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Role of algebraic topology in number theory or algebraic geometry
I am an undergraduate student, broadly interested in number theory and algebraic geometry. As group cohomology and related things are an integral part of modern number theory and algebraic geometry, I decided to take a course on graduate algebraic topology in my current semester. This course covered singular homology and cohomology theory. But I fared quite badly in the course and got a bad grade. I also feel like I have not learnt much from the course.
How much could this hurt my future endeavours in number theory or algebraic geometry? Secondly, how much could this hurt my chances of getting accepted for grad school?
P.S.: I am pretty comfortable with basic point-set topology, fundamental groups, covering spaces etc.

I had similar worries when I was an undergrad; I had to quit the graduate alg top course because it was too difficult, and so I sympathize with your question.  While I have amounted to essentially nothing in math research despite great ambitions (I'm not even at Ph.D. granting institution) and perhaps you probably should dismiss my opinion, I'm writing this answer perhaps as much for me as for you: after 20 years of working my way up the academic ladder (mid0-career at the moment - associate prof with minimal publications at a primarily undergraduate teaching focused institution, which have come to love), I wish I go back and tell myself: You are worrying too much and focusing on the wrong things. Just enjoy learning/doing math, do your best, and live with the results, whatever they are.  That being said, if you are challenging yourself by taking graduate courses as an undergrad, and most of your record in math courses is strong, you should be able to get into a middle-tier R1 at the very least (I'm only familiar with the U.S., though)...albeit that's my sense based on the last time at a Ph.D. granting place (low ranked R1) about 10 years ago, and I don't know if getting into Ph.D. pure math programs have gotten harder or easier.
I should be get back to some administrative/committee work I'm avoiding so I leave with a disorganized hodge-podge of links/comments:
See the following article for a Princeton professor June Huh that who had a negative initial experience in math, was rejected initially by the grad school (top 5 in algebra/number theory according to this list https://www.usnews.com/best-graduate-schools/top-science-schools/number-theory-rankings) where he eventually got his Ph.D. from, and used cohomology to solve a big open problem in combinatorics.
https://www.quantamagazine.org/a-path-less-taken-to-the-peak-of-the-math-world-20170627/
I agree with another answer that many mathematicians need multiple exposures to difficult topics like cohomology.  "One doesn't understand math one just gets used to it" (von Neumann quote).
Regarding algebraic topology and algebraic geometry:

"It was my lot to plant the harpoon of algebraic topology into the body of the whale of algebraic geometry." - Solomon Lefschetz

2 min video of Jacob Lurie on algebraic topology and algebraic geometry/number theory (mentioning Weil conjectures) https://youtu.be/qHwjG5611V4

there are entire industries involving both e.g. motivic homotopy theory, derived algebraic geometry.

The topic of cohomology is vast - there is singular, sheaf, etale, generalized cohomologies (K-theory, Morava E-theories), prismatic, De Rham, crystalline, Dolbeault, syntomic, rigid, and new ones will continue to be invented ... and it is impossible to learn it all, and you don't need to have done well in algebraic topology 1 (or arguably, even remember small details ... IMO the main ideas, conceptual breakthroughs, and big picture are more important)  to dip ones toes into exploring these topics. Instead one has to learn and relearn (a phrase I borrowed from Terry Tao's blog) topics, and if your research problems leads you to need to learn algebraic topology more carefully, then there will be motivation and the perspective of your problem to learn it. (Ok, you may have to learn it to pass through quals ... but can usually get by those by looking at past problems identify the small number of concepts/patterns that are "tested")

As Churchill said, success is going from failure to failure without loss of enthusiasm. For most mathematicians, there are some topics in math one enjoys/understands and others that just aren't their cup of tea.
Every now and then on twitter, there is a "what is cohomology" discussion or dare I say meme:
"Be kind, for everyone you meet is fighting to understand what cohomology is. #inspirationaltopology" at
https://twitter.com/evelynjlamb/status/639087415605526529
and here is a tweet that express confusion with cohomology, and one of the responses is a nice thread giving an overview
https://twitter.com/bathematician/status/1247556791870734336

I won't speak to your chances of getting into graduate school, because that does depend a lot on the school, and on how highly ranked a program you are considering.
The job market for academic jobs in theoretical mathematics is terrible, with far more highly qualified candidates than permanent positions, especially (but not only) for permanent positions with research responsibilities.  If you are a Fields Medal candidate, then you can still find a job easily.  If you are merely very good, you have reasonable chances, but you might not find a job.  If you are merely good, your chances aren't so good.  There are no reasons to expect the situation to improve, and it might get worse.
Now if you really want to do mathematics, then you really want to do mathematics, and it doesn't matter quite so much what the job prospects are, given that it's possible to go to grad school without incurring (more) debt.
Cohomology theory operates at an extra level of abstraction than all the courses you've likely seen before.  Just as many students find their first course emphasizing proofs quite challenging, many students find their first course at this extra level of abstraction challenging.  Many students have to see this material twice to actually understand it.  At our low-ranked PhD program, where as far as I can tell none of our PhD graduates in theoretical mathematics have gone on to do research of any significance (and most dissertations are not publishable except in a write-only journal), we don't really expect any of our PhD students to ever understand cohomology except perhaps in a special case where we have digested it for them.
However, just as most of the most accomplished mathematicians breezed through their first course emphasizing proofs, most of the most accomplished mathematicians managed to learn algebraic topology the first time.  This is only a correlation; there are accomplished mathematicians who needed two or more tries to understand cohomology.  Nevertheless, failure to learn cohomology the first time is evidence against you.
Cohomology is central in current mainstream research in theoretical mathematics; in some sense its presence defines the mainstream.  (It's not so important in many areas of combinatorics or analysis, but those are not mainstream these days.  It's also almost completely absent in applied mathematics, even the more theoretical parts of applied mathematics.)  You do need to learn it eventually to do any serious number theory or algebraic geometry research, and the algebraic topology setting is for most people the easiest entry point.

Ha! :) "Write-only journals" took me a minute. :) But, as it happens, the finite-element method in numerical analysis has evolved to used (basic) (co) homological notions! :)  And mirror symmetry is a big deal in both physics and alg geom. But, yes, absolutely, alg top is the most physically intuitive entry point.

While it's true that it'd be better if you'd aced the course, one way or another, you're already "aiming high", so in that case a failure now and then is not surprising, and in the face of a good body of other advanced work will not seriously harm your grad school chances, even at very good places.
To respond to the other aspect of your question: "(co)homology" is indeed at a slightly fancier/more-abstract level than most other undergrad or basic grad math. The most basic form is basic algebraic topology, which should already start things up by simplicial homology, but after wrangling with technical difficulties for a while, introduce simplicial homology. Useful for many things, like (persuasively) proving the Jordan Curve Theorem, etc.
Meanwhile, c. 1930, Emmy Noether and her school organized prior work on algebraic structures and could describe obstructions to various maps, or descriptions of non-commuting, as elements of "cohomology classes", originally defined in a completely ad-hoc way, and not defining $H^i$ for $i$ other than $i=0,1,2$ or at most $3$. (There was no need.)
Somewhat later, DeRham (re)formulated ideas about Gauss-Green-Stokes in cohomological terms...
Cech (and others) had formulated "sheaf cohomology" in a fashion imitating variants of alg top constructions.
To my mind, Grothendieck's realization that also sheaf cohomology could be realized as a "derived functor", thus becoming "simply" an example of that basic (co) homological stuff was a major turning point. With hindsight, all the "classical" (co) homology theories are/were derived functors of natural things (like fixed-point or cofixed-point functors, or, for sheaves, the global sections functor).
$K$-theory is somewhat different, as it did not fit into that mold. The low-index $K$-groups arose in meaningful ad-hoc fashions, but/and D. Quillen finally saw (late 1970's) a general pattern.
But/and "general" cohomological stuff is not made easily analogous to the alg top version. The symbols often behave similarly, yes, but... "why?" :)
My recommendation to people is to lightly read C. Weibel's "Homological Algebra", in which he goes through many of the standard examples. "Group (co)homology", "Lie algebra (co)homology", etc., are indeed just examples of derived functors of obvious basic functors.
(This in contrast to decades-ago, when trying to learn relevant group cohomology to understand the Artin-Tate classfield notes... the implicit choice of a resolution ("bar" or "homogeneous bar") seemed nutty to me. Oh, ahem, later, I learned that these are just convenient choices of projective or injective resolutions, etc. Whew. And the funkily-named things like "Shapiro's Lemma" are just examples of very general, and not-so-complicated, devices in general (co) homological algebra.)

Do you have recommendations for how to understand the Artin-Tate notes? Did you read it from beginning to end?

@cgb5436, no, I did not at all read it straight through! Not by any means! By this year, I might recommend Jim Milne's notes on classfield theory, as an exemplar of a fairly formal, and correct, treatment. Also, the Artin-Tate notes are anachronistic, insofar as they wrote in a style that did not confidently use modern homological algebra (reasonable-enough, considering the time!).

@cgb5436, also, my own notes on "Number Theory" (at my website, and also at the AMS's free-text site) try to give some motivation for (co) homological description of classfield theory. I don't finally prove the main theorems, but do try to give some motivation for describing things in those terms.

Thanks. But there doesn't seem to be many other references for things like the Weil group, class formations, etc.

Ideally, as and undergrad taking grad courses it shouldn't be much of a factor, but every admissions system is different. In my day, even a good understanding of point-set topology would be really advanced, though times have changed.
If this is for grad school in the US no single grade is likely to make a substantial difference and letters of recommendation from your professors are very important.
But, what's done is done. Don't lose sleep over what you can't control. There are a lot of good grad schools at R1 universities that would ignore a single data point if other things point to success.

As to the relationship between Algebraic Topology and the other fields mentioned I can't be much help. Algebraic Topology and Algebraic Geometry seem to be asking rather different questions, however. Number Theory, on the other hand is so rich that it is "touched" by many other fields. My knowledge is long out of date, though.

Your knowledge is long out of date - one of the major themes in current algebraic geometry research is understanding the cohomology - either in the classical singular cohomology sense or in the sense of intersection theory or more exotic cohomology theories (that might apply in positive characteristic) - of algebraic varieties.

@AlexanderWoo, thanks. The math does flow.


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How much of a "personal touch" on dissertation is OK?
I don't know if this is the case at other institutions but at my university dissertations are published as A5-size books/booklets. There are some regulations on how the formatting is supposed to be but it's pretty relaxed otherwise. Common practice is that the PhD candidate designs the cover themselves.
Typically these covers feature an image relating to the work the person has done in the lab; a molecule, a graph, a microscopy shot etc. Recently a colleague of mine put a painting of herself on the cover. Just for the sake of clarity, not a painting she's done, but rather a painting of her made by someone else. This has raised some discussion among the younger students, such as myself. Thus I wonder, how much of a personal touch is OK really? Would something like I described above be seen as an ego-thing by a potential employer? I am of the opinion that it might be seen as a lack of modesty or "self-distance" (quotes are there as I am not sure if this expression exists in english).
Am I being too critical? As it's a multi-cultural international group of academics here, I wonder if there is a consensus regarding such "customization" of the dissertation.

I think this question is best answered at your own university (or deprtment) because in some places the rules are very strict, in others not so what is acceptable in one place may not be elsewhere.

@PeterJansson I should have been more clear perhaps; given that the university/department doesn't have strict rules beyond the formatting, what is an adequate and acceptable amount of personalization?

Thanks, I see. I think the department/university will have to react sooner or later because people will push the boundaries. In the end if covers become ridiculous in some way then both the Phd and the department/university will risk coming in unfavorable light. So what is acceptable is different for each person/culture/group and pushing the limits will put you closer to what is unacceptable but concensus? no.

You have wide latitude in the Dedication and/or Acknowledgements sections. They are good places to put a individual creative stamp on a document that should otherwise be quite formal and professional.

Where else do you get to say things like "Inspired by work of Seuss [73], ..." ?

This probably depends a lot on how things work at your university.  In the cases I'm familiar with (U.S. math departments), there are only four types of people who have an opinion about your dissertation:

You.
Your thesis commitee, particularly your advisor.
The bureaucrat who measures the margins and decides whether your paper is fancy enough.
Family members and friends who will want to take a look at the nicely bound volume and make polite comments.

Nobody else will pay any attention to your dissertation, unless you do an inadequate job of publishing its contents (in which case someone might be forced to look it up), you become very famous (in which case it will be an interesting historical document), or you do something so weird in it that people pass around copies for the amusement or shock value.
The painting on the cover might fall into the last category if it looks pompous or strange enough.  However, most personal touches are not a problem if the four groups mentioned above don't care.  Furthermore, the bureaucrat won't care unless you violate a known rule or do something so awful that they feel the need to dig up an obscure rule, and your family doesn't get a vote (you'll just be embarrassed if they think you've done something silly).
So the short answer is "ask your advisor".

And if you ever need precedent for going really out there: http://www.amazon.com/exec/obidos/ASIN/0674744438/downandoutint-20 (an entire dissertation done in graphic novel format)

Typically, you want as few "personal touches" on your dissertation as possible, as each one will increase time between your submitting it and the university accepting it. There are many places to assert your individuality within the research community (your speaking style, your writing style in your publications, the types of research problems you tackle, your mentoring style), but this is not one of them.

that's more or less what I thought... However that whole acceptance process is pretty straight-forward (at least in our case) given that the content is OK (i.e. no plagiarism, no racial/religious/sexual offense in the text etc)

We have a very similar practice here, although I think our booklets are usually a little bigger (B5-sized instead of A5).  Looking at the local university press guidelines for dissertation writers (in Finnish, sorry; there's an English version, but I couldn't find anything similar there), they say (translation mine):

"The cover should describe the content of the thesis and invite one to read it.  The cover may either be purely textual, or it may include pictorial elements.  For textual covers, it is worth paying attention to typography and text layout.
If you want a picture on the cover, it can be either a picture from your thesis, a picture chosen by yourself or an illustration selected by our graphic designers.  [...]
If the thesis is published as part of a series, however, the cover must follow the graphical guidelines of the series."

Putting a picture of yourself on the cover of your thesis seems a little unusual, because the cover is normally supposed to illustrate the thesis, and the person presumably didn't write her thesis about herself.  However, as long as there's nothing clearly inappropriate about the cover (I assume it was a picture of her face...), it seems to be her choice to make.
Does that mean you should follow her example?  Probably not, at least unless you believe there's something for you to gain by doing that.
Does it mean you should try to come up with a nice, elegant and unique design, illustrative of your chosen topic, for your thesis cover?  Certainly, if you can!  (Having friends or relatives who happen to be artists or graphic designers can help here.)  At least, it won't hurt, and it just might increase the chances of someone picking it up and reading it.
Does it mean you should stress about it?  Certainly not — "a molecule, a graph, a microscopy shot etc." are all perfectly good choices for a thesis cover, and a text-only cover is a perfectly fine choice too.

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Is it better for a mathematical paper to have a citation or a nice theorem + another coauthor?
I'm publishing my first paper soon with three collaborators.  We made a conjecture towards the end of the paper and intended to publish with the question still open.  Another mathematician heard of the problem and found a solution to the conjecture.  Now we have two options:

publish our current paper on our own, with the conjecture open, after which our friend would publish their solution as a separate paper, or
include their work at the end of our paper and make them a co-author.

Though our paper is pretty good already, the new work is strong and would make a nice addition, so the first option seems nice.  On the other hand, I'm an undergraduate senior (entering graduate school this Fall) and so are two of the other collaborators.  Thus it seems like adding another professor as a co-author may make my contributions (which I have worked very hard on) appear less substantial.  Also in favor of option 2: if the other professor publishes separately, the citation may make our paper look good.
What do you think?

so your work is incomplete and you are hesitating in whether or not you should complete it? I will definitely go with the second option and target a better journal.

I should add, by the way, that our potential extra coauthor has left this decision to me, since the theorem by itself is a bit "low level" for somebody in his position, yet probably enough to constitute a nice short article.  In other words, it's all the same to him.

"since the paper is a bit "low level" for somebody in his position" I will consider this as an opportunity to list my name next to his.

@seteropere That's a good point.

Mathematics papers sometimes include an appendix written by someone else (a MathSciNet search for "With an appendix by" returns 984 hits).  That's one way to include this other researcher's contributions in your paper while making it clear who contributed to what.  It's sometimes used in these sorts of cases, where a paper makes use of or is enhanced by someone's work but their contribution can be isolated in a way that distinguishes them from the coauthors on the paper itself.

@AnonymousMathematician That's interesting.  Do journals generally have policies outlined for this or is this a pretty standard thing?

It's reasonably standard but uncommon. I've never written such a paper, handled one as an editor, or even refereed one, but I've seen a number of them and know of a few written by colleagues. If you search for "with an appendix by" on the arXiv you'll find examples. I would model the formatting after one of them and mention the appendix in the cover letter, but there's no need to worry that it would be strange or nonstandard.

I can add that the timing issue is also important, especially to that established would-be coauthor. Sometimes someone decides to write a paper, and it never comes to life.
However, it is also important how adding the proof to the existing paper would slow down the process of getting it out.

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Number formatting: use of digit separators in manuscripts
I am reading through a manuscript that I am co-authoring with a colleague and I noticed that it used digit separators/marks for all the numbers (i.e. 2,500 instead of 2500). Maybe it's just me but I think this style started after my colleague started doing a post-doc in the U.S.
I have checked the author guidelines of a couple of journals that are likely submission targets in our field and they don't seem to include anything about decimal/digit separators. I also checked my previously published articles and noticed that numeric values were not edited (by press editors that is) to include digit separators.
Thus my question, is there a general rule-of-thumb regarding number formatting, especially considering digit separators?

I don't think there are strict rules apart from journal-specific ones. I personally wouldn't put any separator. I'd use scientific notation for large numbers instead (2.5 x10^3). 2,500 was two and a half for me until I moved to the US.

@Jigg: Scientific notation also carries some information about precision, e.g. 2.5x10^3 means "between 2450 and 2550".  It's not really appropriate when exact integers are intended.  It would look silly to write "Nature published its annual list of the year's 2.5x10^3 hottest organic compounds".

@NateEldredge well it makes more sense to me than 2 and a half hot compound. (Joke aside, you have a point. Although I didn't know about this rule, I wouldn't assume the uncertainty if not explicitly given.)

This depends on the field, publisher, journal, and country. When writing a paper, if you really care about it, look at the house style manual, which may or may not take a stance on it. The AIP Style Manual, for example, recommends using small spaces as separators. Other journals don't really say anything about it.

Digit separators differ between countries, particularly since the decimal seprator is comma in many countries but a period in English/American. Hence in English you may use commas as digit separators while in other countries periods are used. Space is therefore the only separator that is not confusing. A general rule of thumb is to not use separators for single-thousands but start to use them for tens of thousands and up

1000
10 000
100 000
1 000 000

When using spaces in writing, it is good to remember to use non-breaking spaces so that numbers are not broken over lines.

Assuming that the manuscript is written in Word (sad, I know..) does regular space count as non-breaking space?

In Word you can use "Ctrl+Shift+spacebar" to get non-breaking spaces.

...in Windows. On a Mac, use option-space, in any application.

In Word you can enter Unicode characters by typing their four-digit hexadecimal value followed by ALT+X.  For example, U+2007 is a non-breaking figure space: 2007 ALT+X, and U+202F is a NARROW NO-BREAK SPACE (a good choice for the thousands separator in large numbers): 202f ALT+X.  NB: Be careful when the character that immediately precedes the four-digit hex value is itself a valid hex digit:  33202f ALT+X  (inserts a different character).  As a workaround I do this: 33\202f ALT+X, then I delete the '', then I continue typing.
See also: https://jkorpela.fi/chars/spaces.html

I would say that a space is the most confusing separator.

Well, everyone better hold up, @gnasher here is confused. Why would you say space is the most confusing, @gnasher? Are you making a sort of joke based on the technicality that it’s not what is taught to grade schoolers in almost any country, so therefore it will naturally be most confusing by count of the number of people, now including members of “both sides” worldwide, initially confused by this notation?

In scientific literature it is common to employ a thin space to separate groups of digits (see e.g. NIST SP811, §10.5.3). If you're using LaTeX to write your articles you can obtain this spacing in two ways:

Directly with the small-space command \,. For example: There were $10\,000$ people at the concert last night (well, not exactly a scientific example).
Using the siunitx package and the command \num (or \qty for quantities with units), which can take care of the spacing automatically.  For example: There were \num{10000} people at the concert last night (it adds automatically a small space after the 10).

I believe the \, operator works with or without the math mode being operational.

Yes, you can get the small space both in text and math modes, but I prefer, for clarity, to have numbers written in that way delimited by the dollar signs.

@aeismail you are right. As a reference, item one in this answer and this question: Behavior of , in both text and math mode are helpful indeed.

Always using math mode for numbers seems to stretch the notion of "math mode". So you would write I was born in $1983$, and I live in $02138$ Cambridge?

@Sverre In simple cases like the ones in your example, I wouldn't use $$. In general, however, I'm used to employing systematically the features of the siunitx package: for typesetting most, almost all, numbers in my documents I use the \num command. In this way, I can change the formatting style for the whole document in one instance by means of the \sisetup command. For example, I sometimes need to change the decimal separator from . to , when translating from English to Italian and viceversa, and this can be obtained automatically.

@aeismail: The thin space works while not being in math mode as well, however the font changes. A more detailed explanation can be found in When to use math mode?

I think that, in as much as there is such a standard, it tends to breakdown between scientific and humanities fields. In general, I would argue that the modern standard in science is to use only spaces as separators ("2 500" instead of "2,500" for instance), while the reverse tends to be true in the humanities.
However, the best guidelines for these sorts of issues, as usual, is to consult with the guidelines and recommendations of the individual publisher.

so... if the journal has not specified anything it's free-for-all?

@posdef: Basically, yes, so long as you're consistent!

Let the typesetter worry about this. When putting together the manuscript for submission, worry about other things.

@StephanKolassa not so much worry but rather curiosity

@posdef it doesn't necessarily mean that it's free-for-all, they may have a policy but not explicitly mentioned it - they'll tell you if it matters and some details need adjustment at typesetting, I have had such a request for digit separator change.

@StephanKolassa: In case you were referring to a person by "typesetter": In some fields, authors are asked to provide a camera-ready document that is readily formatted for printing down to the letter. No further typesetting is done by the publisher, if it can be avoided.

@StephanKolassa If you care about the appearance of your article, you should never let the typesetter worry about the typesetting details. When I receive proofs for my articles, more than half of my comments will be directed at the typesetter, asking him/her to fix typesetting mistakes or poor typesetting choices.

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PhD student, issued contract at year 3 which will sign over intellectual property. Is it legal?
I'm EPSRC (Engineering and Physical Science Research Council, the biggest UK funding source in the sciences and engineering) funded. Several months into my PhD an industrial sponsor came along. In exchange for additional funds they wanted me and the other PhD students in our group to spend some time during the PhD at their sites and work on industrial problems. This is known as a CASE award. I'm not sure what the university signed, but I have not signed anything. It was a verbal agreement with my supervisor.
I'm now in my 3rd year and writing up. The industrial sponsor has decided to renew their agreement with the university and just issued me with a contract (it states the university and industrial sponsor have agreed upon additional clauses as of early 2015). The clauses/contract that I've been asked to sign states that I will give the industrial sponsor all my intellectual property (to which I currently own) generated over the course of the last 3 years. It also states that the industrial sponsors will review all publications and stop me publishing anything they think will give them a competitive edge (Note I'm not and have never used any of their data, resources or industrial knowledge/work/ideas etc. this is my own work) - I'm just about to publish the remainder of my PhD and then submit my thesis in the coming months. I was in good position to finish early and focus fully on moving to the industrial site for the remainder of my PhD and work on the projects the industrial sponsors wanted me to look at. Clearly for any projects done while there, the IP would belong to the industrial sponsors - however they want everything, including the stuff I did before they even got involved!
Additionally signing the contract means that they can make my thesis closed - i.e. future employers are not allowed to see it. This could damage my future prospects as I was also looking at work outside of academia and they will no doubt want to know what I've been up to. This was never part of any agreement and I would have never taken on a PhD with these terms. Academia is all about the publishing and the free flow of ideas - this all makes me a very cheap slave!
Legally, where do I stand? I understand that as an employee issued with new contract I would have to either sign or walk away, unless it goes against the heart of the contract. But I'm a student and I'm in the last few months of my PhD, if I walk I get no qualification.
I've been told that they can't make me sign it - but won't go into detail as to whether it will affect my PhD or not? Again I'm EPSRC funded the industrial sponsors have paid me extra around 10% of the EPSRC stipend in exchange for me spending several unpaid months at their site working on projects of their choice. I've been told by my supervisor that it's in my best interest to stop resisting and ultimately sign the contract. Can they do this three years in? Has anyone been through anything like this? Anyone have any advice?

Find an employment lawyer in your country, and pay them to review the contract and advise you.

What is EPSRC? Anyway, we can't advise you on the law - you would need a lawyer for that. But it would seem to me that the company can decide under what conditions they want to provide funding. If you don't want to sign, I presume you could continue your PhD, but you'd have to adapt or change your project to be possible without the company's support, and you might  also need a new funding source.

I've added the UK tag, since this is specifically about EPSRC funding.

" I'm not and have never used any of their data, resources or industrial knowledge/work/ideas etc" -- money is a resource. Did you or anyone else spend their money on your research? I'm not saying this entitles them to own your work, or to retroactively change the terms under which the funding was given, just that you need to be precise when you make statements like that.

Before forming out on a lawyer, go and see the post grad rep in your student union, or the rep responsible for education. They likely not be able to help you themselves, generally being elected, but the union might have someone around who can give guidance (that your fees have already paid for). Also, if you are considering an academic career then UCU membership is open to you and guidance in this kind of situation is grist to their mill.

Don't sign a retroactive contract unless you get a strong financial incentive. Your supervisor has nothing to benefit from this deal, so I suspect he just wants things to go smoothly. If you insist on not signing, I don't think he would try to stop you from graduating. It seems to me that they have very little leverage to make you sign. Also, I am sure there are ways to change your supervisor if you are in conflict.

Are you sure you own the IP from your work?  Your supervisor unlikely owns all the IP from his/her work and a portion of your work might actually be his/her work.

The EPSRC has some specific guielines and rules that seem to discourage retroactive contracts, according to a booklet I downloaded from http://www.epsrc.ac.uk/funding/howtoapply/basics/ip/  "Unless arrangements have been made in advance, our guideline is that IP resides with the generating University. ...  A Collaboration Agreement must be signed by all relevant parties before the research project can commence.  ... Each University has a  Technology Transfer Office
(TTO) ... seek advice from your TTO at the earliest possible stage.  ... "

Respond with the PAANDA.

Seems to me that the choices are (a) Go with it; or (b) Finish the PhD without involvement from the company. I don't know whether (b) is an option for you in terms of e.g. outstanding data. But you don't owe them anything retrospectively!

A couple of things to consider:

Do you have a lot of stuff in your thesis they might be interested in patenting?
If you do and they stop you from publishing, once it's patented you can still get credit (+bragging rights on your CV)
Is the company a potential employer? It might be better not to alienate them
Do you have resources to patent the stuff in your thesis yourself? Note it takes thousands of £ and much effort, and you cannot publish anything that is going to be patented
If your PhD is so useful that they want to patent stuff, that's great for you!

I would go for it.

" It also states that the industrial sponsors will review all publications and stop me publishing anything they think will give them a competitive edge" Isn't this against the basic scientific principles?

Legally, you can't be made to sign a retrospective, retroactive contract.
Professionally, if your supervisor or the university person responsible for the CASE studentships decided to be obnoxious about it, they could make the completion of your PhD uncomfortable.
As long as you don't need the CASE money or the on-site experience, this looks like a useless deal for you; in your shoes, I'd be minded to talk to my supervisors, then the faculty graduate tutor. Explain without emotion that you didn't sign up for a CASE studentship; ask if they can give you a good reason why you should sign up, because from where you are, it's hard to see any value in it.
They won't want to stop you finishing. You're EPSRC-funded, and having EPSRC-funded students fail to finish causes a problem for the department when it seeks a renewal of the funding. So you do hold quite a lot of the cards, here.
Ultimately, it's going to be a negotiation. It would be very surprising, and rather irregular, if they did sign up with the sponsor having given the sponsor the belief that this contract will retroactively apply to all current PhD students: I've only seen the terms and conditions apply to those students who start their PhD as CASE students. My hunch is that it's more that someone is just trying to get something for nothing - a free rider.

+1 For excellent specificity in the consequences w.r.t. CASE and EPSRC.

I agree that they are trying to get something for nothing. Companies do this sort of thing all the time in the hopes that you either won't fully read the contract or will be afraid to contest it. Often they will even have unenforcable clauses just to scare people out of suing.

Unfortunately, we won't be able to provide you with legal information. (And you shouldn't trust random strangers on the internet that claim they can.) That said, it does sound extremely strange for a company to embargo your work done before they ever showed up.
I would recommend that you approach your university's legal department. Ask them to specify explicitly what consequences signing or not signing the agreement proposed by the company will have on you and your obtaining a Ph.D. Ask them to answer in writing. This consultation should be free to you.
If you don't like the answer you get there, you can get an outside lawyer. This will be more expensive. And it may be hard to find someone who understands the specific situation, employment-and-academia-wise.
However, the first thing this lawyer can do is review the information you were so careful to obtain in writing from your university. Your university's legal department knows this. Therefore they have an incentive not to cheat you, and you should be able to trust their information at least to a degree.

I've never liked the opinion of university legal departments. I'd skip paragraph 2 and go straight to an outside opinion. +1, by the way. :-)

You suggest asking your university's legal department to answer in writing what consequences not signing will have for your ability to obtain a PhD.  I don't think you're going to get anything useful out of that.  Seriously, what kind of answer are you expecting them to give?  Think from their perspective.  (And remember that the university's legal department works for and represents the university, not you personally, so they might just say "Sorry, I can't help you.")

I disagree with the comment that it will be difficult to find a lawyer who understands the situation, namely the interplay between contract law, academic research and intellectual property. This sort of thing comes up frequently in a patent lawyer's office.

+1 for the WANALF warning. (We (...) Firm)

+1 for don't assume the university/legal will act in your interests rather than their own

Clearly for any projects done while there, the IP would belong to the
  industrial sponsors

Clearly not.
Assuming no employment (explicit nor implied) was in place, works created by you [a student] belong to you. See here.
You can bargain by threatening with 'cease and desist' order for them using your IP.
The blanket character of the contract could mean the strong commercial value has been found in some students work, and they try to secure it WITHOUT pointing to it.

I think that copyright and IP are not the same thing.

"IP" is an umbrella term without legal meaning, typically used to include copyrights, patents, trademarks, etc

" works created by you [a student] belong to you. " it might be different in the UK but in the USA work created by a student belongs to the University. I've known cases where people quit school to avoid IP entanglements with their university for them to become an entrepreneur.

@ChrisMarisic I think there is some variation there, even in the U.S. For instance, in some cases, I seem to recall co-ownership of the IP between the university and the student.

@RemcoGerlich ...which doesn't mean it didn't had any meaning. The law governing copyright, patents, etc. somehow must be referred.

I would upvote for that very useful link for the UK but as @ChrisMarisic mentions, there are usually copyright transfers from the student to the university for all work performed in the course of the student's education which probably applies in the OP's situation.

@Lilienthal I have no recollection of ever signing any kind of agreement to transfer copyright of my work to any of the UK universities that I've been a student or employee of.

@DavidRicherby IPR clauses should be standard fare of any student agreement. I assume most universities require you to sign one or consider your acceptance to be implicit in your enrollment. As an example, the Bristol University Student Agreement states: "This document forms the basis of the relationship between you and us which starts when you accept our offer of a place on your Programme".

Oxford required graduate students to explicitly grant property rights to the university via a contract, as of a few years ago, and may still do so.

@user1512321 IP is, by definition, a set of rights. Owning the "rights to IP" is the same as owning IP. Entities do in fact create IP through a collection of creative choices or insights made by a collection of individuals. A work is not the result of a single act but many acts.

The other answers cover most of the issues, but I'll share one strategy I used in exactly this situation (I was supervising a PhD studentship with a CASE award, and the sponsoring organization did exactly the same thing). First of all, as said, the university should be able to help. In fact, they like the CASE award prestige and funding, but the university will likely take the line that in fact they own the work anyway, not you. (Hence the "IP resides with the generating University".) So in fact, they could sign over the work directly. In practice, all institutions prefer to get everyone agreeing because, also in practice, commercialization is totally doomed without everyone accepting a uniform line, at least to some extent.
So we took this strategy: accept the basic assignment, but add a rider so that if the organization did not explicitly elect to commercialize the work within two (say) years of completion, that it would revert to the student and university jointly. The reality is: they likely won't be able to commercially use the work without employing you and/or the university, so personally I wouldn't really worry about them working on without you. Far more worrying is the possibility it'd be shelved due to inaction, and this is the outcome to guard against. Essentially, you're assigning them an option to commercialize, but they actually have to do it.
The type of intellectual property also matters. They can't patent anything without recognizing you as an inventor. If it's software, there are some lovely approaches I used with open source licenses where the ownership is assigned but (being open source) a right-to-use is set. Then, even if the ownership changes, the right to use remains. This is broadly what happened with MySQL, and it allows
Finally, making the thesis public can probably be easily added to the contract. UK employment law gets very twitchy about actions that make it hard for people to seek work -- again, this is more lawyer issue, but given the work has been open up to this stage, there doesn't seem much point in closing it off now, and I expect they'd get that.
Don't be afraid to negotiate contract clauses. Company lawyers just start asserting everything, but quickly (well, more commonly slowly) adjust to a more realistic position. After all, they've usually just copied another contract and minimally edited it to suit.

Your third paragraph seems to stop in the middle of a sentence.

The problem here seems to stem from the blanket statements in the proposed contract.
The word here is : propose your terms i.e. negotiate.

I will give the industrial sponsor all my intellectual property (to
  which I currently own) generated over the course of the last 3 years

Instead of "all intellectual property" try to negotiate toward "intellectual property in domain x,y,z only."   You know what you've done for them, if there's no overlap try to give away what you don't need, maybe that will be enough?

Industrial sponsors will review all publications and stop me
  publishing anything they think will give them a competitive edge

Try to add "each stopped publication will incur fixed penalty of £1e5, payable immediately."
This way you may not be able to show your work but you may prove it was worth for them to keep it for themselves.

I second all the IANAL advice -- so get a lawyer. You should be able to get someone to give you some general IP/employment advice for a few hundred pounds.
However, in addition, don't be afraid to push back on the contract and ask for terms to be modified. For example, you could propose changes such that you retain ownership but grant the sponsor a royalty free license to use. That wouldn't protect them from the loss of competitiveness they're worried about in the event your dissertation is seen, but they may be making more of a noise about that than they really want to. Alternatively you could offer to meet them halfway, saying that you will allow for your thesis to be closed only for a year, or to be closed for longer but with an exception for job interviews.
Behind contracts there are always people (OK, there are also lawyers...), and people are often willing to discuss. Remember that you currently have a huge upper hand -- you currently own the lot.

I also worked at a top research institution in my nation, and we routinely had Ph.D students sponsored by the industry.
Here's how it worked.
Case 1: Let's assume that the problem being worked on did NOT involve the company's prior IP or proprietary product. In this case, the IP belonged to the institution / researcher. Because the company funded part of the stipend and/or gave some funding, the company simply got an exclusive right to use the IP commercially.
Case 2: Let's assume that the problem being worked on involved incremental work using the company's prior IP in addition to funding. In this case, IP generated within the premises of the institution belonged solely to the institution. IP generated within the premises of the company (obviously using the company's resources such as equipment and money) belonged to the company.
So, the result was a joint IP shared between the institution and the company. Of course, the work done at the institution was "generic" and the work done at the company's place using the company's equipment was specific, targeted and a trade-secet.
Your case seems like case 1. I strongly advise you to Not sign that contract and keep your thesis open.

The above discussion was all from a legal perspective, but there is a second, non-legal perspective that can be tried too: publicity. Here is one suggestion.

Keep good documentation of all communication.
Decline signing the last-minute changes, handing over 3 years prior research. (as already advised above). You might still graduate OK anyway.
But if it looks like there will be a problem, go to the awarders of the EPSRC and CASE funding and explain what the company is trying to pull. Explain that it would look bad for EPSRC and CASE scholarships if companies can attach these hidden strings.
If, (very worst-case scenario), if they don't let you graduate, let them know you wish they had been up front with you with the information from the beginning. In fact, you feel that other prospective students who will be in your shoes have a right to know about this institution, this company, and these professors up front, and you would feel the moral obligation to let those students know all the details of your personal experience on the web, facebook, twitter, etc. so that they will be fairly warned if the same people try to inflict the same thing on them. Of course you would not give any opinions or moral judgements on these named individuals and companies, just the facts of what occurred so that readers can come to their own conclusions. (But before it comes to this, you should get a lawyer to review everything.)

Talk to a patent lawyer. It is going to cost you some money, but this sort of thing -- namely employee inventions, inventions of students, contract terms with respect to IP -- comes up all the time in a patent lawyer's practice.
Approaching your university's IP arm may not be in your best interests. Try and get independent advice.
I am not a lawyer, but I am well aware of sections 39 (Right to employees’ inventions) and 42 (Enforceability of contracts relating to employees’ inventions) of the UK Patents Act 1977.
I do not believe that university students are considered employees for the purposes of s.39 and, as such, any invention belongs to the student. However, to what extent the agreements you entered into, either explicitly or by your actions,determine ownership of your IP will be determined, needs to be assessed by a competent lawyer.
Again, this is not legal advice. You get that from a lawyer, who you've engaged to advise and/or represent you.


text:
Is it morally acceptable to leave an academic project which brings value to thousands?
I am a university professor, Egypt, and one of my academic research projects five years ago, on which I spent a really long time, was to develop and evaluate an online community and library of freely accessible and quality video content. The project allowed participants to record and share video tutorials and presentations easily. It has received many awards and produced 28,000+ quality videos. Today, thousands of users from around the world use my video platform to create and share videos, particularly during COVID-19 pandemic.
My question is: is it morally acceptable to leave and shut down this academic project, since I am very busy, do not have enough resources, and no investor or company is willing to support, fund, acquire or run this project?

If you were one of those that got this project going, congratulations. You have done some good in the world.

(1) Open source it, then (2) start a Patreon, and (3) hire someone to take over your role if the Patreon succeeds? I can't productively answer the morality without knowing the costs and benefits, and while the free market has its faults, it can help you here: If enough people pay to keep it going, then it's immoral to shut it down but you can hire someone else to keep it going, and if they don't, then it's okay to shut it down.

Yes I was @Buffy, I am the researcher and founder, unfortunatelly.

@Will Chen, if I make it open source, no body will pay for the recording tools or the platform membership, and this will make my problem more difficult. The project income helps me to run the project for five years, so far, and my mission is to keep the project for non-profit.

I think if people want to keep the platform going after you are willing or able to run it, they should be willing to put in the person power and resources to run the platform, if you announce you are no longer able to maintain the site yourself and are looking for such input. If no one is willing to step up, then I don't think you have any ethical or moral obligation to keep maintaining a service on your free time.

This is an incredibly important question.

This may not solve the "busy" aspect, but why not switch on advertisements on your videos? Surely that would bring in some revenue. Whether that's enough to fund the operation I don't know (depends a lot on your audience). Also I note most of the videos are used by professionals in the course of their work, surely there must be a way to make them pay a little bit of something each for the convenience...

I think you're asking the wrong question.  It's clear how you feel about the project, but this question betrays a sense of being defeated already.  Why not ask how you can save this project while freeing up your own time in the process.  There are already some good ideas here on how you could do that.

This might be a question for philosophy.stackexchange.com.

Of course it is, or else we'd never let nurses, doctors, and teachers quite or have time off

The logical conclusion of this approach would be that everyone would be morally obligated to sacrifice their lives entirely if anything they could do would help enough "others".

This is a situation I'm fairly well acquainted with since it is not dissimilar to open source software projects -- which is something I have been doing for more than 20 years :-)
It is clear to everyone that people's priorities change over time and that while you may have put a lot of time into leading a project in the past, nobody can expect that you continue to do that indefinitely unless you are paid for it: Life often just intervenes, you may have a new job, a new family, kids, etc.
A question to answer for you is whether you actually care about the project's long-term future. If you were the only one who ran the project, then walking away from it will simply ensure that it is dead. If you think that there is little loss in this, then so be it: It's your project, you're free to do with whatever you please. But you may actually have feelings for it that go beyond it just being a "job". Indeed, I read from your description that it has actually led to a lot of good, and it sounds to me like you think it would be a shame to just close it down. In that case, you'd have to find a way to hand it off to someone else.
Now, good leadership often includes mentoring people to take over from you. Among my proudest achievements as a founder of two open source software projects is that I feel that I could walk away from these projects and very little would actually change: There are people who I have passed all my information on to and who can (and frequently do) fill all of the roles I have in these communities. If you care about the project, and you haven't mentored others who can take over from you, then now would be the time for that: Identify who could replace you (individuals or, better, a whole group of people), have conversations with them about transitioning, and then teach them what all is involved in running the project.
Hopefully you can commit enough time for long enough to bring people into the boat and teach them what they need to know to take over from you. If you manage, the project will survive and your place in its history will be assured.

I don't see an ethical issue if you take a few actions to lessen any disruption it might cause. A scheduled exit that is well publicized and not too soon would be good. Offering to let someone else take over responsibility would be good.
Making the tools open source, etc. would be good. You might consider passing on the domain to someone interested and who seems trustworthy. An organization would probably be better if it can guarantee stability.
I think making it possible for people to retrieve their contributed materials easily would be essential. Perhaps finding an archival site might be needed.
But, you won't, in any case, live forever, and unless the project has sustaining funds and an organization behind it, there is likely no guarantee that it can live beyond it's creator.

A quick perusal seems to suggest that much of the above is already in place, so if it is just one person stepping away from participation there should be no issues at all.

If you're looking to find a source of funding which allows you to continue maintaining the project (at some small % of your time), find a (global) nonprofit technology partner like TechSoup Global Network, and ask them about funding or grants you can apply for.

look also into YouTube (technology) support for nonprofits, google.org or whatever. I can't readily find the right program. Ask their nonprofit community managers.

If you're trying to find someone trustworthy as maintainer so you can hand over all responsibility for the project, then again try the above. Be careful of the open-sourcing route that it doesn't get hijacked by spammers or SEO types, like The top-ranking HTML editor on Google is(/was) an SEO scam (casparwre.de, 6/2021). It's now well-known that there are organizations who offer $$$ to acquire (closed-source) apps with a good reputation so they can trojan them for malware, spam, contact-harvesting, SEO backlinks etc., then it comes back to bite you a year later. Also, make sure your licensing is watertight to prevent this sort of behavior (like: will your license stipulate that no vendor can ever charge a fee for it? forbid forking and resale without attribution?)

If you go open-source, Apache Incubator is a good way to go, and that page has a lot of advice.

Yes, it is morally acceptable.
If you were forced to continuously work on something against your will, this would be simple slavery, which itself is clearly immoral.
The only other moral way we have to force each other is by signing contracts - and if you had a contract which said that you have to support this project for another X months or years, you would not be concerned about morals, but about ways to prematurely get out of the contract.
Of course there are other aspects. Is it healthy for yourself? Is it in accordance with your own personal value system? Will it lead to prosperity and happiness for yourself? Will it be good for your reputation? And so on and so forth - that's where the "meat" of the decision lies, and all of these you can and should decide for yourself. Morals play no role there.
N.B.: as pointed out in the comments, this answer does not suggest to just "leave right now", but addresses the morality of the issue, as this is the title of the question, and the gist of the body, was far as I can tell. I'd suggest to create a secondary question on how to transform an academic open source project into a true community effort with little effort for OP, if required.

It’s a false dichotomy to say the only two choices are “leave right now” or be a slave forever. An orderly exit from the project, after taking reasonable measures to find and help train a replacement (or some framework for keeping the project alive, for example by letting the open source community take charge), seems like the most ethical choice, even if “leave right now” is a legally available option.

This is the best answer.

@DanRomik, I am not suggesting to "leave right now" at all. Ich am saying that "being forced to continuously work" is bad. I pondered whether I should add more to the answer (about how to exit in a good way) but I feel that's more a side issue - OP is concerned about morality, and this answer addresses this very aspect. He got lots of answers which instead focus only on the "how". The morality is the interesting aspect to me, that's why I added this answer. I have added a little NB to address this.

Why not make it open source? I'm going to challenge some of your assertions (or possibly misunderstandings) in your comments, which might explain why this is a good thing.

nobody will pay for the recording tools

Sure they won't. But why do you need them to? If you set up an open-source project on GitHub, GitLab, SourceForge or anywhere similar, then you have no hosting costs.  At the very most you might want to pay for a domain name redirect.

or the platform membership

The platform is YouTube. Whether people pay for the ad-free version, or use the free version and live with the ads, is up to them. It's not something your tools should even care about.

The project income helps me to run the project for five years

Which is great. But presumably that was paying for hosting and paying for your time. You're stopping development, so you have no time to charge against the project. And you can host an open-source project in any number of different places for free. You simply don't need money.

my mission is to keep the project for non-profit

Which you will do by open-sourcing it.

"Open source" is not the same as "the project is alive". Just because you dump a few 1000 lines of code onto github doesn't imply that someone else will actually pick it up, continue to support and develop it, or otherwise care about the project.

Thank you for your technical clarification, @Wolfgang Bangerth, appreciated. Actually, the project is a group of integrated components ike Windows software, Chrome extension, and PHP/JavaScript video and user management platform developed with YouTube Data API. These components are designed to work together.

"The platform is YouTube. Whether people pay for the ad-free version, or use the free version and live with the ads, is up to them. It's not something your tools should even care about." It is when YouTube gives your channel a cut of the funds; YouTube memberships are specific to the individual channel. There are YouTube livestreamers whose full-time jobs involve streaming on YouTube and raking in YouTube membership money from their fanbases.

@nick012000, the platform is different from YouTube, it is developed with YouTube Data API, which is totally different from asking users to upload videos to their personal channels. Users upload videos to the project platform, whch handle, upload and process videos using YouTube servers then return video data and content to our platform.

@AlaaSadik So it's stored on YouTube, meaning it isn't costing you anything to host content.

@WolfgangBangerth True enough, but the code base, build scripts and everything else can be ready for anyone else to pick up. That sorts the OP's ethical concerns. Whether there's ever any future development is another matter, but at least the OP's work isn't lost.

@nick012009 But the OP is quite specifically wanting some way of cutting it loose, so they aren't looking for monetisation.

@Graham "So it's stored on YouTube, meaning it isn't costing you anything to host content." They still have to host the frontend somewhere, even if the backend is handled by YouTube. It sounds like they've monetized access to the frontend, as well.

It's not just morally acceptable, it's inevitable: you will probably not live forever, and so at some point, you will stop contributing to this project. Your only choices are when that is and how well-prepared the project is for that.
With that in mind, I'd argue that there's an active ethical obligation to at least plan for the possibility of you leaving. This is quite a common concept in business, known as the "bus test": if you were to be hit by a bus, or are otherwise removed from the project unexpectedly and against your will, that would presumably be at least as disruptive as you quitting in any other way. As the probability of that happening is decidedly more than zero, you should have a plan in place so that the project survives you (since you seem to care about it continuing).
What that plan looks like depends on details of the project that I don't know about - maybe you have a collaborator who you could prep to take over if needed, maybe you need to recruit some assistants who you can train up slowly, maybe you can do something else entirely. Whatever it is, though, it will work at least as well (and probably significantly better) for you stepping away gradually in a controlled manner now, rather than rapidly and unexpectedly.

Great, thank you @user3482749, I will start to prepare for that in cooperation with one of my colleagues who understand in business planning, and I will do my last try to convience somebody to acquire or adopt ths project.

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


text:
After publishing my manuscript, can I withdraw the manuscript and publish it at a different journal?
I published one of my manuscripts in June 2015 in a relatively new journal (6 volumes so far). The journal makes it clear in the website that it is available online and in print with ISSN. The key idea was getting a printed copy of the issue/journal for promotion requirements in my University. I contacted them many times to send the hard copy but till today I did not get it and I believe that they will not. I contacted them to remove the paper from their website to re-submit the paper in another journal for publication.
The question is: is this possible? and what is consequences for submitting the same manuscript to another journal?

Don't do it. Once the paper is published, that's it - it cannot be unpublished, only perhaps retracted if it is revealed to be flawed or fraudulent. Aside from that, any self-respecting journal would not accept a submission that was already published elsewhere. This is considered unethical behavior, you will either be flat out rejected if you are honest about your intentions, or worse if you hide your intentions and are discovered to have tried to publish the same paper twice.

Have you explicitly checked that a printout (or pdf) of an eprint is not acceptable?  Most journals (at least in my field) do not provide physical offprints to authors anymore.

The question is: is this possible?

If you have signed over the copyright of your paper to this journal, or given them an irrevocable license to distribute, then they don't have to take down the paper just because you have asked them. In fact, if they are a reputable journal and the paper has already been published, they shouldn't just take down the paper without a very good reason, because that would distort the scientific record.

and what is consequences for submitting the same manuscript to another journal?

Submitting a manuscript to a journal that is already published in another journal is called "duplicate publication", and it is considered a kind of research misconduct. Consequences can include retraction of the duplicate publication, being banned from submitting papers to that journal for some period of time, or being banned from submitting papers to that publisher's journals for some period of time.

I think the copyright transfer is a contract. If the publisher does not hold up their end (i.e., providing a print version), I would be surprised if the transfer was valid. That said, that aspect is a legal question and probably requiresome a lawyer. Further, it would not change the prior publication status, at least in my mind.

@StrongBad I'd be surprised to see a copyright transfer that says the publisher will provide a print version.  Especially for an online journal.

The copyright transfer does not say that, of course. However, we have to remember that one of the main criteria we use to publish is the availability of print copy.

one of the main criteria we use to publish is the availability of print copy. [citation needed]

authors: Екатерина Борисова


text:
How to automatically extract submitted/accepted dates of many journal papers?
I am doing a research of the processing times of papers published in journals in my field. I have noticed that the metrics that the journals advertise (e.g. the Elsevier journal insights) do not correspond to my experience, nor to the recently published papers, so I wanted to make my own survey. (My guess is that they take into account papers which are immediately rejected by the editor without being sent to a review, so the average looks quite favourable. I am more interested in the average time of the papers which are actually accepted.)
I plan to cover all recently (last 12 months) published papers in 10-20 journals of different publishers (e.g. Elsevier, T&F, Wiley), which will result in hundreds of papers. Basically, I will take the date when the paper was submitted, accepted, and published online, and calculate the average per journal.
Is there a way to automatically extract this information?

Have you checked this data is actually made available for your preferred journals? IME not all make their accepted/submitted/first-online dates very easily accessible, though it has improved a bit recently.
If it's there, your best bet is probably to screenscrape the HTML. Some journals provide nice clean XML to play with, but this is usually new online-only titles rather than legacy ones from traditional publishers.
Elsevier use a simple HTML tag (class="articleDates") which contains the core dates -
Received 23 March 2015, Revised 15 May 2015, Accepted 18 May 2015, Available online 9 June 2015
Taylor & Francis have similar information to Elsevier: the element you'd need is again "articleDates", but it unfortunately has a lot of linebreaks in it for no good reason!
Finally, Wiley don't seem to expose submitted/accepted dates (at least not for all journals); "publicationHistoryDetails" just gives first-online, which isn't much help.

An excellent example of what you can do if the data is available, looking at the PLoS journals: https://metarabbit.wordpress.com/2013/06/05/how-long-does-plos-take-to-review-a-paper-all-plos-journals-now/

Thanks for the suggestion, I didn't notice that it'd be fairly easy to get the info from the HTML. And yes, not all journals (especially Wiley's) provide such data, but luckily they are in a small minority.

@paginated there's a good chance they'll expose this data soon (the UK HEFCE open-access mandate relies on it, and it would be a lot easier if they reported it, so there's some pressure...) - but for now, I think the html's your best bet. Let us know how you get on! I'd be quite interested to see the results.

This is an interesting question (+1). And I like @Andrew's answer (+1). However, I would like to suggest an approach, somewhat alternative to Web scraping. I mean using meta-repositories and their APIs. For example, you can consider using CrossRef, which offers, along with other services, CrossRef Metadata Services. There is a free of charge subset of this offering, which can be used via what is referred to as End-User Lookup Affiliate (other metadata services seem to be paid).
With that repositories/APIs approach in mind, if you use R programming environment, there is an interesting initiative rOpenSci, which is comprised of an open science-focused set of projects, developing R packages for interacting with various repositories, including meta-repositories. In particular, rmetadata package seems like the project that is the most relevant on the topic (note that it is not a mature project yet). A more mature, but still relevant project is rcrossref package. Hopefully, some other rOpenSci packages also might be of your present and future interests.

Great, I was not aware of any of these. Thanks.

Anything that doesn't involve screenscraping would certainly be an improvement from a practical perspective. However... it's all a bit moot if the other data repositories don't actually contain the relevant metadata! From a quick check of the Elsevier example it doesn't look like they do...

@paginated: My pleasure.

@Andrew: I wouldn't make conclusions, based on sample with N=1. Plus, considering current trends, we can expect at least some progress in representativeness and data quality of repositories and meta-repositories in the near future. So, trying this approach can give researchers a sense of comfort (or lack of) for automating bibliographic information discovery and analysis and help build their skills foundation for, hopefully, not-so-distant time, when this approach will become mainstream.

Here is a program I wrote to webscrape from a Springer journal. It uses the "Download CSV" link that appears next to the RSS feed icon when listing all articles in the journal Environmental Monitoring and Assessment, URL: https://www.springer.com/journal/10661
To obtain the URL to search on:

Click on the link to the journal, scroll down past the recent articles, and click on the [ View all articles > ] button.

To narrow the search, use the Date Published link in the header above the article list.

There is an RSS feed icon there which is easy to find. However, do not use that icon, but instead use the down arrow icon next to it, which is Download CSV.  But don't click on it.  Instead, right click on it and select "Copy link address."

In the code below, in the line which contains os.system, delete the URL after curl and paste the URL just copied above.

Run the program. You'll end up with an allpapers.csv file containing all the Received, Accepted, and Published  dates for all articles matching the publication date range selected.

import os,sys
from dateutil.parser import parse

import requests
from bs4 import BeautifulSoup
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np

os.system("curl 'https://link.springer.com/search/csv?date-facet-mode=between&search-within=Journal&facet-start-year=2021&previous-start-year=1981&previous-end-year=2021&facet-journal-id=10661&facet-end-year=2021&query=' > searchresults.csv")

sresults = pd.read_csv("searchresults.csv")
timedicts = []
for URL in sresults['URL']:
    print(f"===== {URL} =====")
    page = requests.get(URL)

    soup = BeautifulSoup(page.content, 'html.parser')

    times = soup.find_all('time')
    timedict = {'URL':URL}
    for time in times:
        label=str(time.find_parent().find_parent().contents[0])
        datetime = str(time.attrs['datetime'])
        if label[0] != '<':
            print(f"{label} : {datetime}")
            timedict[label]=datetime
    timedicts.append(timedict)

allpapers = pd.DataFrame(timedicts)

allpapers.to_csv("allpapers.csv")

@PabloA Academia.SE does not have syntax highlighting enabled. Source https://meta.stackexchange.com/q/314553/552049

@Anyon Thanks! Would be great to escalate it for staff attention.


text:
How to handle salary negotiations while negotiating a postdoc position?
I am a couple of months off my defence and started thinking about postdoc possibilities. I seem to have an opportunity at a very prestigious lab in the U.S. (I'm currently located in Europe).
After a brief chat with the PI at a conference, and some e-mails back and forth I was invited to come for a visit, meet the people and present myself and my work so far. Considering that we are still in contact and started discussing more regarding the projects and funding possibilities, I feel like they genuinely do want me to work there.
Putting aside all the parameters regarding the scientific matters, I am a bit concerned about the economic aspects. The lab is located at a city which is among the most expensive in the country, based on what I read/hear. I have been in contact with the postdoc-community (turns out there is one) at this university and asked them about how salaries are decided and how it compares to the cost of living in that city. The answer wasn't very simple, but my understanding is that it's not regulated at uni or faculty level but instead decided on a case-by-case basis. I hear figures varying from $30K to $75K, which is a pretty huge span.
So, coming back to my contact with the PI, at no point during our communication the subject of salary came up, and while initially I was cool with that, I am starting to feel like it would be good to know what I am getting myself into before we start putting serious effort into writing grant applications and designing projects.
I realize money shouldn't be the first concern, while negotiating an academic position; but if I'm going to relocate to the other side of the planet without any security of a future there, or back here, I'd like to know that I'm taking a step up from my current life rather than a step down. The issue is that as a grad student in Sweden, you have a pretty decent life and you get a respectable salary (despite being 20-35% down from a comparable position at industry).
Q1: How can I inquire about the salary offer/negotiation without appearing greedy or money-oriented?
Q2: As a follow up, is it reasonable to expect/ask them to match my current living standard?

At my lab, there is one post-doc salary set by HR. At a university I could see (have seen but a long time ago) that the post-doc salary could vary widely by school (engineering vs arts) or possibly by department (civil vs electrical engineering). Certainly the professor has some (limited) budget to allocate to a post-doc, so you might price yourself out of their market.

Hope you don't feel bad about asking about salary.  My postdoc got relocated to London (where my living costs more than doubled), and felt I "shouldn't" press for more money.  In the end I just got resentful and resigned. There were other factors too but the point I want to make here is that, given the current market for permanent academic positions, a postdoc is a just a job and you can negotiate to get something that works for you.  As @Jon Custer says, the issue is whether you price yourself out of the market.

I think all your concerns are very reasonable. Honestly, I am not really buying into the "money is no concern in academic job hunts" story. A postdoc is a job. Part of a job is a salary. I never understood why you are allowed to ask about housing, students, packages, whatever, but not what money you are going to make.

Q1: how can I inquire about the salary offer/negotiation without appearing greedy or money-oriented?

In the past, I have brought up this topic during my faculty visits (i.e., when they invited me over). At this point, nothing is promised yet, but it should be reasonably clear that both sides are interested and will not be scared away by trivialities. That is, if the PI went through the pain and costs to fly you over, (s)he isn't going to drop you just because you said the nasty M-word. Also, a slightly uncomfortable topic is better discussed face-to-face, over coffee.
Usually, there is a point in the conversation where you can drop it in without being overly heavy-handed. Don't make it the first thing you ask, but some time during the day quite naturally the formalities of your employment will come up. At this time you just ask directly for your yearly salary.
"You say that my employment would be full-time for 2 years? By the way, how much in yearly salary would this roughly amount to?"
If this is above what you expect, nod sagely and let the topic go. If this is slightly below your expectations, ask if there is possibility to increase (e.g., with additional teaching, by bringing in grants). I wouldn't really consider this negotiating (as they like to say over at Workplace.SE, one cannot negotiate without being prepared to walk away), but rather an open discussion what you would need to do to get to your expected salary. If the offer is way below your expectations, to the extent that your standard-of-living would actually unreasonably sink from your current position, explicitly say so.
However, keep in mind that there is a good chance that in this third case, you may well have an unfixable problem - likely, the PI will be unable and unwilling to go up very far from whatever (s)he currently has in mind, so there is a good chance to you will either have to take the lower salary for the experience, or be prepared to walk away. However, at least then you know - this is still much better than finding out when you are already in the US that your salary isn't close to what you are used to.
Edit:
There is, unfortunately, also the very real chance that the answer will be something evasive, for instance:

"We'll tackle this when you are here, ok?"
"Salary will follow the university standards / NSF standards / whatever."
"I don't know from the top of my head, but I am sure we will be able to figure it out."
...

If this is the annoying case, I would press the topic. Really. No matter what anybody says, it is not unreasonable to expect to have more or less exact knowledge about salary before agreeing to changing jobs, especially but not only if that "changing jobs" will mean that you move to a different continent. Also, it is a super-bad sign if the PI won't even give you a ballpark number. That alone would make me very anxious about the entire salary topic.

Q2: As a follow up, is it reasonable to expect/ask them to match my current living standard?

Partially. Your current standard of living isn't really of much concern to your new employer, but of course you can use this argument to plausibly explain why you care about having a specific minimal salary goal. Of course for the PI it's not an ethical problem at all to respond with "I don't have this money", or "For this money I can get two qualified people who don't have your expectations regarding standard-of-living". So I certainly wouldn't expect them to match your current salary, but it is not unreasonable to ask for this.

Or the PI might say, "sure, but then your contract will be 18 months rather than 24 months"?

@gerrit Maybe, but there's a good chance that this is actually not even bad for the OP.

@xLeitix well he's not being evasive but the subject never came up and I am not sure if it's on purpose. I can't imagine him being short on research money, given the reputation and their success in literature.

Ask for a copy of the offer letter, once you are fairly certain you have it in the bag.

@aparente001 There was nothing even close to as formal as an offer letter for all the postdocs I did so far. At least here in Europe, postdocs are more like you show up, start to work, and weeks later you magically have a contract and get salary.

@posdef Most won't bring the topic up by themselves unless they think that their salary offer is particularly good. It is your job to make this part of the conversation. (and, sadly, that he is a well-known researcher neither means that he has a lot of money, nor, if he has a lot of grant money, that he is free and willing to use it to pay particularly high postdoc salaries).

Some of the stories I've heard go along the lines that very prestigious labs/departments/institutions in the US actually pay low salaries at the levels below professor because people are beating each other up to get an opportunity in those places and are willing to trade money for reputation. Can someone confirm this?

@Miguel I am not sure how one could "confirm" this. Surely there are labs that do this. I am sure there are others that are paying just fine. That being said, generally speaking paying subpar salary is rarely the optimal strategy if you want to hire the best people (which the best labs def. want to do). The best people usually have offers not only from your excellent lab, but also from your competitors who have equally good reputation.

@Miguel There are at least some prestigious labs in the US that pay reasonable postdoc salaries. Lawrence Livermore pays postdocs $75k—$100k / year.


text:
Strategies for dealing/interacting with a colleague who have suffered from academic burnout
There are quite a few question aiming at or hinting towards avoiding academic burn-out, but I couldn't come across one that targets interaction with a colleague that has suffered from a serious burn-out, which can be very tricky as I am learning nowadays.
Background: A colleague of mine (office-mate actually) has suffered a pretty major crisis over the past year and had to take an extended leave of absence due to stress. The person in question was/is close to disputation but due to the fact that they could not handle being at work anymore, everything was postponed.
After several months away, my colleague is trying to get back in the game by starting off 20%. I heard that it didn't work out all too good the first attempt, a couple of weeks later they are attempting to start again. As we were chatting the other day, I realized that I can't really say much without tripping my colleague off, in the sense  that the subject often raises old issues somehow and causes some frustration/stress for my colleague. That partially originates from the fact that most of what we have in common and talk about is work oriented somehow.
My natural reflex when I realize that the subject causes discomfort is to not feed the conversation and attempt to change the subject. But that doesn't really work too good, as it's not very discrete. I also suspect that specially avoiding small-talk with my office mate isn't very nice either, I don't want the person to feel isolated and alone. I mean the fact that a person had a stress-related problem, it's not something that one should be ashamed or embarrassed about, it shouldn't be awkward socially, but somehow it does feel like that.
Does anyone here have any experience about how to tackle a situation like this?

it's so odd hearing about situations so similar to mine... had to check the date to make sure it wasn't me who was the subject you're on about :)


text:
What degree do you need to present a poster in a conference?
Hi there I just finished my Master’s degree and in a couple of months there is a conference about my thesis topic that I would like to have a PhD about. My question is can I present a poster or should I own a PhD already? I read that you can present a poster even with a Master’s degree but my professor told me that’s not true. Should I ask another professor if he is interesting in collaborating with me for a poster or is it dumb? I was thinking on working with the professor I wanted to do my PhD thesis with and maybe work on something small is it possible in only two months? I don’t know how much time you need to prepare a poster.
Thank you.

Can you describe the conference? Is this the kind of conference which is selective about abstracts and acts something like a peer-reviewed journal? Is the conference aimed at younger researchers (PhD students/postdocs)? Did the conference say anything about poster submissions that give the impression that they are not open to anyone?

Why not just ask the conference organisers? There’s no hard and fast rule as far as I know

@user438383 I thought it may be a dumb question and I didn’t wanna seem like I am overrate myself but yes you are right

@TrevorGunn the conference is open even for post graduate students, the only description was that there would be a 30 mins poster session nothing about who can present. I don’t know how these conferences are called I think it’s just an academic conference where Postdoc, PhD students and professors present their study results. I think that it is aimed in students in general from post grads to post docs.

@Mathematician don’t worry about that, nobody will think you are dumb for asking an honest question like that.

You sound a bit like you want to prepare a new result just for a poster session. It may vary between fields, but at least in my area of math, posters are more used to advertise existing or upcoming results. That being said, I have seen people present the results from their master-thesis, so that might be a simple solution.

@mlk Thank you so much for your answer at first. I don’t want to prepare something just to be at a poster session I just want to start working on new things at mathematics but I don’t have someone to guide me. I just thought that it would be a great opportunity to present something in front of professors with similar scientific interests and it may help me on my future studies. My first idea was doing a bit more work on my master thesis but my professor told me that’s not possible, and I’m a bit confused.

You do not need any specific degree to make and present a poster.
Nobody will check degrees at any point, the only important thing is to produce good work, get it accepted at a conference, and follow conference instructions to build a proper poster, and present it.
In conferences I have seen undergraduate students presenting posters, and even by researchers without degrees (for example, Chris Olah, in Machine Learning).


text:
Should I cite a source for a direct quotation separately if it is inside a paragraph with the same source?
Assuming that Adam conducted an interview with John Doe and Adam is the only source.

Should I source the direct quotation separately?

The chocolate rain machine was invented by John Doe in 1980 and was regarded by Doe as "the most significant invention of the 20th century" (Adam, 2017). He constructed it from wooden bars that were...[several sentences] (Adam, 2017)

Or is the source at the end of the paragraph enough?

The chocolate rain machine was invented by John Doe in 1980 and was regarded by Doe as "the most significant invention of the 20th century". He constructed it from wooden bars that were...[several sentences] (Adam, 2017)

Your quoting Adam (2013) for a citation by Doe ??? Surely, Adam (2013) is not the original source, so you should either quote the original, or explicitly specify that (for example by see Adam (2013) for a recent summary, or similar), or both.

@Walter What if Adam conducted an interview with Doe and thus is the primary source? I will change the year examples to accommodate for that. I did not anticipate that this would become relevant.

Possible duplicate of Should I reference the book I got a formula from, or the source that book got the formula from?

@astronat It is not, because I only have one source.

I added pictures to visualize what I mean.

Dissertation writing instructor here. I completely agree with jakebeal. His suggestion about connecting to the next sentence using "Adam further reports" is what writing teachers refer to as citation boundaries (for googling more info). Connectors (aka transition words) generally refer to words like therefore, and, & however.
Not to be annoying, but your example includes a quotation and a paraphrase, not 2 quotations. This affects the answer to your question bc you could have however many paraphrased sentences in a row, and only need to cite the final one -- as long as it's clear that all the info in them came from the same source (Adam further reports).
Quite honestly, I'd tell my student to avoid the situation because 1) it's awkward, and 2) there are several easy edits that would alleviate the problem.
However, if you have 2 actual quotes (with " "), you would have to cite each. But again, the reader will find it awkward & weird most likely.

The objective of citation is to provide clarity in attribution.  In the case where something might be unclear, it is generally better to err on the side of over-citation rather than under-citation.
In this case, I would judge the direct quote to definitely need a citation, because the source of a direct quotation should always be crystal clear.
It is the second part of the paragraph that might go without a citation. If it was short and you began it with a connector like "Adam further reports..." then it might be clearly enough linked with the quote citation to not need a separate citations. In this case, however, where it appears there is quite a bit of additional material, a second citation is likely to provide more clarity.


text:
What does it mean for my manuscript if the publisher's website says "decision letter being prepared"?
I submitted a paper to Physics of Plasmas. After 101
days the current stage says

decision letter being prepared.

And there is bold sentence saying

days to render final decision 101.

My question is:

Has the journal already made a decision regarding the paper or is the review process ongoing? Because not once it came to me for review.
Acceptance in one go is rare so does it mean a rejection?

Just be patient or ask the editor. He is the only one who knows.

What do you mean by because not once it came to me for review? Did you expect to review your own paper?

I also suggest that you take a look at: What does the typical workflow of a journal look like?

I mean that the first decision report has not come yet, generally when a paper gets reviewed a report is generated and shared with an author. It went for a review and after the review by referee suddenly the status shows " preparing decision report" and the day counter which counts the number of days since submission says" days to render final decision 101 ", so I am wondering whether it's possible that a final decision has been reached without the review being shared with me, will it be a minor or major revision or is it that they have rejected it.

In all likelihood, if a decision has been made without reviews, the handling editor did not find the paper suitable for the journal and has chosen to not even start the review process. My money would be on a rejection.
It is fairly normal that editors do a screening of the paper before the review process starts to avoid wasting reviewers time on papers that are almost certain to be rejected.

No but the paper went for a review as the status shoes review stated and review received

It hasn't come to me even once till now , I mean that I haven't received even the result of the first round of review and the status is saying : days to final decision 101

Hopefully, rejection mail is on the way.