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Editor Assigned Pending to Reviews Completed in Less Than a Day
I submitted to a mathematics journal on August 20, 2023, and the next day the system status changed to 'Editor Assigned Pending'. It remained 'Editor Assigned Pending' until September 18th.  However, yesterday, September 19th, it directly changed to 'Review Completed.' What's going on? Does this mean it's going to be rejected? Because mathematical reviews typically take longer, it feels like a rejection

On the 18th, it remained 'Editor Assigned Pending,' but on the 19th, it switched to 'Review Completed.' This caught my attention. It had been 'Editor Assigned Pending' for a month and I assumed it hadn't reached the editor yet, so it appears as though the review process only took a day.

Possible duplicate of: Can I predict the fate of my manuscript (from information other than a decision letter)?

There is no way to answer your question without knowing the inner workings of the journal you submitted to. Electronic submission systems rely on human input and are therefore subject to an even wider variety of errors. It is of course quite possible that the editor that was finally assigned your paper decided on a desk reject, but there are other ways to interpret what has happened.


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What constitutes a minor journal?
One reviewer of a paper I had submitted mentioned that if I were to submit to a “minor journal", there would be no need to add additional content, the current journal on the other hand would require more work. I'm quite puzzled about this statement – what qualifies as a "minor journal"? My primary focus is within the field of mathematics (graph theory). To avoid any controversy, I prefer not to disclose the name of the journal I've submitted to.

Some journals are considered more "prestigous" or "major" than others. There are several measures like impact factors that are used to rank journals and some are subsequently put in the first quartile, the very best journals, some in the second, third, and the least prestigious/impactful in the fourth. Other journals are not even ranked. The usefulness and correctness of such rankings might be debatable.
But in your case, the reviewer says that for your paper to be suitable for their relatively highly ranked journal, the quality needs to be improved, while other, lower ranked journals might be more open to publish a wider range and less refined kind of paper. If that is really the case might again be true or not.
You will find journal rankings - and possible fitting "minor journals" on pages like scimago, but if resubmitting the paper to a "lesser" journal is the way you want to go (instead of trying to improve the paper and stick with the current journal), I would suggest to first ask your supervisor(s) or colleagues with more experience in publishing their research for recommendations of such "minor journals".

This comment should be only understood in a relative sense: that is, the referee is expressing the opinion that the results in the paper are not strong enough to be published in the journal you submitted to.  There are not "major journals" and "minor journals" but rather a continuum from the best to the worst.  (This is an oversimplification: there are many mathematics journals, but only finitely many, so surely the space of all such journals is discrete.  Also journals
are not linearly ordered; rather each person has their own partial ordering on the set of journals from which an approximation to a collective ordering emerges....)
The most important word in the last paragraph is opinion. The editors of the journal will most likely take this opinion seriously (the better the journal is, the more likely that one referee's opinion will prevent the journal from publishing your paper), but all they can do is reject the paper: they can't force you to agree with their opinion.  If the referee had some insightful comments about your paper that help you understand why it is not as good as you had hoped, you should probably take a fresh look at your entire thought process of where to submit the paper.  In the absence of that...it is entirely reasonable to resubmit to another journal of similar quality to the first.  It is only when you repeatedly receive the opinion that you need to submit to a lesser journal that you need to take that seriously...according to your own precise definition of "repeatedly."

Nice. Thanks. The editor did not reject my paper and give a change to revise, and I add more works in the paper.

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After a PhD internship, I've been offered to finish the PhD at the company. Should I accept?
I'm asking for an opinion here as I don't know many people that can help me with this decision. Any feedback is very much appreciated, sorry in advance for the long post.
I'm a 2nd year PhD student in Computer Science (more in detail I do research on a particular branch of Deep Learning) from a university which is top tier in my country, but is not top tier worldwide (this is just to put some perspective for later on). Also I would like to mention that I do not know yet if in the future I would like to work in academia or in industry,.
I was offered a research internship in a big company (it's not FAANG, but almost). The internship was in a different branch of Deep Learning, that is not directly connected to my previous research, and this made me quite undecided. In the end I accepted as I thought that coming from a university that is not top tier I couldn't afford turning this down (in fact it was the only company that gave me an interview out of 10+ internships to which I applied).
The supervisor at the company didn't give me much freedom, so I mostly had to execute his projects, but I did have my say in them, and I am still very proud of the work done. On a personal relationship level, I didn't quite connect with the supervisor and I didn't like his approach to research, but I always acted professionally and did my job. Now that I'm at the end of the internship, the supervisor has given me the opportunity to finish my PhD while staying at the company. I am very undecided and I would like to have some opinions from more experienced persons. I've made this list of pros (+) and cons (-):
Pros/Cons of finishing the PhD at university:
(+) Relationship with supervisor: I have a very good relationship with my uni supervisor, not only at a professional level, but also on a personal one.
(+) Freedom: I would be able to continue working on my original PhD topic, and I would have total freedom on the projects. While I didn't dislike the topic done at the company, I find it less interesting, and I'm afraid my company supervisor would not give me too much freedom.
(+/-) Possibility to have other external opportunities: I would be happy to perform another internship in another company, or to visit a lab in a different university. Of course I don't have any guarantees this will happen, but I believe that at least for the second case there would be good chances of making it happen.
(-) Less collaboration opportunities: at my university I have very little opportunities to collaborate with other researchers. While it didn't happen that much during the internship, I could probably have more chance of doing collaborations at the company.
Pros/Cons of finishing the PhD at the company:
(+) Resources: at the company I have access to much more computational resources than at university. I was able to do some experiments that at uni would have taken me double of even more of the time.
(+) More networking opportunities: the company has many really great researchers that would be much easier to get in touch with if I'm working there.
(+) Money: while I am very lucky to not have to worry too much about money, there is no doubt that the company would allow me to have more financial independence.
(+) Permanent position: there would be high chances of me getting offered a permanent position after my Phd.
(-) More Stress: during my internship I felt much more pressured to bring results than at university, and this has been quite stressful for me.
(-) Relationship with supervisor: I did not connect very well on a personal level with the supervisor at the company, and this caused my some very stressful moments.

Talk this over with your supervisor at the university. They are your best source.

Define freedom: how many peer-reveiewed papers did you publish on your topic? How many are in the pipeline? if the total number is <2, I would say the topic is too broad, so yes you are enjoying freedom, too much freedom.

Interesting difficult choice. I wouldn't dream of trying to advise you. My quick scan of your reasoning suggests to me that years down the road you might be happier (by some definition) having followed the academic track. But I think you can think of this as a win/win situation - I'm sure there are many people who would be delighted to  have to make this kind of decision.

One piece of insight: is this where you want to end up?  Imagine 5 years down the line, you're working for the big company, you have your PhD, you're reasonably well-paid, your work is meaningful if somewhat less personally interesting, and your work life is perhaps a notch or two more stressful than it was as an intern.  You look down the road, and you can see that setting the pattern for your life for the next 20 years.  Is that a good life, as far as you're concerned, or do you want something else?

"Also I would like to mention that I do not know yet if in the future I would like to work in academia or in industry" - this is maybe the major thing to make your mind up about. Other comment: If you stay at university, look out for opportunities to get into contact with others, workshops, doctoral schools, talk to people at conferences etc. You don't need to rely on your supervisor/university for networking/collaborations.

My advice: Do one major thing at a time and do it well. Unless circumstances dictate otherwise, finish your PhD, then move on. A very good challenge you're being presented is how to express to the potential employer that you're very interested (if you are) but unable to accept at this time. Happens all the time, Diplomacy 101. No guarantees the position will later be available, but c'est la vie. At the same time it does sound like you're uncertain about where you'd like to end up, but that's a different craps game.

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Advisor on medical leave only a few weeks before dissertation defense
My doctoral advisor has been on medical leave for several months now. As such, he has been extremely hard to maintain contact with. He lives in a different part of the country and checks email only about one or two times a week. This usually has not been a huge issue because I know what I need to do for my dissertation and have been doing it.
In keeping with a discussion that he and I had about three months ago (which was a continuation of several prior discussions on the same topic), I have agreed to terms for a full-time job starting in six weeks. Part of the contingencies of the job require that I actually have successfully defended my dissertation.
Today, he sent me a terse email to inform me that he needs to take care of some of his medical issues, and then he will contact me and we can try to "finish" the dissertation. This is a deviation from previous agreements he and I had. Outside of any last edits he would want to add though, the chapters for the dissertation have been done for some time now. I am just biding my time, waiting for him to give the final go ahead to submit the dissertation to the committee. I have conveyed these thoughts in email to him, but he has ignored these emails.
My question is this: Has anyone ever declared their advisor "medically unavailable" just weeks before trying to defend their dissertation? I am essentially faced with the decision of delaying the start date for my job (while still paying rent all the while) and keeping in the good graces of my absent advisor, or, alternatively, going to my department and seeking to have my advisor declared medically unavailable. Because he would possibly still need to sign off on my defense paperwork, I am worried that my advisor could try something to still block me by refusing to consent to signing the paperwork.
ADDED
I will add here a few details about why my advisor is on medical leave. He is not sick or dying. He had a routine procedure done on his knee about five or so months ago. Millions of people have undergone this procedure and return to work within a week. This is not a case of a poor old man who is terminally ill. I do not think it is unreasonable to ask a guy who had routine knee surgery to respond to emails five months after the surgery.

You're strangely hostile toward someone who is on medical leave ... but he has ignored these emails. I understand your frustration, but I sincerely doubt he is ignoring them willfully. || going to my department and seeking to have my advisor declared medically unavailable Why haven't you done this a long time ago?

I have already looked into declaring my advisor unavailable. He was ever so quick to respond to a department inquiry and declare himself completely fit and able. He sure seems to be ignoring my emails willingly. Whenever someone "official" emails him, he all of the sudden can respond immediately. It must be some sort of medical miracle.

Since your adviser responds promptly to messages from department officials, I suggest that you ask your department chair (or, in a large department, the professor in charge of the graduate program) for help. Perhaps the chair can persuade your adviser to approve your thesis, or to let someone else be your temporary adviser during the medical leave.

@Vladhagen There's a big difference between sending an "I'm alive" email and being able to usefully critique a dissertation. That said, I hope you may get some useful info on how to more peacefully negotiate with him, as he may feel pressured to keep up appearances to the department. It may help to know if you have any other professors who could potentially help advise you.

just wondering, you said he lives in a different part of the country, so surely the department is already aware that he is not available in the sense that a "normal" phd advisor would be?

@PandaPants Department leadership was not aware until recently that he was living out of state. That did not seem to be part of the agreement.

I have heard of cases where an advisor took part in the defense via skype because he couldn't be physically present (for whatever reason).

Any chance the new job can accommodate your situation, given the circumstances? Because the real problem seems to be you are out of time. Your dept will almost certainly accommodate your situation and help get you graduated one way or another. But within a few weeks? Might be impossible. Meanwhile can you get the committee's feedback on the thesis at least informally?

"I have already looked into declaring my advisor unavailable. He was ever so quick to respond to a department inquiry and declare himself completely fit and able." - This makes it sound like you asked the department for this without communicating with him first that you planned this course of action. In effect, your coup attempt failed, which puts you in a much worse position than you were before. You probably managed to offend your advisor quite a bit while he is dealing with medical issues.

@BryanKrause I had not been able to get ahold of my advisor for three weeks at that point. Phone calls, Skype, email...all went unanswered. There came a point where, yes, I had to go to the department.

While it might not be the best course of action, there is a possibility that your advisor is on medical leave for something else than the reason he gave to you. (Including potentially being terminally ill.) You did not give a location, but in many places, you don't have to give away the reason for medical leave to your employer as long as it is valid and given by a doctor. But you also called it an "agreement" in the comments, so is it an actual medical leave or a special agreement for him to do "home office" and/or reduced hours with the department?

Something (somewhat) similar happened to a friend of mine. The key to her solution was to get another chair while at the same time allowing her advisor to "save face" in the department. Basically she made it a matter of logistics (rather than irresponsibility or personality).
She approached another (full professor) member of her committee to act as an ally. Then she copied the ally on a friendly email to her chair suggesting that the ally had "volunteered" to be a "co-chair" for the logistical purposes of the defense/graduate school paperwork. She explained that of course she wanted to keep her original advisor as the chair, but that the work start date seemed like it was making that arrangement impossible. She and her ally were able to arrange it so the original, medically unavailable chair would still get credit internally for having her as a student and would remain on the committee (as a "distance"/Skype examiner).
I have found that, in general, difficult professors respond to subtle pressure from their peers (never their students) and prefer solutions where they can save face!


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Timeline for notification of teaching duties for Grad TA
As part of the support for my PhD, I teach a class every semester or so. I dual as a research assistant and have outside funding. I receive the same pay whether I teach or not. A few weeks ago, my department posted a list of teachers and their assigned classes. I was not on the list and received no indication that I would be. Naively I assumed that this meant that I was not going to be assigned to teach this semester and that I would just be a research assistant (which I already am funded for). I mean, you would think that they would notify teachers of their assignments, right?
However, I now have been notified today (December 19) at 2:30 p.m. local time that I am in fact assigned to teach a class starting in January. I have never taught this particular class, and (obviously) have no lesson plans or materials for the class. They have given me two weeks' notice. Since school is on holiday, I cannot go into the department and pick up a textbook for the class or anything. (Plus I live out of state from the school and I have gone home. I am not flying back until January 2).
Should I speak up and do something about this, or just grit my teeth and check it off as department ineptitude? For those of you who are in department administration, is this a common practice to notify an instructor two or so weeks before they have to step in front of a class and teach, especially when they have never taught the particular class and do not have access to the textbook during the ensuing two weeks?
For further reference, the department has done this to a few other students in the past. Usually what happens is that a professor decides last minute that they "cannot" teach a class. Several times the reason has been that the professor is tired of teaching said class or is just tired of teaching in general. The department chair is on board with this, since he knows he can just force a graduate student into the position and it keeps his friends happy. Since no students have ever pushed back on this practice, he keeps doing it. That is the reason why I wonder if I should formally address the issue of dumping teaching assignments onto the graduate students.

I understand their needing an unexpected "cover" for a class. The odd thing was how they passed it off as just my normal duties that I should have been planning on. No mention of being in a pinch. Who knows, maybe they are covering for yet another professor who can't do something for "personal reasons."

When you say "speak up and do something", what kind of outcome are you hoping to achieve?

Unpleasant surprise. It can happen, esp. if suddenly a lecturer drops out (e.g. leaves the department or falls ill), but clearly it would have been good form to ask you first, before dropping you into a class with bare 2 weeks warning over Christmas holidays.

@NateEldredge As part of my end of year reports, I have to report to the graduate college on my progress, including any issues that have come up with finishing my degree, etc. The administration to my department is not exactly running with a clean sheet in the eyes of the university right now. I have added some more details in my question.

That doesn't really answer my question.  Is your desired outcome "not having to teach the class"?  Is it "teach the class, but get some extra support and resources"?  Is it "teach the class, but ensure that reforms are made so that this doesn't happen to more people in the future"?  Or something else?

In other words, are you asking about how to address your specific situation right now, or how to push for structural changes to address this as a general concern?

@NateEldredge I guess we could say the desired outcome is to indicate to the department that they need to stop being so sloppy. I will grudgingly teach the class, since there is not much I can do about it otherwise.

Most likely something fell through at the last minute and they had to find coverage. It could have been handled better (i.e. asking rather than just telling, explaining the situation), but it does happen that a class might suddenly need to be reassigned much closer to the start of the semester than normal.
(Adjunct professors often get last-minute teaching assignments, and last-minute cancellations.)
You can certainly ask them if they can reimburse you for the cost of the textbook shipped to you at home. I've had my department reimburse me for expensive overnight shipping for stuff I needed for prep when they assigned a class to me at the last minute (a week or two before classes started, in a subject I barely knew. That was fun.) You can also ask if, given the late notice, they can help you out with materials and lesson plans from the last person who taught it.

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Cold calling external researchers to evaluate a manuscript for a tenure/promotion file
Suppose one is seeking external comments on the quality of one's research for a tenure/promotion file. Assume that my institution requires such a letter and my chair has advised me that "it would be desirable to have an outside expert comment on the quality of this paper."
What about contacting experts in the field who you don't know and asking them to write a letter about one of your papers? Has anyone ever done that? Is it highly unusual? Or even rude or a cultural faux-pas?
Also, does it matter whether the manuscript is in draft form or already published (or in-between)?
Maybe the answer will be field-dependent (and more generally culture-dependent)? I am in math and in the USA.
I understand that, generally, one would ideally have a large research network to call upon for such things, but I do not. Furthermore, my recent work is in a subfield where I simply do not know anyone with relevant expertise.
For clarity, I am at a teaching institution where the research requirement is quite minimal, but it is still valuable to get external expert comments.
Obviously people are busy, and there is a high chance that such a request would go unnoticed or ignored. That's fine.
===
Edit: Given the comments and answers, it appears that my institution is quite distinct from the vast majority on this. I think there is a standard for the institution to seek such evaluations of a candidate which are essentially anonymous to the tenure/promotion candidate. This is not the kind of evaluation I am seeking. I am just seeking, e.g.,  evaluation of the quality of a specific paper. This is quite distinct from the more general anonymous evaluations of candidates which occurs at research-focused institutions.
The general consensus is that I should not contact those who I have no personal connection to and make such a request. I should at least have the department chair do that.

Does your tenure evaluation require this?

You should ask your department chair and your promoted colleagues how this is done at your university.  In most departments (even at teaching-oriented departments), you are required to have external letters and these are solicited by your department chair, not you.  But some departments differ.  If you have confirmed that you are expected to solicit these letters, please edit the relevant guidelines you have been given into the question.

^ This is a clearer way of asking my question.

I can have the chair send the request, but there is no specific requirement at my institution on who sends the request. I understand that this all may sound very strange for those at institutions where research is essentially the top priority. So it's important to understand the distinction, and these comments make me think that is actually an important factor (type/class of institution) regarding my question. If it helps, assume the research is "R1 quality."

Is there a requirement for such letters at all?  Or an expectation?  How many are expected if any?

Both you and your university will want letters that actually address the actual research expectations for your position - expectations that your letter writers may not understand.  How is this problem customarily handled at your university?

@AlexanderWoo I think most people have external researchers they know who can write such letters. I just don't personally know anybody capable of evaluating the research. Part of the issue is that I just don't have much of a network, but also because it is in a subfield I haven't worked in before.

@jdods That's not good. You need to know people in your field. You can't substitute that with cold calling.

@jdods - we can try to give you advice, but I think you really need to sit down with your chair and get a better idea of what you're really asking for before we can give you good advice.  I was thinking about putting in a close vote for "depending on individual factors," but I think the external-to-your-institution-facing aspects could make a good question - you just need to tell us enough about the internal-to-your-institution-facing aspects to actually ask the question you want the answer to.

@BryanKrause yet, one needs to deal with the situation they have whether ideal or not. Maybe I can take away from your comment that I should contact the people I do know to see if they know anyone with the relevant expertise.

@AlexanderWoo I edited the question to say: Assume that my institution requires such a letter and my chair has advised me that "it would be desirable to have an outside expert comment on the quality of this paper."  Maybe that satisfies what you are asking for?

Suppose one is seeking external comments on the quality of one's research for a tenure/promotion file.

This is a  problematic way to begin a question. It is difficult for me to suppose such a thing - quite simply, this is not how tenure reviews are conducted at major US universities I’m familiar with (nor at universities in a few other countries I’ve had experience with, for that matter).

What about contacting experts in the field who you don't know and asking them to write a letter about one of your papers?

Again, you are assuming a premise which I believe is false, which is that you as a tenure candidate should be taking an active role in your own tenure review which includes soliciting opinions from people outside your institution. That’s not at all how the process works usually.

Has anyone ever done that? Is it highly unusual? Or even rude or a cultural faux-pas?

Let’s assume that you are in an institution that actually allows you to reach out to people and solicit opinions about you for your own tenure review. The thing that you should probably be aware of is that this is not a policy that communicates seriousness or competence. If I were on the receiving end of such a cold call/email, I would assume that either you don’t know what you’re doing, or your department chair doesn’t know what they’re doing and gave you poor advice, or your institution doesn’t know what they’re doing (and I’m not sure which of those options are worse).
In other words, yes it is unusual, and has at least the impression of being a faux pas, even if within the walls of your institution it’s considered the normal way of doing things.
My suggestion to you is to find out more about the policies of your institution. It would be best for you to not communicate directly with external reviewers for your tenure case if possible. If for some reason you feel like you must reach out to such people yourself, because your institution’s policies demand it or because your department chair isn’t capable of handling this task themselves, proceed with extreme caution. At the very least, your cold email should contain enough details to reassure the people you’re sending it to that you are acting within the appropriate institutional protocol and that this isn’t some kind of weird mistake. Reviews are often solicited from people who don’t personally know the tenure candidate, so that part by itself is not unusual or a cause for concern.
Good luck!

This makes me think my institution is highly unusual. The answers and comments here successfully talked me out of sending the email though! So that's a win really. But, yes, candidates can solicit letters at my institution. That is the norm here as far as I know. I have had success cold calling in the past, but also experienced the letter writer asking to be contacted by the chair instead. I of course always instruct them to send the letter to the chair and not me!

As I remarked below - this is actually not a completely unheard of policy - it does happen with some frequency at institutions for which research decidedly a lower priority for tenure and promotion.  You are correct this is not a policy that communicates seriousness, but these institutions are not that serious about research.

I find cold calling is seldom productive. People are busy. If they don't know you and have no incentive to respond then they are unlikely to do so. Even if they agree, you might not get the best feedback nor timely feedback. The more "expert" they are, the more likely it is that they are too busy.
Hopefully you have other academics in your field whom you know and who know you as well. Ask some of them. Have you met folks at conferences and meetings? they are a good source.
If you wan't some independence in the evaluations, ask a colleague to make a request on your behalf of someone in their circle of contacts/collaborators.  Such requests are harder to ignore.
Alternatively, ask a recently tenured colleague if they will share their materials so that you can compare them. Or ask them to give you feedback, assuming they aren't part of the decision process.

These are helpful suggestions, thank you.

I think it helps here to understand what the usual practice is for tenure/promotion letters, even though the original question is not about the usual practice.
Usually, the chair or the dean, not the candidate, solicits several letters from experts on the candidate's research.  The experts are asked to comment on the entire research record of the candidate, not on a single paper (though in some cases, that record, or the part of the record that is under the writer's expertise, is a single paper).  These letters are solicited from people without any conflicts of interests, which usually means they cannot be collaborators of the candidate or people who have worked with the candidate in any capacity.  (I once got a panicked call from the chair of a department because one of the letter writers for a tenure/promotion candidate had just started a collaboration with the candidate after agreeing to write the letter, not realizing the problems this would cause.  He needed a letter in a week or so.  I was unable to help as I was also collaborating with the candidate, but I did manage to suggest someone else.)
Professors are accustomed to being asked for such letters and frequently agree to write them.  Note this is framed as a favor to the chair or to the university, not to the candidate personally.  I have written several such letters for faculty at primarily undergraduate institutions whom I have met only once or twice at conferences, whose research work I had only a passing familiarity with.
My suggestion is that this will go most easily if it conforms to the usual practice.  Find some experts in your area who are known to understand and be sympathetic to the realities of research at PUIs.  Ask your chair to write one of these experts asking for a letter, clearly stating what kinds of comments are being requested and what the approximate standards for such comments are.
The website of the Provost's Office at my university actually has a template for an email/letter a chair could use to make such a request, publicly available because every department needs it and hiding it would be too much trouble for a document for which there are no confidentiality concerns.

My sense of the question is that the OP wants some reassurance about their application materials prior to submission and the start of the formal process. What you describe comes too late for them to make improvements based on suggestions of others. Also, the OP says the chair has made a request that they obtain letters, so their process is, perhaps quite different.

@Buffy my goal is to have an expert comment on the research to aid the relevant institutional committees in evaluating its quality. I think differences in institutional culture might be an important factor. Of course my specific individual factors may be key here (e.g. being mid career with no research network and specifically none in the relevant subfield). It's a matter of making the tenure/promotion case as strong as possible (as far beyond the bare minimum as possible). I don't need personal reassurance as I have my own opinions about the quality.

I think this answer makes a good point about confirming to the standard practice the expert getting the request is accustomed to (and not the standard practice of my institution). My thought though is that I like to reach out personally first. However, maybe it is advised to simply skip that step.

I had to smile when I read "a. template for an email/letter that a chair could use". In my college (perhaps even in the whole university), these letters are specified word-for-word (except for the candidate's name & pronouns) by the college administration. The chair is not allowed to deviate, even slightly, from that "template".

A (possibly) more useful comment:  As far as I can remember, whenever I've been asked to assess the research of a tenure candidate, the request always came from the chair, never from the candidate. And in my department, any letter solicited directly by the a promotion candidate could not be included in the promotion file, i.e., it wouldn't count at all.

@AndreasBlass it is indeed standard practice at my institution for the candidate to solicit ALL letters. So now I am really curious about this. Is it a SLAC vs R1 difference? Or is it a ranking related thing within those categories? Or is it a cultural/demographic related thing? A question for another day...

@jdods: Chairs/deans solicit letters at almost all colleges and universities - the exceptions are almost always colleges and universities at which research was formerly of such low importance that letters were not requested at all, but now research is now slightly more important so that candidates are encouraged to ask for letters.  Note that one would not expect candidate-solicited letters to be as objective since presumably the candidate chooses writers who would have favorable views.

@AlexanderWoo yes, I think that matches my institution. Research was historically less important and has become moreso, to a degree. You seem to understand the situation, then. Thanks for all least confirming that this is indeed a real phenomenon. I'm not sure many are aware that such places exist!


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Citing your own related (unpublished but under review) research necessary?
The main idea of this questions is to have two papers under review simultaneously which are somewhat related but do not rely on each other in any way (except in the temporal sequence of discovery for myself). Should the second submission cite the first?
Question 1: Suppose one has a paper under review and are writing a new paper which extends the methods to a different class of objects. Should the paper under review be listed as a reference?
My thought is that if it was someone else's unpublished paper that inspired me to extend the methods, I would definitely cite it, and that tells me I should cite it even though it's my own paper. But it also feels a bit weird too as the papers don't rely on each other in any way really. They are just two different applications of the same proof technique. The applications are somewhat similar though.
Question 2: If I cite it, would I need to include the unpublished manuscript as a supplemental file during submission of the new paper to a journal?
My thought is to not include it, as the work is mostly not relevant, plus it is a much longer and more complicated paper. SO it would make the submission seem very cumbersome. The current paper is much shorter and doesn't rely on the other in any way. Reading the other paper will not help evaluate the current paper. The only thought I have is that an editor/referee might argue that in light of the unpublished work, the new paper isn't a sufficiently interesting new application of the novel proof technique (which was novel in the unpublished paper but now isn't so novel). And that would be a fair point, but I'm not sure if it would be the deciding factor at this particular journal. And I wouldn't want to not include the citation for the sole purpose of avoiding this possibility.
My thought is that both papers are highly relevant, because the results are non-trivial and will almost certainly have other applications that I can't foresee.
These are a math papers, but I imagine the question could be answered more generally.
Edit/note: I believe I am looking for ethical guidance here. I wanted to make sure I was following expected practice of the discipline and what most journals/editors would have wanted in this matter. I.e. if excluding the citation is likely to be seen as unethical, then I definitely want to include it. If it doesn't really matter and opinions are too varied, then I might just exclude it.
I went ahead and submitted the paper excluding the reference though. I'll try to update this if ultimately the reference does end up in the paper though. Hopefully, I get a chance to ask the editors/referees what they desire on this matter.

you might wait and add the citation of the first paper to the second in the last stage of the review process of the second paper. It is possible that the first get accepted and receive doi during the review process of the second one. You can also think of arXive. but check if pre-publishing in arXive is acceptable by your goal journals (and if they have any condition for it).

Pure mathematician here.

Question 1: Suppose one has a paper under review and are writing a new paper which extends the methods to a different class of objects. Should the paper under review be listed as a reference?

Sure, that's not a problem. Our culture in math is to cite papers that we rely on but also papers that are thematically related, that the reader might want to check out to learn more. You write "if it was someone else's unpublished paper that inspired me to extend the methods, I would definitely cite it" - so then you should definitely cite it, even though you wrote it, because it might interest the reader! In fact, you might consider updating paper 1 to also cite paper 2, as another instance where this proof technique was extended in a similar way.
Now let's turn to the issue that paper 1 is unpublished (so far). In math, this situation is very common, because the speed with which papers are published is much less than the speed we produce preprints. It is common to wait a year for a first referee report, maybe another six months until a paper is formally accepted, and more months till it is published.
The best way to combat this issue is to put your papers on arXiv when you've finished writing them and before you submit them. You can then update the arXiv submission after incorporating the comments from the referees. This allows other researchers to build on your results even while they are under review at a journal.

Question 2: If I cite it, would I need to include the unpublished manuscript as a supplemental file during submission of the new paper to a journal?

You can cite the arXiv version and therefore will not need to include a supplemental file. Also, since the work in paper 2 does not depend on paper 1 for correctness, probably the referee won't need to check over paper 1 at all. Almost every paper I've written cites some other preprint of mine that is still under review. Perhaps your paper 1 will be accepted by the time paper 2 is accepted, in which case you can update the citation to point to the published version. Good luck!

For now, I'm not putting the papers on arxiv since I want to get several other related results written up first. I do plan to put preprints on arxiv eventually though. I decided to leave the citation out for now, but maybe will talk to editors about that if the opportunity arises, depending on how the submission process plays out. Thank you so much for the answer!

I suppose I was looking for ethical guidance here. I could quite put that to words until now. I wanted to make sure I follow the guidelines that the journal would want. I've added a note to the question to clarify that.


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Related work in an article
(This is a junior researcher's question.)
Scientific publications contain a part discussing related work and the context of the paper. However, it is not clear where to put the section discussing related work of a paper.
Where does the section on related work belong in a scientific publication? Is there any universal standard, or is it arbitrary?

I heavily edited the question, hopefully now it asks what it was meant to ask in the first place. Perhaps the downvoters could reconsider their vote.

If you're writing a conference paper, put it in the same place as it appears in the conference papers you read.  If you're not reading any conference papers, you're not ready to write one.
If you're writing a journal paper, put it in the same place as it appears in the journal papers you read.  If you're not reading any journal papers, you're not ready to write one.
If you're writing a dissertation, put it in the same place as it appears in the dissertations you read.  If you're not reading any dissertations, you're not ready to write one.
If you're writing a $PAPER_TYPE, put it in the same place as it appears in the $PAPER_TYPEs that you read.  If you're not reading any $PAPER_TYPEs, you're not ready to write one.
Also: Ask your advisor.

I think this advice is very good and sensible.  I do wonder though about room for doing things because it makes sense as opposed to because that's how it's always been done.  Of course, there may be good reasons why "it's always been done this way", but then occasionally someone sticks their neck out and imagines a new way of doing it.

Generally, put it in the introduction. This partly motivates further study of the field, i.e., by showing that previous experts have worked on similar problems,
and that such problems are well established.

Like so many times, it depends on the field. The options in general are either at the beginning, after the intro; or at the end, before the conclusions.
Look at previous issues of the journal/conf you are targeting.
Also, ask your advisor.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Are there any universal rules for bibliographic references recognised all over the world?
There seem to exist many bibliographic reference styles and many universities have their own guidelines too. I wonder, whether there exist any universal guidelines for formatting bibliographic references in publications?

There is no truly "universal" system—that's why packages like EndNote and BibTex both come with hundreds or even thousands of different bibliography styles.
That said, there are some common approaches—the Modern Language Association and Harvard formats are quite common in the humanities. The sciences have more widely spread systems, but I think the most common I've seen is the "abbreviated style," containing authors, journal, volume and page info and year. (There are some variations within that style based on different publishers, and some publishers, like ACS, are now starting to take advantage of electronic distribution by including full titles.)

The link to MLA seems to be down.

The answer is no. Within fields, there are often a single style which makes some approaches and components more common or even that makes a single style dominant.
Get yourself some software like BibTex, EndNote, Zotero (my personal favorite), or similar so that you can simply rely on someone else to automate importing the data into a database and outputting according to whatever rules a particular journal or venue requires.

This is already contained in Benjamin's answer, but let me stress it once more. You shouldn't edit bibliography entries by hand. It is time-consuming and error-prone. There is software for doing that. It might take a little while to learn how to use it, but it is extremely beneficial in the long run.

As aeismail said, there are no truly universal rules and the bibliographic reference styles differ across scientific disciplines, and even within these there is often large variation. So normally, you need to consider the journal/conference/... the publication you are writing is aimed at and consult their rules. Most of the time, you will find quite strict requirements articulated in the venue's "submission guidelines", or "author's corner" sections - usually on their website. If still not sure, contact the responsible editors/PC chairs to advise you.

As everyone says, there are no universal systems, although there are a few very popular systems. Of course you should use reference software, but if you are asking which style you should use for general purpose citations outside of publishing, I would just pick one of the most popular, depending on your discipline.

Chicago style seems flexible and perhaps the least field specific.
APA style is popular in the life sciences and psychology, of course. But, I don't know if it is so popular in the humanities.
MLA style seems to be the most popular in the humanities.

If you are not instructed to use a specific one, all of them give the necessary information in a bibliography/reference list format (that is, the full title, authors, dates). I think the issue that might be field specific is in-text citations, but that is not your question. If you pick one and use it consistently in any given document, I am certain it will be internationally understood.
Keep in mind you do not need to learn all the details- just select the option in the software and make sure any imported references (from old PDF's, etc.) are correct. I like Mendeley.


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Data Collection in Academia: Insights?
Data Collection is a primary objective in many academic fields and can be approached primarily through three different lenses - qualitative,quantitative and mixed methods.
With particular attention to computer science and HCI (human-computer interaction), what are some primary approaches to data collection? Specific references to primary, secondary and tertiary sources would be much appreciated.

I'm wondering if this might be a duplicate of “book or survey about conducting experimental studies”

The first introductory text I used is Survey Research Methods by Babbie. It gave (and still serves as a refreshment of) a pretty comprehensive look to the whole process, and the writing and layout are quite easy to understand.
I'd also consider a Google search on different syllabi using phrase like "research methods syllabus filetype:pdf" and see what most instructors recommend. You can modify the search phrase to make it closer to your field; you can also change the pdf to other extensions such as doc, docx, or even ppt if you desire other types of document.
I'm sorry to say that we can't be ready to run a study just by one book. Common methods such as interview, focus group, and questionnaire are their own field of research: For interview and focus group, you'd have to expand into the field of communication and qualitative analysis. For questionnaire design, you may have to further tap into some psychological manifestation of questions, measurement theory, and item response theory.
To build a better foundation, I'd also recommend flipping through Craft of Research by Booth et. al. and it will also pay off to befriend some statisticians or people major in statistics because you may need to learn something about probability-based sampling as well.


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My paper was rejected, and some colleagues say this is due to the "reviewer's mindset." What does this mean?
I'm pursuing my PhD (fourth year). My institute has the following rule:

At least Two SCI papers is mandatory for awarding
doctorate degree.

I tried for publishing an SCI paper recently and got rejection. Two reviewers provided comments, given below in concise manner, for rejection

Language is not good;

Proposed method is just a composition of couple of existing methods;

I am undergoing panic since I am in pre-final year of my doctorate degree.
But, I keep on asking colleagues  and other friends in my academic network how to handle the situation and I categorized their suggestions in to two categories:

Majority of the people are saying that it is totally or mostly up to the mindset of the reviewer(s). The selection of journal is wrong according to them. They are saying that I need to search for the new journal, accepting such papers, by improving the language alone. If I keep on trying like that, one day I will get acceptance.

One person is saying that since the core of the proposed method cannot be improved and the language alone can be improved. It is better to drop the idea of sending to multiple journals and need to try for totally new technique or method and developing a new paper and then sending it for review.

None of the the people giving advice has published in an SCI journal.  They are just giving me a guidance.
Is it true that reviewer's mindset play a role? Is the guidance to resubmit the same paper (with improved language) to a different journal a good idea?

I don't really understand what you mean by "reviewer's mindset".

By "SCI paper" you mean a paper in a journal indexed by SCI? Your advisor doesn't even have a single SCI-indexed paper, nor do any of the other possible mentors around you? That seems quite bad, I don't know why anyone would get a PhD through an advisor without a reasonable publication record. In any event, this is far too specialized a question to ask as far as what to do next about your individual research project. You need a mentor close to you to help with this, Academia.SE won't be a suitable substitute.

The comment 'composition of existing methods' is the most critical aspect.  This means you have not convinced reviewers that your method is new.  It is not about mindset.  Ask yourself, what is new in your paper?  Fusing a bunch of methods together is not sufficient.  You need to show that your assembly/method is new.

"low-quality publications such as [...] Scopus journals"  I didn't know Scopus-indexed journals were low quality.

Wait, neither your advisor, nor any of your mentors have a publication in a journal indexed by SCI, yet it is a requirement to obtain a PhD!?

Is it true that reviewer's mindset play a role?

I'm not entirely sure what you mean by "reviewer's mindset." The reviewer is just trying to decide whether your article is more worthy of being published than other articles that have been submitted. It is true that the process is a bit random; submitting the same paper to an equivalent journal might yield nicer reviewers who make a different decision. But this is unlikely: if a paper is rejected from one journal, it usually means that the paper either needs to be improved, or it needs to be submitted to a less selective journal (or both).

Is the guidance to resubmit the same paper (with improved language) to a different journal a good idea?

Impossible to say without reading the paper, but resubmitting the same paper to a less selective or more relevant journal could indeed change the decision. But you should also consider whether it's possible to improve the paper.

Language is not good

This is a very common problem. As a reviewer, I am shocked by the quality of the writing that established groups submit to reputable publishers. These problems range from basic English mechanics (understandable for non-native speakers, but still needs to be fixed) to basic manuscript construction problems (poor organization, haphazard presentation of background and method, ambiguous results with unclear figures, etc.)
Many students really learn how to write by iterating with their advisors 30+ times. This is a crucial skill; if your advisor is not helping you write up your results so that they are publishable, you may need to consider finding other sources for this guidance, and be prepared to completely rework the paper.

Proposed method is just a composition of couple of existing methods

If this is true, it means that your paper is not very exciting; you combined some existing methods and got some unsurprising results. There is nothing wrong with this per se, but you will indeed need to select a less selective journal; top journals will prioritize more novel approaches with more exciting results.
Another possibility is that your paper is exciting, but it's written so poorly that the interesting bit is buried and your reviewers didn't understand the key point. If this is the case, revising the paper could address this objection.

I am not getting a constructive guidance from mentor. And I am in an environment that none of the persons around me has an SCI journal till now including my mentor.

I think this is the real problem. Normally I would say that your advisor knows what to do, you just need to communicate better with them. But you say your advisor is themselves unable to publish in these journals (which is all the more confusing; how can your university expect their PhD students to achieve what their faculty cannot)? I'm afraid I do not have the solution, but I am concerned for you. Good luck.

I recognize the panic. Especially when pursuing your PhD. It may feel that too much depends on getting your work published.
I have had similar experiences and still got my work published. You will have to try again, and again. There are constructive editors and reviewers out there but it takes some time and effort to find them.
Publishing is to some extent a lottery and subject to many biases. I hate to say it but you may want to consider asking an established professor or researcher to join you as co-author (and improve your paper). A mentor who does not publish and does not have a reputation is not helpful.
Also get assistance with your language. I had reviewers who called work ‘sloppy’ because of 2 typo’s in 10.000 words. This was just nasty.
Look for SCI journals with lower rankings. MDPI does not have the best reputation but they are known to be less picky and more inclusive.
And do not panic. Writing publications is a skill to be learned and needs perseverance. Put yourself together and continue. This is what a PhD is about and most of us had similar experiences. We just do not talk about it openly because it feels like a personal failure. There is shame in talking about work being rejected. You are for sure not alone in this.


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Potential Collaborators insisting on Joining Supervision Panel
TLDR: Researchers wanting to join supervisory team instead of collaborating, why?
I have started my PhD for awhile now and I am gearing up for my confirmation presentation (research proposal defence). I am quite happy with my supervisory team, who I know well and work very well together. I met some researchers by accident with the potential of collaboration on some interesting off-shoots of my thesis, I was hoping to publish.
One researcher worked on the same topic as mine but from a different discipline, so I thought I would ask her some theory questions I had and potentially get her help for a methodology paper at the end of my thesis. Another researcher I approached before my PhD but she did not answer my emails. I have since met her and she was keen to be involved. I thought I could include some questions relevant to her area in my survey and hopefully publish a separate paper. I felt the topic did not meld well with my overall thesis.
Both researchers insisted in joining my supervisory team with some force. Both refused to volunteer or discuss specific questions that I posed, that would have been helpful in my thesis. Both insisted that I speak to my supervisory team and let my team decide whether they can join. They did not call nor spend time with me and getting to know me and my thesis better. One of them did not even read the draft thesis proposal that I emailed her before she offered to join my supervisory team, which I thought was rather rude (was I being unreasonable?). In both instances I felt quite disrespected and demeaned as both thought that my supervisory team should make the decision to join with seemingly no consideration of my opinion. Is this common? Why is that so?
1) What are the possible motivations for both of them to insist they join my supervisory panel? Both of them seem reasonably thin on PhD supervision even though they were both quite hard to get a hold of. Both seem keen to develop links with my department.
2) Why the forceful insistence for my supervisory team to decide whether they can join? Why am I not a relevant decision-maker in their eyes? I can veto them joining the team, so why don't they seem to appreciate that I need to be onboard?
3) Why are they not generous in spending time answering what I thought were simple conceptual and theory development questions that I had? Just one or two lines pointing in a general direction would have been helpful. Why did they focus on joining my supervisory team before discussing their topic areas? I am now concerned that they are not competent in their topic areas, but at the very least they do not seem interested in scholarly discussion.
4) If I am offering publication, why is that not sufficient? I thought publications are a great outcome and sufficient reward for collaboration. I don't understand why joining the supervisory panel participation is more important in their minds than publications and potential collaboration with me and my department in the longer term?
In the end, I was unfortunately forceful with both of them. To one, I outlined how I got to know one of my current supervisors that I who I did not know previously, about how I was able to find out what they were capable of, what they were comfortable with, also their availability and current work pipelines.
To the other one, I offered that we look for a potential student(s) in order to pay justice to the topic. I told her that I am happy for her to meet my supervisors and collaborate with my department either way. I have not heard back from her. I suspect she is upset. I feel horrible being forceful and direct with both of them and I wonder what other ways I could have handled the situation? Is there another approach that could have achieved a successful collaboration instead, if I somehow knew their agenda better? Instead, I am left with the feeling that I was some child answering to some doorknockers insisting on speaking to my parents...

It was the right decision to not let them join the team, but it would probably have been better to have said something to them as "I'll discuss it with my supervisors" and do precisely that (if you trust the latter). That way, this does not become your decision only, but of the whole team. They seem to be young, ambitious and with some disregard to the legitimate interests of others. The joint papers/discussions may have been a good starting point for them later to join the team, but "crashing the party", so to say, is not on. You may have been more diplomatic, but ultimately, you did right.

I can't speak to my supervisors. My primary has already indicated that she is not keen for more to join the supervisory team.  She prefers a leaner team so decisions are easier to canvass and the level of commitment is not diluted. I agree with her. Organising meetings is already tough, so adding unreliable ones would make things worse. I never indicated nor hinted that joining the supervisory team was an option.

Well, then you are even in a better position. You just could have let them know that this is currently not possible, but you are open to collaboration. Rinse and repeat. No need to be forceful, just firm. In fact, in this case you have an advantage that the decision is not even yours, so no reason to feel slighted - it's an advantage to not be able to decide. For what it's worth, I completely agree with your supervisor, small teams are better. Anyway, no need for you to regret, you would have probably regretted much more if they joined your team. Good luck with your PhD.

Thanks @CaptainEmacs. That's true. I forgot that the decision was pre-determined. I guess, I had the option that of telling both of them that from the onset. I never fully appreciated that. My primary was already hesitant and annoyed that I looked for a third supervisor, so a fourth would be a definite no no. Maybe a part of me was worried that if I told them that from the onset, they would have reacted poorly.

Another thing that annoyed me was that both of them knew that I already had a full panel of three. I have not seen many panels of four or more (unless there were content experts with clear roles). For them to assume that they could join without much negotiation really got my goat.

As the wise man says: you can control your reaction, not theirs. If they invite themselves to your party, they have only themselves to blame if they are "outvited". One caveat: if they have contributed important ideas from their stock in the discussion with you, they may be entitled to co-authorship on the relevant papers. But I guess that's what you offered them, in any case.


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How does a PhD student go about doing a meta analysis of a research question?
I just thought that I would put this question out here because I am currently working on a meta analysis of a particular research question in my field (HCI/information science). Moreover, this question is new and has not been answered in very detail so far.
I have done most of the usual ways described in other resources as follows:

I have done a comprehensive review of the relevant literature pertaining to this particular research question. This is a new area and the number of directly relevant papers are ~<50. I have also compiled an exhaustive bibliography of the indirectly relevant papers in this area. That number is ~<150.
Out of this set of directly relevant literature, I have identified 23 quantitative empirical studies, 14 qualitative empirical studies and the rest are theoretical pieces/position pieces/framework papers.

The challenge I am currently facing is how to meta-analyze the data. In HCI, it is not common to freely distribute empirical datasets (although signs of change are imminent in the atmosphere. :)) and I have sent out polite emails to the relevant researchers inquiring if I could have some manner of access to these datasets. The rate of response is ~50% so far in responding to my email but only about ~5% want to actively share their datasets.
Therefore, the only other option (that I can see right now) is to compile, summarize and make sense of data and results already reported in the qualitative and quantitative papers.
I was wondering if any of you experienced (and also not-so-experienced :)) academicians/researchers had any insights into how to actually go about doing a meta analysis from the bottom up.
The main online resources which I have been using so far to tackle this problem is given

www.statistical-solutions-software.com/what-is-meta-analysis,
www.wilderdom.com/research/meta-analysis.html,
www.psychwiki.com/wiki/Meta-analysis and
echo.edres.org:8080/meta/.

Please do note that I am not expecting any detailed step-by-step "spoonfeeding" response. Pointing me to some helpful resources is fine. In addition, personal anecdotes or valuable experiences will be really appreciated.
Thank you for taking the time to read this question.

For meta-analysis you don't typically need the original dataset, only summary statistics related to the study and intervention (which hopefully are available in the publications). You might also want to add the Cochrane Collaboration to your list of websites.

Thanks! The Cochrane Collaboration website is really cool and looks very useful. It looks specific to the biological sciences or medicine though but I am sure that many of the main concepts carry over to HCI.

Also note that Cross Validated is always able to lend a helping hand with any statistics questions.

@ThomasH thanks for the tip! I do visit there occasionally as well.

The Handbook of Research Synthesis is very helpful on these details.

@Thomas thanks for the link. ordered it from the library !

Good luck to you. I'm trying to do something similar and found that few HCI papers publish enough summary statistics to conduct a proper meta-analysis. Indeed, a lot of the time, their stats seem quite sloppy.
I've styled my analysis similar to two review papers I found. One from the HCI area as well (Dehn & Van Mulken, 2000) and one from a bit more outfield (Jones & Gosling, 2005).
Neither is a true meta-analysis, but they get as close to formal as I think it's reasonable to get when an actual meta-analysis is simply not an option.

Dehn & Van Mulken (2000) The impact of animated interface agents: a review of empirical research
Jones & Gosling (2005) Temperament and personality in dogs (Canis familiaris): A review and evaluation of past research

added the papers to my current reading list and upvoted your answer by one. if I don't get anymore in a reasonable time frame, I will accept yours.

accepted and also awarded bounty to you.

Isn't sloppy stats almost the rule in computer science? Performance measurements often don't even report standard deviations.

@Blaisorblade Unfortunately yes, but HCI straddles more than one field. Most conferences I go to, the split between computer scientists and sociologists/psychologists is nearly 50/50. The latter should know a lot better and the former should stop making excuses or take the science out of their name (NB: I'm the former).

@Shion Thanks for the bounty, I completely missed that :)

@ThomasH: things are so bad that we have papers calling to action: see http://dl.acm.org/citation.cfm?id=1297033 or http://dl.acm.org/citation.cfm?id=2442781 (though the latter has a slightly different focus). And people are slowly getting their act together, finally (at least wrt. reproducible evaluations). Maybe people like you should do the same in your community? Though doing it is of course much harder than writing comments :-)

@Blaisorblade There are some papers in the HCI community specifically as well, but it's a manifold problem. For the most part, neither authors, nor reviewers nor editors have the necessary statistical background to distinguish good from bad statistical practices. So no one along the chain of publication stops the papers being published, so the practice continues. Reviews are one way of drawing attention to the problem, so I plan on having a section "giving out" about other people's stats.

I really second the use of the Cochrane Collaboration website for meta-analysis and systematic review.
Another good resource is the PRISMA checklist which is often used for journals and reviewers in health fields when evaluating papers. PRISMA also has good guidelines for how to format/present your included papers and create a flow diagram of your review process (again, often required in health-related journals). Good luck!

+1; came here to mention PRISMA, which breaks down the whole process into very clear straightforward steps and is a gold standard for systematic reviews and meta-analyses. It sounds like the OP is specifically looking for advice on what to do in a field where researchers don't like sharing data though - you might want to add something addressing that specifically.

One take on this, regardless of field, is to create a framework to place the existing research in.  Perhaps you have two dimensions, colour (red, green, yellow) and smell (sweet, sour) - and you review all the prior literatures and place it into your framework 'buckets'.
What this is really doing, and why you want this in your dissertation, is setting up your contribution.  By classifying all the prior research, you will have (hopefully!) identified a hole, which your work is going to fill.  So... choose your buckets carefully!
ps, I realize this is not a statistical answer - but I hope this is of use, or perhaps sheds some light that will help you see a useful way forward.

One note, besides the very helpful ones you have already gotten. While you have embarked on a "meta-analysis", which often has the very specific goal of producing a single (or small number) of summary estimates for an entire field, you should not view having to fall back on writing "just" a systematic review as a failure.
Instead, "the literature in this field is incapable of being statistically summarized in its present state" should be viewed as a finding in and of itself.


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Plagiarism from preprint of paper (from the Arxiv)
Recently we have written a research paper and posted a preprint on the Arxiv to obtain some non-official peer review and to increase the quality of our paper. Till now we have not submitted this paper to any conference or journal (it is unpublished), but we are interested in sending it to a conference.
While testing our paper for plagiarism using free sites, we obtained results showing 83% plagiarism from the version we posted on the Arxiv. In other words, the software is saying that we plagiarised our own paper. We also tried pulling down our paper from the Arxiv to avoid this plagiarism, but it’s not possible. Does that mean our paper will get rejected by all conferences? What should we do?

I agree with Chris, but let me just say that in my opinion your arXiv posting is actually a helpful thing, because it makes clear to people where the material was taken from

I can't imagine that anyone who runs a plagarism checker and gets this result won't also see what's being flagged up and realise it's from the same people. Assuming they don't prohibit papers having been published in arXiv before (some do...) they'll be used to this sort of thing happening.

Presuming that you cite your preprint on Arxiv.

Take it easy. Plagiarism software is spectacularly bad in detecting plagiarism in maths papers. It flags totally innocent things like "Let $G$ be a graph." as plagiarism... I used to work at a university in Asia that implemented mandatory plagiarism checks on PhD theses, and my last PhD student there had problems with these checks, despite having original research results in the text...

@Andrew, unfortunately, some editorial boards are lazy and just run a text similarity checker over a paper without interpreting the results. Software cannot determine plagiarism, only text similarity. A human being must take the decision as to whether or not a text similarity constitutes plagiarism. Quoting the arXiv paper is the best way to go.

Quoting the arXiv paper is the best way to go — What?  There is absolutely no reason to quote an earlier version of the same paper!  If you want to safeguard against this sort of thing, the proper defense is the cite the earlier version(s) — arXiv preprint, technical report, PhD thesis, or whatever — preferably in a footnote on the title page.

You say (it is unpublished), but that isn't really true.  The arXiv is a publicly accessible forum from which any member of the public can view your paper.  That is the very definition of "published", if you ask me.  Now, I know academics use this kind of language all the time, but it doesn't make a lot of sense.

But while testing plagiarism using free sites we found that results were showing 83% plagiarism from our paper only which is posted on Arxiv.

Two questions:

Why did you test your paper for plagiarism in the first place?  I have submitted about 50 papers and have never done this...partly because I never thought of it and partly because I know haven't committed plagiarism because I wrote the papers!  Were you in doubt whether you plagiarized or not?  I don't get it.
If I understood you correctly, you seem concerned that a plagiarism detector found your paper on the Arxiv.  But that's super weird – a paper cannot plagiarize itself, and you are not the first or ten-thousandth person to post their preprint on the Arxiv.  Why would that be a problem?

Based on what you said, it is surprising that you only got 83% plagiarism.  I guess the reason that it's not 100% is that you did make some nontrivial modifications in your paper (and neglected to mention that in your question).  OK, so...I recommend that you post the updated version on the Arxiv.  Then the plagiarism detectors will either figure out what's going on or report that you have plagiarized 100% from a preprint with the same authors and title...a puzzle that even the most harried conference editor should be able to sort out.
Finally, since the question was originally posted on Math Overflow, let me say that in mathematics it would look absurd for a paper to cite its own Arxiv preprint.  If that is actually a halfway standard convention in other fields, I would be very interested to see examples.

It's a bit odd to put questions in the answer section.

it is surprising that you only got 83% plagiarism – it may also be due to the equations. The plagiarism checker probably considers the Arxiv’s PDF, whose equations are different than their TeX source (at least to the plagiarism checker) or a PDF of the same paper generated with another style file.

I have a paper which cites the arxiv version in the supplementary material section since the journal didn't support uploading supplementary material (so we simply direct people to arxiv which does support it)

The situation as I understand it:

You wrote a manuscript A and uploaded it to the arXiv. You do not intend to publish manuscript A in a journal or conference.
You later wrote a manuscript B. You intend to submit B to a conference. This manuscript B shows 83% overlap with manuscript A.

Thus, you are worried to have problems with publishing manuscript B.

While both are your work there is a potential risk somebody may think you are committing self-plagiarism. (As if you would you try to publish both A and B in a journal or conference there could be an actual problem.) To avoid this perception you should make the status of A clear.
You can do this via:

Adding a footnote to the front page of A saying that it is a draft/technical report/etc. and not intended for publication. You can also include this remark as "comment" in the meta data on arXiv.
Mentioning the draft A in your paper B, like: "A preliminary version of these results with more detailed proofs is available on arXiv." or whatever fits you context.

Doing either of those should suffice, but doing both might add some extra safety.
(Assuming there is no policy that results must not be circulated beforehand for the conference where you submit. But in mathematics this should virtually never be the case.)

My reading of the original question is that OP wrote manuscript A, posted it to the arXiv, and then some time later wants to submit a revision A' of the same paper to a conference.

@JeffE The answer seems to coincide with your comment? Just let B = A'

What you should do:

Not worry about it.
When you upload your paper to a conference/journal, include the arXive paper in your citations.
Write a cover letter to the conference chair / editor stating that this paper is based work that you have posted as a pre-print on arXive, and state if/what is additionally in your submission

No, citing the arXiv version would be quite absurd. A paper should not cite itself.

Citing itself? I assume that the paper being submitted for peer review is not identical to the paper on arXive, but contains the same general idea. If it is the same manuscript, then of course skip #2 and go to #3.

The main point of arXiv is to put the paper there first and then submit that exact paper (modulo some formatting) to journals/conferences (and then to update the paper to reflect reviewer comments so that it matches the published paper).