both versions). Whether you prefer to cite it with a ProQuest DOI or with a link to the university repository is up to you, though possibly a given journal may have an opinion on which they prefer. Depending on how formal the citation style is, you could do something like:

Bleckh, A (2015). ProQuest citation; DOI. Copy available from [repository]

which would let you use both access methods.
For DOIs, it's unlikely that your repository will assign a DOI to their version - most repositories aren't set up to issue DOIs. The repository is intended as an alternative way to access it rather than a different publication, and so material hosted by a repository tends to give the bibliographic details of the "real version" rather than provide their own.
(Also, I'm not sure what you mean by "maintaining" - are you envisaging updating it over time? This would be quite unusual for a doctoral thesis...)

Thank you for your insights (+1; acceptance is pending, based on potential feedback from others). I didn't mean to use both citations within the same referencing document, but one of each, based on that document's audience and its assumed access. Your suggested combined citation makes sense, but I want to hear more opinions from people here to make up my mind. In regard to "maintaining", I implied similar meaning as "citing", not updating the document - I will remove the confusing and unnecessary word from the question.

In regard to DOI, I could consider posting my dissertation to Figshare, which, as far as I know, assigns DOIs to all artifacts. Then, I would simply prefer citing the Figshare's version to the one from my unversity's e-repository.

Is there a pressing need to have a DOI rather than a URL/URI? The figshare approach would certainly work, but putting three copies out there might confuse people - if you do this I'd recommend including a coversheet on the figshare version pointing to the other two copies and clarifying that the content of the thesis itself is the same.

Not a "pressing need", certainly. I'm just exploring options. Thank you for all suggestions.

Regarding strategy for assigning a DOI, my personal preference is to use my university library's repository for that. I prefer to use my own university's repository as the canonical source of bibliographic information about my publications to remain maximally in control of it. My university library happens to be able to assign DOIs. I realise that not all repositories do this and in that case, I would recommend using a repository such as figshare or Zenodo because they provide open access to the published material and you retain your copyright. It seems ProQuest offers the latter but not the former.
A special case where one has to be careful is if you do not own the copyright to all of your thesis. This was the case for my own thesis which consists partly of papers for which Springer and IEEE own the copyright. They allowed publication on my university's own repository but I could only post the introduction on figshare, because that implied CC-BY licensing.

Thank you for the answer (+1) - your insights are helpful. As I said in comments above, I was considering figshare and Zenodo repositories (and actually use Zenodo to assign DOI to software that I've developed for my dissertation data analysis - though it's a bit tricky - I will post a separate question on the issue). I just checked and found out that ProQuest didn't assign DOI to my dissertation. Since my school's e-repository didn't either, the issue remains, but it's not a high priority one.

BTW, while ProQuest doesn't assign DOI, it does assign ISBN. While ISBN is focused on physical products (books, journals, etc.) rather than their digital counterparts, I just read about the existence of a service for "mapping" between DOI and ISBN systems, called ISBN-A ("actionable ISBN"). Unfortunately, ProQuest seems not to be using the service.


text:
Publish an article in the journal in which one is an associate editor
I want to know whether is it normal to publish an article in the journal in which one is associate editor. For example, one of the co-author article in this article in this journal.

If you are curious, you could ask the publisher what their conflict of interest procedures are, but I'd be very careful about asking regarding specific papers: it's difficult to avoid having it come across as an accusation.

It is not normal, but it can happen. Usually under such circumstances the article is handled by a different editor, and the submitting editor is treated as would any other person submitting to the journal.
Also note that a paper can be submitted to a journal like Physical Review Letters, and them get transferred to another journal where the conflict could be created. (This happened to a colleague.)

I think how normal it is depends on the field and the type of journal.  For a very prestigious journal with a small editorial board, it would be highly unusual.  For a mainstream journal with a large editorial board, especially in fields where big collaborations are common, it may be difficult to avoid.  Every journal that allows publication by editors should have formal procedures in place for how to avoid conflicts of interest.  They really ought to put these on the web, but often they don't.

In my field (Epidemiology) it is quite common to publish in a journal where you are an associate editor. It's a fairly regular thing to see articles with authors who are also on the editorial board appear in an issue of the journal, and no particular fuss is made about it.
If nothing else, the Associate Editors for the American Journal of Epidemiology is both quite large (well over 70 people), and in some cases make up a large chunk of the senior faculty of a given department. With how prevalent collaboration and large co-authorship papers are in the field, not submitting would lock huge swaths of the field out of a particular journal.
AJE also has one of the most robust paper anonymization systems I've encountered for review, which I think makes the threat of any particular conflict of interest fairly small.

It is entirely normal, with some uncommon exceptions. For instance, check out how many publications Prof. Tony Cai (former Editor in Chief) has in The Annals of Statistics.
In this case, the papers have to go through the usual peer review process, handled by another editor/AE.

Can the E-in-C see the names of the reviewers handling the papers?

I do not think the situation you describe necessarily creates a conflict of interest, and thus I believe there is nothing inherently unethical about publishing from time to time in a journal where you are an associate editor.
The question, as Anonymous Mathematician nicely phrased it, is more "what measures does the journal take in this case?" At a minimum, it must be a different editor who handles the paper, maybe the editor in chief. And the system must be designed so that the anonymity of the reviews cannot be breached by the author/editor.
If this is enforced, then I don't see any major ethical issue. The one risk I see is that the author/editor might get a slightly more "deferential" treatment, but this is also a risk for some other authors, e.g. big names in the field. One case which might become worrying is if an editor were to submit the large majority of his papers to the journal he works for... Even if everything is ethically above board, it may look like collusion, and should probably be avoided.
Now, I want to highlight some reasons why it is desirable that editors are allowed to publish in the journal they work for.

If they are editor for a major flagship journal in their field, it is not fair to ask them, their students and coworkers to avoid it entirely. It could make a large negative impact on, e.g., graduate students' careers. (Imagine a chemist who could not publish their major work to JACS, or a physicist to PRL.)
If they want their journal to succeed, they want to attract the best papers. If they rightfully believe that their own work is good, publishing it in the journal will sustain its quality. I am not an editor, but I do that myself sometimes: publishing in a journal because you think it's a nice venue for the community, and you want to help it grow. I imagine an editor, who wants the journal to succeed, might feel the same.

There is nothing wrong with an editor publishing in the journal with which they are asociated. Put it differently, why should ones right to try to publish somewhere be limited?
All editors, at least should, be aware that publishing this way has some possible repercussuins. If an editor starts pouring out works in "their" journal, it will soon reflect negatively on both the editor and the editor. Hence, such behaviour is "self-regulating" in the longer term.
It is of course possible that a research field is very narrow and so the journal may be the only major outlet for papers in the field. In such a case there may be no escape but I would then also argue that the science community concerned may know each other quite well, peer presure should then be a major factor keeping things on course.
I am personally Editor-in-Chief (EiC; one of two, with 12 associate editors) for a journal. My fellow EiC has published one paper, I have not (there are enough journalsin my field so that it does not affect me too much). We make sure, in fact our electronic submission system ensures, any editor submitting a paper cannot see or affect it in the system. We also take care of papers from each others departments to avoid any suspicion.
So, the "problem" is quite common and unavoidable to some extent. It is only a problem if it is abused but that will likely soon back-fire on both the journal and the editor.

Even then I believe there is a conflict of interest here but you are correct to say that "if it is abused but that will likely soon back-fire on both the journal and the editor".


text:
How can I cite a workbook?
I want to cite someting from this workbook. How can I cite it? The year is 2009 but what should I put between brackets if there is no specific author?

The pdf file has "Gilles Couzin" as the author. You could contact that person and ask if he(?) indeed is the author ...

I would treat it as an online resource since it is not published and might be replaced by a newer version at some point. To cite this, you don't need an author but make sure you state the date when you retrieved the resource. In BibTeX it is done using @misc entry for example.
Another, but less formal, possibility is that instead of a reference, you use a footnote where you will place an URL and the date you retrieved the resource.

As this is published by IT services and not an academic part of a university, I would treat it the same as a sales brochure from a company.  The author is the institution.
Note that if you follow the guidelines for getting a copy + associated documents as in the document, you get to this page, which states "The publicly accessible documents on this page are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 2.0 UK: England & Wales License. Their "original author" is the University of Bristol which should be acknowledged as such in any derivative work." (my emphasis)

Incidentally, the PDF author is apparently http://www.bris.ac.uk/contact/person/getDetails?personKey=iLhaBgn6CGP8pOCJqjV1K2BQLzJ6aI

So can I say Information Services (year) ? and in the references refer to the University?

@Kaser I would probably use "University of Bristol Information Services" - just saying "Information Services" is rather vague.  It's definitely personal preference by this point though.


text:
Will the bad grade in a proposed studied subject be a red flag in my application?
I am currently doing final year project on a subject which I did not have a very good grade(I took three courses in this subject with grade A-, A and B+, only top 5-10% can earn a grade of A and A+). I am quite interested in it and plan to continue in this subject in graduate school. Will this grade have bad effect for my application? Can I indicate my interest clearly in my PS given that my grade is not perfect?

By the way, the B+ is actually the grade for the graduate course. That is why I am so worried. Said...

@UV-D Thanks for UV-D's reply. Actually I have not consult the administrative people about this question (Actually I doubt that I could ask such questions to them?). As I am preparing for my PS, and I read in one post said a bad score in the interested subject is a "red flag". I am quite worried about this. UV-D, do you mean that I could still indicate my interest in my PS? Thanks!

@Daniel: "A bad score in the interested subject is a 'red flag.'" This is true. But a bad score is well below a B+, particularly if only 5% of students get an A or A+!

@aeismail: Thank you for pointing that out clearly. This brings me another question. We all knew that grading system varies from department to department. For certain application form, I could indicate it clearly as the space is provided; for others, shall I state it clearly in my PS? Thanks

This may be handled with your university transcript, in which case further explanation isn't necessary, unless there are exceptional circumstances about which you want to make the committee aware. (For instance, serious illness, family emergency, etc.)

I don't believe there is a serious stigma associated with an undergraduate getting a B+ in a graduate-level course. It is generally understood that undergraduates taking true graduate-level work (with graduate-level course numbers, etc.) are taking exceptionally advanced subjects, relative to their own preparation. Therefore, it is entirely understandable that you might have an A-, B+, or even a B in a graduate-level subject without it having a strong impact on your chances for graduate-school admissions. Exceptionally weak performance (corresponding to "failing" grades—usually C+ or lower) would be an exception to this, but I see no reason here why you should worry too much.

Thanks for the detailed answer. I found it is hard to decide what to put in my PS. Maybe I will write a new post on this issue later. Many thanks!

One solution to this would be to ask the instructor of the course to write one of your letters of recommendation. If you were indeed performing at a graduate-level while still an undergrad, then he or she should note this in his/her letter.


text:
The best ways to cite a theorem whose assumptions/conditions are written earlier in the source?
When one cites a theorem from a source in mathematics, the following problem usually arises: some assumptions/conditions of the theorem are written much earlier in the source, which do not appear in the statement of the theorem.
What are good strategies to solve this problem so that the writing could be more reader-friendly?
On the one hand, citing the theorem simply as "By theorem 3.1.4 in [Fang 2013] ..." means the reader may miss some of the conditions of theorem 3.1.4 if they appear earlier in the source.
On the other hand, yes, restating all the conditions of the theorem is considerably the "best" way. But if one has to cite a lot of hard theorems in a proof, restating everything may distract readers from the main issues.

Let me construct an example: if a chapter in a commutative ring theory book begins with "All rings in this chapter will be Noetherian", any theorem containing the word "ring" in this chapter would not include the word "Noetherian". If I cited one theorem in this chapter merely by its "number", a reader may be easily misguided if he/she directly read the theorem without reading the first sentence of this chapter.

People who write papers with uncontained theorems are the worst.

There are a number of ways to handle situations like this, depending on how much prominence you want to give to the result you are citing.
If the cited theorem is quite important to your work, and you think the reader will benefit from seeing it written out, then you can include a complete statement:

Theorem 1.2 [Smith 1953].  Suppose $X$ is compact, Artinian, and hyperfinite, and $\sqrt{Q(X)-57} > \pi/4$.  Then $U(X) \sim \gamma$.

[Oh right, we don't have MathJax here. :( ]
Then elsewhere in your paper you can say "By Theorem 1.2, ..."
If the hypotheses of the theorem are particularly complicated and you don't feel it's helpful to include them in your paper, you could write:

Theorem 1.2 [Smith 1953].  If $X$ satisfies the assumptions of Section 5 of [Smith 1953], then  $U(X) \sim \gamma$.

Then you can write elsewhere "We can easily check that $Y$ satisfies the conditions in [Smith 1953], so by Theorem 1.2., $U(Y) \sim \gamma$".
If you don't care to say much about Smith's result (perhaps it's well known, or you're just using it as a black box), you can just cite it, perhaps with a brief comment about its assumptions:

Since $X$ is hyperfinite, by Theorem 5.6.7 of [Smith 1967], ...
By Theorem 5.6.7 of [Smith 1967] (which requires $X$ to be hyperfinite)...


text:
Adding co-authors after acceptance
I am writing a paper, need some review. I want to send it to IEEE, without the name of my co-authors. I might get acceptance. I need to know, in that case, will I be allowed to add my co-authors or not?

why would you even want to do that ?

Apart from anything else, there’s a good chance that one of your co-authors would be picked to review the paper. Now that would be awkward, wouldn’t it?

@KonradRudolph if by awkward you mean “unquestionably unethical”, then I agree :)

Sometimes peer-reviewers do more to advance a paper than some of the less-significant co-authors.

@F'x Well I was thinking more from the direction that said coworker gets the review copy and thinks “wait a minute, I know that paper. Why am I not on the author list?”

I am writing a paper, need some review. I want to send it to IEEE, without the name of my co-authors.

Short answer: Hell no!

Depending on the editorial policies of the venue you submit, they may or may not allow to add co-authors during the review process. Some may even accept you to add co-authors after acceptance of the paper.
However, note that in all cases, it is unethical not to have a correct/honest list of co-authors at time of the first submission. All persons who have made significant scientific (or “intellectual”) contributions to the work should be co-authors in the submitted version of the paper.
“Hiding” co-authors during the first submission, even if you intend to add them at a later point, is a clear ethical violation. It probably also violates the journal's (or conference's) policy, which typically stresses the importance of having an appropriate authors' list (and even sometimes provides criteria for authorship).
The reason that editors may allow you to add authors is for special cases or circumstances. The main reason why it would be used is when, during revision of the work to address reviewers' comments, someone who wasn't a co-author of the initial manuscript has been brought onto the team. For example, if you asked someone to run some extra analyses and his contribution warrants authorship of the revised manuscript.

I completely agree, but regarding your example of a special case where this would be appropriate: if the revision included significant contribution from a new author, why wasn't the revision submitted with this author's name on it? Still seems unethical to me.

@Bitwise yes, that's what I mean: if someone contributes to a revised manuscript, his name should be on the revised manuscript (even if he wasn't on the original manuscript)

I agree with F'x's answer, but let me expand on it a little: intentionally submitting a paper without listing your coauthors is a potentially career-ending mistake.  If I caught you doing that at a journal I edit (or as a referee), I would fully inform everyone - your coauthors, department head, university administration, etc. - and I expect it would lead to severe consequences, such as expulsion from grad school or tenure denial.  Ethical violations vary in how serious they are, and deliberately omitting coauthors is among the most serious.
Even if you confess and ask for your coauthors to be added, people may not believe you always planned to add them.  Instead, some people will suspect that you initially intended to take all the credit but lost your nerve or feared getting caught.  You may know that was never your plan, but your word won't mean much when you're already confessing to something unethical.
It will be even worse if you get caught during the process.  For example, one of the referees might already be aware of who is involved in this work, or might even be a coauthor.  If they turn you in, you'll be in a particularly bad situation.
In either case, your coauthors will likely be furious with you.  They presumably don't think the paper is ready to submit (if they do, then you should submit it with their names on it!), and they also don't want it circulated with just your name on it.  Regardless of the journal's policies, you'll have to answer to your coauthors.
Even if you manage to salvage your career, this will stay with you forever.  In short, don't do it.

As @F'x and @AnonymousMathematician said, don't do that by any means.
If you feel there is some good reason that @Suresh cannot find then on the basis of that reason you can request a double-blind review.
Due to the way you worded the question, my guess is that you don't have good reasons to do that. You should agree with your co-authors whether you want to send a paper or not before sending it for review.
Besides of the ethical reasons provided, there could be legal consequences, AFAIK you are not the holder of the copyright of what your co-authors did, and if you disclose, publish or attempt to publish some information without their consent then they could start legal actions. If you had their consent, holding their names for the review would be very dodgy and ruin your reputation.
Therefore, to answer the question: "will I be allowed to add my co-authors or not?", the answer is "no", and it doesn't really matter if you try to add them or omit them, this has many chances of backfiring in a dreadful way. Hopefully you didn't send it already, if you did and no review was started then withdraw it asap. If the reviews started, then start to apologize deeply to everybody.

You can't "request" a double blind review in most places. It entirely depends on the journal's policy...

@yoda please check the link, this is a specific question and answer. If this wasn't specific of IEEE then most probably you cannot "request" a double blind review, but then you can search for venues that do that (upon request or by default). Thank you for the clarification in any case.

@Trylks Even in double blind review processes, we are supposed to mention the collaborators during the submission. It will be just hidden from reviewers. The authors needs to be mentioned because of COI reasons.

In general this depends on the conference regulations, so the advice is to check them.
Usually you must put information about all authors before the submission deadline. For instance, here are the rules on EDAS submission system regarding this matter.

You can add other authors later and you can change the order of
  authors. Note that some conferences do not allow that you add or
  delete authors after the submission deadline, to prevent that authors
  try to defeat the conflict-of-interest detection mechanisms by
  omitting authors.


text:
arXiv identifier near the end of month
If one submit a paper (today) on Oct 30th at 20:00:01 GMT (16:00:01 EDT) on arXiv, which announces on Nov 1st 00:00:00 GMT, is the identifier 1311.xxxx or 1310.xxxx?
What is the general policy of arXiv to have 1311.xxxx or 1310.xxxx when submitting a paper near the end of Oct? When is the cutline between the twos?

http://arxiv.org/abs/1310.0079

Why do you want to know this? Why does it matter?

The information on arXiv's help pages implies that the identifier is based on the submission date, see e.g.:

Submissions are assigned identifiers and appear in the listings in order based on the submission time (the last time the "Submit" button was selected at the end of the submission process). An edit and subsequent "Submit" will reset this time and thus change position in the listings. Edits are permitted between 16:00 and the 20:00 announcement time. However, doing this will remove the submission from that day's announcements and delay it until the next day.

If so, a manuscript submitted today should get the identifier 1310.xxxx. This also seems to fit with a couple of random papers I looked at, e.g. this one (Submitted 27/09-2013, announced 01/10-2013).
However, note that arXiv seems to use 20:00 GMT as the daily deadline for submission (see e.g. here), so submissions made after that are transferred to the next date.

Thanks, but, are you sure??? Like this one: http://arxiv.org/abs/1310.0050, from 1310.0001-1310.0050, they all submitted in the end of Sept, but their numbers are 1310.xxxx. Can you explain it?

@Idear I only know what I have read on their help pages, and I'm not affiliated with arXiv. However, in that particular case I suspect that the reason is that the paper was submitted after 20:00. See quote above and here - "...there is roughly 1/4 hour remaining until the next deadline (Wed 30 Oct 13 20:00:00 GMT).".


text:
Is it ethical to keep authorized readings after course is over?
I was the TA for a course a few years ago.
As part of the course, I was able to obtain a set of business case studies.
At the bottom of each page, it is written something to the effect of:

This document is authorized for use by [my name], from [start date] to [end date], in the course [name of course] at [name of school]. Any unauthorized use or reproduction of this document is strictly prohibited.

Is it ethical for me to keep these readings after the course is over,
and to read them some time in the future?
Conclusion
I appreciate the opinions of all who answered and commented.
I had asked this question because the licensing agreement
sounds too bad to be true.
The students had to pay more than $100 for all the readings for this course.
If the students were to purchase a textbook,
at least they are allowed to keep it and read it in the future.
I suspect that the publishers wishes they had the technology available
to make the case studies like the
"Mission Impossible" style self-destruct messages
which would explode once it is past the license end date.
This seems acceptable to me for software,
but strange for something like readings.
At the end of the day, I have to make my own decision
about what is the right thing to do in this instance.

One "right thing to do" is to complain vociferously to the department head about this choice of material/license.  While there may be some benefit to using real world case studies instead of carefully crafted synthetic ones, it surely isn't enough to justify robbing the students of their class materials, which they purchased, at the end of the term.

"This seems acceptable to me for software, but strange for something like readings." Holy smoke, this hurt so much you may as well have punched me. Software is speech, too. https://en.wikipedia.org/wiki/The_Right_to_Read

Technically, it may not be ethical to keep a case or data set past its license period. Most dataset licenses also specifically state that the holder should not hold material of both physical or digital form (or even preprocessed form) of the licensed matter past its license term. It also stated that the backup of all forms should be deleted.
Having stated above, it is still a widely practised taboo to use cases and datasets past their license periods. You may attain knowledge from it but will only get into trouble if you were to publish any material that relates to the dataset/case that you currently possess beyond its license. This also depends on how strictly the license owner enforces the license.

The legal/moral status doesn't depend on the owner doing sloppy enforcement of their rights.

As included in the first paragraph, it isn't legal to keep documents owned by another entity which is licensed to you beyond limited period. I just stated the level of risk involved depends on what you do with the document.

That is a highly specific restriction, I'm not going to discuss whether or not it is legal and to what extent, but take it as it is. It clearly states the extent of your use of the readings, so after the licence expires you can't use them any longer.
That certainly includes presenting them in another course or the same one next year or putting them online etc. But, I don't think there are ethical reasons why you couldn't keep them for yourself, since you already had unrestricted access to that information for some period of time. So in that light, you could've learned them by heart or transcribed them into your notebook by the time the licence expired.
Bottom line, from the ethical point, I don't think the restriction applies for your personal use. From the practical point, you could contact whoever licensed the readings in the first place and inquire the specifics.

The answer is implicit in the condition that you mentioned: the document is authorized for use by you, for a specific period, and only for a particular course. Anything else is prohibited. You may ethically keep the objects (printed pieces of paper) as long as you do not use them in any way whatsoever, which would include reading them. Bottom line, the restriction does not say anything about a personal use exception. As with any contractual matter, you can always ask for a free modification of the conditions, but you must ask.

I don't see how the ethical question can be answered completely without the legal question whether the statement is binding or not and to what extent.

It is certainly ethical to find out whether the conditions are legal in your country - particularly, if the conditions seem to be "too bad to be true".
The fact that a publisher writes some conditions does not necessarily mean that they are binding in your legislation.
Copyright legislation here (Germany) allows teachers to copy e.g. a chapter of a book for their course - the university has to pay for that (via VG Wort) but doesn't need to ask for permission - unless the publisher offers e.g. a dedicated teaching pack - which may or may not be the case in this question.
My "legal feeling" again for my legislation (Germany*) is that there is a big difference between going on the use the course material as a participant of a course (OK) vs. going on to use the course material as a teacher for a new course (not OK).
In this question, what is ethical for me coincides with what is legal. I don't see any reason to apply ethical guidelines here that are more strict than what my legislation asks for. Nor do I think there are good reasons for not paying the legally required fees (AFAIK 0,008 EUR/text page/course) for use of teaching material (the more so as university teaching is privileged here over commercial courses where that easy procedure does not apply).

I'm not a lawyer, but my understanding is that the kind of disclaimer you've described is legally baseless in the USA, and you shouldn't feel bad about ignoring it. Feel free to keep your readings, refer to them, and cite them in the future. Once you've purchased a physical copy (without some agreement otherwise) nobody can legally place restrictions on the ways you use your physical copy.
If you want a strictly ethical answer, I would say that it's unethical for the editor of your readings to try and restrict the ways in which students use the material they've purchased. They've got no legal basis to do so, unless you've signed a contract or otherwise mutually agreed on some restrictions. You may upset someone by ignoring their wishes, but that's not the same thing as being unethical.
The relevant US legal concept is called the First-Sale Doctrine. It says that once you purchase or otherwise obtain a physical copy of a written work, you are then free to do with it whatever you want. You can take that physical copy and keep it, you can read it, you can sell it to another student taking the class next year. Once the owner sells the physical copy, they lose any interest or control in the physical copy, and you are free to do with it what you wish.
Note, however, that copyright law prevents you from freely copying a work. You have your physical copy and can do most anything with it, but you're not allowed to make your own copies and then distribute them.
As an aside, any teacher who is telling students that they can't keep written documents and notes from their class, without an extremely good reason (the course material is considered secret or privileged), is probably not a teacher you want to have. My guess is that the person who added that statement wants to encourage every student to purchase a new copy of the course materials every semester at full price. I would call that behavior grossly unethical- students are not a cash cow to be milked at every opportunity.

It looks like the use outside of that particular course and date range is prohibited. You might probably keep the documents/data, but you can't use it at all. Even using it for a completely unrelated purpose (say as practice data for statistical analysis in another course) is not allowed even during said date range.
The conditions imposed are quite draconian, and might even be considered unreasonable. But that would be for a court of law to decide, and you don't want to go near that. You agreed, abide by them.

actually the OP asked whether it is ethical, not whether it is legal, so that's not a question for a court of law. Some things are ethical that aren't legal, and vice versa. Given that you recognize the legal restrictions are draconian, one may plausibly argue that it is those restrictions that are unethical and that there is nothing wrong with breaking them. In fact, even the law recognizes that a contractual obligation entered into willingly by a party may be invalid for ethical reasons (look up "unconscionable contract"), so even a court of law may not agree with you.

@BenCrowell, then OP was not entitled to use them during the course either.

@vonbrand: What rights does the OP not have, without this license?  He wouldn't have the right to make copies, but it doesn't sound like he wants to.

The definition of Ethical Behavior as defined in an entry from www.businessdictionary.com is:

Acting in ways consistent with what society and individuals typically think are good values.
Ethical behavior tends to be good for business and involves demonstrating respect for key moral principles that include honesty, fairness, equality, dignity, diversity and individual rights.

As you are discussing your decision and your action and in general our society has an expectation that people will honor the terms of the contracts that they enter into, then in order to act ethically you would likely need to either

Destroy all of the copies of the business cases that you obtained under the license and not use them.
Request an extension as user6726 suggests
Purchase a new license to the material
Borrow a copy of the material from a library that has license to lend the material to you.

If you entered into and agreed to a contract, whether implicitly as was the case here, or explicitly, then violating the terms of the contract without agreeing to a change of terms with your contract partner or receiving a legal judgement that the terms of the contract are illegal and therefore you are not obligated to follow them would be an unethical choice.
To further add to this would be the idea of fairness, as you mention with regard to the fact that the students that took the class were required to pay for the readings where as you received the material to use in the context of teaching them. The license was either paid for by the school, which means indirectly by the students or from a grant obtained by the instructor for the course, or was a comp from the publisher for the instructor selecting the material for the course in the first place. So while you could argue that your use is not really harming the copyright holder, the fairness argument to those who had to pay for the license, namely the students, calls into question the ethics of using them and strengths the case for not using the material.
That being said, I find the ethics of the publishers that chose these types of limited licenses highly questionable. When I have seen these types of licenses, they are generally for texts that get updated with great frequency, and the updates to most every chapter are at most a few sentences or a figure or two. It is part of a broader business model to make used textbooks less valuable and to force students to purchase the version of the text that the instructor is using. This is more the case where an instructor assigns homework problems and the problems are renumbered or parts of the problem are changed so that either the instructor needs to manage responses from multiple editions or they need to insist that everyone buy the new version. Another way to devalue used editions is to sell and get instructors to use online material which is licensed only to a single user and expires with the end of the course.
The problem is that two wrongs do not make a right. So just because the publishers are behaving questionably does not mean that it gives license to act unethically in response. Can you do it and live with yourself? Sure. But that is entirely your choice. And as you said, only you can answer that question for yourself. Strictly, in a legal framework you are breaking the terms of your contract and their copyright. And as a few of the commenters above stated, if you were to then use that material for new work produced, you could likely find yourself in trouble not only with the copyright holder, but also your institution if you published based on material you did not expressly have license to access.


text:
Wearing dressy clothes in the "lab"
I'm a Ph.D. candidate in a theoretical field, so there is only math and programming involved (as opposed to a wet lab). The environment is very casual, everyone just wears jeans and a t-shirt everyday. Sometimes I dress semi-formally (e.g. a dress shirt tucked into nice slacks) just because I like to. I notice people tend to give me quite odd stares when I do this. In the blue hair thread, a highly voted comment remarked:

I only remember one situation in my field where somebody’s looks were commented on and that was somebody wearing a tie and a suit as a PhD student.

and further in the conference appearance thread (which is a dressier occasion than daily lab work):

if you are young (<30) , wearing a suit and a tie would probably seem a little weird.

I'm likely over-thinking this, but is it inappropriate for me to wear dressy clothes in the lab? Obviously it's not offensive or anything, but I wouldn't want to make anyone else feel uncomfortable or have them dislike me for what I wear. Any thoughts?

You know, the answer to this is actually trivial (imho). Why do you care? People get used to things pretty quickly and if others look more at your appearance - especially if it is good - than your work you should probably not deal with them anyway.

So long as you're not violating any university dress code (and I can't imagine you are), it's probably an issue of why you're changing your routine. Again, nothing to make a big deal. A well-timed joke or two (not making fun of them, of course) might break the tension and put the whole issue behind you.

Even if you are over 30 do you need to suit up in the lab? - that is a weird custom.

A good part of theses comments come for the fact that it's fashionable to look unfashionable as an academic (I dress goofy/too casual, hence I'm a genius, right?, right?). Just ignore the hype. I wore a shirt, proper pants and decent shoes everyday to the lab (that occasionally included experiments for which I wore a lab coat) as a postdoc in the US and nobody frowned upon the practice.

I notice people tend to give me quite odd stares when I do this. There is only one way you can solve this. Get a ridiculous bow tie!

Cedric Villani?

@CaptainEmacs Ya got me

This question is similar to: Dressing etiquette for interviews in academia. If you believe it’s different, please edit the question, make it clear how it’s different and/or how the answers on that question are not helpful for your problem.

It is perfectly appropriate since most university dress codes for students is to make sure nothing offensive or too revealing is worn (local definitions for both of those are widely variable). It sounds like you are having trouble working out if it is simply that you are unusual or if it is actually a problem. The simple solution is to ask some of the folks in your lab what they think.
If it turns out you are worrying on their behalf when they don't care, then keep wearing nice clothes.
If it turns out they care then you actually need to address that, whether by asserting your right to wear what you choose to within the official dress code or by making adjustments. Since clothes are social markers it might be what they perceive to be your statement that is the problem and not the clothes themselves.
It is always possible they are glaring at you for completely unrelated reasons. Again feeling that out is worth your time.
A personal story, I wear Hawaiian print shirts every day while teaching. One day I wore a plain button down shirt and my students asked what was wrong. It was laundry day. So don't discount the possibility that the only thing going on is that you stand out from the norm and nothing beyond that.

True labs, of course, have their own additional requirements to ensure safety of personnel and visitors.

There is nothing wrong in dressing formal. The whole point of dressing "casual" is to feel comfortable. If you like dressing up then for you this is comfortable.
I myself have noticed that people in science/tech start treating their "casual" wear as some kind of a uniform, like forcing everyone to wear a jeans and a t-shirt just because Steve Jobs did. This obviously misses the point of "casual" wear.


text:
Do reviewers of research proposals for a fellowship read the whole application, or only the scientific part?
If you are applying for some fellowships, there are many fields which you have to fill in. For example, what will be benefits for a host country, what will be the benefit for your home country, what will be the benefit for you or for your host supervisor, what will you learn, what have you learned yet, etc. There can be a scientific abstract, lay abstract or questions like what will be the impact of a fellowship on your future.
Who will read your whole application?
Scientific reviewers of your project will get only your research proposal, or is it their role to read all this fields?  Are these field kept just for cases, when there are two similar candidates to get support, and than these fields can be critical?

I've never heard of most of those fields.  You may need to specify which fellowship you're talking about.

From my experience, reviewers get the whole proposal and also read the whole proposal. Reviewers try to get a complete picture of the applicant and skim the proposal for all relevant information in this regard. This means, that probably no reviewer will read every word of the proposal, but potentially, every word will be read by some reviewer. The reviewers base their review on the whole picture they get, but usually their feedback is only for the part for which they are specialists (e.g. the scientific strength of the applicant and so on…).

I'd say it could depend. I've been part of review committees (not for fellowships) were I got only a part of a proposal (say the scientific proposal, or the funding summary) to analyse, others in which I got all. Sometimes I got all, but was to evaluate only certain aspects.