text:
Advisor manipulated/threatened me into sharing my first authorship
My last Phd work was submitted to a high impact journal (IF >35). The manuscript came back for revision with 2 positive comments and 1 no-suggestion on my last day in his lab. Given its positive comments, I expected to go for next round of review as long as the comments are fully addressed. The comments requested simulations and experiments, which I supposedly would not be able to perform as I graduated and was leaving the next day. So my advisor threatened me on my last day to submit to IF (~5) journal or share my first authorship to someone (person X) who was not involved in the project at all. For the later, he reasoned that X needs to commit full-time ~ 4 months just for revision and stop all other works. Although I explained to go through comments first and discuss and that I can revise, he did not agree any of it. He asked me to choose 1 of his options, no negotiation (like giving co-first after X shows to put significant effort). I agreed to give X co-first authorship under the condition that major revisions will be done to address all reviewers' requests and convince them. Then my advisor privately told X will be the co-first and to revise none, minor, or major; choice is up to X. They spent 1.5 months only for quick revision, without addressing all comments. I told X about the problems with the revision, but no any reply. It was rejected directly by the editor. (At this point, they already broke the deal.)
Then they submitted to another journal, got rejected by the editor again.
Another journal (IF >10) finally passed the editor and came back for revisions. All 3 reviewers are positive. Yet the editor asked for all the comments/experiments to be fully addressed. My advisor did not even notify me about this decision. X told me that they wanted to submit to IF ~5 journal because too many experiments need to be done for the revision. X said need ~ a month or more to revise, and my advisor wants X to focus on looking for a job. So X asked if I am okay with this decision to submit to IF ~5 journal. (This is how I know there is a revision requested.) I am very mad because how X can deserve a co-first if they did not even put in effort and time! The revision comments are very positive, but they said they think it will not go through. (I am basically #w$%t&f?)
Similar things happened repeatedly during my PhD in his lab. I am very mad, but I am helpless. I used to hope this work would help my faculty job search if it gets published. This time, I did not want to "waste" this work while it originally even had the chance to go through IF>35 journal, but they messed it up since then.
Note: My advisor is a complete a**o who used to call/write bad recommendation letters for those who were against him.
Any suggestions on how to handle this?
UPDATE 1: So they agreed to submit a revision. Knowing that they will not treat it seriously like last time again, I revised the majority myself, incorporating old experimental data. There are still many simple experiments (~ 2 weeks worth of time) needed to be done. How can I make sure they will do the job and do it right?

Astonishing is how all this was mishandled. It could have been a nice starting point for a new student and everyone could have been happy. I know this doesn't help you but I had to comment.

Whose job would it be to be doing the extra experiments that the reviewers asked for?

@CaptainEmacs Supposedly, X would be the one as X's name was added for revising purpose. Based on last experiences and per X's request, I did most of the revisions to minimize X job for this newest revision. I am worried X would not complete the rest to fully address the comments and would not respond if I am not satisfied with the revisions.

I think the "best" way forward is to cut your losses, try to get it published reasonably well, and never work with these people again if you can avoid it.

These are your options:

Focus on your new project in a new lab working with better colleagues.
Do the revisions yourself.
Let the former advisor do whatever they want.

I agreed to give X co-first authorship under the condition that major revisions will be done to address all ...

You agreed to the co-first authorship.  You should not break that agreement.  Unfortunately, revisions being "done" is subjective so you cannot punish the other party for breaking their part of the agreement.  Next time, only agree to someone's authorship after they have earned it.

I haven't downvoted, but you say: "Next time, only agree to someone's authorship after they have earned it" - well, that wasn't an option in the first place.

Yes, you are right that only agreeing authorship after they have earned it. But it was not an option for me. (edited to clarify) He told me not to proceed with the revision unless I agree first. So I agreed with a condition (listed the revision tasks), but X was only informed about getting the co-first no matter what X does with the revision. It seems my paper destiny depends on what X wants to do with it.

Go back to your first principles of your own personal ethical code. Your situation is complex so calmly apply the question is that right or wrong. If it's wrong then decide will I let it go or will I act on it. If you decide to act on it you will know you're acting on principle and are in the right. Also try to think, what is the other person's point of view. Do they think they're right and I'm being unreasonable. When you're calm, try to speak to the coauthor as it sounds like the supervisor is not a good avenue for you. Get it published, out of your hair and draw a line behind it. It's not that big a deal about the impact factor and impact factor is currently used inappropriately as a standalone ranking. Read up on that, you may be using/ thinking of the impact factor in a way it was never intended to be used. Co- first author is also no big deal, try not to be egotistical, if the other co-author gets this over the line and it gets published then you've been spared that work. Try to be relaxed, these things happen literally the whole time in academia.


text:
Advisor doesn't let me graduate and prevents me from working
Posting for my friend
Brief background:
I am in the middle of my 4th year PhD at a US university. I opened up a new direction for the lab, which led me to 2 impactful publications and 1 manuscript ready for submission.
My lab has 2 lab locations (L1 & L2), and the tools required for my research is only available in L2. Since stay-at-home order started back in March, I was not able to get my full access back to work in the lab. My advisor did not grant my access to L2. He reasoned that L2 is at a max capacity and only people with prelim. data will get priority access. I repeatedly asked for the access (4 times in 6 months) as I have on-going projects and my collaborators have been asking for my devices. Over the past 6 months, he granted access (L1 & L2) to everyone else in the lab, including current members, one new PhD and a new postdoc. Without a choice, I worked only in L1 with very very limited tool and asked one member for help for further process in L2. However, one process takes ~ a month to finish instead of 3-4 days due to this.
In the meantime, he refused to hold meetings with me. Until I repeatedly requested, he would meet me once a while. He met with all other members twice a week. He did not agree/want me work on any of the projects I was working on or proposed at that time. When I asked what kind of projects he would be interested in, he did not know. It seems that he just did not want to give me full lab access and did not want me to work on my projects, basically wasting my time.
Due to all of these, I decided to graduate at the end of 4th year. So I asked him about my graduation plan. He then required me to complete a 4th impactful project and have it published in order to graduate. (This was not even fulfilled by many of his past PhD students.) He provided project suggestions with unrealistic goals (which he agreed). Then he "proposed" to me the projects I proposed to him earlier in my PhD. He said he would consider granting me access to L2 if I can provide preliminary data for these projects. His motive seems very vague and actions are very contradicting.
I would say that I have done enough (opening up a direction, publishing in high impact journal) to meet the average PhD quality here at the least. Do you think it is appropriate to tell him that I want to graduate? He did not give me same opportunities as the rest while hindering my PhD career. If he doesn't let me graduate, is it okay for me to take the case to the chair and higher-ups?
NOTE: My advisor has been abusive to me (and also other members) since I joined. He has been sued by his students in the past. This is also part of the reasons make me not wanting to continue my PhD longer in this environment.

What is your plan after graduation? Are you going toward something or just away from this?

@Dawn I am not planning to go to academia. I will be looking for an industry job.

So if you have a job lined up, then my advice here is relevant: https://academia.stackexchange.com/questions/114193/what-to-do-when-an-advisor-repeatedly-changes-graduation-requirements/114196#114196

Let me suggest a couple of things. You may not be happy with the suggestions, I realize, but it is a "safety first" recommendation.
I suggest that you agree to 4th project and that you commit to it. But I suggest that you don't leave it open to a follow on 5th, 6th, etc. Try to come to a firm agreement that this next big thing will be the last he asks and that you will then be able to move on with good recommendations. Hard to get a guarantee on the last part, but it is what you seek.
There are two major reasons I suggest this.
First is that it is now a terrible time to be graduating. Higher education is in flux because of the pandemic and it will take another year for it to settle out. Hopefully it will by then, but a "novel virus" presents an unknown future.
Second is that fighting with your advisor is not a recipe for academic success. Going to the chair with a complaint might poison the relationship and leave you without a future path. I don't know if the advisor is abusing you or just thinks that with a final push you can open more doors in the future. Doing more than the average is actually expected, though not always achieved.
If your funding is in place to continue and you want to maximize your future, consider following his advice.
And if you are actually depressed, go see a professional. The university probably has a counseling office for such things. What you are feeling is pretty natural, actually, but you may need advice about how to get through it.

I am not planning to go to academia. The problem is that he has abusive behavior and this will keep tormenting my mental state if this continues, so I want to end it asap.

I do not agree at all with the second reason.  Continuing to work for an abuser is encouraging abuse.  Talk to the omsbudsperson or chair or some other appropriate official.

And maybe not getting the degree or needing to start over.

Do advisors have that much authority to not give me a degree even if I satisfy all the requirements?

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text:
How common is it for a student to finish a Master's degree at a school and to be rejected for a PhD at the same school?
This question likely doesn't make much sense in the US and other countries where separate Master's degrees are uncommon. However, here in Canada, the vast majority of graduate students must first apply for a Master's degree, and then apply for a PhD program (usually filling out applications during their Master's degree, as the deadlines fall).
Students are highly discouraged from completing their undergrad, Master's, and PhD all at the same school for many reasons. But it seems quite common to do one's undergrad at one school, then both grad degrees at the same school.
My question is: how common is it for students in this situation to be rejected from a PhD program at the school where they are currently doing their Master's? And what might be reasons for such a rejection? I imagine that some reasons would be lack of willing supervisors (which begs the question of how they were accepted for the Master's anyway), unsatisfactory work during the Master's degree, or some extreme situation such as academic dishonesty.
My field is math, so I guess we can restrict the question to that discipline, but I'm curious about answers from all fields.

I've added the [tag:canada] tag, as, for example, in most of Europe it is not at all the norm that one pursues a PhD after a Masters degree.

@servaes really? I would say the situation in Europe is exactly the opposite: the vast majority of PhD courses require you to have a Masters.

@astronat Both your statement and that of Servaes can be true at the same time; they have different denominators.

@astronat That is indeed true. What I meant is that the vast majority of students that start (or finish) a Masters degree have no intention of pursuing a PhD. In this context the question doesn't quite make sense, hence the tag. I hadn't considered your alternative reading of my comment.

I don't think separate Master's degrees are uncommon (but yes, among PhD-bound people, less common than Europe).

One very obvious thing would be availability. My department has around 100 masters students each year, but will only have 7 PhD places. We pretty much take as many masters students as we can (because they pay). As you can imagine, this is not always popular with the people that have to supervise them for their dissertations.
Master degrees are funded by the student (either directly, or via a loan). PhD positions are funded by external funding bodies or scholarships.

In Canada this is not true: at least in Science, a Master's is funded like a PhD is, though usually it pays less.

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text:
Is it more common to refer to subplots as a "frame" or a "panel"?
In scientific publications, when referring to a figure with multiple plots, often labeled using (a), (b), etc., is it more common to refer to each subplot as a "frame" or a "panel"?  Are both correct terms? Is one more correct or commonly used than the other?

Sounds entirely a stylistic choice to me. Just be consistent within a paper.

This was my first thought but I wanted additional input.  After I finished writing my dissertation, everyone reviewing it has used "panel" when referencing a subplot.  I used "frame" throughout.  I am not sure if this difference was from my inexperience.  I do not want to change it throughout the entire document.

At the worst, that's what "Find and Replace All" is for :-)

Are you sure words such as "frame" or "panel" are used in papers, rather than on a meta-level, by typesetters? I have heard the word "panel", but only ever with respect to typography and page layout.

Here are some "panel" examples: 10.1128/JB.186.18.5973-5977.2004, 10.1021/ct900653p, 10.1016/j.bpj.2013.05.021, 10.1128/JB.01200-09, 10.1103/PhysRevLett.99.038104, 10.3390/nano5010246

I am having a hard time finding "frame" examples.  Perhaps it is best to avoid either but in situations where it is necessary to use "panel".

Have you ever seen "subplot" in the same context?

I can't recall having seen the word frame or panel used to refer to a subplot. More commonly:
In the text, e.g.,

Figure 1(a) shows [...]; figure 1(b), instead, shows [...].

In the caption, e.g.,

Figure 1. Comparison among blah blah: (a) function f [...]; (b) function g [...]

I've never used frame or panel either, but it could easily be a style variation between disciplines. See if any of the major professional societies in your field have a style guide, or see if the major journals have one. You might find an answer there.

I list a selection of example publications above which use panel but in my quick search, I could not find frame examples.  The use of panel is rare which leads me to think it best to avoid its use if possible in favor of the options provided here.

@stvn66 looking at some of the examples you provided, it might be that the authors chose to use the word "panel" because of the specific close-packed arrangement of the sub-figures, and of their type -- mostly photographs.

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text:
Hiring Committee Conflict of Interest?
If you are being interviewed for a job and find out afterwards that a member of the interview\hiring committee had a past romantic relationship with another candidate what should you do?

This seems like it was inspired from this question: Should you recuse yourself from the hiring committee if you have had a past romantic relationship with an applicant?

We need a bit more information to be able to help.  Please check the published policies, if any, for the particular institution, and post the gist in your question.  (Cick where it says "edit.")  I suggest you paraphrase if you want maximum anonymity.  If you're okay with the name of the institution being known, post a link to what you found.

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text:
If I use non-government funds to pay for flight on non-U.S. carrier, can I then use government funds for other costs of that trip?
The Fly America Act states that all U.S.-government funded travel must be done via U.S. air carrier service (there are some exceptions, but none of them apply to my scenario).  I recently received a travel grant from my university, independent of any government research funds, and I know that I am allowed to fly non-U.S. carriers with that university travel grant money.  However, the grant does not cover all of my expenses for this trip, and I wanted to use government funds to cover the remaining.
Can I fly on non-U.S. carriers and pay for the flight portion of the travel costs using the university travel grant?  Would there be any issues with this?  To reiterate, I would only use the government research funds to cover non-flight portions of the travel.

"The Fly America Act states that all U.S.-government funded travel must be done via U.S. air carrier service" - Or via one of the several other governments for which there is an agreement (this information is in the link you included).

To clarify: I'm considering air travel that would not fall under that category.  That is, the home country of the airline I'm considering has no agreements with the U.S. government.

It sounds like that should be fine, but the only way to get a definitive answer would be from the office in your university that handles reimbursements.

Yeah, I'm asking my department administrators, but they seem uncertain, so I wanted to see if other people at other U.S. universities had experience with this.  I want to know if there are any federal guidelines prohibiting what I'm describing.  Also, why the downvotes?  I think this is a very relevant question to academia that should be of interest to anybody at U.S. universities trying to do academic travel on limited budgets.  If you would like to reword it, please make suggestions.

I think the current version of your title might be attracting some negative attention - it sounds like you are aiming to do something subversive, which I don't really think is your intent.  You really just want to know if the Fly America Act applies to entire trips or only to airfare funded by US govt funds.

This could be problematic if the OP intends to use the flight to meet Cost Sharing requirements on a Federal grant. It's been a few years since I was really involved in cost allowance stuff, but I believe that all cost-sharing contributions must themselves be allowable costs.

The text of the Federal Travel Regulations explicitly states:

You are required by 49 U.S.C. 40118, commonly referred
  to as the “Fly America Act,” to use U.S. flag air carrier service for all air travel funded by the U.S. Government, except as provided in §§301-10.136 and 301-10.137 or when one of the following exceptions applies:
[...]
(g) When the costs of transportation are reimbursed in full by a third party, such as a foreign government, international agency, or other organization.

In this case, since you are not requesting federal funding for your air travel, you can use a non-foreign carrier. Clearly, foreign travel will most likely require lodging and per diem costs at non-US-owned venues—unless you happen to like staying at Holiday Inns and eating at McDonald's, Starbucks, or Pizza Hut. Moreover, the above portion of the regulations say that if improper air carriers are used, only the transportation costs are ruled unallowable. It does not talk about the per diem expenses for lodging, meals, and incidentals.

I was looking for some language like this, thanks!


text:
How to find PhD co-supervisor?
I am looking for a co-supervisor to assist me during my research journey based on online / remote supervision.
Does anyone knows how I can make an ad or search for such a thing?

I would prefer to find him myself and to avoid my supervisor assistant since I know that he would not be helpful to do so.
Do you know nay website that I can find some ?

If you already have a supervisor, ask him first, he would need to agree either way and might have some ideas or contacts. If you don't have a supervisor yet, look for one before thinking about co-supervisors.


text:
How much do grades from beginning of bachelors impact PhD admission?
Do low grades in standard 12 and first year of bachelors (including a few repeats) hamper the admission to a PhD course in Europe if one has a research paper published and a masters degree in relevant discipline with decent grades?

Possible duplicate of Does a bad grade in one course (with otherwise OK record) affect graduate admissions?

This may depend on the country as well as university/institute. You should have a look at the corresponding websites, as most information regarding PhD admission can be found online.
For example, the TU Munich website [1] states:

Results are considered to be above average if studies were completed
  with an average grade of at least 2.5, or at a minimum passed with a
  grade of “good.” In exceptional cases, your above-average
  qualifications can also be proven through academic work (e.g.
  publications) completed after your course of study.

This means that your bachelor or earlier grades to not affect PhD admission as a hard citerion. However, when you hand in your application the professor will have a look at ALL your grades. It is his/her finial decision whether to accept you, so all your grades might have an influence on the outcome.
Personally, I have experienced that having publications beforehand helps a lot. Thereby you prove that you have at least a basic understanding of scientific work. This may give you an advantage compared to other applicants.
[1] https://www.gs.tum.de/en/applicants/application/requirements/


text:
How to get recommendation letters for graduate admissions when my social anxiety makes it difficult for me to make connections?
I understand references make a huge difference when applying to graduate programs.
Over my years in university, I have spoken to professors about projects / exams / papers. I definitely make use of their office hours.  I also go to a top school and am set to graduate with high honors. I am an extremely determined and motivated person. Although I have made use of the available resources, this is an extremely difficult/rigorous school and thus very few people achieve anywhere near a 4.0. My cGPA is a 3.5 and my GPA over the last 2 years is a 3.7. I have also been involved in a lot of organizations related to my field of interest/research. Including, volunteer on three projects at a renown research hospital and research for an undergraduate science magazine.
However, I have severe social anxiety. I understand this is “no excuse” in academia for not making connections, but it is extremely difficult for me to be around other people. It is severe. It has been a huge step for me to even go to the office hours (which I am proud of myself for doing), but I have not stood out from the crowd and I doubt any remember my name. I have never wanted anything more (graduate school), and yet my mental illness is a severe restriction on my life. I have been seeing a psychiatrist and have made huge improvements since high school (when the social anxiety became severe).
Is it necessary that I only acquire references from professors with whom I have developed a close relationship? Should I discuss these struggles in my application?

See e.g. Details an applicant should include/exclude in an introductory letter to a prospective grad school adviser? (for previous version of this question)

There is also already a Q&A about whether to discuss mental health issues in an application for graduate studies.

Thank you!! And I significantly shortened my question now (took out the "what to include in an initial email" since it was less personal and I assumed I could find that somewhere else on these forums).

I can see this is a difficult spot for you.  After all, to be good at your work doesn't necessarily require you to love interacting with people, but to get into the field you require letters of recommendation, which are best achieved by... interacting with people.
A few thoughts:

Are you more comfortable communicating over email?  If you can combine a good email correspondence with good course work, I think there's a path to overcoming this.  You can easily email your professors (using the less verbose style of your revised OP!) and ask about graduate school, research interests, and finally letters of recommendation.
Have you taken classes with the same professors repeatedly?  This is one piece of advice I give to undergraduates a lot.  Each good semester with a professor helps reinforce the positive impression.  Assuming you still have one semester left before finishing, I would prioritize doing this again.  Speaking for myself, student's names I only see once are often quickly forgotten unless I've gotten to know them in person well, but student's names I see repeatedly start to stand out regardless, especially if they've done solid work.
Related to 2, have you taken only very large classes with the professors you want letters from?  If so, and if it's possible, you might try to get into a smaller section they're teaching even if it's of less (but not unrelated) interest to you academically.
You would be surprised how far showing up to office hours with good questions will get you, I think.  You said you've managed to overcome your anxiety enough to do this, and I don't think you should underestimate the benefit.

In summary, find alternative ways to build relationships with the professors, through repeated interactions and electronic communication.  You don't have to be chumming it up regularly with your letter writers in person to get good letters of recommendation, though even the few visits to office hours you have managed will have likely helped.  Also make sure you read the posts others have linked in the comments regarding mental health issues and PhD admissions.
Good luck!

Thank you, this is a fantastic response!! I did especially like the one link ff524 provided about what to say in an initial letter. I have taken 2 classes with the same professor before. These were both very small classes and this professor did know me by name, at the time. I took these classes in my first and second year of University. However, I am now in my fifth year and haven't spoken to him in about 3 years. Thus, not only is he unaware of my performance since his classes (both of which I performed well in), but he may not remember me. I did have another professor earlier this year...

... for another small class. I spoke to her once in office hours and it took her months weeks to learn my name. So she likely has forgotten it by now. Both of these professors are very nice. I'd like to mention that the first professor did help me write a letter of purpose to get into my undergraduate program (it's second-year entry). But again, I have not spoken to him in years (although unrelated, my younger cousin is actually in a first-year class with him at the moment).

@aspire94 In that case, while I think email is possible, coming by to say hello in person may be your best option.  I don't know how difficult that would be for you, so you'll have to weigh the benefits there.  But they're probably a lot more likely to remember you when you give him/her a face to associate with the name. You can re-introduce yourself as if you're assuming he doesn't remember you, tell them what classes you took with them and when, and that you're considering grad school and ask advice. It might help if you don't go asking for a letter straight away! Less pressure.

Excellent suggestion. Yes, it will be very difficult (I'll likely have heart palpitations the morning of / night before). But I can see where it goes. Perhaps I should wait to hear back from a potential supervisor first? Finding a supervisor before applying is essential for this program. I also forgot to mention that the other professor taught a class that is directly related to my masters program (they have the same name) and I took this class earlier this year.

@aspire94 - If it's easier for you to go in person, go in person.  If it's easier to write an email, write an email.  If it's easier to ask the Student Disabilities Office for help, ask them for help.  There are multiple ways of approaching professors, and you don't need to add to your anxiety levels by trying to figure out which approach is better.  Go easy on yourself and choose the method that triggers less anxiety.  All methods are fine.

You doubt your lecturers remember your name, but do you think they don't remember you? Maybe a little background info about you (in an email or even in person) would jog their memory?
I was in a similar situation as you, and was really surprised to find that my point of view, which was that I was practically invisible, was not only not true, but the lecturers I asked for references actually had a good impression of me (note: I had performed well in all their respective classes).
Also, even if they don't remember you, that doesn't mean they won't write you good recommendations, especially if you've performed well in their classes.
My advice is to probe (perhaps informally, say after a lecture) a number of your lecturers how they feel about writing you a recommendation, then try to gauge from their responses how likely it is that they will write you a good recommendation, and then finally ask them for actual recommendations in the order of their likelyhood of writing you a good recommendation.

Thank you! It's nice to know someone was in a similar situation. This is extremely frightening for me.


text:
Can I negotiate an acceptance to print delay, post acceptance?
Update: My withdrawal request was accepted and I was also offered to be published in the immediate issue of the Journal. I took back my withdrawal request.
Edit : Mentioning Journal
I have an accepted paper. But it is slated to appear in 2021. And both print and online versions appear around same time. I was hoping online would appear much faster than that, but its not the case. According to copyright I cannot host it on my website also for an embargo period of 12 months. So it's not even sharable, let alone citable. I have a followup paper already being written, and more ideas in pipeline that are built on top of this. This publication wait period defeats my whole purpose of publishing as I cannot share it with others and I cannot cite in furthur works. I cannot use it for advancing my career too. I also have plans to seek research positions or phd fellowships. I am kind of stuck. I cannot withdraw it now as it is already accepted. Is there anyway I can negotiate to get it out much before than the slated time?
Edit:
An excerpt from the copyright.

Retention of Rights

The Author/Editor may deposit an Author-created version of the Article
  on Author’s/Editor’s funder’s or funder’s designated repository at the
  funder’s request or as a result of a legal obligation, provided it is
  not made publicly available until 12 months after official
  publication. Author/Editor may not use the Publisher’s PDF version,
  which is posted on www.publisher.com, for the purpose of that deposit.
  Additionally, the Author/Editor may deposit the Publisher’s PDF
  version of the Article on Author’s/Editor’s own website or
  Author’s/Editor’s institute’s designated repository, provided it is
  not made publicly available until 12 months after official
  publication. Furthermore, the Author/Editor may only post the Article
  provided acknowledgement is given to the original source of
  publication and a link is inserted to the published Article on
  Publisher’s website. The link must be accompanied by the following
  text: “The final publication is available at www.publisher.com”. The
  Author/Editor is requested to use the appropriate DOI for the Article.

Update : I have made a gentle and polite withdrawal request citing delay as reason, to which I got a one line reply, "Thank you for your message". I don't know how to interpret this one line  reply. Does it mean that they will get back to me on this? or I should assume that it's been withdrawn?

Would you mind sharing what discipline you are working in? And are you sure you are not even allowed to share a preprint version of the paper until it appears in 2021? It’s hard for me to imagine such a kafkaesque situation, which would not be even remotely acceptable in math or several other disciplines I’m familiar with. Perhaps if you blog or post on social media about your experience, pressure can be brought to bear on the publisher to relax the restrictions?

@DanRomik : It is mathematics. I have posted an excerpt from the copyright.

" The following agreement is effective if and when the Article submitted to be published by Publisher, Inc. (the "Publisher") is accepted".

interesting. Is this a math journal or a more general science journal (Nature, Science etc)? I’m asking because this is completely at odds with anything I’ve ever seen in the math world. If it’s a math journal, I can only guess that the journal is a predatory one trying to make itself look legitimate by copy/pasting a policy they found elsewhere and don’t really understand, or is otherwise a weak journal run by clueless people who similarly don’t understand what they’re doing. No serious mathematician I know would submit their paper to a journal with such policies.

... The bottom line is, beware. I see a lot of red flags here, and the BS embargo may be the least of your problems if you publish in this journal.

@DanRomik I have not signed any copyright statement. Surprisingly they haven't asked for one. Do you advice to withdraw my paper? I have not yet responded to their acceptance letter.

I cannot advise you on withdrawal without knowing the specific journal and without knowing more about your work and your career situation. All I’m saying is, this smells quite fishy to me. Perhaps the best advice I can offer is, find an experienced professional mathematician to give you specific advice about your situation based on detailed, specific information (of the sort that would be inappropriate to post here) about you, your work, and the journal in question. Based on looking at your other posts, it’s clear to me you are in need of this type of advice. Good luck!

The cause of the problem is probably that the journal has accepted more papers than it can afford to publish next year.

@AnonymousPhysicist : Is it appropriate to mention the publisher's name here? (its copyright policy is common for all its journals and not specific to this journal).

@user102868 Doesn't matter.  Anyone can google to identify the publisher.

@AnonymousPhysicist : Its in top 10 publishers as per some raking. Do you think it can be predatory? Or has such policies?

I don't see why having this kind of copyright policy makes the journal predatory.

@DanRomik : Answering your question, it is a journal dedicated to applications of a branch of mathematics to areas like finance, CS, physics, etc... It is applied in nature.

as I cannot share it with others --- Regarding this aspect only, I don't see any reason why you couldn't share it (email) with anyone who specifically asked for a copy or someone you know who you sometimes exchange preprints with. However, I'm guessing you're only asking about actually placing the manuscript in a publicly accessible web location.

@DaveLRenfro : Yes, as one cannot cite it when just shared in an email. I myself cannot cite it in furthur work

cannot cite it --- This wasn't even on my mind, but since you mention it ... (repeat of a comment I made in Academia 8 months ago) [[ Indeed, I suspect that when flipping through a typical issue of a typical journal in most any field, one will find several papers whose references include items listed as "to appear", or "forthcoming", or "under review", or "submitted", etc. ]] (back to present) Certainly I've seen this many, many times in references, and also rather often even things like "personal communication" (which I've actually used, but not as a formal reference item).

@DaveLRenfro : Then in that case, how would a referee view that reference. A preprint should have been hosted somewhere atleast, right?

Obviously I can't answer for others, but clearly such things aren't that much of a hurdle because (at least in mathematics) it shows up fairly often. Incidentally, I was wrong about something in my previous comment. I just noticed that I've actually used "personal communication to author (Feb. 27, 1995)" as one of my references, but this was back in 1996 so it might not be as relevant in the more formal and structured environments now.

It's hard to tell from the outside why they aren't posting online versions of your accepted paper now. If the publisher is the root cause, you could conceivably change their mind by negotiation. I would not be hopeful because they're likely to keep to the status quo purely out of inertia, but your objection would probably be filed away as a data point for when they finally decide to modernize.
On the other hand if the editor-in-chief is the root cause, the publisher is not likely to overrule the editor-in-chief, and you'll have to convince the EiC. Chances are the EiC has entrenched views of this (as opposed to the publisher who's more likely to simply be doing what they've always been doing), which makes convincing him/her harder. Still, you could try. Be sure to mention you have follow-up work already lined up.
It's unlikely that there'll be negative consequences for trying and failing. Your paper's already accepted; they're not going to rescind it for non-academic reasons.
One thing I would definitely check is whether you are permitted to upload preprints. You mention there's an embargo, but quite often the embargo is only on the accepted manuscript. You can still post preprints. Some publishers (e.g. Elsevier) allow you to post the accepted manuscript as well, on a non-commercial personal homepage or blog.
Edit: based on that paragraph, negotiation is the only way out, because they're preventing you from making anything else publicly available. If you have transferred your copyright then they can actually publish without your consent now (still, they might let you withdraw anyway as a gesture of goodwill). You say you haven't signed any copyright transfer, but that's not sufficient; the journal might have policies that say the copyright is automatically transferred upon acceptance or even upon submission. You'll have to check. If you haven't transferred the copyright, then you could withdraw and submit elsewhere. It's a decision you'll have to make.

I am tackling here a different "side" of the question. Most other answers talk about making the earlier (accepted, but not yet published) paper available to the general audience. This is a proper thing to do and needs to be considered. But what about the next manuscript?
What has been sometimes done with two manuscripts in different journals that depend on each other, is: while you submit the second manuscript to a journal, provide the first one to the reviewers as a supplementary material for review. It is confidential, it is not a public availability, should be fine.
So, basically, when submitting the next manuscript, additionally show the previous one.
Notice, however, that I know of this practice with a submitted manuscript. You seem to have a post-review manuscript (or even a camera-ready version, depending on how it is seem and whom you ask). I am not quite sure, you are allowed to distribute that to other reviewers, but you can at least show the initial, pre-review manuscript to the reviewers. Explaining in a letter to editor that it is accepted, but you provide a version you are sure, you are allowed to provide, might be helpful, too.
Oh, and about citing: You can cite it as "User102868, "On foo, bar, and biz", Awe. J., to appear" or "... in press". This is somewhat a bad style, but it's little you can do, if you do not retract the article all together.
And yeah, for the rest of us: such an issue is precisely the reason arXiv exists. So, use it. Please. But, as always, ask your supervisor / your coauthors first!

The difficulty with your last paragraph is that some journals - notably Nature - frown upon handling papers already on the arxiv as it “kills” the novelty factor once the paper is published.  Of course Nature Publishing are primarily looking after their $$ interest but still.  Other “high impact” journals also follow the same model of giving 2 strikes to papers available on arxiv or elsewhere...

Yeah, that's the asking part. For most journals / publishers there is a statement if they are Ok with "preprint servers" or not. And of course, this needs to be checked before submitting to arXiv or whatever. My point in the last paragraph was rather that coauthors might not want it, too.

No, I don't think there is any way for you to negotiate to get the paper published earlier as you have already agreed to the publishers terms and conditions (by signing the acceptance agreement). In your situation you now have two options:

Formally withdraw the paper from the journal (get official proof of withdrawal) and submit it to another journal. This is technically possible but now you run the risk of an additional long period for your paper to undergo review at the new journal. There is also the additional risk that it would be rejected at the other journal (and obviously you can no longer submit it to the original journal since you withdrew it) so you would then have to start the process at a third journal.
Check to see if can document your preprint. In some cases you are allowed to host the preprint on Arxiv. When I say preprint I specifically mean the version of the paper that you had before you submitted it to the journal and before any peer review and/or correspondence with the journal editor and/or reviewer took place. This original manuscript is not subject to the terms and conditions, however the manuscript that you submitted to the journal when it underwent the peer review is actually under copyright so you are not allowed to share that version. As a result you are allowed to document the original preprint in for example your CV or website and include the snippet that this was accepted by Journal X with Manuscript Number Y. You are not allowed to document the version of your manuscript when it was received by the journal. You could site your paper as follows:

J. Smith, ''My paper title'', Journal X, 2021 (accepted manuscript Y)

I have not signed any agreement.

I understand. In this case you must now make a specific decision to either accept the offer to publish or reject the offer to publish. Until you make a decision either way you are not allowed to do anything as the paper still "belongs" to Journal X until you reject their offer.

Talk to your university’s legal department about how much you need to change to post a “preprint” copy elsewhere.
This sounds like the sort of question that you’d need to talk to an IP lawyer about, with the text of any relevant contracts in hand. Fortunately, universities generally have legal departments that address these sorts of issues as their job. I’d recommend talking to the team at your institution.

Not sure why I’m being downvoted for “ask you university’s lawyers since they’ll know what the actual legal rules you have to follow will be”.

I am not a downvoter, but probably because you are talking about IP, which is in the eyes of most people about some product. The question was about paper publishing. I have not heard about any instance of university IP layers (basically, something going in the direction of "patent lawsuit") helping to negotiate better publication terms of research papers. They appear to be in different worlds.


text:
Pros and cons of publishing in a journal not indexed in SCI but under ESCI?
A Journal is indexed in Scopus and Web of Science. But under Web of science it is under Emerging sources citation index and not under SCI or SCI expanded. What are the pros and cons of publishing in it if you are a serious researcher looking for phd admission? Its not predatory for sure and no charges for author whats so ever. Its also from a reputed publisher. The feild is applied mathematics

Have you already published a lot in math? Have you submitted a lot of papers? Or are you just exploring?

In general you publish in the most prestigious journal that will accept your work. There are reasons for this: more prestigious journals tend to be more visible (more readers), more impressive (helps with graduate admissions), or are even tracked by promotion committees ("to be promoted to [role], you need to publish [number] articles in SCI-indexed journals"). So your question is rather difficult to answer. There's practically no reason to publish in an ESCI journal instead of an SCI journal.
That said, you should of course discuss with your advisor which journal to submit your article to. SCI journals might be more prestigious, but if your work is not significant enough and they are going to desk reject it, you might as well save yourself the time and submit to an ESCI journal.

The concerned SCI journal is not in MathSciNet.

I'm guessing that where you are in your career it matters very little. The important thing is to get published in a reputable journal. I also doubt that experienced scholars worry very little about such things.
Pick a journal that seems appropriate for your work. Send it off. Then write the next paper.
And if you are not yet in a doctoral program, then publishing is a big win, no matter where, as long as the journal is reputable.

What do you precisely mean by a journal being reputable?

Primarily, not a predatory journal. But good ones are produced by professional associations (say ACM or AMS) or by known professional publishers. For starters, probably the ones that publish the papers you base your own work on.

It is generally considered a journal that accepts research papers that are then sent by editor to two experts in your field to be peer reviewed and accepted or rejected by the editor.
It is difficult to advise you with out further information:
where is the institution you are associated with, your academic achievements and future plans.
  Normally you would have an academic advisor who had supervised your research.


text:
How to interpret this rejection email from Journal of American Math Society? Anything to read between the lines?
I had submitted a paper manuscript to JAMS (J. of Amer. Math Soc) and recieved the following email 2 months after the submission. Can you help me interpret this email, as to what the situation is and what would be the best way moving forward.
Are there any positives/negatives that can be taken. I have not received any referee reports or any technical points on my work, which is what disappointing me. I would like to understand the circumstances/rationale behind this decision.
I am new to journal publishing. I want to know how i can take this decision moving forward, while choosing another journal for submitting. And also self evaluating my work from this. Is there anything to loose heart?
email : (names and references removed for privacy reasons)

Dear Professor XXXX,
This message concerns the manuscript
XXXXX    by XXXX
submitted to the Journal of the AMS.
We regret to inform you that we cannot accept this paper for
  publication in JAMS. The reviewers who evaluated this submission did
  not think that it meets the acceptance standards at JAMS.
JAMS is the premier journal of the AMS, with extremely selective
  acceptance criteria. A paper must be truly exceptional to obtain the
  unanimous approval from the editors, which is required for
  publication. We publish fewer than 30 papers per year in all of
  mathematics. As a result, less than 10% of submissions are accepted
  for publication, and many excellent papers are rejected.
One reviewer suggested that the discussion in your paper should
  include a comparison with the following reference:
XXX, XXXX, XXX. XXXX: XXX.XXXXX XXXXX XXXX, Journal of XXXXX.
  5555;5(XXX):5555-4444.
Sincerely,
XXXXXX, Editorial Assistant Journal of the American Mathematical
  Society
--- Sent via EditFlow by JAMS Editor  <journal.american.math.society@gmail.co

Dear Professor XXXXX,
The reviews we received were intended for the editors' eyes only, so
  we are unable to send them to you.
Apologies, XXXX

Not sure what you are looking fot. The situation seems to be quite clearly laid out in that email.

JAMS is a top journal.  Most papers, even excellent papers, will not meet their publication criteria.  Do not despair...try for another journal.  If you want AMS publication, you could next go for PAMS or TAMS (based on the length of your paper).  Or you could try for a subject-matter journal: one that publishes only papers in your particular area of mathematics.

Trying hard to read between the lines: maybe "should include a comparison with the following reference" means "someone else thought of something similar, first"

There isn't anything between the lines.  It's simply a rejection. The editor and reviewers feel that your paper is clearly not strong enough for this journal, and they're telling you so.
Note that JAMS is an extremely selective journal, generally considered one of the top four out of all the many hundreds of journals in mathematics.  It is very very hard to get a paper published there.  Most of the papers they publish will be major breakthroughs in an area, or solve a famous open problem.  The "10%" is actually misleadingly high, because the vast majority of papers are never submitted there in the first place because the authors know they have no chance.
Such journals often do a quick first round of reviews, where the reviewers are only asked if they think the results are potentially important enough to warrant publication in JAMS.  Only if they say yes does the paper go on to a full technical review.  In this case, it sounds like they said no.  You didn't receive a detailed report because they didn't need to do a detailed review of the paper to make a decision.  Remember that their job is ultimately to make the decision; it's not their job to give you feedback or help you improve your paper.  Sometimes that happens along the way, but when the decision is clear, they won't spend time on a paper that, in their view, can't be made publishable in this journal.
The reviewers can, as in this case, make comments about things they happened to notice as they were doing their quick review.  That's why you got the note about the reference.    You'll have to read the reference to determine exactly what was meant here; it may be that the reviewer thinks that paper may already contain your results, or at least that they are similar enough that you need to carefully explain the difference.  But it sounds like the reason for rejection was the overall significance of your paper, and this was just something they noted in passing.
How to move forward: submit to a different journal.  If you want feedback on your paper first, you'll have to get it from someone else, e.g. a mentor, PhD advisor, collaborator or fellow researcher.  Such a person could also help you get some ideas of journals for which your paper might be better suited - where it would have a better chance of acceptance or at least a full review.

@Kimball: "Great minds think alike..." ;-)

@NateEldredge ... but great enough to submit a joint answer to JAMS?

Fools seldom differ? ;-)

@NateEldredge : If they reject without full review, and if the reviewer thinks the cited reference contains the result, then shouldn't he explicitly say that? Ok, if he was not sure, and he has no time to read/understand my paper fully and ascertain the fact himself, then whats the point of him suggesting that I do the comparison and include it in discussion of my paper, when I am not given any chance to revise and submit. All he is suggesting is to include a comparision discussion, but with no chance to revise and submit. I don't understand this logical. .....(contd.)..

..(contd.)..Havng seen the reference, In my opinion, the reference suggested to me is no where close to my paper or its theme, and I don't know what to discuss and compare, when its not related. On the other hand, the papers I havev cited and compared, and which I am directly competing against, are published in top journals. So I don't understand why my paper is not important.

I had written to the author of the papers I have cited in my work and with which I am competing against, and he has agreed that my work was correct.These papers of him were published in top journals, which prompted me to submit to a top journals. I should include that the author has said it was correct, but I did not dare to further ask that is my method/paper superior than his papers.

Moreover, what I am excited about is, that my method has real world applications in a field, and I cannot describe/demonstrate them here as I am submitting to a math journal. If I want to submit to a journal of that field by including the applications/demonstrations, my worry is the reviewers of that field won't understand the mathematics to be gin with, so they might be skeptical.

@user102868 Submitting to a math journal does not mean you can't describe the real world applications. But being correct and citing work in top journals is in no way sufficient for the work itself to be publishable in a top journal (in fact, this describes by far the larger part of my own paper, but I have certainly not written any that could be published in JAMS or the like). As an aside: The fact that you describe the person you cite as your competitor makes me worried that your view of research is very different from your peers.

@TobiasKildetoft :  hmmm...I don't mean the person as a competitor, my paper gives a completely different perspective and poses and solves a different math problem on the same topic of the competing paper. Neither is better than other, I just used the word competing to mean both being on same topic of interest. perhaps "competing" is a wrong word here.

@user102868 If it poses and solves a completely different problem, then just being on the same topic (which I assume is why you are citing the other paper) has nothing to do with how interesting the results are.

well no point in trying to arguing. from my point of view, the perspective and problem I pose is more interesting and beautiful than others. I also know my problem has practical applications, which I indicated, but cannot publish all the experiments as its a math journal and its not appropriate to establish superiority by showing non mathematical content. There is a different place for that.  I believed they would appreciate the aesthetics of the math, but they were not impressed is what it seems.

@user102868: "All he is suggesting is to include a comparision discussion, but with no chance to revise and submit. I don't understand this logical."  What I am trying to say is that I don't think the lack of this discussion was the main reason for rejection.  It was a comment that the reviewer thought might help you going forward, but the straight "reject" decision should be understood as saying that even had you included such a discussion, the paper would still be rejected.  That's why there wasn't a "revise and resubmit" decision: resubmitting to this journal would just waste your time.

@TobiasKildetoft : "your view of research is very different from your peers", Can you explain what this means. I am not able to get what you are trying to say. Is it technical?

@user102868 1. It is usually to a good idea to address every concern of the reviewers in some way; there is a good chance that the next reviewers in the next journal will have similar concerns otherwise. If this is still unclear, check if some has asked about it here already or ask a new, separate question.2. In many fields of mathematics addressing possible applications is welcome and appropriate. More specific advice is hard to give without more info. Maybe ask a question about how to address applications in a pure maths paper, if such has not been asked yet.

Top journals, and JAMS is at the very top (most mathematicians probably will not have ever seriously considered submitting there), typically have 2 first passes before a proper peer-review (referee): (1) editorial consideration and (2) "quick" opinions from experts.  Which is to say, there are 2 common ways for a paper to be rejected before it is sent for a full peer-review: (i) the editor decides from the title/abstract/info that it is not appropriate, or (ii) the editor solicits experts for an opinion of whether it is worth the effort of a full peer-review.
Based on your letter, and since you didn't receive a referee report, I would say the most likely scenario is (ii), and this is not surprising because unless you have done something really spectacular (I don't know that you haven't, but playing the odds...), you shouldn't bother submitting to JAMS, Annals, etc.  (It can also happen that a referee who is asked to do a normal review, just sends back a few lines in the case of recommended rejection, in which case a full report would not be passed on to you either.)
So my suggestion listen to the expert's advice and compare what you've done with what's in that paper.  Then, if possible, ask some more senior people for advice for where is an appropriate place to submit your work.

I have read that reference fully, and I am surprised that mathematically there isn't much to compare with my paper. Neither there is anything to compare in terms of theme, except to say that the suggested reference is an example of various traditional techniques being used in a field X (not mathematics), and that the theorems I have proved in my paper will give rise to tottally new techniques which overcome disadvantages of the cited traditional techniques. The suggested reference is not a math journal.

So my conclusion is, the rejection is largely might be due to standards not being met, rather than the cited reference. Infact citing that reference in my paper would actually help my cause.

@user102868: "Infact citing that reference in my paper would actually help my cause."  Hmm, up until now I have been defending your right to resubmit the paper as is.  But now you have me confused...if the citation helps your cause it means that it's (i) relevant and (ii) helps your cause!  So you definitely should cite it, no?

@PeteL.Clark : Its just one of  hundreds of such papers written about a class of methods and its not even foundational for that class. Its actually trivial that my method does not belong to that class. I don't think its a must to cite that particular paper. It would look like a random pick, if I cite it. The reviewer could have suggested to just mention about these class of methods and say that mine was different from that. This would take only a line. Over all its a positive suggestion is what I am feeling. May be that particular reviewer may not have voted for outright rejection.

@user102868 Or maybe that particular reviewer happened to know that that particular paper is about similar methods, but does not know the literature about that method very well.

Here's a positive from this experience that nobody's mentioned:
You got your answer in 2 months.  This is actually quite fast for an answer on a mathematics paper.  This is much better than waiting 12 months or more, then getting that same response.
You should address the cited reference (which may be duplicating some of your ideas), and resubmit to another journal.

It's not much of a positive! A rejection after a year would have come with constructive comments about how to improve the paper; getting rejected after two months for not being significant enough for the journal isn't much better than hiding the paper in a filing cabinet for that time and then submitting it to a more appropriate journal.

@DavidRicherby I've submitted two papers to JAMS-level journals, each with multiplicity two.  First paper: 2 months rejected with quick opinions at first journal, 5 months accepted at second.  Second paper: 6 months rejected with quick opinions at first journal, then 15 months rejected with 8 reports none of which were sent to us at the second.  2 months is a good turnaround for a quick rejection, and long rejections don't always have meaningful feedback!

@NoahSnyder Jeebus. I don't know whether to boggle more about the fact that eight referees were involved, or that none of their reports were sent to you!

The thing is, the paper didn’t really need significant changes (it’s now accepted at another very good journal, with relatively few changes).  It’s just that the opinions must have been pretty split about whether it was significant enough to make the cut.  It’s not so clear how helpful it would be to us to see those opinions.

Most likely is that your theorem is just not ground breaking enough.  It is possible there are other issues with the paper (writing quality of the text or logic of the math).  But we really can't tell because the paper was not deeply reviewed.  Go to a lower tier journal (more specialized) and submit it there.  This will either get published or at least give you better feedback on your manuscript.
Note even on the off chance that your discovery should be at that top level journal, it is still their choice and people make mistakes.  Nothing is perfect.  Move on.

The second paragraph of the mail is just boilerplate that everyone gets. The final recommendation is all you really need to be concerned with, but I'll guess that it is a big concern for the reviewers.
Is it the case, perhaps, that you missed an important earlier paper (the one cited) in developing your own? If so, you need to go back to your work and see how much you add to the earlier work. It may be that you only need a simple update before resubmission, but it is possible that you are left with too little that is new for you to proceed successfully without a lot of work.
But, no, nothing seems to be hidden or implied that isn't stated directly.
As for your comment about submitting (as is) to a different journal, they will likely have exactly the same reaction. Possibly even some of the same reviewers.

Its clear that there is a wide difference between the reference recommended. I think its just a suggestion to include a reference as a scholarly practice. incidentally its from a non mathematics journal.

In your answer, by 'resubmission', do you mean to same journal or a different one?

After revision you can try JAMS again. Rejection doesn't mean "we never want to hear from you again". But you should, perhaps, do a new lit search to make sure you don't hit the same wall again.

Actually, I doubt there is much chance of this paper being accepted in JAMS given that they already rejected it for not being up to their standard (I am not even sure if they allow resubmission, but I didn't check).

@TobiasKildetoft, perhaps, but it depends on how important that citation was and how much of a revision is made. With a lot of revision it becomes, essentially, a new work. But yes, the standards are high.

@Buffy : The paper was rejected not because of the reference. I don't think it has has nothing to do with it (having seen it). No point in resubmitting.

You certainly know best. But revise before you submit anywhere. Any advice you get on any paper should be "considered" for revision. That doesn't mean every reviewer is correct, of course.

I downvoted because of the last paragraph.  Many papers in mathematics are rejected upon first submission, resubmitted as is, and then accepted.  Moreover your answer misses that where the OP submitted was in the top 0.1% of all math journals, a level of eliteness that doesn't exist in many other academic fields.  Being rejected from such a journal says almost nothing about the value of a paper.

@PeteL.Clark, perhaps, but a recommendation to submit without considering reviews and revisiting the paper seems to me like particularly bad advice.

@Buffy There are no reviews. The paper was submitted to an absolutely top-flight journal. Before even doing full peer-review, they rejected the paper because, even if it's 100% correct, it's not significant enough for this particular journal. There's no basis on which to revise the paper, except perhaps to add the requested comparison. The correct course really is to submit it to a journal at a more appropriate level.

@DavidRicherby, sorry, but the OP mentions "the reviewers who evaluated....".  How was I to assume otherwise? There was at least some feedback (a citation). How was I to assume that should be ignored? The "comparison" might involve a complete re-work (or not).

@Buffy The asker explicitly says they didn't receive reviews, which is a strong indication that they don't exist. The other answers (which were posted after yours, but well before your reply to Pete Clark's comment) are written by people familiar with the journal and explain the situation, confirming this. And the asker has already commented to say that they don't think the suggested reference is very significant to their paper.

@Buffy: I don't think anyone is or should be telling the OP not to look up the reference.  As it happens, they already did and did not find it of clear relevance.  To be more explicit, I object to "As for your comment about submitting (as is) to a different journal, they will likely have exactly the same reaction." That's not how it works at all, because there are so many different levels of math journals.  You seem to be conflating "Your paper is not publishable in JAMS" with "Your paper is not publishable in a reputable math journal."  That's a serious mistake.

@PeteL.Clark, no, I'm not conflating that at all. I'm commenting on the fact that many subfields of math have a limited number of reviewers, so you may well get assigned to the same person again, who will likely object again. Perhaps even more strenuously. I hope you aren't advocating journal "shopping". Papers should always be revised in the light of new information.

It just seems wiser to me, especially as advice to a young researcher that when you get a rejection (from anywhere) think "what does this paper need in order to be improved" rather than "what other, possibly lower quality, journal would accept it.

I think it would not be bad at all if the OP resubmitted and got for a referee the same person who had previously made the comment about the other paper.  Another thing that you don't seem to be taking into account is that the OP's paper was not refereed; they only got "quick opinions," which top journals use to identify papers that are not likely to be of sufficient quality.  It is not clear that the writer of that quick opinion "objected" to anything, and it is not clear that this comment of theirs had anything to do with the rejection of the paper...

To me, the language used by the editor suggests otherwise, but it is not sufficiently clear -- that lack of clarity is in the nature of "quick opinions."  If the OP gets the same person again as a referee, they can then explain what they meant more directly.  "Papers should always be revised in the light of new information." New relevant information, yes.  Referees can say the darnedest things.  Making revisions that you don't agree with to please a referee who may or may not see the paper again is not a wise use of time.

Finally, if by "journal shopping" you mean trying to get your paper published in the best journal you can: um, yes, of course I am.

@PeteL.Clark Perhaps the use of the word "quality" needs clarification. A paper published in JAMS, Annals, etc., needs to be important enough to be of interest to the wider mathematical community. So being rejected by such a journal is less a statement about the quality of the paper as publishable mathematics and more about whether anyone outside the subfield would care.


text:
Why is it reasonable to believe that this student handed in a term paper from another class?
I have a student who has handed in a term paper from another class, only changing the title page, and he claims that he only put the due date for the current course's term paper on the cover sheet of the old term paper to remind him of when the new term paper was due. He claims he was then cutting and pasting (appropriately, of course) between the old paper and the new paper and must've gotten the two files mixed up. Of course, the "wrong" file (old term paper with new due date) was "accidentally" uploaded to our learning management system and he did submit the "correct" file two days later (that was extremely poor quality), but only after I pointed out the problem to him.
Now he is claiming I am unreasonable because I don't believe him and have failed him for the course. We are about to go to a grade appeal at the department level. I was wondering if everyone on here could provide suggestions for why it is reasonable to stick to my decision, despite the student arguing very vigorously that I'm unreasonable, unfair, and even irrational for not believing this was "just an honest mistake". (Given my university's fondness for "student friendly" I may not be supported very vigorously by the committee.)
Any help is greatly appreciated.

It's called self-plagiarism.

I am troubled by the idea that you've failed the student for self-plagiarism, which presumably would mean that you are very confident of his guilt, and yet you're posting here asking for arguments to support your case. If you need uninformed strangers on the internet to give you reasons to believe he is guilty, to me that's a sign that you're not really very sure of his guilt. In that case, it's probably better to let him enjoy the benefit of the doubt (frustrating as that may be) and instead of failing him for self-plagiarizing, give him a bad grade for submitting work of very poor quality.

@DanRomik Who doesn't feel this sort of way when they've failed a student for committing academic dishonesty and they have to go before a committee about it?  Sounds like little more than proof that the OP's human (and probably doing this for the first time).

Why was he cutting and pasting between two different papers, are the two similar in scope? Some opinions I agree with: REF1, REF2.

He may have meant something like copying papers between folders, rather than copying content between them, or copying a title/signoff page with a set structure - I did this once, with a /Module/Jon_Story_Assignment1.docx type file structure, and grabbed the wrong file when uploading. Fortunately I noticed before the deadline and uploaded the correct file and there was no problem, but I can attest to the fact it can happen and is surprisingly easily done, particularly when doing a repetitive task like renaming 5 files to add your name, and then uploading them.

Specifically to this case, I don't find it completely unreasonable that he may have been copying the title page from one file to another then saving it, and accidentally saved them in the wrong locations. It could be an excuse, sure, but it's well within possible

Please explain what exactly is wrong with handing in the same term paper, as long as it's the student's own work, and otherwise meets the assignment specifications?

@jamesqf many departments specifically forbid the reuse of assignments. As to whether that is a reasonable policy is a separate question.

I might be having a completely different stance on the topic, however I feel it needs to be thought about. The primary goal of a school would be to asses whether the student in question has achieved a certain level of competences.
In order to test those competences you'd give all sorts of assignments to see whether the student has both competences AND skills required for their studies.
As @Significance and @DanRomik mentioned before, filing the other paper can be seen as self-plagiarism. However, if you consider that filing this paper is invalid you could also say that he never filed any valid paper in the first place. Meaning he crossed the deadline that was given for this paper.
School is a place to prepare a person to work at companies and more. So it would not be a bad idea to treat a student as if he were an employee. He filed his work late, couldn't meet the deadline and would obviously be penalized. Now since school is a place to learn from your mistakes you could throw him a lifeline. Rather than smashing him down, I'd accept his paper that was of extremely poor quality, but penalize the grade of this paper based on crossing the deadline.
Now, in the end he may still fail due to the poor quality + crossed deadline. But at the very least he would have learned to be more punctual about his work.
After all, being able to deliver good quality work on a timely way are some of the most important competences a student has to learn.

Neither agreeing nor disagreeing with you with the following, I just felt it's worth pointing out that in a business setting it's pretty common for someone to attach the wrong file and nothing is thought of it! I probably get a couple of "Whoops, forgot to attach the file" or "Whoops, disregard that, here's the right attachment" emails a month, along with one where I have to ask for the correct document

While I hate comparing academia to industry, there are behaviors in industry (e.g., intentionally deceiving your boss or customers) that will get you fired.

In the absence (or even presence) of a clear policy statement about incorrect submissions, just let the department committee sort it out. If your department wants to be "student friendly" let them be. If you really want to fight the "student friendly" approach, take it up at the next faculty meeting.

In case of such doubt, I'd ask the student to show evidence. I.e., show me on your computer the file that by mistake didn't get uploaded, and I'll check if it wasn't written yesterday (yes, that can be faked, but...) and I'll consider grading that one. In any case, whatever grading penalty there is for sloppy work or similar will apply, and probably also the penalty for turning it in late (as applicable).

It can be faked incredibly easily... and if they had the wrong title page, they could easily argue that they have since edited the file to correct the title pages. While I see where you're coming from, there's no way to be sure about it: modifying created/modified dates is trivial

@JonStory, I know.  But if you ask them cold to show you the work of their computer they are carrying around, they don't have time to fake what they didn't turn in, and even less fake file dates.

Here is my problem with the student's story: Every LMS I've ever seen allows you to review your submitted documents. We learn as a function of not wanting to fail our classes very quickly that we need to make certain that the docments we submitted are free of technical fault. This includes making sure that: you submitted the right document, there are no formatting issues, that our file isn't actually broken or inaccessible.
In all those cases, regardless if the student had plagiarized or not, he would still be penalized. If I make the assumption that he did not want to fail this assessment, and that his due effort still resulted in the submission of a fraudulent document, I would undoubtedly hold him as accountable for academic dishonesty. If I assume that he was careless, and that his lack of attention resulted in the submission of the wrong document, I have to dig deeper:
Compare the quality of paper 1, and paper 2 (the poor quality one). Does it look to you like he threw paper 2 together hastily in an effort to cover his tracks, or does it look characteristically like his attempt at a term paper? There should be marked differences between a paper he took the time to polish and something he attempted to churn out in the two days that he knew there was trouble.
Now, as serious as the offense may be, I don't believe in derailing on-time graduation or graduate school prospects. I believe in instilling values that down the road when, for example, he contends to self-plagiarize something that he no longer holds copyright or publishing rights on and ends up in a bit of legal trouble, it just doesn't happen.
I think that instead of failing him, you can work this out giving him an honest grade on his final submission, penalized for the late days, at a larger percentage of the final grade.

My former department used Turn-It-In and while it had a review feature, the program typically took hours to process so the ability to review the document did not happen until after the deadline.

@StrongBad That's strange in my experience, when I used Turnitin as an undergrad we could generally view our own submission within 10-15 minutes (we used Canvas for everything else, just one class in one term used Turnitin).


text:
Is single parenting compatible with success in academia?
Good day.
I'm currently a PhD student in computer science. I was married and have a daughter with my former wife. There is a probability that our daughter
will live with me. Could you please tell me is it possible to be successful in academia and to raise a child alone? By "to be successful in academia" I mean eventually to receive a professor position. Could you please share your experience?
Additional details: my university has a kindergarten and I live in Germany. My concerns are more about is it enough to have 9 working hours per day for writing the PhD thesis.

I know people who did it, so it is certainly possible. The chances and the commitment needed, however, depend a lot on the age of your child, where you live, whether your university has supporting structures, etc. And, of course, your resilience to a stressful life. With the details you provided we cannot tell anything but: yes, but who knows? Therefore, I have to vote to close.

Your question is very relevant and asks for research-based answers instead of anecdotal evidence. Where do you want to become a professor, Germany or would be another country also possible? If you want to stay in Germany, do you consider FHs as well?

Best of luck. I believe you know how things end up working.

My head of department at some point referred to her PhD work days split into "the time while the kids were in school" and "the time after they went to sleep". So it is certainly possible as I know at lest one successful example. How probable or likely it is, or what it depends on... I wouldn't want to guess

Summary: The older your child is, the easier it is. But by no means it will be easy. Personally, I don't even think it is possible. I present my own observations to support my claim.

I am an early career researcher myself, having just graduated with a PhD in a STEM field. I also got married a year before my dissertation defense and became a parent literally a month before I was to defend and graduate.
First, of course, anything is possible. While I may not personally know of any such success stories, I am sure others here do and I am sure you can google and find a few success stories.
But I will describe what I think is the average case instead of the extreme case, resulting from my own experiences and what I saw around me; friends, colleagues, lab partners, advisors, coauthors, other professors, people I met and got to know in meetings and conferences, people with whom I have interacted during my career...a sample size of 30-ish people.
Grad school is hard. Grad school in a STEM field is really really hard. It is very consuming. It consumes your time, eats into your social life, takes up your mental energy, your physical energy, and your emotional energy. It always has an adverse effect on your mental and physical health unless you are very disciplined and exercise, eat, and sleep regularly.
Likewise, being a parent is hard. Being a good parent is really really hard. Kids demand so much energy and they need so much love and attention. Raising a child is more demanding than going through grad school. If there are two of you, sure it helps. But both parents have to put in a lot in raising a child. Being a single parent is even harder because in a way, you are filling in for both parents.
Now on to hard data! Master's is easier so we will only consider doctoral students and above. These are all in STEM fields. I only know of two cases where they had children before starting doctoral studies. One had three kids, another had one kid. One had already made quite a lot of money on wall street and wanted to come back to school to get a PhD so he didn't worry too much about TAing or financial aid. The other was a typical student. They both did finish successfully but it took them about a year longer than was average in their respective fields. And I want to emphasize that they were both with their partners who were both full-time stay-at-home parents.
Next, I only know of myself and one another student, who had children while in grad school. We both had children very late in our studies, when most of our work was done, a paper or two was published, a paper or two was submitted, the thesis was being written or half done. Every single other person that I know of who wanted to have children, were waiting to graduate or even later to have kids.
I have never known nor heard of (a friend of a friend of a friend) a single case, a single parent who has wanted to start a PhD, or has started a PhD, was/in in a PhD, or has successfully finished a PhD.
In all honestly, I don't think that in your case, you can put up hard boundaries between your personal life and your professional life. How can you separate raising a child as a single parent and work on your computer science PhD? It doesn't matter what hours you decide, nine hours a day or 4 days a week. You will come home and think about your dissertation problem. You will think of your thesis. You will think of the comp sci question you are trying to answer. You will think about big and small inevitable conflicts with your advisor, your lab colleagues, your coauthors, your thesis committee, and whether you'll get a TAship next semester or not. Similarly, how can you stop thinking of your child when at work? What happens when the child is fussy or upset and doesn't want to stay with the babysitter or go to daycare? What if the child gets sick or there is another emergency? You'll run out of your lab without even thinking and there goes your rest of the nine-hour-planned-day out the window.
Furthermore, let's say a miracle happens and you get your nine-hours-a-day workdays. From a 24 hour day, taking out the time for sleep, how much time will you have for yourself? When will you decompress? When will you destress? When will you have time for your physical exercise and mental wanderings and distractions such as your hobbies? How often will you be able to just sit in front of the TV and eat cereal the whole day? When will you relax with your own alone me-time? Without hobbies, exercise, relaxation time, grad school will absolutely kill you. Every single person I know who tried this either dropped out or was an absolute wreck by the time they graduated. And these people were not even parents, much less single parents.
In conclusion, the statistics are against you. Sure, your child's age is a factor which makes it easier the older your child is...but it will still be very hard. You are taking two things which are notoriously difficult and intrude upon every aspect of life, and you want to try them both simultaneously, and hope you can keep them separate and succeed in both. I really wish you the best. Good luck!

Summary: Although it is possible to succeed in academia as single parent/father, it is rather unlikely.
Nonetheless, if you are single parent, then it is probably a good idea to:
 1. Build networks with other parents (not exclusively in academia).
 2. Make strategic use of institutional support, like kindergartens, parent-and-child offices or parental leave, which facilitates your work-family balance.
 3. Read and learn about the experience of other single parent academics.

As there is empirical research about the impact of parenting on academic careers of mostly women, there is no need to stick only to anecdotal evidence. I think that much of this research can be generalized to the situation of fathers who actively (and sometimes equally) engage in care work for children. Qualitative research by Sallee (2014) shows that the problems of these more engaged fathers resemble the well-known problems of mother's work-family balance.
Overall, most studies have shown that care for young children lowers women's productivity in terms of publications (Hunter/Leahey 2010). Note that results for the selective group of women engineers and scientists seem more complex. There is no consistent evidence for a motherhood penalty in academia, but there seems to be a fatherhood premium (Kelly/Grant 2012). The latter is likely the result of fathers who work more (to earn more) and take over less child care. Mothers, especially of younger children, show higher levels of family-to-work conflict (Fox/Fonseca/Bao 2011).
Thus, parenting in academia comes with a significant cost. This research applies to careers in academia in general. If you would leave academia after your PhD or a first Postdoc, the productivity loss would be possibly not so problematic. However, it would make it much harder to attain a professorship (especially the hierarchical German system). Single mothers often show up as an especially disadvantaged group in the studies. Probably, single fathers face a similar situation. As a caring father you experience similar constraints as mothers in academia but you would get no equivalent institutional support in form of women's representatives and special funding opportunities.
If you are single parent, then it is probably a good idea to:
  1. Build networks with other parents (not exclusively in academia).
  2. Make strategic use of institutional support, like kindergartens, parent-and-child offices or parental leave, which facilitates your work-family balance.
 3. Read about and learn from the experience of other single parent academics (use e.g. Ward/Wolf-Wendel 2012 as a starter).

Literature about parenting in academia:
Fox, Mary Frank; Fonseca, Carolyn; Bao, Jinghui (2011): Work and family conflict in academic science: Patterns and predictors among women and men in research universities. In Social Studies of Science 41 (5), pp. 715–735.
Hunter, Laura A.; Leahey, Erin (2010): Parenting and research productivity: New evidence and methods. In Social Studies of Science 40 (3), pp. 433–451.
Kelly, Kimberly; Grant, Linda (2012): Penalties and premiums: The impact of gender, marriage, and parenthood on faculty salaries in science, engineering and mathematics (SEM) and non-SEM fields. In Social Studies of Science 42 (6), pp. 869–896.
Mason, Mary Ann; Goulden, Marc; Wolfinger, Nicholas H. (2013): Do Babies Matter? Explorations of Place and Belonging. Piscataway: Rutgers University Press.
Sallee, Margaret (2014): Faculty fathers. Toward a new ideal in the research university. Albany: State University of New York Press.
Literature with actual tips:
Ward, Kelly; Wolf-Wendel, Lisa (2012): Academic Motherhood. How Faculty Manage Work and Family. New Brunswick, NJ: Rutgers University Press.

It certainly is possible. I know a lot of professors who are single parents and they are very successful. At least in the US, it is illegal to discriminate against someone seeking employment based on whether or not they have children, or their marital status (among other categories). You will have to find the balance between your work and personal life.

-1 Professors who are single parents doesn't quite work here unless you know for a fact that all those people went through grad school, graduated, went through postdocs, assistant professorships, and then got tenured while being single parents. The might have been single themselves, or had no children while they climbed the academic ladder and became single parents much later in their careers.

I know it has been a while since this post, but I want to encourage others who may stumble across this. It is possible! I am a single academic mother in STEM. It’s not easy, and you won’t be the top student, most likely. If your advisor is understanding and you are paid it certainly will help. Also do you have to work 9 hour days? Be as efficient as possible. Academia is hard but so are a lot of careers. It has been my experience that, although there are few single parent academics, most academics are pretty empathetic and will understand if you have to flex your schedule at times. Be strong, it can be done if you really want to. Ask for support from family, if possible. Don’t worry about what anyone else thinks. As your child gets older, she will enjoy traveling with you to conferences and being in an interesting environment when she goes to work with you.

Certainly, the responsibility of being a custodial or sole parent might take away some hours of your research and writing time.  On the flip side, raising a child is extremely rewarding and can actually improve one's discipline and focus.  Caring for a child can have a civilizing influence!
I will now back up a step and try to imagine what might be going on.  Perhaps your daughter's mother is not able to care for her at this time, and your daughter is in need of a different living situation, and perhaps you feel a responsibility to step up and create a home for your daughter, as an alternative to... I'm not sure what, perhaps going to another relative such as a grandparent, or going into foster care.  Maybe you are wondering how much of a personal sacrifice would be involved if you were to step forward, in other words, maybe you are wondering whether you would have to choose between taking responsibility for your daughter vs. finishing your PhD.
The only part of this I would be able to answer is that last part.  In general, people do not find it necessary to abandon their PhD studies because of childrearing commitments.
As to whether it would be the right choice for you, and for your daughter, I can't say.
Tip: Parenting is always easier when one has a good support network, regardless of how many adults the child lives with.  (I do not mean to suggest that you can't do it without a good support network.)  If you are seriously considering taking this step, it could be helpful to start building up your support network now.  Ways to do that include:

talking to your relatives and close friends about the project: as you talk this over with them, they may suggest ways they would like to help
lining up a primary care provider (doctor or pediatrician), and finding out practical things like, do the doctor and nurse have a special phone hour?
getting recommendations of private babysitters in case you need extra hours beyond the kindergarten hours
find out which parks and play areas give you a good vibe
looking for a weekend playgroup where you can interact with other families; you can start to attend already, and start to form relationships with the other parents

Note, my experience with such playgroups is that even if most of the parents who attend are women, men are always welcome.  (I say that having attended playgroups in Denmark, Germany, France and the United States.)
A book you might enjoy reading: Commando Dad: How to be an Elite Dad or Carer, From Birth to Three Years.  You can safely ignore the quasi-military theme, and you can skip the early chapters about baby care.  But the general attitude of this book could be helpful for your self-confidence -- which is really the key to parenting.
Please note that there are many ways of being a responsible parent.  Being the sole custodial parent is not the only way.  I lived in Mexico for a number of years, and saw a huge variety of ways.  For example:

An acquaintance, a mother, sent her child to live with her parents in the countryside for his first five years; and then she brought him to live with her in the city, where she managed a small store.  Her son played in the store outside school hours.  She felt that the store wouldn't have been the right place for him when he was a baby, toddler and pre-schooler.
Another acquaintance, a young man, was in high school when his child was born.  During his college years, he traveled to his parents' place whenever he had more than three days off school, to spend time with his daughter.

In short, even if you decide that your daughter's primary residence should be somewhere other than with you... I hope you can still find a way to maintain, or build, a relationship with your daughter, even if she is living primarily with someone else -- even a foster parent.
Personal note: I met my father three times before he died, which happened when I was in my early teens.  I am very glad I had those three opportunities.