text:
Preparing an IEEE conference accepted manuscript for arxiving
What exactly do I need to do when arxiving a accepted manuscript to an IEEE conference? Which license to select on arxiv? Do I need to add the reference/doi not only to the arxiv metadata but also the document itself?

Background.
I've a paper that has been accepted at an IEEE conference. After I've received the reviews and acceptance notice, I was asked to incorporate changes and include a copyright notice that was provided to me, something like

123-1-1234-5678-0/12/$31.00 c 2015 IEEE

I assume this last pdf then is the so-called postprint or accepted manuscript.
I want to post this on arxiv and wondered what I need to do. It seems the accepted answer to the following question does not really match my case:
Conditions for uploading IEEE publications to ArXiv.
Also it somewhat doesn't match
An FAQ on IEEE Policy Regarding
Authors Rights to Post Accepted Versions of Their Articles:

Does the policy affect how authors post their articles on preprint
  servers such as ArXiv? Yes. The IEEE recognizes that many authors
  share their unpublished articles on public sites. Once articles have
  been accepted for publication by IEEE, authors are required to post an
  IEEE copyright notice on their preprints. Upon publication, authors
  must replace the preprints with either 1) the full citation to the
  IEEE works with Digital Object Identifiers (DOI) or 2) the accepted
  versions only (not the IEEE-published versions) with the DOI. IEEE
  journals will make available to each author the accepted version of
  the article that the author can post that includes the DOI, IEEE
  copyright notice, and a notice indicating the article has been
  accepted for publication by IEEE. IEEE conference authors are free to
  post their own version of their articles, as accepted by an IEEE
  conference.

Which in turn is somewhat different from the information provided in
An FAQ on Intellectual Property Rights for IEEE Authors:

Can an author post his manuscript on a preprint server such as ArXiv?
  Yes. The IEEE recognizes that many authors share their unpublished
  manuscripts on public sites. Once manuscripts have been accepted for
  publication by IEEE, an author is required to post an IEEE copyright
  notice on his preprint. Upon publication, the author must replace the
  preprint with either 1) the full citation to the IEEE work with
  Digital Object Identifiers (DOI) or a link to the paper’s abstract in
  IEEE Xplore, or 2) the accepted version only (not the IEEEpublished
  version), including the IEEE copyright notice and full citation, with
  a link to the final, published paper in IEEE Xplore.

What's the difference between the two? Both seem to say that you update your preprint (accepted version) with the copyright notice, citation, and link to Xplore, and post that to arXiv.

To me it seems the first differentiates between journal and conference articles, where the latter can be arxived "as accepted by an IEEE conference" -- so in my case, the conference already asked me to include the copyright notice, but no citation or doi (or Xplore) link -- this pdf is then almost indistinguishable from the one available at Xplore...
Also, what copyright should I select on arxiv?

When it says "IEEE conference authors are free to post their own version of their articles, as accepted by an IEEE conference" it just means that the conference won't give you the version to post (as opposed to "IEEE journals will make available to each author the accepted version of the article"). As far as I can tell, the accepted answer to Conditions for uploading IEEE publications to ArXiv does match your case, and this question is a duplicate.

I see, that's what it could mean: for conferences one needs to add that info while for journals one is provided with the pdf.
I guess I disagree with that answer matching my case -- if you follow that link in that answer, it shows you a way to add footer info, yes, but looking at their output that's neither the provided copyright "123-1-1234-5678-0/12/$31.00 c 2015 IEEE" nor does it contain the full citation nor do I know where they got that sentence from..

this is the obvious answer, but i think you need to correspond with someone at or affiliated with the IEEE.  if they want you to put a copyright notice on the arXiv copy with a price tag, they might want it behind a pay wall.

If your question is how to add the info in latex, then it's a question for [tex.SE]. (And it's already answered there: see the second answer on that linked question). If that's not what you're looking for, then it's really not clear to me what your question is and you should really [edit] your post to clarify.

My question is not how to add that info to latex. But, if the two answers to that other question are both correct, then what information exactly needs to go on the accepted manuscript pdf before posting it on arxiv? The second only adds the copyright line "123-1-1234-5678-0/12/$31.00 c 2015 IEEE" while the first adds a notice that is similar to 8.1.9.B. In that sense these two answers provide different information?
I struggle with the imho rather obfuscating information provided by IEEE and different threads

Further sources of information -- http://www.ieee.org/publications_standards/publications/rights/thirdpartyservers.html -- and -- "IEEE conference authors are free to post their own version of their articles, as accepted by an IEEE conference." in http://www.ieee.org/documents/author_version_faq.pdf
I feel all that slightly different IEEE information is rather obfuscating what exactly can and needs to be done. To me it seems the concerns are not addressed in the mentioned other thread. I've also sent an email to ieee but not response yet.

It's been 11 days without IEEE responding now...

Here the relevant bits of a correspondence with copyrights@ieee.org.
Question:

I am having trouble understanding the policies on what exact
  information needs to be included in an accepted manuscript before
  posting it to arxiv.
Given an accepted manuscript at an IEEE conference, am I right in
  assuming that I need to include the following?
  (a) the full reference of the published version,
  (b) the doi linking to ieeeXplore,
  (c) the copyright notice as shown in 8.1.9.B, http://www.ieee.org/publications_standards/publications/rights/rights_policies.html
If yes, is there a standard procedure how to include those in a
  standard IEEEtran tex or does one just add them in any way convenient?
  If no, could you please clarify?
Note, however, that the accepted manuscript of a conference paper
  sometimes already contains a copyright notice of the following form
  "123-1-1234-5678-0/12/$31.00 c 2015 IEEE" i.e. the accepted
  manuscript, the version finally sent to ieee for publication and prior
  to copyediting etc already contains a copyright notice that is
  different from the one mentioned above. Would this one need to be
  replaced by the other one or which exact notice would need to be
  included?

Response:

Sorry for the delay in response. To the best of my knowledge there is
  no standard format to provide the information. You would need to
  provide the copyright notice as shown in 8.1.9.B from the PSPB
  Operations Manual:
“© © 20xx IEEE. Personal use of this material is permitted. Permission
  from IEEE must be obtained for all other uses, in any current or
  future media, including reprinting/republishing this material for
  advertising or promotional purposes, creating new collective works,
  for resale or redistribution to servers or lists, or reuse of any
  copyrighted component of this work in other works.”

Not sure this really clarifies the situation..?

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text:
Is it reasonable to worry about lack of potential for dating in postdoc positions?
I am 25 years old, and in a few months' time I will have to decide whether to get a job in London or apply for a postdoc somewhere.
Apart from all of the usual pros and cons (eg. job security, salary, lifestyle) associated to each path, one thing that worries me most is my loneliness. I am worried that if I were to get a postdoc (say at some small university in some small city), that I would never meet someone to date and get married to eventually. Most math postdocs tend to be male (I believe) which is fine for me since I am gay. But it seems to me more likely that I will find true love taking a city job in a metropolitan environment where there are many more people. And I am really not sure that the "single life" is amenable for doing a postdoc in a foreign country (where I'll likely have to look to find a postdoc in my field).
I apologise if this thread is not suitable for this board, but it is an important consideration in a potential academic's life. I would truly appreciate your thoughts and experiences.
Edit: I guess I am asking whether I am right to be worried about the lack of potential for dating in a studious and bookish environment like academia, and whether anyone has any advices about how to deal with this.

(a) postdoc is (usually) a short-term position, not a life-sentence. (b) Could you get a postdoc at a "large" city with many people and variety of communities nearby, and have both social and academic life?

In my experience, and this will depend a lot in the culture, you may get more social life in a smaller city. If you go to a large place, there are so many options that you are responsible to find them on your own; whereas in a smaller place people at your work are more likely to engage you into their social circles.

"I am asking whether I am right to be worried about the lack of potential for dating in a studious and bookish environment like academia" You are not. Of all the things I have heard about postdoc life, being unable to find a Significant Other is not one of them. If you would find somebody with a job in industry, you'll also do fine as a postdoc.

@RanG. (a) I agree, but I have heard it is much harder to get a normal job once someone has done a postdoc (eg. due to age). (b) I hope I will have that luxury.

You seem to be under the misapprehension that the UK contains nothing between London and "some small city". That's actually rather patronising to the rest of the country.

Personally, I think that doing whatever makes you happiest also optimises the odds for dating success.  I don't believe it is necessarily harder to find love in a community of 10,000 than in a community of 10,000,000.

@xLeitix: Sorry to contradict you, but you have heard it now. I met several interesting people when I was doing my postdoc, but when they found out that I was going to be forced to move cross-country in a year or two, they cut things off. (See Nate Eldridge's comment below.)

UK "small city" universities are great places to meet people. 1) The cities usually aren't that small - anywhere over 400,000 people will have a lively, varied, metropolitan social scene. 2) Smaller cities have more community. The university will be a great hub for like-minded people, and everywhere being not too far makes people more spontaneous. In London, everything is scattered. 3) Seeing people is less complicated. London is notorious for friends barely seeing each other because they live far apart and don't get around to scheduling a meet up. In small cities, they just meet up.

@Ben: meh, the median age of first-time fathers in the UK is around 30 now, I think. Everyone is postponing "adulthood" in that sense. Historically most people had children by 18, depending exactly when you consider "history" to be, so you could say the same of undergraduate studies ;-)

Many comments assume that OP is exaggerating how small a "small city" is. Maybe that's reasonable in a relatively compact country like the UK, but at least in US a big university could actually be really isolated.

@SashoNikolov The UK has 61 million people in an area not much bigger than Washington state (and 53 million of those are in England, which is a good deal smaller than Washington). There's no such thing as an isolated university here.

worry more about the "two body" problem once you find someone - if you find a fellow academic now you have to try to get jobs for each of you at the same institutions (or at least the same towns which in many cases is the same thing) - non trivial. For that reason some people try to resist forming bonds until they know where they will end up living.

@DavidRicherby Not intending to be patronising. I am at Warwick now -- not a small university and not a small "town". But it is very difficult for me to find "true love" here.

How is Academia different that any other job? You work for a number of hours a day, and then you are free to use your time solving jigsaws at home or socialising with other people.
Perhaps the academic environment has the advantage of multiculturalism. In most industries, the large majority of the people are from the country; but at universities you can find much more diversity, and thus, easier to find people you feel more comfortable with.
Lastly, in large cities there are, statistically, more potential "suitable partners", but they will be more difficult to find. As a mathematician, you may want to model it as an Erdős–Rényi graph, for the fun of it.
In the end, I think either path will have comparable a priori chances of finding love, so this should not be your main criteria to decide what to do with your life. Being happy with what you do will make you a nicer person, and have a larger impact that the city you are in.
And, to put at ease your concerns, most professors I know are married, and they certainly went down the postdoc path.

Not all mathematicians are specialists in Erdős–Rényi graphs, and life.

I know professors who found their professor partners long after getting a permanent job (in fact, I know one who married her PhD student), and I know people who were already married with children as they started their PhD studies.  The two-body problem may arise, though (see e.g. this question).

I must be doing something wrong. So far I am not managing to work a few hours a day and then be free to solve jigsaw puzzles. As far as the difficult to find point: dating websites, online meetup groups, etc. And finally, social networks are well known to look very little like Erdos-Renyi random graphs.

"You work for a number of hours a day" -- the upper bound on this number is relevant here. It does not seem to be uncontroversial.

@Raphael the same happens in industry. In both worlds there are people ranging from a strictly bounded schedule, to people putting insane hours.

From the anecdotes that I am familiar with, there seem to be two key questions:

Is the community that you are going to dominated by the academic institution?
Would you prefer to avoid dating undergraduates or potential colleagues?

If the answer to both of these questions is yes, then you may have a difficult time finding romance.  This is particularly true for some U.S. institutions that are not near anything else (e.g., State College, Pennsylvania), because most of the potential matches that you will meet would be too "close" professionally.  Likewise, if you have highly unusual tastes, your only option may be to go to a large city where the population of people you are interested in will be non-trivial.  Otherwise, however, your dating prospects are likely to be dominated by constraints on your social life rather than the number of possible matches.
There is a further consideration that is not in your post, but which I think is also important to keep in mind.  A postdoc is inherently a temporary position, so if you find a serious romantic partner, the two of you are likely to soon have to confront the two-body problem.  This doesn't have to be a show-stopper, but it's probably worth thinking about the degree to which you might be willing to adjust your career goals to match with the goals of a partner...

+1 for the last paragraph. In particular, if you enter a relationship which lasts until the end  of the postdoc, your partner has to be open to relocating, or you have to leave academia, or you have to do some complicated long distance thing, or break up. That's a nontrivial consideration.

Well, if you consider "potential colleagues" to include only people from within your own department or from closely related departments, State College still has a decent number of options. I know a lot of people who met their partners in grad school there, people from other unrelated departments or who were unaffiliated with the university entirely. (But of course you're right that it's about as isolated a college town as you can find anywhere in the US.)

@DavidZ There are worse at the postdoc level: consider, for example Los Alamos National Labs. Now that truly is a very small community where one might step very carefully around questions of romance...

Great question! I would not worry about the lack of potential for dating. I was a postdoc for three years, and although it was quite a lonely life, I had a lot of friends, mostly PhD students from outside my own department. The reasons for this were (a) it is quite hard to befriend PhD students in your own department when you are a postdoc; it's like an officer trying to fraternise with privates and (b) younger academics with permanent positions tend to be married/have children and are not looking for social life.
So although I was shut in my office all day, the graduate community in general was a great way to meet people. However, I did not find anybody. I think key reasons for this were (a) uncertainty about my future (I was doing a postdoc in a foreign country and in an area in which I felt insecure and probably wasn't going to continue, and I think that women found this lack of confidence and future plans unattractive) and (b) incompetence.
Now I am working in industry, and I don't find that single life in industry is any better or worse than single life as a postdoc. It's actually harder to meet people because there is no campus, and the people I do meet tend to be less interesting.
Summary: ignoring the other pros and cons which you mentioned, there might be plenty of potential for dating graduate students from outside your field.

I can't say I've ever had any difficulty befriending PhD students (or, for that matter, faculty) in departments where I've been a postdoc. Sure, you're senior to the students but you're not, to continue your military analogy, in the chain of command above them.

@DavidRicherby agreed. To add to that, being a PhD student hasn't been an obstacle for me in that regard. As long as I respect the person and don't make an issue of "status", age is by far the biggest factor in how to get along with someone.

Unfortunately, based on my experiences, I am somewhat more pessimistic than other answerers to the question. As a postdoc I met a couple of interesting potential dating partners, but they weren't interested in getting involved with someone who had to move across the country in a couple of years.
I then began a tenure-track job in a rather small, quiet city. For some people this is exactly their cup of tea and they are quite happy. For me, it represented some compromises that I had to make if I wanted to continue my academic career. Among them, I've found it difficult to meet people with whom I have much in common.
There are many ways in which your situation could turn out well! And, I think most people that decided to go into academia are happy with their choice. You might get a job offer in an appealing big city. You might end up in a small town, meet someone there, and discover that you love it. And at no point, even once you are tenured, do you ever have to commit to any job for the rest of your life. You can always apply for other academic jobs or go into industry.
Nevertheless, I'm afraid that I believe that your worries are indeed reasonable. Best wishes to you, whatever you decide.

How do you know that there isn't someone in this small institution that is thinking, "Damn, there are no dating prospects here."
And then when you meet said someone, well there isn't much competition.
But the fact is if you have a campus that will give you 10,000 choices vs another with 20 choices, it really comes down to there is only "1" and you don't know if that person is in the 10,000 or the 20.

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text:
I submitted a paper to two journals, and the first published it, but I agreed to publish in the other; what can I do?
I submitted my research paper in journal X on 7th July, 2014. Journal sent me one thanks email immediately. After that I waited for one month for any response from editor but nothing came from editor side.
Than I submitted my paper in other journal Y. My paper was accepted in that Journal and sent for review from editor side.
At 30 August, 2014 I received one acceptance email from the editor or journal X that my paper has accepted and I was asked to submit publication fee of 90$. But I could not reply this email due to busy schedule and I was also not interested to publish my paper in journal X. After that I could not receive any email or revision or anything from this journal X.
I continued to work with journal Y, modify paper according to reviewer comments, sign copyright agreement and now paper is in publication phase.
Yesterday, by chance I open my Google scholar account and find paper that was published in journal X to whom I was not interested and who was demanding 90$. When I checked the online paper, I was astonished that the journal published my paper in its July issue and date of publication was 1st July, even I send this paper on 7th July and journal X notify me about acceptance and fee payment on 30th August.
How its happened that Journal X published my paper without my consent and published it in back dates. Now what I should do because the same paper is in final publication phase in journal Y to whom I have signed copyright agreement also. Please guide me tell me any forum to raise voice against that journal X. Because I send many emails to editor of journal X but receiving no reply from editor side. Any penalty or any other thing which I can do.

I am not too sure Journal X is really wrong except that they had early submission date. You submitted your paper to them. They accepted it. You did not raise objection. Then they published it. It seems to me they did nothing wrong.

I never heard of a serious academic journal that allows dual submission except if one submission is to a preprint server, conference proceedings, non-refereed publication venue in a foreign language and the like. If you didn't explicitly tell Journal X that you would like to withdraw your submission, and if Journal Y doesn't allow dual submission, I think the only option you have is to withdraw your paper at Journal Y. By the way, the review process can take long. For example, in mathematics, it can easily take a year or two or even more. 2 months till acceptance sounds quite normal to me.

Journal X accepted paper but did not get my consent or sign any agreement. They contact me on 30th august for acceptance but published it on 1st july without my consent or even informing me.

You made a mistake when you submitted the paper to Y without telling both X and Y that you already submitted it to X..

Most journals do not reply in one month. I have the feeling that both journals are probably of low quality or scam journals. Either way, as @scaaahu comments you made a dual submission, which is a major mistake in Academia. And what is that: "I could not reply this email due to busy schedule", you did not reply to the journal you have submitted your work to? This is plain silly.

I'd like to amplify the apparent skectchiness of Journal X. If they did not have a copyright transfer agreement from you in writing, then at least in the US, they are in violation of the law and do not have the right to publish your article.

@BillBarth: While maybe true in the U.S., this might be different in other places. While a signed copyright transfer agreement certainly strengthens a publisher's position, other legislations might define this as a case of dispute, in which case judges and/or lawyers start analyzing and interpreting to what extent journal X could be seen as acting in good faith. Depending on the wording of the original CfP and the submission system, the mere submission by the OP might well be interpreted as condoning publication, for lack of anything more tangible. Hence, it depends on the publisher locations.

@O.R.Mapper, I'm sure you are correct, but I would hope that no legitimate publisher would publish an article without a signed copyright transfer agreement no matter what its local laws said given that the US is such a big market. Seems sketchy to me.

@BillBarth: Sure, I totally agree it is absolutely sketchy. I just wanted to point out that, dubious as it seems, they are not automatically violating any laws and might very well get legally through with that procedure, while in turn the OP might face legal charges.

@O.R.Mapper, I wouldn't overstate the risk of being sued by either journal in this case.

@Bill many "sketchy" publishers have an automatic copyright transfer clause that's probably for scenarios just like this one...

@ff524, that doesn't make it a legal copyright transfer in the US.

The OP has violated academic ethics. Journal X has violated copyright law (almost certainly). The OP should retract the paper from journal X. Assuming it has no print edition and that it actually takes the paper down, this may be the cleanest solution.

@TheodoreNorvell: That's it! I'm quite surprised that none of the answers cover that possibility (to retract from X and continue to Y). Can anyone further explain why this is not a plausible solution?

@justhalf Assuming Y prohibits dual submission, it is highly unethical to hide his or her misconduct and proceed to publish the paper in Y. Moreover, upon OP's submission, most likely X obtained the copyright, although it is unclear from OP's writing if it was done in a legally valid way. Either way, OP did not object publication in Journal X. Therefore, it is unquestionably unethical to retract it from X for the purpose of publishing it in Y. If anything, I feel that OP should disclose everything to both X and Y. This may result in getting banned from them for some time, though.

@YuichiroFujiwara If you are right that X owns the copyright, then everything else you say makes sense.  I was working on the assumption that X did not legally obtain copyright. They are in violation of the OP's (now Y's) copyright and so it was unethical (and illegal) for them to publish. In that circumstance the only ethical (and legal) thing for X to do is to retract the paper. None of this undoes or exculpates the OPs original mistake of dual submission; that is done and can not be undone.

Your mistake. Move on and withdraw from number 2.

It really irritates me when I spend valuable time reviewing a paper only to find that it's already been published somewhere else in the time frame I had allotted to review it. To avoid this problem (and others), journals generally frown on dual submission. Elsevier discusses it here: https://www.elsevier.com/editors/publishing-ethics/perk/questions-and-answers#duplicate

date of publication was 1st July, even I send this paper on 7th July I could not stop laughing. It seems Journal X lack communication skills

The fault here is yours.
You should never have the same paper be submitted in two different journals at the same time. This is an absolute rule that protects both you as an author and the journal as the publisher from duplication of effort, as well as avoiding situations like this.
If you had wanted to stop the publication in journal X, then you should have sent them a letter clearly retracting your submission. This would have ended the process at journal X, and allowed you to submit the paper to journal Y with a clear conscience.
Now, however, since the paper has been published by journal X, you are stuck. If journal Y publishes your paper, you will have the same article published in two different journals, which is also a violation of ethical standards, and could lead to both copies being retracted by the publisher. So, unfortunately, you are stuck paying the fees to the journal X, and the work you've done to improve the paper with journal Y is now "lost" to the literature.
As has also been pointed out, journal X appears to be quite sketchy, and I would avoid any future contact or involvement with them. But for now, consider this a lesson learned for the future.

"which is also a violation of ethical standards, and could lead to both copies being retracted by the publisher" - and not only that. Note how the OP pointed out to have "sign[ed] copyright agreement" for journal Y. If that agreement includes a clause about exclusive publication rights for journal Y, the publisher of journal Y would legally be in a position to sue journal X for copyright infringement, which (given the voluntary unretracted submission to journal X) might very well be passed on to the OP.

(The lack of a signed copyright agreement between the OP and journal X weakens the position of journal X, but the situation could well be in a realm where it is up to a court to judge whether the OP is, either intentionally or negligently, responsible for the copyright violation.)

@O.R.Mapper Somehow, if at least one of X,Y is a scam journal, the OP can still easily claim that one of them broke the policies, not the OP. However, this is again highly non-ethical.

I don't think it is clear that the OP is obligated to pay the fee. This may be the case, if the terms of submission specify this. But otherwise, the OP might not be obligated to pay. (If, for example, the journal is one which does not even tell you it charges until it 'decides' to accept your paper and only then tries to get money. Although I don't know why X would have published in that case. But they may be both sketchy and disorganised.)

Pretty much this, you published in X, send a letter/email to Y explained your mistake and ask for retraction.

I am sorry to say that you have ended up in a tricky situation totally on your own, and apparent lack of understanding of publishing. What you need to do? On the face of it the paper is accepted for publication in X and you need to withdraw the paper from Y.
Your description contains so many twists where you have seemingly dug yourself deeper that your best outcome is to learn from the mistakes and go on.
Some pointers:

You should never send papers to a journal where you really do not want to publish, or, I do not see the point of sending papers to a journal where you do not wish to publish
You should never send papers to more than one journal at a time. If the first choice rejects your paper, it is ok to pass it onto another
If you send a paper to a journal that charges for publication, there is no excuse not to follow up on those charges. Yo have essentially agreed to paying by submitting.
Your own time crunches is solely your problem. If you cannot answer E-mails or other correspondence in time, the world will not stop and wait for you.

So regardless of how you dislike journal X you have put yourself in a situation where you may have to accept the fact that the paper is with X and because of that Y should not be able to publish it.

+1 for ..If you cannot answer E-mails or other correspondence in time, the world will not stop and wait for you

You ask what to do with journal X, but I think it is more important to do the correct thing with journal Y first.
You should reread the copyright agreement that you signed for journal Y and see if you misrepresented the status of your work.  (Typically when one signs these agreements one is representing that the work in question has not been published before and is not under submission at any other journal.)  If so, you should immediately inform journal Y of your mistake and of the true publication status of your work!

I can't believe how everyone is blaming the OP.
Since you clearly did not sign an agreement with the journal X, I think you should talk to the lawyer and sue them. Laws may change from country to country regarding this, however it seems quite illegal to me that they demand $90 from you for something you did not agree for.
Does your university have a legal department to deal with such cases?
EDIT: I clearly understand that it's OP's fault to submit into 2 journals. However I clearly see 2 distinct issues here: 1. The OP unethically submitted to 2 journals. 2. Unethical Journal X supposedly published without the OP's agreement, as OP himself stated.

The journal may have an automatic copyright transfer clause, which says that submission of an article for review constitutes agreement to publish. Both journals almost certainly have a policy that prohibits dual submission, which the OP has violated. It's certainly not a straightforward legal battle, and it's one the OP may not have the resources for.

@ff524, good point, but I'm assuming that there is still some space for the OP to battle since there was no payment made, and the last agreement was not signed. It's however not a clear case, and involvement of the university would help a lot.

Whether or not the journals are also predatory is beside the point.  Dual submission is pretty much always considered unethical in academia, besides generally being explicitly against policy in journals.

@jakebeal, you're right, but that is a separate issue. Pointing it out really doesn't help the OP now. Journal X clearly did something wrong, this is what the question is about.

@Elchin: You can't separate the two problems here; the fact is that the unethical behavior of journal X does not excuse the unethical behavior of the OP.

@aeismail, on contrary. If I grow weed in my house but it's found through an illegal search, the evidence is inadmissible.

@Elchin: That's a bad analogy. The facts are that the OP submitted the same paper to a second journal without retracting it from the first. That is against the policies of pretty much every journal. The fact that the first journal is sketchy isn't an excuse; the second journal would be well within its rights to not publish the article.

I'm not sure why this answer is so highly voted. It doesn't seem to me that the OP has much of an argument that they never agreed to publish the paper, given that they did submit the paper voluntarily to the journal. Of course we don't have the journal's name, so we don't have the details. But I see no actual evidence given that the journal has acted unethically or in bad faith.

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text:
Should I write "we" or "I" in my research statement?
I am currently in the process of applying for tenure-track assistant professor jobs.
I was wondering whether I should write "we" or "I" in my research statement.
While it is true that I did not do all the research on my own,
I have heard that in a research statement,
I am trying to sell my research agenda
and thus should use "I" rather than "we".
Nevertheless, I get an odd feeling as if I am taking all the credit for something that was done with other researchers.

possible duplicate of Use of first person in a PhD Thesis

@EnthusiasticStudent I strongly dis-agree that this question is a dup of the one you are linking. This one is about research statement and the other one is about thesis. They are totally different things.

@scaaahu research statements, thesis, papers and books are all academic publications. I don't think there is any difference between the usage of the fist person in these documents. If there is, it should be clearly indicated in the question that what is really special with a statement of research that OP did not find in another post and has posted a new question.

A research statement is a mix of past and future.
When you are talking about the past, you should be honest about the fact that you are not working in isolation---in fact, that is a good thing.  Use "we" or "my collaborators and I" or whatever most accurately describes what actually happened.
The other key part of a research statement, however, is your views about the future: what you think is important, what your ambitions are for the future, etc.  Those are unambiguously your own opinions, and should be "I" statements.

But what about when there is just one author? "I" seems the appropriate choice then but it sounds so self-centered. But "we" sounds strange to me.

The conventions of passive voice and saying "we" when you mean "I" are unfortunately widespread.  Personally, I am highly in favor of using the singular "I" when it really is just you.  I even have a number of solo author papers where this is the case, which sometimes gets static from reviewers.  For a personal statement, though, I think there is no question: use the word that conveys the truth most accurately, and don't be afraid of taking personal responsibility for things that you are proud of.

I wonder if people from more fields can chime in on this old question.


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Is it ethical to have mandatory questions in an online crowdsourced survey with paid participants?
Our School Research Ethics Committee requires when designing an online survey that each question is optional for the participants. These rules were devised before the era of crowdsourcing when researchers had to rely on the goodwill of others to gather the necessary responses.
However as I am paying each participant to complete this survey (using Amazon Mechanical Turk) do you think I have a case to argue that I should be able to make some, or even all, questions mandatory?
I have not approached the Research Ethics Committee about this yet, I just wanted to see what the norm is in other countries and institutions.

By "mandatory" you mean "if you don't answer this question you don't get paid"?  Ethics aside, this may have an effect on your study's accuracy: if a participant encounters a question they don't want to answer, but they don't want to forfeit their money, they may just give a nonsense or random answer.  If you make the questions optional, you can probably have more confidence that the questions which are answered, are answered accurately.

Mandatory is a difficult concept. I think it is ethically questionable to not allow a participant to withdraw from a study at any time. There may be edge cases, for example drug studies, where further follow up treatment is required, but even here I think that treatment would not be considered part of the study. When a participant withdraws from a study we still need to provide them with whatever inconvenience allowance was agreed. We are not even allowed to prorate the inconvenience allowance, however, we break our longer studies into hour long segments and pay an hourly inconvenience allowance. It is perfectly reasonable to use a "forced choice" response system where participants are required to give a response in order to continue with the study. Using the Mechanical Turk, I think ethically you should provide an easy means of dropping out that is constantly available that will not penalize the participants. When it is so easy to withdraw, forcing them to answer a question which is not inherently necessary, seems silly. If they do not want to answer it and they have no other option, they will just withdraw.
Consider two experiments that consist of two questions. In the first experiment you either show either a circle or a square that is either red or blue. If for whatever reason the participant does not want to tell you what shape they saw, you can still get meaningful information about the color and therefore it would make no sense to force them to answer the first question. In the second experiment you show them a face and ask if it is a man or a women and based on that response you ask them if it was either Alice or Carol or Bob or Dave. For this experiment they need to answer the first question.

I like your suggestion. A "forced choice" response system where any mandatory questions have an N/A option or an option saying they don't want to answer. I will also add an easy and obvious means of dropping out that is available on each page. Participants will of course be clearly informed before starting the experiment/survey that certain questions are mandatory but that they will have the option of stating that its either non applicable or that they don't want to answer. Partially completed responses are discarded of course and the participants have to be made aware of this before starting

While this will definitely vary by review board, my personal experience has been that it's a standard that you are explicitly required to inform participants at an appropriate point (disclosures, usually) that they are allowed to refuse to answer any question they want by leaving it blank or marking it in some fashion. Sometimes this even means that, if they leave any question off, you have to throw out their whole set of responses because it's useless to you, but they must still be paid/credited for their participation even if it makes it useless to you.
The question is both ethical and practical - if you require an answer you may also be encouraging dishonesty, and possibly invalidating the usefulness of your survey anyway. "I'm not answering that" is better than "I'm not comfortable answering that truthfully, so I'll just put down nonsense." And this set of rules actually goes far beyond just the idea of unpaid volunteers, as it applies to things like medical patients, paid employees, etc.
Now, this is not to say you can't do it - ethics review boards have approved electrocuting and burning people based upon appropriate balancing factors, so it's up to the board and how you design and present your study.
But setting form fields as "required" will require appropriate disclosure to the participants and review board, and will likely be considered a negative that must be appropriately justified and handled. You will have to show that autonomy, right to withdraw, informed consent, non-coercion, and ethical payment are all handled appropriately. You will be making things hard on yourself, so if you don't have to do it this way, you probably shouldn't.
You are generally welcomed to pro-rate payment, so if a person refuses to answer all items you only have to pay them for the items they did answer - and you must put this in the informed consent forms and present this to the review board. Whether or not the particular online payment system or setup you use will support such a method might restrict your realistic study design, but that hardship is probably not something the review board will be particularly concerned about.

Some very good points. I will have to look into whether or not it is possible to provide partial payment using AMT.

The IRB that I serve on would never approve of a paid participation survey in which the participants would be denied the compensation if they didn't complete the survey.  Furthermore, if someone decides that they don't want to complete their participation in the study it would be unethical to make use of any partial responses that you'd already gotten from that participant.
In short, the answer to your question is "no."

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


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How do you reference a dissertation that is turned into a book?
I recently reconfigured my dissertation to publish as a book.  How do you properly cite, reference, or acknowledge the original dissertation (or is that even necessary)? I obviously want to avoid self-plagiarism, but also think it is silly to cite my dissertation at the end of every paragraph in the book.  Any thoughts?

What do other similar books in your field do?

In my field (in which publications are normally in the form of journal articles), a dissertation is treated more like a preprint (or a collection of preprints) and not an independent formally published work. In my understanding, citing the earlier preprint version of the article is not necessary. At most the relationship between the two versions might be noted in the acknowledgement.

Related question: How to avoid self-plagiarism when adapting dissertation into a paper?.

Assuming that you still hold copyright to the dissertation, it is enough to say, perhaps in the forward to the book, that it draws heavily from the dissertation including long passages taken directly from it, giving a citation to the dissertation.
The important thing is that a researcher is pointed to the original work to get complete context on the ideas including what you don't put in the book.
It is much harder if you have given copyright to someone else, the university or a publisher. Then it isn't a question of plagiarism but of copyright infringement. But some publishers who hold the copyright might permit such things if asked.


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Supervisor had an article retracted (I am not a co-author). Will this affect my career?
An old research article of my PhD supervisor with his previous student who worked in  cancer is retracted due to similarity in images. My supervisor was the corresponding author. I was not a co-author. If my supervisor suffers reputational damage, how would this affect my own career? Can there be difficulties publishing my own work with my supervisor, given that they had a paper retracted before?

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

I tried to make a couple of edits to emphasize what I think you're worrying about, but feel free to add further clarifications or evert the changes if they're misleading. I don't think more details about the alleged misconduct are needed, but further spelling out your concerns could be helpful. Either way, it seems a reasonable question to ask, so I've voted to re-open.

Was the "similarity of images" a plagiarism issue (stealing ideas no attribution) or a copyright issue (over copying with attribution)?

@Buffy I assumed it was a data manipulation issue, but it would be good if OP clarified that.

Is "similarity in images" a euphemism for "pretended images of the same biological specimen were images of different samples"? Because if so it's massively problematic that your advisor would characterize it that way
("similarity of images") and further that you'd repeat that same language...

If my supervisor suffers reputational damage, how would this affect my own career?

Probably not at all.  "Image similarity" in medical research often means there was fraud.  Most people will not judge you based on your supervisor's former student's behavior.

Can there be difficulties publishing my own work with my supervisor,
given that they had a paper retracted before?

Probably not at all.  Publishing decisions should be made on the content of the paper, not the identity of the authors.  To do otherwise would be unethical.
If your supervisor happened to commit grant fraud, that could be a real problem.  Usually scientists who are caught committing grant fraud loose their funding and are banned from getting new funding for a period of time.  Then they cannot pay their PhD students.

Thank you so much. This has helped me alot. I was really worried when I heard of the misconduct.

It can happen to good people that they make a mistake and have to retract an article. (Somewhere on youtube is a talk by a statistician who points to a retracted article by himself. There was a problem in entering data into a spread sheet.) Voluntary retraction of an article would actually speak to the academic virtue of the retractor. Under such circumstances, you should not expect any disadvantages of publishing with your advisor.
Being a corresponding author does not mean being responsible for everything. If your co-student fabricated research results, then your advisor might not have been in a position to detect this before submission of the article. In this case again, no blemish on your advisor and you should not expect some disadvantage of publishing with your advisor.
If however your advisor was grossly negligent or dishonest, then any of your advisor's publication might draw much more scrutiny (as the academic community in a special field tends to be small and therefore more cognizant of trespasses) and this would be to your disadvantage. However, people will also realize that you were not involved in this incident and that changing advisors can be difficult.

Hmmm. Actually, every author is responsible for everything. And a supervisor has a special responsibility. But some cases are problematic and others less so, as you say.

I respectfully disagree. No supervisor will redo experiments / simulations done by a competent graduate student. No supervisor will be redoing field interviews. They will talk with the student about the results and methodology, but supervision will not be watching over a student's shoulder while contributions to the paper are made.  In the case of Schön from Konstanz, the respective institutions judged (with the tacit approval of the communities) that many co-authors were not only innocent, but also not culpable.

Sorry, but if your name is on the paper as author, you take responsibility for everything in it. If not, then you ain't doin' your job.

@Buffy: I'm not sure I follow your reasoning here. How would this work, e.g. in interdisciplinary research? For instance, I am a mathematician specialized in functional analysis and I'm currently working with economists on a mathematical problem in trade theory. Of course I care also about the economic background, and they have considerable mathematical background knowledge. But we are using some extremely specialized mathematical tools to analyze trade models which have very extensive economic background. Assume for instance that I write a paragraph about [...]

[...] how one of the mathematical techniques that we use developed and I happen to severely misrepresent the development of this technique. How could my colleagues from economics take responsibility for this, given that it took me many years to accquire the necessary background knowledge to understand the development of those ideas? Similarly, how could I take responsibility for the economic context to be presented and interpreted correctly throughout the paper? It requires years of experience and high familiarity with the relevant literature to get those things really right.


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Blurry digital signatures in letter of recommendation on letterhead
My referee has issued me a letter of recommendation on letterhead in hard copy form , but with very blurry digital signatures. The letter has the university stamp on it. There is contact number and address of the university's old campus, but with current university website mentioned on it. Moreover, the referee's email and phone number are not mentioned in the letter.
I am applying for a highly competitive scholarship. The referee has sent the letter in email to my abroad university supervisor. Now I need to apply using online application by uploading a scanned copy of the letter. In this scenario do you think that there is a chance of losing the opportunity because of the blurry signature, and lack of email and phone number of the referee?

What country is receiving the letter?

Country is Australia.

This is closely related to the asker's other recent question: https://academia.stackexchange.com/questions/138125/letter-of-reference-without-referee-email-and-phone, adding in only the blurry signature.

Wikipedia says: A digital signature is a mathematical scheme for verifying the authenticity of digital messages or documents. https://en.wikipedia.org/wiki/Digital_signature

The answer mainly depends on the pipeline of the scheme you are applying to. Without knowing their exact rules and regulations, it is not possible to answer your question exactly.
Having said that, if I received a LOR with signs of digital manipulation / forgery (such as blur signature), my first step would be to contact the referee directly. First, I would try to locate them online and use email / telephone from their official university page. Failing that, I would try email / number from the LOR. If it is absent, I would consider dropping the case, unless the rest of the evidence shows completely outstanding candidate.
Unfortunately, it is not uncommon to see forgery, lies and other dishonest ways of gaining advantage in academic applications. After all, Universities are reluctant or incapable to assign any penalty for this, encouraging such dishonest behaviour.  The duty of checking the paperwork falls down on academics appointed as "admission tutors" or "scholarship administrators", who usually do not have tools and time to perform rigorous checks. In case of doubt, they may decide to drop the application or at least de-prioritise it.
tl;dr: if your LOR looks forged, it may negatively impact your application.

If I take another letter of recommendation with appropriate sign and stamp, but without email and contact number on it. Would it work then? My university website does not have my refrees email.

Why don't you want to have your referee to put their email and contact number on the letter?


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Takehome Exam Plagarism Help
I was writing a take home exam where I was allowed to use notes. I copy-pasted some of my lecture slide show into one of the answers, to speed up the process of referring between my notes and the slide show and this way I could easily reference my notes. It was around two sentences and the font was completely different than my answer. I ran out of time on the test and I am not sure if I deleted the two sentences copied from the slideshow.
My question is: Do I email my professor and let him know this just in case I did not erase it? I do not want him to think I plagiarized, I had no intention of keeping it there, and it is blatantly obvious that I was not trying to pass it off as my own (because you can tell it came directly from the slideshow and is not incorporated into a sentence).
Do you think I should be worried about getting in trouble?

I'm curious about the logistics of this. If you wrote a take home exam on a computer (as implied by copy-pasting), do you not have a copy of the answer file to check for sure if you erased it or not? Or is this handled through some sort of web interface?

That said, if you can't tell whether you did or not, emailing the professor seems like a good idea. This way you can make sure he knows where the two suspicious sentences came from - he might not remember they were in your slide show.

Without the instructions for the takehome exam we can’t be sure... if one instruction was “make sure you reference everything properly” then claiming “different font” or “I forgot” may not be sufficient. You can but ask...

As an instructor, I usually appreciate when my students let me know about a potential problem in their work before I even have a chance to discover it myself. It signals to me that they're 1) concerned about their work, and 2) aware of their own work -- which, sadly, not all students are.
I can't imagine it would hurt to send that kind of email, unless your instructor feels a certain kinship with the Grinch.

Regulations in your University may be different. In where I am students tick a declaration saying that they submit the work which is entirely their own and all citations are properly labelled and attributed. So formally copy-pasting a sentence from another source without attribution may be considered a bad academic practice and result in penalty.
Formalities aside, I also think that copy-pasting someone else's text and changing it to make a part of your own submission is indeed a very shallow approach to learning and I would discourage my students from adopting it. You are supposed to work with concepts, ideas and methods, not with words, sentences and fonts.
To answer your question — I recommend you to get in touch with your lecturer, explain your mistake, and mention what you intend do in order not to repeat it.


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Ask Area Chair/Editor to reveal one of the reviewers of my paper
We submitted a paper to a venue and got accepted. The venue is single-blind, reviewers know our names, but we don't know who they are.
During the review process one reviewer made very good suggestions that will potentially lead to another paper.
We would like to collaborate with the reviewer.
Is it okey to email the area chair, to tell the reviewer to contact us? An email similar to:
Dear AC,

We are the authors of paper XXX, we liked the discussion with reviewer YYY.
We are considering extending our research and we would like to invite the reviewer.

Would it be possible to ask the reviewer to contact us?

If it's not okey, why?

"invite the reviewer into a collaboration"...
Yes, asking the editor to ask (not tell) the reviewer is fine under these circumstances, though they may not want to do it. The two of them can make a decision. But the connection should come from the reviewer, not the editor, which you seem to know.

I dont know who is the Area Chair/Editor, but I can contact them via email.

For a conference it is probably the "program chair". For a journal, whoever you last communicated with about acceptance.


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When writing a review article, is it okay to cite recent preprints?
I am currently writing a review paper (for the first time) on an emerging topic, and the problem is that almost all the sources that I found regarding this topic are preprints on arxiv.
I wanted to know if citing them in the review paper is okay or not.
This paper is going to be a chapter in my thesis later on.

What do you mean "including"? Mentioning, quoting, and citing, I hope.

@Buffy my suspicion is that OP is simply asking if they can cite pre-prints. If this is the case, I think it's fine but best to avoid whenever possible (coming from a computer science background).

@Buffy, I am sorry for not being clear, but I meant it as in citing and including them as part of the papers that are going into the review.

I do not know about "okay". However, for some topics, considering "published" means the work is at least 1 or 2 year old, I would say that a review including pre-prints has a higher chance of giving a good idea of the actual state of the art. At least pre-prints can/should be included as evidence about where the field is now heading and the variety of directions being undertaken (rather than as sources of well-established knowledge).

Have you had a chance to peer review any conference or journal submissions yet?  If so, then read the pre-prints yourself, make a judgement call on the quality of the research, let the authors know about any potential issues, and cite the paper if you think it is good science.  As a scientist, you are now among the ranks of arbiters of what counts as science and what is just junk.

Your goal is to provide your reader with an overview of where the field currently stands. "The field" is defined by what people have done, and that includes not only publications that have already gone through peer review, but also those that have not yet, and that consequently are only available as preprints. As such, it makes sense to include these papers, though you have to pay attention that possibly not everything you can find on arXiv has the same quality as what you can find in the peer reviewed literature: You have to make a judgment call on each preprint yourself.

And there is always the possibility to add a sentence along the lines of "At the time of writing, the research of A. et al, B. et al. and C. et al. has only been published on a preprint server." so readers of the review will know that these sources might not have been properly peer reviewed yet.

@user253751 Sursula's attribute was "only published on a preprint server". The "only" is the important part.

There are journals that don't let you cite unpublished materials in review article submissions. Others won't have an issue with it. So do read the author guidelines for wherever you intend to submit.

Do they specify that preprints don't count as published? I can understand not wanting to cite resources that are unavailable.

Personally I would recommend going the other way. Write the best work you can. Then see where you can get it published. Seems quite stupid to leave out important works because some journal has stupid author guidelines.

Do they forbid "personal communication" too?

If you use something you need to cite it. It doesn't really matter whether it was "formally" published or a preprint. It should be clear from the citation where it appeared, say on arXiv.
If you need to quote something be formal (punctuation). If you paraphrase make it clear that you do so and cite as well.
But, as you prepare your review, watch out to see if your sources appear in a more formal way and adjust if necessary. It is preferable to cite from a formal publication as it is less likely to change or disappear.
But, yes, it is OK. Probably necessary.

Disagree, citing a open access preprint is much better then citing anything behind a paywall.   Think of what's best for most reader who don't have someone else to fund them.

@Ian, but the "official" publication is possibly more accurate and complete than a preprint. They aren't always the same. The published article has been through review and the preprint may not have been. Accurate sources are better than cheap ones, actually.

If we just say ''accessible is always better'' then we start running into problems, what needs to be done is make peer-reviewed research articles much more accessible for everyone.

@Ian If a preprint exists for a journal article, any moderately intelligent student without institutional access to the article will be able to find it.

This is significantly field-dependent.
In many fields, including my own (mathematics/theoretical CS) citing preprints is very standard, for all the good reasons described in other current answers and their comments.
However, there are other fields — e.g. medicine and biology — where citing un-peer-reviewed work is rare, and generally viewed as bad practice except in exceptional circumstances.  (Caveat: my knowledge here is second-hand, based on what I’ve been told by colleagues who work in those fields.)  And it’s not hard to see the reasoning behind this: in maths, if you rely on an under-scrutinised study and it turns out to be flawed, no great harm is done; but in medicine, it could have very serious consequences.  So the relative weighting of the principles “use all available information” and “guard the literature against contamination by bad work” is different.
So in sum, you should know and follow the norms of your specific (sub-)field — read what other comparable papers do, and follow that.  (Or, if you find you disagree with your field’s current norms, you can of course choose not to follow them; but be aware of what issues this may cause with e.g. journal publication, and bear in mind also Chesterton’s fence.)

If your review paper or peer review should include an assessment of new approaches, it can be helpful to include a review of recent preprint research.


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Two different gre scores
so I gave my gre for the second time and got a score of 160 in quant and 146 in verbal. However first time I got 158 in quant and 150 in verbal. Which score do I send to the university or do I send both the scores.

This is something that you may well ask your prospective universities.  Also depends on which fields you are planning on pursuing.  Second score seems overall better, but your question doesn't have a lot of information to go off of.
I would note that if your program doesn't weigh GRE nearly as much compared to GPA and research experience (let alone making it optional for reasons such as COVID) that this wouldn't necessarily be something worth tearing your hair out for.


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What are some formal methods in measuring socio-economic impact or broader impact of research topic or individual research papers?
By formal method I mean a broadly known, standard and as objective as possible. For example, one of the major criteria for NSF grant are “broader impacts” which is not hugely objective(likewise with other funding agencies).
In recent years, Altmetrics and similar tools and indexes have been devised to measure informal citations and calling them "social impact" – e.g. social media or non-traditional citations/mentions.
In terms of economics and decision making for the policy making in academic research, is seems reasonable that should be some measurement method, performance index, or framework to evaluate “broader impacts” of the work we report in scientific publications or can refer to. Can you provide any references to such methods, indexes, or frameworks?

There are interdisciplinary researchers who study such questions.  It's labeled with various names: "Sociology of Science", "Science, Technology, and Society" (STS), and similar. You should look at journals in those fields.  For example, Science and Public Policy has these articles:

"Opportunities for impact: Statistical analysis of the National Science Foundation’s broader impacts criterion"
"The state of the art in societal impact assessment for security research"
"Introduction: Future pathways for science policy and research assessment: Metrics vs peer review, quality vs impact"


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How acceptable are the outputs of automatic LaTeX converters for journals with LaTeX requirement?
Is there anybody there, who uses this combination as the pipeline of document production in his/her work? IF so what are the common bugs/imperfection that one should expect.
From a latex-noob point of view, it seems faster and easier to work(collaborate) on a paper in Microsoft Word (For months) and then use a plugin or some other quick converter to make it into a latex on the last week(ideally a day) if there exist a smooth conversion tool to get to .tex format?
a reliable/acceptable converting should address the journal template/format, tables, table of content, footnotes, margins, figures, equations and bibliography. Is there a bulletproof conversion out there, and if not why?

1- I edited the question, hope now it makes sense why it is an academic-related question. collaborating and quick creation on the doc is much easier that latex, but the final product of a scientific report is much better looking in latex(especially if some math involved).  2- I am not sure who else other than academician would use latex or would be curious to know about the reliability of such quick methods otherwise, I would add it on those forums.

I think there is some value in this question, although I fear it's difficult to answer in a useful way since it depends on many factors that are specific to your personal situation. I'm willing to retract my close vote and see where it goes.

Whatever you do, don't do it on the last day.

@CapeCode thanks. I am hoping to hear from people who do this on a regular basis. or hear on what else they do after an automatic convert. does it make sense to use it or is it easier to start from scratch.

I think it would really depend if you have only text, with figures / equations it becomes non trivial. Usually, journals will take other formats as RTF which are easy to produce from Word.

It would help if you tell us what discipline you work in. Also, what makes you think that there are any tools that convert content (including I assume math equations) from Microsoft Word to LaTeX? Can you point to an example of such a tool so we can get a sense of how such a conversion workflow might work?

If you work in a field that expects papers to be written in LaTeX, why not learn LaTeX?

@DanRomik For instance, Pandoc.

The core philosophy of LaTeX is to separate content from formatting. You can do the same in Word: collaboratively write the text, not caring about the final formatting and figure placement, and lastly convert it manually to LaTeX.

The most probable answer to what acceptable is the conversion from word to LaTeX is probable too little. The main reason is that word is more based in local format (visual appeareance) rather than semantic tags.
For instance, you need to specify that a group of specific paragraphs are the abstract. LaTeX made this using an instruction like
\abstract{ ... text ...}. A converter needs to look in styles to learn the meaning of the text fragment against its list of heading, leyends, abstract, section, subsection, etc.
But if what you want is have a simpler medium to wrote and rewrote contributions to the text, provided that you have a a solution to create graphics in jpg, png or pdf format and a transfer the more complex tables to LaTeX way, you can use Pandoc to convert from word to LaTeX.

I like this fundamental explanation of how these two are treating the content and its composition. And Pandoc seems like an interesting Swiss Army as well. How do you assess tools (Lyx, OfficeLibre, etc) or formats (RTF, HTML, XML) that Microsoft word can save-to in this probable pipeline?

@Amir. You should save word in docx, because this is the understood format for Pandoc. If you want to move between Word docx and LibreOffice odt, try to not make styles changes from the standards used, until the very end. You can also use some web based solutions that take out of author's sight, those problems and allows other authors contributions and version control in a different way that word does (draft, authorea, penflip, sharelatex, overleaf, online latex eq editor, etc.). I should add that LyX is interesting and easy to use.

MS-Word to LaTeX in general
There is quite a few Word to TeX converters out there but none of them worked well for my case. This is mainly because a load of spatial constraints imposed by Word making it difficult (though not entirely impossible) to reproduce in plain LaTeX generically.
For Journals
A big NO; it is not recommended you use Word to LaTeX converters for journal manuscript submission for the following reasons:

Most journals usually have LaTeX templates with pre-coded class files and have a mandatory requirement to use the same.
Tailoring a Word file to a LaTeX format for a specific journal is counter-intuitive. You would be spending more time on the presentation than the actual matter -- something that LaTeX was invented to prevent.
It makes copy editing even more troublesome. The class files provided by the publishers would contain tools that would assist not only the author but also the publisher to add further information (such as volume and issue number). Automated converters usually don't use prescribed journal class files.

Points to note
It might be a bit difficult at first but as you practice more at it, you would certainly feel that it is much more rewarding and efficient to write your papers, reports, and thesis in LaTeX than Word.
Moreover, most of which you noted: journal format, table of contents, footnotes, margins, figures, equations and bibliography is much easier in LaTeX than in Word (IMHO).
This is from my first-hand experience and heard the same from nearly all of my colleagues who moved to LaTeX -- all of who had to switch to LaTeX from Word just because of a journal requirement.


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Is there any standardization of figures for scientific publication in any field?
Short Version: Making the data behind the figures openly available is undeniably a massive help to the research community. What are some enabling systematic efforts (standard, file format requirement, tools to extract data from the figures) who are pushing for this openness available? This is not to ask for people to share their tabular data, but to use a figure file format that is easily extractable.
Imagine a day that we can do a meta-analysis on a large number of scientific papers to build a big AI. Or a software that can extract all the figures and build a massive database of data that can put the research into a quick use by engineers or others. Perhaps if there is a standard or framework for figures it would help this happen faster (the same goes with the objectives and hypothesis of papers).

Are you aware of any effort in this direction?
Is there any framework for figure structures, locations of content in the figure that is mandated/suggested by journals for better OCR in any field or certain experiments?
For example, the data in Matlab fig files (no matter how many curves or dimensions) can be accurately extracted. Is there any journal that asks for such file formats from which data can be easily extracted?
Link here: https://www.mathworks.com/matlabcentral/answers/100687-how-do-i-extract-data-from-matlab-figures

As an example of figures that work as a scientific report, but their data if extracted can help the bigger scientific developments, here are some examples. I doubt if an OCR-like algorithm can extract 100% all these data accurately.

It seems to me that making the data behind the figure openly available would be much easier than trying to extract the data from the figure.  There are many efforts to do the former.

What do you mean with "the data in Matlab fig files can be easily extracted"? Do you mean by OCR, like in your previous point? That seems false to me. And that format looks like opaque binary data.

@DavidKetcheson Looks like this could be a great answer.

@FedericoPoloni  Fig files seem to be a rich object you can extract their data with high fidelity. The great example is that that you can extract z-values from a 2-Dimensional image. It will have very low loss comparing to a OCR.
https://www.mathworks.com/matlabcentral/answers/100687-how-do-i-extract-data-from-matlab-figures

@DavidKetcheson I would agree. but also I know people who are very afraid of sharing their raw data. can you refer some successful practices in this field.

@grochmal I don't understand how can you state that "there is no need for it".  What I meant is extracting from the . Most scientific portals let you download the image of the plot separate from documents and there is less need to run a code to find the figs in the document. But each plot has thousands of data points that are very useful for building AI machines. It seems to be hard to extract all these data points accurately. So some standardization from Journals in the format they require can be helpfull.

@DavidKetcheson I added your comment as the part of the question.

There is no need for it.

Or a software that can extract all the figures and build a massive database of data that can put the research into a quick use by engineers or others.

This is pretty much what Information Retrieval systems do (Yes, I'm looking at you Google).  I worked with interpretation of images through AI in the IR area and finding that something is a figure or not is easy.
First of all there aren't many document formats, almost all papers are either in PDF or PostScript, which have a stamp that something is an image or figure.  The same is valid for Word documents and even HTML.  Then the question simply becomes what is a figure (in the sense you mention in the question, i.e. something generated from data) and an image generated by a snapshot of reality (e.g. a photo).
A figure (in the sense above) will have few edges in an ordered fashion, whilst a photo will have many edges in an unordered fashion.  Even a photo of a white table on white background has enough noise to produce more edges.
The interpretation of what the figure shows is a completely different thing.  It is much, much, much harder to do with AI.  But then again, a standardised way of placing the figures or placing content in the figure would not help with that.  Interpretation of a figure is something we humans have some difficulty to do.  More often than not, looking at only the figures in a paper does not make you understand what the paper is about.
To produce a meaningful interpretation of figures in papers you would need to understand the paper first.  Just like we humans do.

One note on MATLAB's .fig I'd like to add is that asking for specific file formats that are not publicly available may produce a lock-in problem.  This is not a particularly good example of a lock-in since MATLAB provides discounted student (and sometimes general academic) licences.  Yet, there are some countries where these licenses are not available or in which even the discounted ones amount for a big sum due to monetary differences.
Therefore requiring specific file formats may lock some researches/students out of a journal.  Something that would not be a good sign about the journal's openness.  The tech wars, notably between file formats are sometimes more fierce than between options about well debated scientific topics.  I'd prefer a journal that stays out of those (although guidelines on how and article should be formatted that are independent of the software used are definitely good).

MATLAB student licenses aren't free.  Very favorably priced compared to professional licenses, yes, but not free.

@BenVoigt - Thanks for that.  I just checked and it is 100% correct, the student licences are simply much cheaper (less than $30).  I was misguided by the fact that my institution always gave it to me.  I've corrected the answer.

@grochmal In the US... in other countries it is generally much more expensive, neither institutional licenses are common.

Also, depending on your topic, you may not easily be able to make your figures using Matlab. In bioinformatics, many people would use R or python (+matplotlib), in cell biology it's common to work only with Excel, and sometimes Prism for more complicated stats...

Matlab license is not free. bug what a Fig object does is a good example of what people can submit to journals instead of flat images of their plots.

Matlab Fig was an example of a file format that you can extract the raw data from it. (3D plots, Contours, axis-title, etc). Are there other formats like this? and if so is there any journal that requires it?

@Amir - The only portable data format is ASCII plain text, preferably with an explanation of what it contains.  But no journal would force you to publish that because journals do not publish plain text files.  Requiring any other formats would cause more evil than good.  On a brighter side several governmental funding bodies (at least in europe) require you to make the full data available in a "publicly available place and a publicly readable format" (but they do not define what these are).


text:
At which part of the paper is it better to cite R packages?
I'm sure we need to pay credit to every R package developer. Just in line with this post.
My question is, how better to integrate the citations of R packages into my paper. Should it be part of the methodological part? I saw papers that just throw the citations into the reference list. But it just doest not seem right.

There is a similar question on Academia. My focus is on the way one should incorporate the actual citations into the paper.

You should cite the software packages that you use just like any other piece of scientific work that you build on. If they are significant enough to make it to your main narrative, then cite them there just like the other key techniques you build upon. If they are useful but uninteresting methodological detail (e.g., equivalent to a microscope model or reagent brand) then they should  in just the same way be relegated to an equivalent methods section, appendix, or other piece of supplemental material.

How would you cite ggplot2?

@Ilya Honestly, I don't think I would, unless there was something fundamental about ggplot2 that enabled the analysis.

@Fomite I don't agree.  It is crucial to pay credit to those who contributed their time helping others.  Also, I think, you should mention all the packages used for reproducibility.

@Ilya Except this will rapidly become cumbersome. Do I cite Git? matplotlib? Numpy, because I really like their CSV export function? Requests, because its how I pull down a config file off Github to make sure I'm always using the current one?

@Fomite No)) The idea is to cite everything that is needed for reproducibility. You cannot obtain the figure you use in the paper without ggplot2, but you can easily reproduce the analysis without Git

@Ilya Yet you could obtain the figure using base graphics - a scatter plot is a scatter plot.

This should be included in your Methods section towards the end of the section.

The analysis/statistics section of your manuscript would be the appropriate location. It is here that you should mention what R version, what additional packages were used, etc.


text:
Is it possible to measure/evaluate one's progress or development in quantitative terms?
I often end up frustrated over the pace of my work, or rather the lack of "worthy" results. During my feedback talks with my colleagues and superiors I usually get good feedback but I find it distressing that most of it is qualitative arguments.
I sometimes feel like I have not progressed as much as I would have liked to, but not sure how to assess whether or not I have developed "enough" over time. Which led me to wonder if it is possible at all to measure how well a PhD student is progressing.
The usual measures in the community appears to be:

number of publications
which journals the publications appeared in (or rather the impact factor)
number of hours in the lab (regarding how "hard-working" one is)
number of credits taken from courses during phd studies

I personally find none of the above to be a good measure. Publications are a fact of research, or the goal rather. But they should not a be measure of how well a PhD candidate is doing in research. I believe the pragmatic demand on "more publications" has essentially lead to overall lower quality and novelty in individual publications. But even without that subjective comment, it should not be a revelation to anyone here that the amount of publications (and especially in which journals they are published) is more dependent on the seniors on the paper rather than the grad student who wrote it.
As for the other two measures I point to, they are just too naive variables to mean much. I mean you can be in the lab for 18h a day, but not learn much new or even worse not even remember those things you have learned. Besides one can also argue whether or not it's actually better for a grad student to be obsessed with number of hours in the lab, or courses taken.
Summary: Is there a good way to measure your progress through-out your studies? How can I evaluate my development as a scientist, in quantitative (and unbiased) terms?

You mean, a quantitative evaluation that doesn't reduce to a set of naïve numbers? Seems like a contradiction to me. If it's quantitative, it's gonna be simplistic.

well I guess you are right about that. What I meant was a fair way to evaluate a person's work and development. I see that this might be rather tricky to do as an outsider, but for self-assessment one would perhaps need to look at factors other than where and how many articles one has published.

But “in quantitative terms”? I don't see what much more you can say of quantitative self-assessment other than production metrics. (Or: on a scale from 0 to 10, how happy are you?)

Tried to rephrase the question a bit.. I guess your answer is "no it's not possible" which is also a valid answer. If that's how you feel then perhaps you could write it as an answer, and perhaps elaborate on it a bit?

I wish the question was: how to measure/evaluate one's progress

@seteropere I might be splitting hairs here, but aren't all measurements based on some quantitative parameters?

@posdef I am not sure but I know from my work on decision theory that qualitative information is more general than quantitative ones (some qualitative information cannot be represented/mapped to quantitative ones) but on the other hand they are less descriptive.

@posdef I have a similar problem, but since I'm just beginning my PhD, my question was a bit more focused on the beginning stages. Still, I think answers contain a lot of points relevant to your question, so you should maybe take a look.

@penelope thanks for the link, it does have some insights, though I must have missed the bit about self-evaluation; how I (or others) can measure how well I am progressing is the core of what I am trying to ask here..

@posdef I was basically asking how can I evaluate when the time has come to move on from just reading the literature (not producing any output, but still important work) to starting to produce something -- for me, it looks like this is the hardest time for self-evaluation, cause no output is produced (or expected) at this stage, but I still want to somehow measure my progress.

To reduce anything to a quantitative score, you need a valid metric. There are very few valid metrics you can use in research, as you state in your question. The only other half-common metric that you didn't list above is Papers read/annotated. We all know reading is really useful, and you should definitely aim to read X papers a week (where X is some random number that makes sense in your field). That said, the goal of reading is to gather information, and how much information was gained (and retained) is a lot harder to measure.
That said, I have two half-answers:

Make up your own metric based on hours of productive work. At the end of each day, just write down in an excel sheet or something how many useful hours you worked that day. You can use some service like Rescuetime to help you in this, or the Pomodoro technique, or just simply buy a stopwatch and keep track yourself. At the end, do a simple # useful hours/total hours worked to see how productive you think you're being. That'll probably be more useful than anything else you'll come up with.
Make task-specific metrics. I tracked my progress on my thesis using a custom shell script I wrote that tracked how much text I added in a given time period and plotted it out. (Yes, I probably spent more time making the shell script than I gained in motivation from using it. Whatever.) I tracked progress on one of my projects by how many datasets I had analyzed. I tracked progress on another project by how much coding I completed each day. These are much more useful than broad, overarching metrics.

posdef, this is something that I've struggled with as well. Instead of knit picking over what the definition of 'is' is, I would like to offer the approach which I have used.  Your mileage will vary but I've found this approach to work well for me and it may work for you as well.
First, the crux of the problem for me was that progress is either analog or digital, qualitative or quantitative, right?  This is what we are led to believe and I think that in the case of education, it is not true.  There are discrete quantitative measures by which you can, and have, gauged your progress.  40 classes to get your Bachelor's degree.  If you complete 20 classes, you're half way there.  Quantitative progress.  If you're half way through and your GPA is 3.5 then you can make a qualitative assessment of your empirical data.  50% complete, doing well with room for improvement.  So throughout our undergraduate work there is a pretty consistent set of standards and metrics by which to measure our progress and the quality of our work.
Graduate school, for me at least, has been somewhat different.  With a Masters program you've usually have either seven-eight classes and a thesis or ten-twelve classes and some kind of a project.  For the first portion of the program you can track as before, but then you get into the core of your research or development and encounter something, which I think you are alluding to, 'the perception of quality'.

"How many papers did you write?" 10 - High(Quant)
"How good did people think they were?" 4 - Low(Qual)
"How many hours did you spend in the lab?" 100 - Low(Quant)
"How good was your lab output/finding?" 10 - Exceptional(Qual)

I haven't started the doctorate yet, but I can make an educated guess that this only intensifies with candidate work.
What it really boils down to at this point in your academic career, at least in my experience, is 'how well is your work received?' and how to do you track that to evaluation your own progress. What I've done is to take a two pronged approach to each aspect.
On the quantitative side I've set up a simple database with my course work, grades, number of publications, number of lectures, number of citations, everything I can think of to track my progress.  You could also do this with a spreadsheet pretty easily.  The basic tenet of this approach is 'What do I have to accomplish & what have I accomplished."
On the qualitative side I've asked professors, facilitators, leads, reviewers, even peers in some cases, to evaluate my work against the task objectives.  Usually you get something like "you're doing fine" but if you can get more detail, do so.  A question that I like to ask is "Would you feel comfortable with me teaching your syllabus?"  This seems to get their attention.  It's interesting because it puts the qualitative assessment back on to themselves and forces them to think of your mastery of the material in terms of dissemination rather than assimilation.  "Do you feel comfortable with me teaching this material/running this lab/managing this team  that has your name on it?"  Good bad or ugly I write it down and give it a 1, 2, 3.  1=no faith. 2=some faith. 3=complete faith.  If, after 6 courses (for sake of argument) you have a qualitative score of 15+ then you know that more than half of your superiors have faith in your mastery of the content that you are consuming or presenting.
To be fair... I'm a bit of a numbers junkie and this may not be the kind of system that works for you but it has worked for me so far.
Best of luck.

Thanks for the reply, I appreciate the time and the effort. It appears as this question has awakened some controversy (see comments).
The problem with this type of evaluation is, PhD courses are pass/fail courses (at least here). A further problem is that I work very cross-disciplinary, meaning that I have a more or less unique niche in the dept. Which of course gives rise to my doubts over whether or not my superiors have the expertise to judge my progress objectively. In most cases I know more about the practical bits of the projects than they do.

@posdef: knowing the projects better than your supervisors is kinda what the PhD experience is all about if you ask me ;)