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Is it rude to ask an unaffiliated student to leave the PhD student office?
I work in an office space shared by 3 professors. We have bullpen style desks and around 75% of them are full. The lab is somewhat spacious.
One of the first-year PhD students (not my advisor's student) brings in her friend with her to the lab everyday. They hang out mostly, often taking naps and such. The friend uses the lab microwave and has lunch in the lab everyday. They are generally very quiet and not disruptive. The friend is not a PhD student and as such not a member of the lab.
Would it be rude to ask this person to not come to the lab? I've spoken to the rest of the people in the office and they don't care at all, but it bothers me that they are treating the lab as their living room (given that they are here from 10 AM to 8 PM, most of it involves sleeping or using their mobile phone). What would be the right thing to do here? Do I just ignore them or do I ask the person to leave given that they are not doing, nor will ever do research for any of the 3 professors.
Has anyone faced a similar situation before?

This must depend on the person. Something similar happened to me before and I interpreted it as rude (very rude, in fact - I refused to have anything more to do with the person kicking me out). It's especially bad if they aren't breaking rules, only your personal judgment on who should be allowed in the lab. I'd look to see if there are already rules in place, and if not, try to set some up. It's possible you're in the minority though, in which case you'll have to live with it.

@Allure obviously its a very easy thing to live with but I prefer to look at the PhD office to be just like any other office in the corporate world or at a medium-sized company in the US. This behavior would be incredibly unprofessional in a regular office space.
I've had other issues with them previously where they've done 'language practice' in the lab which involves reading sentences out loud. Obviously I put a stop to that. I'm worried that not speaking out on this now will be an indication that the lab space is just another place for them to hang out instead of doing research.

@Nat I never said their behavior was rude. Not to mention, the "generally quiet" behavior is a consequence of me talking to them several times beforehand. As I mentioned in another comment, they used to do "language practice" in the lab and used to kick their feet up and have loud discussion later in the evening. I put an end to that obviously. I'm looking to speak to them about bringing random people in to nip this thing in the bud. At this moment they seem to be quiet. I apologize if I didn't put all this in the question details :)

@Nat exactly... that's what I'm worried about. But I'm also wondering if this is premature. Maybe they are going to remain quiet for the foreseeable future... Then me asking them to leave wouldn't exactly be the right thing to do. Either way, from all the other comments here, I'm going to just ignore them and if something comes up or if the get disruptive, I'll just go speak to her advisor.

@mboze yes but corporations will probably have written rules about where one can bring visitors. Being asked to leave because I'm breaking a rule feels different from being asked to leave because one person out of many thinks I shouldn't be there. That's why I suggested setting up rules.

If they're not a student, what does the friend do? Sleeping in your lab all day can hardly be paying the bills. How long has this been going on? I'd expect it to solve itself eventually as friend discovers that they need to do something with their life...

I will mention that while Nicole Hamilton's answer is fundamentally correct—this is an issue for your advisor, as well as the other PI's in charge of the office space, not you—there is one issue worth elaborating on.
In particular, it is an issue if someone who isn't part of the department is using the department's facilities, because of the liability issue if something were to happen. For those grounds, it would be especially helpful to mention that one of the people coming into the space is not actually authorized to be there at all.

Presumably people who work in that space are authorized to bring in visitors. In an "office" type space (not a lab with special equipment, etc) I would be surprised if the PhD students working there were not permitted to have guests visit.

@ff524  This is not an occasional guest or visitor.  The OP has described someone not affiliated with the lab who's all but living there.

@Nicole yes, the OP has issue with the frequency and duration of visits.  But that's probably not a liability issue, as long as they're following the rules about bringing in visitors (and I've never seen such rules specify maximum frequency or duration of visits).

@ff524 I think arguments about liability are pretty thin.  They're not setting fires.  They sleep there and use the microwave.  The risk someone might get hurt or facilities damaged because they're sleeping and using the microwave strikes me as remote.  Citing liability as a concern in this case is the kind of thing you'd expect from a total bureaucrat, not someone with a brain.  The real issue is much simpler:  They probably shouldn't be there.  The OP's adviser may/may not agree but it's their call either way.

@NicoleHamilton thanks for the answer. Based on all the comments, I'm just gonna focus on my research. If things get bad, I'll just speak to her advisor who I'm on good terms with.

@ff524: This may very well depend on locale. In the US, it might not be considered a big deal. But in other countries, it's probably a bigger deal—it certainly was in Germany. I wouldn't cite liability in the email, but I would mention that someone from outside the department is using the office on an extended basis.

What if they break the microwave? What if they have a medical emergency? At least in Germany, there might be an insurance issue behind this. Would you be okay with someone staying in your home while you are out if you did not invite them to do so, just napping on the couch and using the microwave once? If the answer is no or "I am not sure", then the same caution applies for office space.

Don't say anything to them yourself.  You don't own the lab.  Discuss your concern with your adviser and let it be their problem.  If your adviser decides it's okay, try to live with it.

I think this is reasonable, but I'd also first consider Nat's comment on the original post. If you can't tell your advisor very specifically why it bothers you, it's less likely anything will happen, and more likely your advisor will get annoyed.

@AJK The OP's concern certainly seemed specific and clear to me:  Someone who doesn't belong in the lab is all but living there and using the facilities.

While I am a strong advocate of the relaxed atmosphere the academic environment affords, it is worth considering the outward appearance. While a first-year student might be forgiven for taking a nap in a lab once or twice after hours, I can't think of a good reason this should be accepted during normal hours, let alone at any time by someone not affiliated with the lab. This makes your lab appear like hang-out space rather than a place of business, which it really is.
This is your place of work, and you (along with your colleagues) fought for that space. Establish some guidelines and enforce them.

It's not the OP's lab nor their place to make rules for it.

@Nicole Hamilton per my interpretation, it is, or at least 33% of it. OP states it is 'shared space' with 3 professors, and OP is a professor.

Unlikely.  The OP remarks that the student who brings in her friend is "not my advisor's student".  If the OP has an advisor, I'm pretty sure that means they're also a student.

@Nicole Hamilton Yep, my mistake, OP is probably not a professor. But I stand by my answer. The PI 'owns' the lab but the graduate student keeps it running.  He or she should take personal responsibility in protecting its image and keeping it a place of research, not of napping.


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Funding after getting an Integrated Masters Degree
Im going to get my Integrated Masters Degree in Production Engineering and Management in about 6 months.My next goal is to take another Master's Degree in Artificial Intelligence.The country I want to study is the UK.So will i be eligible for a postgraduate student loan even though I have an integrated master's degree ?

Best people to ask would be SLC (the student loans company). But as far as I know and integrated Masters counts as an undergraduate degree and you're therefore elegible for a postgraduate loan.

I think that this kind of loans are delivered by the UK Government and not a specific company.

The SLC is the government owned company which deals with student loans for UK students. Do you definitely mean a loan and not a stipend or bursary?

I googled "postgradute student loans eligibility" and found the relevant government website. This should give you all the information you need...

Yeap I know the website.I was just asking to check if there are any exceptions not mentioned there.The website states that if you own a master's degree or an equivalent or higher qualification you are not eligible for a postgraduate loan .Hitting the link of "equivalent or higher" gets you to a page that ranks the education in levels.The integrated master's degree is on the same level as a regular master's degree so therefore I will not be eligible.Is that right ?I have to state that Im not a resident of the Uk .I live in greece .

After much searching on various goverment websites, it turned out Find a Masters had the answer.
You are not eligible for a UK postgraduate student loan if you already hold an integrated Master's degree.

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U.S. humanities professors: Can you get back into academia if you leave?
I'm a tenured professor in a humanities department at a second-tier research university in the United States. My Ph.D. is from a top-ten program in my discipline. I have an above-average number of publications for my age.  I have about five years of undergraduate and graduate teaching experience post-Ph.D.
I have an opportunity to take a job as a writer/editor for a marketing company. I'm inclined to take it (for reasons I won't detail here) but am worried that if I don't end up liking my new job, it will be impossible to get back into academia after having left voluntarily.
I'm not expecting that I would get my current position back, or necessarily be rehired to a tenured position. I'm just wondering how hard it would be to go back on the job market and find a tenured or tenure-track position somewhere in maybe two or three years' time if I end up hating the new job.
I want to emphasize that I am in a humanities discipline. I gather that in the sciences, it is common for one to leave an academic position to go work in "industry," then later return to academia. I have never heard of anyone doing this in the humanities, however. Does it happen?

Do both jobs?  Reduce hours at current job by some amount less than 100%?

Taking a leave of absence seems to be the best option. You lose nothing, and in a year you should know whether you like your new job or not. If they like you enough where you are, they should be inclined to allow for a leave of absence, in fear that otherwise you might leave forever. How you describe the opportunity (one year unique opportunity, improved experience, etc.) will also play a role.

i dont understand why you dont just decrease a load???

+1 simply for specifying 'humanities' and the country in the title.

@user some colleges don't allow any sort of absence except for the rare medical emergency.

We do hear from time to time how a best-selling novelist takes a university position late in his/her career.

FWIW my experience in academic science does not support the claim that it is common to leave and return to academia.

Do you like your current job?

Speaking as humanistic social scientist at an R1 (but who has also taught at small liberal arts colleges), I would say it would be next to impossible.
There is an absolute surfeit of stellar recent PhDs in the humanities. Any position that opens up will get 200+ hungry applicants. Why hire at the associate or full level if you can get a stellar assistant at a quarter of the cost.
Furthermore, if a senior position did open up and a search committee were to look at your CV, I would think they might wonder whether you left academia because: 1) you were pushed out (sexual harassment? Title IX violation?); 2) were burnt out of teaching; or, 3) something else unmentionable. If you left because you hated academia, why are you trying to get back in? Academic hiring is risk adverse because of the stakes of tenure.
However, as an alternative, you might be a candidate for some peri-academic positions such as the director of an institute, dean of student affairs, etc.
tl;dr: Talk to your provost or dean or chair about taking an unpaid leave of absence that retains your tenured position.

Is a search committee really going to think that leaving academia is indicative of a sexual harassment claim or Title IX investigation? Wouldn't that require that a large proportion of people who leave academia do it for those specific purposes? Is there a problem with sexual harassment in the humanities that I'm not aware of?

Leaving a tenured position is unusual and requires good reason. The OP is then applying to get back into academia. Suspicions will be aroused. If you leave, you won't find it easy to get back in

What if the OP just wanted to try something different, struggled to find something else or what they did find wasn't as good, and now decided that really academia was what they wanted to do after all?

That's why they should do this during their sabbatical or take a leave of absence.

What the reason for leaving is doesn't matter - if they're going to invest in a tenured position, they'd prefer one that doesn't already have a history of leaving a tenured position!!

I don't know. I'd expect you'd have real trouble getting back to a top-10 program, but a smaller school that's more teaching focused instead of research might be very eager to have someone with experience at that level. She still have to compete with the hypothetical 200 resumes, but good references from her current program could help her stand out from the crowd.

More or less next-to-impossible than reaching the original tenured professor position in the first place?

In what I've observed as a mathematics professor, it is common for professors to be able to take a year of unpaid leave. A typical scenario is when a professor gets an appealing job offer from a different university: often the professor will accept the position, take a year of unpaid leave from her current position, and then can decide later which position to keep.
My (limited, and in mathematics research departments only) observation is that permission to take unpaid leave is usually granted. (For one year; if you want to do this for consecutive years, then you have to make the case that it would benefit your university.) I would recommend finding out whether this option is available to you.

Yes, in my experience (also in math) someone may take a leave of absence to go elsewhere, and those of us still here selfishly hope he will dislike his new job and return to us...  In fact, even if his intention was to resign, our chairman may try to convince him to take a leave of absence instead.

It's worth noting that this is much less true at smaller institutions/in smaller departments, where filling the absence is a costlier proposition. (This exact request by a friend of mine was recently denied at our institution—not in math, but in a much higher-demand field than any of the humanities.)

A sabbatical or a leave of absence is one thing, but it's also very difficult in mathematics to re-enter academia if you leave (and for pretty much the same reasons as mentioned here, plus the fact--- which is probably true in the humanities as well--- that there are very few things one can do in industry that an academic hiring committee would care about).

@anomaly "there are very few things one can do in industry that an academic hiring committee would care about" - That probably says as much about the ignorance of hiring committees as it does about what mathematicians do in industry - but I wouldn't disagree with the statement you made!

I had at least one mathematics lecturer (a full professor) who'd done work "in industry". He'd worked at Bell Labs in the early 60's, I think they probably considered it relevant ;-)

@SteveJessop: There a very few things one can do in industry that an academic hiring committee would care about, provided one is under the age of 70 or doesn't have access to a time machine. (More seriously, there are a few places like Microsoft Research that might be applicable, but they're extraordinarily rare these days.)

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How/when will I know if my conference paper will be selected for a special issue?
My paper was published at a good conference (in the field of theoretical computer science). The proceedings mention that some papers will be selected for publication in a special issue of journals X and Y.
How will I know if my paper is one of them? If it is not, I would simply submit it to some other journal later on. In general, will the conference organizers let me know of a timeline? Basically, I wonder if I should just wait for (say) a few months, and if I hear nothing, then assume my paper was not selected.

One data point: Last year, we received an invitation for a special issue submission six weeks after the conference. It's unlikely that this duration had to do with other invited authors declining (as suggested in one of the answers), since our paper also won the best paper award. However, the six weeks were in the mid of summer, where many people are on vacation.

If you haven't received an invitation a month after the conference, it's safe to assume that your paper won't be invited to the special issue.
Special-issue papers for theoretical computer science conferences are normally selected by the program committee chair (or a small subcommittee), based on nominations and discussion from the program committee.  The two natural times to solicit those nominations are (1) at the end of the review cycle, months before the conference, when all the papers and reviews are fresh in the PC members' minds, and (2) immediately after the conference, when all the talks are fresh in everyone's minds, and the PC chair's work is otherwise finished.
Once the PC chair selects the papers, there's not much else to do.  Under normal circumstances, the guest editors (usually the PC chair, but sometimes other members of the PC) email invitations to the selected authors shortly after the conference.  Occasionally the invitations go out even before the conference, but that's rare.
That said, sometimes additional papers are invited later, especially if some invited authors decline, and some PC chairs are just less organized than others.
If you have good reason to believe that the PC thought your paper was especially strong (for example, unanimously strongly positive reviews, or PC members telling you at the conference how much they liked your paper), it can't hurt to send a polite note to the PC chair or a close colleague on the PC asking whether the special issue papers have been selected.  (Asking whether your paper will be invited is a bit presumptuous.  Just don't.)

Usually, after further review and rounds of discussions among the program committee members, a final list of the articles are prepared. The authors are then notified about the same. I guess the process takes some time (at least 1-3 months), as there are other logistics to take care post the conference.
If your case is so late, then there is no harm in writing a gentle email to the program chair asking the same. Probably, you could ask indirectly when would the list of extendible papers would be put up on the conference website.
In the present phase, you could continue working on its possible extension. Please note that it is not necessary that you have to submit your paper to the suggested journal by the conference. It is absolutely your choice where you want to be published.
The review process is no different expect the fact that a minor version of the report has already been accepted at the conference.


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Is having similar suggested responses to questions from questionare considered plagiarism?
Is it ok to use a question similar to a question from someone else's questionaire? The question is not that specific, but the possible answers are similar. For example the question similar to yours measures level of involvement on a 7 point scale, while you measure level of importance on different scale. Howerer, possible answers that are measured are similar (some are the same, but not all of them). I know that when scales are used in social sciences, they are cited, but this is not a scale, more like a descriptive question.
Is this considered plagiarism? The advisor thought that it's not.

You're posting a question every couple of days about this paper you've already submitted. It really seems like you're putting yourself under an unsustainable level of stress right now over something currently outside your control. If you were a friend of mine, I might suggest looking into what options your institution has for mental health counselling. A counselling session can be useful in helping you find perspective, develop strategies for dealing with stress, etc, whether or not you are ordinarily in good mental health.

If I understand the question and some of your comments, you and your advisor think there is no issue with plagiarism.  What is the basis of this question?

Terry, I think this is a good question. I teach research methods and have a big unit on surveys. I get this question from students fairly often. I am surprised we have not had a similar question here before.

Ah, this prompted me to check! Possible duplicate: https://academia.stackexchange.com/questions/49927/is-using-others-survey-questions-verbatim-considered-a-plagiarism

Your advisor is correct, this is not a plagiarism issue.
Whenever possible, questionnaires should use validated survey questions and responses from previous research. These should be used word-for-word if possible, as small language changes can affect how respondents answer.
If you are totally making up new survey questions when there are good questions that measure constructs out there, you are probably making a mistake.
If you are changing a word or two here and there solely to be “original”, you are probably making a mistake.
Cite appropriately, of course. Usually citing the original source of the validated questions is best, and maybe one or two other influential papers that are directly related to your topic.
Note that you do not need to cite every paper using a similar question to yours. There are fields/questions where hundreds of papers use the exact same question—imagine how long those citation lists would be if you had to cite every other paper with a similar question.

It is not a scale, not a validated question, just a descriptive one, something like "which of the following methods your company uses...". My advisor said that for scales and validated questions there should be a citation (you adopted or adapted it), but this one is a descriptive question that could have come out of theory...

Your advisor is giving good advice. It is unlikely that anyone would consider such things to be plagiarism for a number of reasons.
First, other than in exceptional cases, there isn't much "creativity" in the questions. The questions are not especially likely to capture the "thoughts and ideas" of the questionnaire writer.
Second, and related to the first, is that there are a limited number of ways to say such things.
Thus, questionnaires of this kind tend to be very similar.
Watch out for exceptional cases (the creativity issue), but in the main, there should be no issues.
Note, importantly, that plagiarism is about misappropriating "ideas" and concepts, not just repeating words. If it isn't an issue overall with your paper, using similar/same words for known concepts won't be an issue either.

Thank you for your answer. Is it ok if some suggested answers are the same, such as "legal councel" or "product manager" and things like that? Of course, not everything is the same, biut there are overlappings.

Probably fine. However, if your work is based on the work of an earlier study, you should cite that study. But it would be overkill to make a separate citation for each such (small) case.

It's based on one specific study and that study was cited multiple times. However, some questions from questionare used in that study are modified and one seems to be very similar to a question from another study (possible answers are similar). That second study isn't cited. Moreover, the second study happened to have very similar structure like the first, therefore there are similarities...For example, authors of the second study never mentioned their questions being based on the first study even thought there are similarities in suggested answers.

Easy enough for you to cite the second study, noting the similarities. Make it easy for readers.

The paper is already submitted. Maybe I can add after reviewers coments. My advisor thought it was the best to cite the first study because the model suggested there was adapted, not the one from the second study. Just one question from questionare was similar to the second study.

Time to relax, then. Onward to the next thing.

Take Buffy's and Bryan's advise serious. Your paper is submitted. The only thing that you will achieve by worrying is increase your stress level. If this is your intended career, then you will have to go through this process over and over again. You will be a complete wreck by your third article. So this is not sustainable. It is hard, but you have to find another way to deal with this. My trick is to just forget the article ever existed once I submitted it. You will have to find your own strategy, but what you are doing now is really hurting you. We are worried about you.

Remember that articles are written by humans (at least they are supposed to be). The thing about humans is that they are not perfect, and the things they make are not perfect. Mistakes happen, also in scientific articles. People, including reviewers and editors, know that and will take that into account when reviewing an article.

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Publishing a paper as an independent researcher, without funds
I have written a small paper that I have written in the field of computer science. I've had several people read it, and one recommended that it's of enough quality they think I should be able to publish it in a journal. I'd like to explore this option, but almost every reputable journal I can find requires a large sum of money to publish in their journal, which is not an option for me, as I am not affiliated with any institution and cannot spend that amount of money.
Are there any journals in computer science that don't require a large amount of money to publish with? Or will I simply have to do something along the lines of publishing on something akin to arXiv and not continuing past there?

[tag:independent-researcher]

Many journals will forgive page charges for publishing in certain cases, probably cases like yours. I doubt that all will, and you need to ask, but you don't need to ask before you submit the paper. If it passes review and is something they want to publish, staking their own reputation on it, then they might be amenable.
Open access journals are probably less likely to do this, since author fees are the main source of revenue for them, but traditional journals have other revenue sources.
But first, you submit the paper without discussing fees. There is time for that later.
Note, however, that in CS, publishing at conferences is the main venue. But that requires funds for conference attendance and travel.

I agree, publishing at a conference would be the ideal, but as you've stated, that's just not realistic for me right now. I'll look into negotiating fees with journals, thank you!

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Is it ok to call professors for LOR?
I'm a student who has completed a Masters in physics and taking a gap year. I currently need to receive letters of recommendations from professors of the institution I got my masters from. But because I already left school, I cannot visit them in person. Would it be inappropriate to call professors via phone if they don't reply to my LOR requests?
Edit: I have already sent email requests reminding them of who I am and what class I took from them. But I did not hear back and was wondering if I giving a call would be inappropriate.

"Would it be inappropriate to call professors via phone if they don't reply to my LOR requests?" as in "I got in touch with them by email"?  If so, add this information (Because then, the professor in question already has an address to get back in touch to you, too.  Because this email may recapitulate briefly your profile like *I attended you advanced class of basket weaving 305 in 2020/21, was in the top x% of the final exam, got awarded "best poster at conference x" for presenting results of the lab class, co-authored paper x which was submitted for journal y / got accepted, etc.)

Just give it a try if you have the phone number, your request is reasonable. Standard communication conventions apply.

Thanks for the advice. Would you say it would be better to contact a postdoc of the professor first?

@VVC, that depends heavily on various factors unknown to us, such as your relationship with the professors, their personalities, their current workload, their current mood... but if you have their number (either directly from them or from a publicly available source), they should have a way to deal with you calling directly.

@VVC Situations may vary, but it doesn't seem right to me to treat a postdoc like an administrative assistant. A postdoc's job is research, not answering the phone for their boss.


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Pros and cons of CV and cover letter for Ph.D. position in the same document
I am going to present my candidacy for a Ph.D. position. For this, I have prepared a version of my CV using Latex and moderncv. The moderncv template includes both the CV and the cover letter in the same document. This is the first time I have seen this, and I wonder what are the pros and cons of including both of them in the same document vs. sending them in separate PDF files. Also, which approach is the most common?
Just in case it is relevant: several positions are offered (each one in a different topic under a different advisor) and I am presenting my candidacy for the subset of topics that I am interested in. The recipient of the email is the department account, so I have no idea who is actually receiving and dispatching my request.

Separate is the most common thing to do in general (for graduate programs, jobs, etc), probably because it is the most convenient for applicants, who will often have only one CV but different cover letters for different applications.
Also, you will keep updating your CV throughout your career, and use it for many things, whereas cover letters are position specific.  This makes it somewhat more covenient to keep your CV separate.
The only pro I can imagine to keeping them in the same file is that it will take whoever's looking at your application one less click to see your information, but it seems unlikely that the person receiving this will care very much whether they get one or two pdfs (if they do, they should say what they want in the instructions).


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Is it OK to use the content of my own paper which is not yet submitted, in my other paper?
I have finished writing one paper, but have not submitted it yet to a journal. I am working on a related but not identical subject, though many of the definitions and theorems are same (but they are true in a very different context compared to the first paper). Now, is it okay to use the same figures that I had used for illustrations in my first paper? What about the theorems and definitions? I feel like changing the theorem statements is not worth spending time on, but is this correct?

possible duplicate of Is copying an image from a previous paper of mine considered self-plagiarism or unprofessional?

I recommend to search this website for self plagiarism. There are many questions very close to yours.

@EnthusiasticStudent I checked them, but the difference is that my previous paper has not even been submitted for review, let alone published. As such, there is no question of citing it yet.

@Arani: There's nothing wrong with citing a paper that hasn't been submitted yet, especially since presumably it will have been submitted by the time you submit this one, at which point you can update the citation.

@Henry Since I do not even know if the paper will be accepted or not, how do I cite it?

@Arani: As unpublished notes, or as a preprint.  (I don't know your field, but if it's math---as the mention of theorems suggests it might be---this is quite common, and a quick look around the arXiv will find plenty of articles citing other preprints on the arXiv).

@Henry Its Computer Science

I have seen a few articles cited as "unpublished".

@Davidmh - Yes that happens in happens in Physics too. Worse still - ''private communication''. But that's very irritating, how can the reader look at the precise text, unless the full text is hosted somewhere?

@New_new_newbie I guess it always depends on the context. For example, last time I encountered it, they were setting a certain angle to 20º, that is a reasonable value, for a certain computation. But if it so happens that a better value is 25º, the rest remains valid, and only the numerical results will be slightly affected.

The first paper is whatever you submit first and the second paper is the paper you submit after the first one. Put the theorems and all other stuff in the first paper, cite the first paper in the second paper. Alternatively some other reasonable options could potentially be: make a zero paper with the fundamental stuff and cite it in both first and second or make a full paper and put everything in it.

Most journals require that the submitted manuscript has not been submitted total or partially to any other journal. Of course different policies apply to open access journals. If I were you I would check the journal's policy regarding this issue and contact the editors if necessary to get their opinion (probably they will require details on what will be duplicated). To the very least discuss this with your supervisor. You can find yourself in a very unpleasant position if you are not careful (not to mention having your papers rejected), as indicated by @Enthusiastic Student

The journal that I am targetting does not require total new content. I have checked.

You have to check on both journals. And you have to be careful about self plagiarism. That being said, it is probably enough to use common sense. Imagine you are presenting in one of your manuscript a method, but an application of such method is published before the  method (this happened to me). You will have to give a briefing on your method an maybe use some figure to make the point. You may reuse that figure later, assuming you have the copyright. In the case of previous results, if the main goal of both studies is not duplicated it may be again be possible (but check copyright issues).


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PI asked me to remove a student from author's list, but I disagree
I am a postdoc at the lab of, say, Prof. Johnson. Together with a few students and external collaborators, we performed a research study and sent a manuscript for publication, where I am the leading and corresponding author. Prof. Johnson and I verbally agreed on the author's order and role before first submission. All other coauthors agreed as well (but this is not documented).
The manuscript has been accepted. After acceptance, Prof. Johnson asked me to e-mail the editor requesting changes to the author list. He wants me to remove one of the students (say, Jane) from the author's list because he (quote) "does not clearly see her contribution." I also know that Prof. Johnson and Jane recently got into a personal fight with each other. Apparently Jane borrowed money from Prof. Johnson and has not paid Prof. Johnson back. Jane has now left the lab.
I worked together with Jane, and I know she contributed with data analysis and creation of some figures. This is something I believe can be documented. I also believe that removing Jane could lead to an accusation of unacknowledged appropriation of her work.  Additionally, if Jane's contribution is not enough for co-authorship, we would have to remove another co-author as well (which is not under discussion).
For this reason, I manifested my disagreement to Prof. Johnson, but he maintained his position. I asked if I could get written permission from Jane, but he said "this is not necessary." Finally, Prof. Johnson said that he would request manuscript withdraw or retraction, if I don't agree to remove Jane from the author's list. The institution where I work has a publicly known history of ethics violations, so I would not trust the internal committees to reach a fair decision.
What would you advise me to do? I would like to avoid a confrontation with Prof. Johnson, but I am afraid that such a request  to the journal would cause the paper's acceptance to be rescinded. Also, recent ethics violations in our institution have been reported by international media.

Update. It has been more than a year since my last update, and I want to thank everyone for your suggestions and your empathy. I am no longer in Prof. Johnson's lab and have found a tenure-track position elsewhere (in a different field). Jane started a different program in another country, as far as I know.
The paper was accepted and ready to be published, but Prof. Johnson insisted on removing Jane's name and adding six new authors who, in my view, did not contribute to the paper. Prof. Johnson complained to the editor, and the paper was never published. A few months later, Prof. Johnson and her group of six published another paper in a top journal, which included many intellectual contributions made by me when I was in her lab. Naturally, I was not included as an author. I have evidence of my contributions, but after careful thought, I decided not to pursue the matter. I lacked the energy and wanted to focus 100% on my new position. I still see that Prof. Johnson presents this work at several conferences as if it were her own ideas.
By the way, Prof. Johnson is a young female researcher who, during the day, is a passionate activist for various women's causes in STEM. At night, she uses her position to take personal revenge on students (also female), sabotages the members of her lab and plagiarizes her postdocs. It aches to see how these necessary and fair causes are polluted by people like her. However, she works at a top institution in my country which, aside from its high academic level, is also publicly known for frequent ethics violations, work and sexual harassment cases, just to name a few (and nothing ever happens).

Does your institution have an INDEPENDENT Ethics board?

Comments are not for extended discussion; this conversation has been moved to chat.

Thank you for the update. Sigh.

Oh my. I suspect there is no good answer to your question. Here are several ideas to consider. Whether any of them is feasible in your situation depends on information only you have.

Prepare a rough draft of the paper that removes Jane's figures and
data analysis and ask Prof Johnson if he thinks the paper without her
contribution is still good.
Find someone at your institution you can ask about this matter.(They
would not be the official channel for resolving this, since you don't
trust the official channel.)
Consider involving (or threatening to involve) the journal editor in
the controversy. Since the paper is in its second round of reviews
there, this change might (should) influence whether they will
publish.

Good luck. Please report back on this site with what happens.

Edit in response to update in the question.
Since the paper has now been accepted, I suspect and hope that the editor would not allow you to remove an author without that author's permission. That might not sway Professor Johnson, who seems willing to withdraw the paper if Jane's name must be on it.
If Jane has not only left the lab but permanently left the field then she could agree to have her name omitted at no cost to her. That would still be somewhat unethical, since she did the work, but she might be willing so that you are not denied the publication.
You could still try rewriting the paper omitting everything Jane contributed.
This is still a quandary.

Most journals will state that cannot and will not involve themselves in authorship disputes. However, some journals will not allow an author to be removed after review unless the author themselves consents.

That sounds like a potential avenue for resolution.  OP can blame the journal for not letting him remove her.

Bullet point one does not seem fair to Jane, unless she can publish her work separately.

@Kimball There is no resolution fair to Jane other than including her as an author. My hope in suggesting the first bullet point was that the professor would not want to exclude that material, so would see the error of his ways.

I get it, but I wouldn't encourage the OP to actively remove Jane's contribution (do the unethical part) and see what the already hostile professor's reaction is.  Clearly communicating Jane's contribution to the professor seems a better approach to me, though I'm not optimistic about success.

@kimball does do we know?

@Kimball This exactly what Ethan is proposing: removing Jane's contribution will make it apparent how large it was. The worst unethical action to be avoided is to publish Jane's work without attributing her. Not publishing Jane's work at all might be unfair, but that's the professor's decision, and OP's capability to defend Jane is limited.

Some opinions sure to be extremely unpopular so downvote away.
First: is Dr. Johnson right?  It's possible.  His INSISTENCE makes it sound like he's seeking personal revenge, but maybe he's right.  I'd love to ask him why he approved the authorship in the first place, but that's the kind of discussion that probably won't help anyone.
But let's say he's wrong, and this is only his personal vendetta.
How are you going to be if you force the issue?  Are you going to lose your position?  Will you be able to advance your career?  Will you be able to work in the field further?  That's the potential cost.  What's the potential benefit?  Is there ANY amount of stink you can raise that will get Jane and the other smaller contributor's name on the paper, and if so, how much of a help will that be in their careers?  It's good that other answers are conspicuously "virtue-signalling," advising taking the moral high ground, when it's not their career that could be affected.
In fact, that's normally my personal play even at risk to myself.  But if the potential benefit is zero, there's going to be SOME cost which it is not a smart decision to incur for said zero benefit.
Life is about learning experiences and we've learned a bunch here already:

vet institution before joining
commit decisions to ink (email) not do informally, no matter how friendly or good the people are; even morally-upright friends can have huge misunderstandings
do not fight with bosses, as apparently Jane did.  No fight SHOULD result in this retribution, but we have to acknowledge that there are abusive people who will engage in this retribution.  Jane did so, and you have to be selfish for a second and note that she's put YOU in a bit of a dangerous position with that, along with anyone else in her clique in the department.  Don't hold it against her (or at least I wouldn't) but it's an important angle to understand.
it's too late now, but don't take action (such as your approach to Johnson) until you've figured out that this is your best move.  In my career I've made this mistake several times.
as another commenter mentioned, don't be Prof. Johnson when you get into such a position.  Seeing such revenge first hand actually could help you be a better person than you would have been otherwise.

So what to do?  You haven't shared all the potential costs and benefits and its probably impossible to summarize in a short note anyway.  But:

Verify with the journal whether authors can even be edited at this point, and if possible talk with the editor verbally and imply you're looking for a no, if there's not a written policy.  This no will avoid all future discussion.
I wouldn't get the more minor contributor axed as well.  Leave the poor guy out of it.
Jane obviously is going to find out if she's removed, and the more likely that is, the more likely you should let her know the situation.  She might have good information, such as a trustable party in the institute you can talk with.  Or, she may confide that she was wrong to fight with Johnson and was going to apologize anyway.  Or that she's not concerned about this minor authorship as she's onto something bigger, or that she's decided to leave academia.  Or something.  I might try to present this as "we've got a problem" (you and Jane) and ask to brainstorm solutions on you two's mutual problem.
You're a good person to want to help Jane out with trouble she apparently has landed herself in, but just as you can't take home all the kitties and puppies in the pound, this might not be YOUR fight to fight.  Maybe the solution is for Jane to fight this, if she wants to fight it, and you two connive for you to give maximum aid commensurate with not damaging your own career?

Personally I think this is good advice. Not the moral high ground, but very pragmatic.

It would be OK to advocate for a moral compromise on practical grounds if you were honest about it: "Cave in to the abuser because standing up for the innocent victim will be costly while doing no good". However, you are not honest: she's put YOU in a bit of a dangerous position and help Jane out with trouble she apparently has landed herself in is practically a definition of victim blaming, something that's simply not true: no-one has put OP in a dangerous position but prof. Johnson.

If removing her from the authors list, should we also remove all the data and figures she contributed to?

Not the moral high ground, but very pragmatic.  Imagine if Schindler, of Schindler's List fame, made a public speech that the Jews shouldn't be rounded up and killed.  He wouldn't have saved ANY Jews in that case, agreed?  In life you have to play the "long game."  Trying to maximize instantaneous level of moral-high-groundedness probably won't maximize area under the curve.

practically a definition of victim blaming -- Sometimes people do things that increase their chances of getting unfair and unmoral consequences visited upon them.  We're left to choose whether to point this out to people, allowing them to make an informed decision to avoid those consequences, or not.  Say a tourist is standing too close to the cliff edge.  You can victim-blame, saying that other people who do this tend to fall to their deaths, and reduce the chances this sightseer dies in turn.  Or you could scoff that to do so would be victim-blaming and let the guy die a splattery death.

should we also remove all the data and figures she contributed to? -- This may be a brilliant out.  OK, you morosely tell Johnson, I'm taking her out but she points out she did the analysis only in return for the credit.  Where can we find someone who can re-do her work and is willing to do it knowing a priori they won't get credit?

I would advise you to try to avoid a direct confrontation with Pr. Johnson but to refuse (very politely) to remove Jane.
You could e.g. say that unfortunately this is not possible because you believe the journal doesn't allow the list of authors to change between submissions (which is probably at least kind of true). Or you could say that you understand if he wants to contact the editors directly but that you don't feel comfortable doing that yourself. If possible, say all this by email so that there is a written record. If you are willing to compromise a little bit, offer him to become the corresponding author instead of you and let him take responsibility with the editors; or tell him that unless Jane herself agrees to renounce authorship, your hands are tied.
In any case, even if you take a risk by confronting Pr. Johnson, you also take a risk (possibly greater) if you agree to do something clearly unethical such as removing Jane, unless you have proof that you were coerced to do so.

Op should find out if it's possible or not to remove authors --just saying you don't think it is possible (or worse lie and saying it isn't when you haven't checked) is weak and will just piss off the pi, who most likely already knows the journals policies

Unfortunately, based on the description in the question, I don't think it's possible to refuse to remove Jane, without being in a direct confrontation with Prof. Johnson, no matter how politely this is done.

I would suggest involving the chair of the department or lab (assuming it is not Prof. Johnson), because the upcoming harassment suit is going to be very, very painful. Even, I might add, if that isn't the cause of the personal dispute, because that's how it will be framed. If this is Prof. Johnson, I would move on up to the dean. Jane is going to notice the absence of deserved credit, and it won't get better from there.
The last journal my wife submitted to required repeated certification that all researchers had received appropriate credit.

It depends on how much of your own benefits will become void If you keep your ethics.
I will feel really sorry for her if I were at your position, but I would be more worried about my consequence if I support her.
I probably will let her know that the professor is kicking her out anonymously, and it's up to her to fight against the professor. I might give her some anonymous evidence too but it depends.
Either way, I strongly suggest you to keep some evidence of your professors kicking Jane out, in case you will be in the same boat later.

... or in case Jane manages to defend her right to be on the author's list and Prof. Johnson makes the OP the scapegoat by claiming that removing Jane was their idea.

It's not entirely clear from your description the following two things:

How closely reliant are you on this PI? i.e. is he your primary/sole sponsor, or one of several you work with?
What was the nature of this "fight" between Jane and PI, and is she a grad student with him as advisor?

Also let me add broader question (3) What are your priorities, between 'doing what seems just/fair' and 'grease a few wheels to advance'?
If he is your primary sponsor AND he is not Jane's advisor, then side with him. If he IS her advisor, maybe what he really wants is to get her to quit or switch advisors. Even if you convince him to keep her on this paper it really just drags things out for both people who don't want to be in the relationship.
If you are not reliant on him for support and on merit things should go with Jane in terms of the fight, well, propose withdrawing your further work with him and he can have fun with sub-par students like Jane. If such action is too adversarial, suck it up and remove Jane.

If he is your primary sponsor AND he is not Jane's advisor, then side with him. - While this makes sense from a self-preservation perspective, this is not necessarily the ethical choice.

sub-par students like Jane - I didn't see anywhere in the post that suggests she's a sub-par student.  Where did this come from?

@Kimball it depends on your ethics. I am sure prof. Johnson's ethics will find personal survival is the ethical choice.

I like how this answer candidly exposes the power games inside academia. A long time ago, they were power games only for the sake of own's ego, luckily in the past 20 years  with the fundings becoming scarcier and closer to a competitive system, also money are involved.

@Kimball Indeed. The present response is as relevant as Jane was sub-par; sub-par enough to utilize material she made for the publication. If this was ironic by the responder, they should have put it in quotes.

For the neutral part:
You are being the victim of a weird system. Please note that Prof. Johnson is as much an active actor in this system as a victim.
Prof. Johnson is strongly entrenched in their request to remove Jane. If you are completely expelled from the academia because of this friction with Prof. Johnson, you will leave your place to someone that may or may not be as good as you at advocating for fair authorship.
So do whatever you have to do. if the paper is 100% necessary for your career, make an half-assed attempt at changing the authors list, write to the lowest editor of the journal an email with your prof Johnson in cc, asking the removal of Jane from the authors list.
Now, assuming your side of the story is the right one.
Keep in mind a couple of things for the future:

If you have strong arguments with your subordinates, do not be revengeful and avoid resentment (well, this is true even if Professor Johnson was the right one in the big argument with Jane);
do not be Prof. Johnson.

For the present keep in mind this: becoming a professor is like winnning a lottery. You need a lot of stars to alignate for that to become reality. The small star being the +1 paper with famous/influential prof. Johnson is negligble. And the other co-authors may find you a jerk for blocking the publication of the paper on this  conflict, but even if they are in absolute need of that paper for their PhD, they are at risk of a much bigger jerk, so I suggest you to clearly explain your concerns privately to them.
On the other hand, as a postdoc you do not fully realize your potential of finding a satisfying job outside the academia. Do not forget that.
Good luck!

Can you please clarify what you mean that the professor is a victim in your opening paragraph?

1/2 @infinitezero it is against the human nature to be mean to close people. Students are close to professor. Prof. Jonson had at least a minimum of interest (maybe dictated by their ego, who knows) to have a model role.
I wonder (not really) how come that a smart person is so shortsighted to be mean and so irrational. It cannot be their own fault only. It must be (past) ambient influence, too.

2/2 However, nowadays prof Jonson is an actor in this ambient. How to break the vicious circle? How to stop becoming prof Jonson?
1st: realizing that hard working is just the other side of the exploitation medal ---> stop celebrating that.
2nd: stop believing in suffering and hardship as a learning tool.

I might see your point, but the way you present it suggests you're excusing the actions of prof. Johnson. He is an independent person, and from what the OP writes, is not actively influenced by any external factors. He is not a part of any vicious circle. Maybe he was exposed to some bad role models in the past, but certainly, as a professor, he had a chance to meet good role models. It is entirely up to him to make right and ethical decisions.

@user1079505 It's 2022 and we are still discussing issues that are present since the late 80s (and probably before, I limit to my personal experience). I have enough of this crap, and enough of seeing people trying hard to find the bad guys (and quite often being deceived by the moral fighters apparently fighting for the good of everyone else). Let's fight the future the prof Johnsons, not the many prof Johnsons being around

@EarlGrey today Jane certainly won't become a better future professor, if the encounter with today prof. Johnson discourages here from pursuing an academic career.

@user1079505 I do not care about the Janes future academic career. This Jane in particular showed thick skin, I am sure they will do whatever is needed to become a professor. I care about people like OP, they are squeezed between their empathy for students (and people at large) and their careers. Experience tells me that one exclude the other.

"Experience tells me that one exclude the other" - how is empathy for students excluding a good career? They may be orthogonal, perhaps, but excluding?

@CaptainEmacs you have a finite amount of emotional endurance.
Either you spend it towards your career (do the job you love to do, to say it in a  naive-Stevejobesque style, becaming the median self-entitled&titled full professor on the way) or you spend it towards the students.
I have seen too many postdocs, assistant professor and other peers saying things like "I want to have only exceptional good master students to do their master thesis with me" to believe they are really caring about the students. If nothing else, for the simple reason that exceptional good is a relative metric.

@EarlGrey Of course, I want only exceptional students. But sometimes I helped colleagues with problematic/weak students and helped them get through. This helped my career because I was considered a good mentor to colleagues and students.Your life experiences may be different, sure, but in my "halo" of people, this does not seem to be the case.

@CaptainEmacs do you mean your colleagues are irrational because they had problematic/weak students? If you had better career than the colleagues you helped you are proving my point (not needed, I know the difference between statistics and anedoctal bias).

@EarlGrey I am not sure what's you mean by the link of the colleagues being irrational and their students being weak? At most it might indicate that I am better at choosing or mentoring students. I do not see how that proves your point. Rather the opposite.

@CaptainEmacs You are better at the competitive game that it is academia, exactly because even if you are good at mentoring students, you pick only the excellent ones.
However, this is a fundamental difference in how to think about tertiary education, if it should maximize the outcome of few individuals (winner takes it all) or if it should maximize the outcome for the society (being poor&unlucky in the talent draw done at birth in Germany is less worse than being so in the US) therefore we can stop the discussion.

@EarlGrey I do not want to overstretch the discussion, but there is an important point: You overlooked the statement "choosing or mentoring". Significant parts of my career are built on the latter and many of these were what other people would consider at best middling students, where I instead saw potential. That's what I am trying to say. And as for US versus the Others: the US is the US, and, while dominant, it does not constitute the whole world of academic import. Anyway, I won't keep you any longer.


text:
Advisor not responding to MS student, not sure if he hates me
So I'm a MS student in Computer Engineering just doing a capstone project as one of my requirements for graduation.
My advisor had been nice and assigned me a partner to work on the project.
However, the partner just did many rude things to me so I told my advisor that I want to leave the team and work on my own. He agreed, saying that's understandable.
But after a few weeks, I couldn't get much work done on my project because I've been so busy with other things. Then I noticed my advisor kicked me out of our lab Slack channel (I was deactivated). I met up with him once just to update my progress, and to me he seemed mad/annoyed. I'm not sure if he was actually thinking that way because I think many professors are just not good at communicating or busy.
I felt scared so I thought I'd just only communicate with him when I have made presentable results. At the end of this quarter, I show him my finished project, and he hasn't responded. I need his signature to graduate. Do I read this as my advisor being mad at me for not making progress in the beginning and for not getting along with a team member (who was good at making himself look like a good student, and he was close to my advisor so I'm wondering maybe he made-up some rumors about me) and he just decided to cut me off?
I don't think he'd cut me off without telling me since I have an expensive equipment from his lab. I sent him an email asking for a sign to approve my project and I need this to graduate but he didn't reply and the form deadline has passed but the office gave me an extension. He's still a young assistant prof but his lab has published many papers, and he usually replies to email super quick. Do I see this as him disliking me or is he just busy? And does it happen often to not let a MS student graduate?

If your advisor was mad at you for some reason, refusing to communicate with you would be a very childish way of expressing this (much like, you know, writing a fake RateMyProfessor review for someone you've never met in response to getting feedback on this site that rubbed you the wrong way). Unless you have reason to believe that your advisor is a particularly petulant person, probably there is no need to imagine catastrophic scenarios. The simplest explanation, namely that he just hasn't gotten arond to reading your project or responding to you yet, is probably the correct one.

I don't think it's reasonable to jump from "he didn't add me back to Slack" to "he doesn't want to advise me". Normal (i.e. not passive-aggressive) advisors do not engage in sending veiled hints to their students in this way. I think the reasonable way to respond is to just wait for your meeting with your advisor and to avoid, if possible, ruminating over the worst possible scenarios in the meantime. Other than that, it's impossible for anyone here to guess what's going on in your advisor's mind.

Some people don't like it when there is no progress and they lose interest. (Not saying it is in your case). However, since you need his signature to move on, you could contact student office and ask how to proceed.

There is no way to guess what is going on in your advisor's mind.
Professors are human beings so they have the same range of personality traits as humans in general.  But deliberate "ghosting" would be clearly unprofessional.  Of course that must happen sometimes (see above "professors are human beings", but it's not the conclusion I would jump to.  Other possibilities include:

They are having some kind of personal crisis and are not able to respond in a timely fashion

Due to some technical issue, they are not receiving your emails, or you are not receiving their replies

They have some issue that they need to address with you, but are trying to work things out (gather information, research institutional policy, etc) before they contact you

You can surely think of more if you try.

Regardless, clearly nothing will be resolved if the two of you can't communicate.  If he won't respond to your emails, try something else.  Visit his office in person, or call on the phone.
If that doesn't work, then get someone else involved: e.g. a department chair, graduate program chair, or another faculty member who you trust.  They can help facilitate communication between you, and if it turns out there is a conflict, they can help mediate it.  They may also have additional context about the professor's situation, in case they have something going on that you don't know about.

The thing is he is not on campus except for once a week due to paid family leave. The only communication I have is through email. The deadline of the extension the office gave me to file my forms is tomorrow and they said I won't graduate if I don't get the signed form. So I take this as if I don't get a reply from my advisor (he's not on campus tomorrow), I just have to suck it up. Have you personally seen advisors that just cuts-off communication and stop advising their student without telling them?

No, you don't have to suck it up.  If you have a deadline tomorrow, then telephone or visit the department chair at 8am on Monday or whenever is the normal start of business hours.  Do not delay, and do not rely on emails that may not be read until later.  Yes, I know phone calls are awkward and uncomfortable, etc, but just do it.  Also, call whatever office is imposing the deadline, and explain the situation.

@happypenguin: No, I have not personally seen that.  If I did, I would immediately escalate it to the department chair, as it is unacceptable behavior for a faculty member.

By the way, the fact that he is mostly on leave would crank up the probability of the "personal crisis" option in my answer.

I see, thank you. I hope to believe that he isn't the person to do this because he was very nice at the beginning. It's just that I saw him update his professional twitter account on the weekend while not replying to me so I had thought maybe he's not too busy with his child.

It's true that replying to you ought to have higher priority than updating Twitter.  However, because as mentioned they are human beings, professors do not always prioritize their time the way that they ought to!  (Case in point, right now I am on Academia.SE instead of doing something productive for my students or research :)

Haha thank you, your work here has really helped me and many other people I believe :) Sorry one last thing, do you think it happens a lot where advisors don't want to let their MS students graduate? I don't see any downsides for them but he might just be mad because he doesn't like my work. I'm just really worried due to issues pertaining visa and just need some comfort...

@happypenguin I have seen people going AWOL for a whole bunch of reasons. The fact you do not get a comment may be because they don't like your work, because they are ill, because some member of their family are ill, because they have a crisis, because ... - this is out of your hands. Get help from the department.

Thank you! I will ask the dept. for help.

@happypenguin: Having their students graduate is an advisor's job.  Intentionally refusing to do one's job is going to have serious negative consequences, in academia or any other line of work.  Whether or not it is important to the advisor personally, it is definitely important to the institution to graduate students when they meet the criteria for doing so.

@happypenguin: A situation where a student may be prevented from graduating on time should constitute an emergency for the department.  Be as persistent as you need to be in getting help from anyone who is able to give it.

Okay, thank you so much! Just super stressed...

Update: Turns out he had been reading my emails but kept ignoring them. He only replied when the graduate office got in contact for me and said I didn't do "enough" so he doesn't want to pass me. I beg to differ with that statement, I spent many hours and produced results. Seems like other profs don't want to give me a solution too because they don't want to step on another prof's student. Politics...


text:
Finding correct articles for SLR from different databases?
I have to do a systematic literature review (SLR) as part of a university course. I have found all search terms etc, but now I have to narrow down the search to research articles. I've been stuck for a week, since each database has its own name for these papers and I'm not sure which publication/source type to select from each database, so they are all correct and comparable.
Below I have listed each database and the different publications they have:

ACM: "proceedings" vs "journals" vs "research articles"
Google Scholar: "review articles" vs well, non-review articles
IEEE Xplore: "conferences" vs "journals"
ScienceDirect: "research articles" vs "review articles"
Scopus: "article" vs "conference paper" vs "conference proceeding" vs "journal"
Springer: "conference paper" vs "article" vs "conference proceeding"

Thanks for any advice.
Best regards
PS: If I had to choose, I'd take ACM (research articles), Google Scholar (review articles), IEEE Xplore (journals), ScienceDirect (research articles), Scopus (article), Springer (article)

If I understand your question correctly, you seem to be stuck on the term "research articles" as if that describes a specific genre of article. But it does not. It can mean many different things. I suspect that what it means is "peer-reviewed articles" (as opposed to practitioner studies or non-peer-reviewed scholarly articles), but you will need to clarify from your professor precisely what they mean by the term. I am sure that they will be able to clarify this for you. Since this is a school assignment, then it really does not matter much what answers you might receive from here (including my answer); what matters is that you correctly understand what your professor means. So, ask your professor for clarification.

Hi, Thanks for your answer! The professor said it's up to me to find the correct publications....
If you could answer, if I choose the following publications/articles from these databases, I think they are coherent in terms of research quality and usability for a systematic literature review?
ACM (research articles), Google Scholar (review articles), IEEE Xplore (journals), ScienceDirect (research articles), Scopus (article), Springer (article)

I find it odd that the professor would not clarify such a basic question. But I think you should search for "peer-reviewed articles" in each database. Sorry, but I am not able to check each of the databases you have listed to see what terminology each one uses, but the notion is a peer-reviewed article. These might be both journals and conference articles.

Thank you very much for your answer! :)

@QuarterlyReport, if this answer answers your question, please click the check mark to accept it.


text:
Self-Plagiarism in PhD thesis
I am a final year PhD in UK in a scientific discipline and I am writing my thesis. I have already published 2 journal papers and I have submitted 2 more papers for publications. My department does not allow a "publications-based" thesis so I need to write a thesis in the context of a book etc.
As I write my thesis in a couple of places, especially in the literature review, I tend to reuse sentences from my publications. I try to restate them a bit, maybe change some words for their synonyms etc. but it is practically me writing about what I wrote before. It goes without saying that I cite/quote me at the end of a passage if I say something non-obvious (I found that slightly funny. :) ). The problem is that occasionally I am just explaining for instance how a certain estimation technique works; in that case I cite the original authors and not myself. The syntax in those occasions though is practically the same as the original passage I used in my publication; as I have explained it once and was consider good, I find no reason to reinvent myself (I do a mild rewording as I mentioned but that is quite insignificant). Same things goes for listings. I do cite my paper in the beginning of a big list as the list's source but the list itself is almost identical as the one in "my" paper; in those cases I don't use quotations, just attribution "[]".
Is there an obvious guideline? The basic definition of plagiarism "reproducing the work of another person's as your own" is not (directly) applicable to me because I am the other person (almost *); if I am using other people's work I do cite them but I don't cite myself, citing them, in quotation marks!
I am a bit "fuzzy" about how not to plagiarize myself in my thesis (I have had no problem regarding my journal publications).
(* In all publications mentioned I am the first -but not sole- author.)

Did you look at the other question ?

@scaaahu: This is a slightly different question, asking about how to use papers when a "stapler" or "sandwich" thesis is not allowed, although the answer is similar.

This is one reason why this entire "self-plagiarism" notion is ridiculous. The word has been usurped to mean something which it is not, stealing another's work. It should be called what it is, duplicate publication. There are issues with copyright when reusing ones own work, however the ethics should be clear, plagiarism is stealing another's work and presenting it as one's own, which is far worse than duplicate publication, or passing off past work as new. The latter is unethical, but it is not plagiarism!

Additionally, companies like iThenticate are now capitalizing on this trend. As a scientist, I want a concise, clear, and well worded paragraph describing some method, phenomenon, or mathematical model. For many scientists, such paragraphs are often reproduced over and over again since they work in narrow subfields, even when the meat of a publication is new, the introduction, methods, etc. may be refined to a point where it is about the best it can be. Should this then be re-worded just to avoid being flagged by iThenticate and clones? I don't think so, but it appears that we are headed there

Even if your department does not allow a "stapler" thesis, it is entirely reasonable to expect that you should be able to freely use this material in a thesis. In general, I would expect that you would have to include a copyright statement similar in form to hose that would be used were you to copy the entire paper outright.
To cover against charges of plagiarism, I would simply acknowledge something like "Some passages have been quoted verbatim from the following sources," and list them. Also, when you reuse figures, I'd include the "reprinted with permission" tag.
Finally, ask your advisor or other members of your department for guidance! Since you're not the only person subject to this restriction, they've gone through this situation before, and can provide you with information on how former students have handled this.

The letter of the copyright law is extremely weird in such cases (formally you may need to request a permission from the journal editor to reproduce something, especially a picture, you made and submitted there yourself a few years ago, if you have assigned copyrights-some journals require copyright transfer, some do not). However, the spirit of the law is that you are free to use your own work several times even if you assigned your copyright away as long as you clearly state that it is not the first time you present (this is not required if you both retain all the rights and no originality expected) it and that the previous publications are such and such. To be on the safe side, write to the editors and request a permission to reprint (it is automatic unless the editor is an evil villain having personal grudge against you). However anyone trying to accuse you of using your own work without his permission will make such a fool of himself in the scientific world that his reputation there will plummet to negative infinity, so I don't think the chances of trouble are above those that some crank will accuse you of plagiarizing his work or that the outcome of the accusation, if it occurs, will be essentially different.

Thanks, given your answer and that of Peter's I guess I need to come in contact with an editor indeed.

Correction: you are mostly right about plagiarism issues, but not about copyright. Self-plagiarism is a real thing (and misconduct in some cases)—but reusing your papers in your thesis (with citation!) is completely fine.
"The spirit of the law is that you are free to use your own work several times even if you assigned your copyright away" seems wrong about copyright. Publishers' copyright transfers can have specific provisions for theses (ACM has), but I strongly believe they're needed.

The papers you have published and that my be under review in a journal require permission to rproduce. It is therefore necessary to write to the journals and ask for permission to reproduce the contents in a thesis. I have heard of journals that refuse but they are very few. What you should remember, however, is that the copyright usually covers the final product or versions of the manuscript that have been altered as a result of work done within the journal, in other words gone through or in some stage of review. It would therefore be safe to reproduce your original submitted manuscript. You will need to acknowledge the permissions in your thesis (e.g. if you include a list of published paers and manuscripts in prep.).
All this may seem complicated but I have not experienced any publisher that has refused reproduction (either of a reprint or the text itself) in a thesis. After all, publishers live off of scientists writing papers and a PhD candidate (and scientists involved with her/him) is another "customer" to put it bluntly. It would therefore potentially be pretty self-destructive to refuse use of materials for a thesis with very limited distrubution.
Under any circumstances, please contact publishersand tell them what you intend to do andaskfor permission. Also check on the copyrights (which you usually sign at some point during the publication process. It is "better safe that sorry" that applies. And, I repeat, I would be surprised if you are given a no.
EDIT: A good way to find out what "your" journal adheres to is ot use the SHERPA/RoMEO site classification for self-archiving. They use a four part classification as follows:

green - can archive pre-print and post-print or publisher's version/PDF
blue - can archive post-print (i.e. final draft post-refereeing) or publisher's version/PDF
yellow - can archive pre-print (i.e. pre-refereeing)
white - archiving not formally supported

The level or archiving indcates what also falls under the copyright agreement of each journal and hence also what you may be free to reproduce in a thesis, and what you are not.

Most of the copyright transfer agreements I met so far explicitly say that you retain the right to reuse your paper for a thesis. Depending on the exact wording, you may not even need to ask for permission.

and that my be under review — Huh? Transfer of copyright only happens after the paper is accepted. What am I missing?

@JeffE The fact that one may easily sign the transfer without reading after all passages are reproduced but before the thesis appears in print, i.e., that human beings are forgetful and lazy by nature (I am, at least). However you are 100% right from the formal standpoint.

Also, many publishers have either explicitly posted policies stating exactly what is required or "clearance websites" where such permissions can be obtained.

Thank you for the SHERPA/RoMEO website, it was really helpful. (Apparently my currently submitted work is on "green" journals, my published one on a "yellow" and a "white" one...) I will look the copyright agreements in detail.

I use sentences like "The results described in this chapter have been published as [xx]." or "This chapter gives the argumentation published in [yy]".
However, my primary reason for this is less concern about self-plagiarism (papes and thesis are in different languages) than  pointing out that these findings/developments have passed peer-review during a publication process. But if you give the appropriate citations also to your paper, I think it is important to make it easy for the reader to see whether the citation is your contribution or not.

slightly off-topic: I even go one step further and at the very beginning (in a section about abbreviations, symbols and conventions) explain that papers [1 - x] were written in direct connection with the thesis, and are put to the front of the literature list to allow the reader to easily detect my contributions to the field. You could also solve this by giving reference lists "my contributions" and "other people's contributions" (similar to how some fields give primary literature lists and secondary literature lists).

Interesting suggestion (about the literature lists), thank you.

With regard to your slightly off-topic comment, that only works in fields where the norm is for the bibliography to be sorted in order of citation. In many fields (e.g., pure maths and computer science), the bibliography is normally sorted alphabetically by first author so this trick wouldn't work.

Are your papers really your own papers, or maybe you have some coauthors? That's when it becomes complicated. It will be hard to claim that the text you copied is exclusively your own work when the original paper is drafted and signed off by other people. On the other hand the thesis should be your own work exclusively.

That is the primary difference between "stapler thesis" style and the reuse discussed here -- in the stapler method the thesis will contain contributions of coauthors.  But repeating one's own contributions is still perfectly fine, and the automatic assumption will be that the parts so used are the portions which the thesis author was responsible in the earlier work; only the coauthors themselves will have any basis for thinking otherwise.  So it's worth noting that one shouldn't claim the work of coauthors as one's own, but that possibility hardly disqualifies use of prior published work.

If you quote from your own paper, you may have to justify to the degrees committee how much of the paper was your work. If you are first author, it should be no problem, otherwise can you put a figure on what percentage was your own work ? Even if not all your own work, if the actual research was done by you, it should be possible to put a different slant on it. Having your ideas published already helps with the defence, as you can demonstrate successful peer review

Talk to your advisor/sponsor of your thesis!!!
Read your school's and department's policy of plagiarism.  Some will include "self-pgagiarism" some don't.
It is all up to the advisor and school.  If they accept it, then it is fine.  If they do not accept it, it is not fine.
If you are the copyright holder (or have rights), then there is no legal issue.  Even if you aren't the holder, there are provisions in the law for academic references.


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Is it okay to upload the PDF of my non-open access papers in academia.edu or research gate?
Is it legal to upload a PDF of my non-open-access papers to research networks, such as ResearchGATE and Academia.edu?
I am pretty sure that it could cause some problems, because normally people should buy them from the publisher. But I have seen many researchers put the PDF of their (non-open access) papers for free there so as to get more citations.

It should all be written in the copyright transfer agreement you signed before publication. If some things are not clear, you can always ask the journal. If your question is a very general one asking about all papers out there posted by the authors themselves, it depends. For example, there are high-profile journals that are "hybrid" in that they are in general non-open-access (so their papers look like tightly copyrighted by the publishers) but do offer an open-access option for each individual paper if the authors so wish. If your filed is EE, many IEEE Transactions are like this.

Well, My works are in high profile journals (IEEE Transactions, Elsevier and Taylor & Francis). Also I haven't paid the extra money to make them open access. So In this case, I am not allowed to upload the PDF for free ? @YuichiroFujiwara

Most likely not unless it's an unusual case or some of the journals you published in have a different policy than many others. In any case, as I said in the first comment, you should read the legal document you or your co-author(s) signed, and if you are still in doubt, you should ask the journal(s) directly. Some journals do allow you to post the published versions on your  personal website, your institutions' server, etc. But I don't know a journal that is fine with uploading to a large network that systematically distributes papers for free.

@YuichiroFujiwara Exactly so. Read the fine script in the contract. Allowing authors to freely distribute their papers negates the business model of open-access journals.

@Electricman "high profile journals" -> these people have legal departments.

@Electricman IEEE allows you to distribute a pre-print version of the article (so a document YOU have prepared and not the one that you can download from IEEExplore) as long as you clearly state the copyright status. Most publishers would actually allow that. You just need to make sure what is the exact process. Also, in terms of the business model it is more based on subscriptions and not on individual sales of articles.

@Electricman you need to look at the policies those specific journals/publishers make available - eg/ http://www.elsevier.com/about/company-information/policies/sharing for Elsevier. There's no general answer for all journals (beyond "no, unless they say you can")

FYI: Has the stance on questions pertaining to legal issues changed?

See also: https://academia.stackexchange.com/questions/62752/does-a-preprint-include-revisions-made-in-response-to-peer-review

The current best source for answers to this question is the SHERPA/RoMEO database, which categorizes all journals by their policies.
This tells you, for most respectable journals, what you are legally allowed to do in terms of posting versions of the paper on other sites (this may, of course, be modified by local laws; for example, documents produced by US government employees are not generally protected by copyright).
For a large number of journals, you are at least legally allowed to post preprints.  In such a case, I see no advantage in flouting the law by publishing the journal's final version instead: I believe a preprint is generally sufficient to make your work more readily accessible and gain you the open access citation benefits.
As for journals that do not allow you to post preprints: you need to make your own moral and personal judgement on whether you will submit to such journals at all, and if so, the degree to which you will comply with the law.

SHERPA/RoMEO is certainly very convenient and a wonderful resource, but I wouldn't call it "definitive".  (In rare cases it can be wrong or out of date, and then the actual publishing agreement is definitive.)

@AnonymousMathematician Good point; I have weakened the language accordingly.

What this answer does not tell you is what the journal is allowed to impose on you, the author. This depends also on your local law ... and also on the local laws applicable in the country of incorporation of the journal's editing body. However, we are in agreement on "whether you will submit to such journals at all" - this is, indeed, your decision to make.

@ALANWARD Actually, it does: "this may, of course, be modified by local laws."  What those local laws might be, and how they might be interpreted in a particular court of law, of course, are a different and much broader question.  My key point is that much of the time we don't need to answer those questions in order to resolve the original question.

Policies vary by publisher. Relevant links to policies from Elsevier, Wiley, and Springer. The details you will have to read for yourself and for your particular case, but generally speaking:

Publishers distinguish between three versions of the manuscript: the preprint (i.e. before submission), the accepted version, and the published version.
You are usually free to distribute the preprint wherever and however you wish.
You are usually free to distribute the accepted version wherever and however you wish, as long as it is for non-commercial purposes and after the embargo period.
You are not free to distribute the published version.

It is quite common to find that a pre-print of the paper (before the journal editors have got their hands on it, and therefore added value) may be found on the author's website, containing almost all the value of what you would get from the journal. Even if not, it is always worth checking the author's website to see if there are large results files, software source codes, or other materials which would allow the research to be reproduced and/or extended for other purposes.

Hi and welcome to this site. This answer, while interesting, does not answer the original question about the legal implications of uploading articles on academic social networks.

even I was looking for answer to same question and looks like its not legal in most of the cases
found informative articles here https://blackboard.swan.ac.uk/bbcswebdav/institution/LibraryISSResources/Material%20for%20researchers/SharingPDFs.pdf
Also about example of journal policy here
https://www.elsevier.com/authors/journal-authors/submit-your-paper/sharing-and-promoting-your-article

This question can basically be analyzed from the standpoint of copyright law, much as in any other topic related to publication.
In your paper, there are clearly some parts to which you hold rights as the author: the text itself, figures that you have created, etc. However, in the version published by the journal there may be certain elements to which you do not hold any right: general presentation, typesetting, etc. Even editorial corrections that have made your text better in some way may be seen as generating rights for the journal. Additional work done on your text may also intervene here, such as correlating citations with existing papers published in electronic form, which helps the reader navigate from citation to citation and thus may be seen as increasing the value of the paper.
Some questions you need to ask yourself are:

What have you signed? Have you signed or otherwise agreed to transfer some rights to the journal? All rights? Are the rights granted to the journal exclusive rights? Are they limited in time?
Which is the applicable jurisdiction? All copyright law is not equal. For example, in some jurisdictions an author's granting access to colleagues may be considered "fair use", but this concept may not be applicable or even exist in other jurisdictions.

In certain jurisdictions, the transfer of exclusive and universal rights may be against the law, invalidating the agreement signed by the author at least in part. For example, the right to be mentioned as the author of a text -typical of copyright law- may not be waived in Spain. The author may choose to assert or not such a right, but the journal could not publish the paper anonymously (even in extract form) without the author's explicit approval.
It is worth mentioning that the agreement signed with the journal has been prepared exclusively by the journal, in the form of "general conditions" for the use of a service. This places the author somewhat in a position of inferiority, since he or she has not contributed to the wording of the text. Some jurisdictions will take this into account when interpreting the finer points in the text, often in favor of the author. Since the journal had more time and a better bargaining position to start with, it is up to them to have come up with a fair and balanced agreement that both parties can stand by.
So, while observable facts are as stated by the OP in the question (there may be a potential legal problem, but some authors have no qualms in providing open access to their papers), unfortunately the legal situation is so complex that it would be very difficult to give a single, authoritative, answer.
If you are worried about a specific case, the best guidance to be given would be to consult a lawyer with experience in handling copyright law in your jurisdiction. Your university's legal department may very well have had to handle similar circumstances and have guidelines set up.
Otherwise, it is always wise to remember that there does exist a legal distinction to be made between public communication (making a text available on-line) and private (an email). Editorial companies have a much better case to have public communication halted - in the first place, because they can easily prove it actually happened. I, personally, would not have any difficulty with supplying a colleague with a private (proof) copy of a paper if so requested by email.

I agree that the key question is "what have you signed?", but I'm not convinced by much of the rest of this answer.  For example, it's not clear that the author retains any rights at all to the text or figures (some publishing agreements are very demanding).

@AnonymousMathematician That is indeed so - my point being that such demanding agreements may very well not hold up in court. This depends on local law. I have edited the answer to be more precise in this respect.

This is a rather misleading answer: while many of the things are technically true, they do not correspond with the realities of standard practice or most legal systems likely to be encountered by authors.  The biggest flaw is the fact that copyright transfer is pretty much always never partial: usually either the entire document is transferred (possibly with grant-back rights) or else none of it is transferred but the publisher is given  publications rights (either explicitly or else implicitly via an open license).

@jakebeal Unfortunately, your comment makes no sense from a legal standpoint. You seem not to understand that "ownership" of an intangible is a relative concept. In what you call "transferring" a document, what are in fact received are not the document in itself, but rather the economic rights or rights of exploitation concerning said document. Giving a publisher publication rights amounts in fact to a partial transfer of the rights on the document, often without exclusivity. Perhaps it would be worth your time to go over this with a lawyer, it certainly surprised me when doing my BA in Law.

@ALANWARD Could you please provide some references for your assertions?  They seem rather at variance with typical descriptions of copyright transfer, or perhaps you are just using words in a different manner than I have typically encountered them?

@jakebeal: as Alan refers to Spain as example the difference may be due to the "philosophical" differences between the concepts of copyright between Anglo-American and continental European legislations (where the author typically has quite a number of inalienable rights - sometimes including an inalienable right for secondary publication, such as putting the manuscript online).

@cbeleites It would be very interested to have a link to some sort of reference there, and particularly to know if anybody has seen how this has played out in international conflicts, e.g., vis-a-vis the DMCA and various international IP treaties.

@jakebeal: Linkable reference is difficult - I learned this in a lecture about copyright law... But e.g. for Germany here's the relevant reference to some inalienable rights for secondary publication (of the authors' manuscript; including some conditions that have to be fulfilled): §38 UrhG. In Germany, the Urheberrecht (≈ copyright) can not be transferred by a contract.  AFAIK this is very different from the Anglo-American copyright concepts. The Urheber (author) can only license the use the work (§29, 31). Does that help?


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creating a reading list
Is the first time I write to this group and my question may be very basic (so I apologize). I'm getting ready to start my PhD and I'm collecting useful material for reading. I try to organize the list of articles and books I choose but I have a basic question. Once this material list is presented to my supervisors is it wrong then to make changes; I mean how it is possible to know from the beginning all the articles I will use the first period; Usually such lists are not created by reading in stages;
Thanks.

It is not very clear what you mean. You want to develop a bibiographic search strategy?

Have you asked your supervisors how they suggest you handle your reading?
My reading list is a folder in my reference manager that keeps changing as I discover new items, decide that I no longer need to read others, and have skimmed or read yet other items. It would be useless to stick to one list no matter what. In my case (I'm a postdoc) the reading list is mostly a reminder to myself. In your case it additionally serves to discuss your priorities with your supervisors who might already know some or most of the papers.

Thank you for your advice. And yes, you are right, my list will help me to discuss and clarify my initial  priorities with my supervisors (with whom I have not talked about the format of the list yet). Thanks again.