text:
Worried about bad undergrad grades for phd admissions
I have a very bad undergraduate percentage (BSc maths, 58.3%) and from a no-name university. Mostly because I was not interested in pure mathematics and gave all my time to CS components of the course. However, I worked hard and got admitted to one of the best research institute in India (CMI) for MSc CS and maintained a consistent A grade. I also bagged some good internships at very prestigious Indian institutes (IIT-K, ISI). I was also offered PhD position in CS at both CMI and ISI last year.
I wish to join PhD outside India mainly due to stipend (very low in India, wont be enough for a family of 3). However, my BSc marks keep haunting me and often leave me very disappointed.
What are my chances to make it to a good university (<300 rank) in US or European countries? How much does BSc marks matter for a PhD candidate?
Also, should I take a PhD position at a low rank institute (~700 rank) if the professor is well known and has very high research throughput?
Also what rank and how many colleges should I apply to to maximise my applied-accepted ratio?
Thank you very much for giving it time to read.

You're very confused if you think PhD positions pay much in the US. You basically get payed slightly above minimum wage

@FourierFlex In india phd stipend is around 400 USD. So a US stipend’s saving is equal to whole stipend in india.

Do you think you can save 400 USD a month in the US, with a family of 3? I am honestly asking this reality check. Maybe if you got a good paid PhD in Urbana, IL ?

@EarlGrey By family of 3, I meant me and my parents. They’ll be staying in India only and 400 USD in INR is good sum for 2 people to live good life

Ok let's do the math, a PhD position gives roughly 2K a month, 800-1k is going to rent(probably more tbh), at least 250 food, you will also need a car, car insurance, cell phone, various other expenses. The idea you're going to send back any substantial amount of money(even 400) is pure delusion.

I think your MSc, thesis and internship are far more important. But I want to address the elephant in the room: it is not your grades but the fact you are not in the country where you are applying. Many supervisors prefer candidates they can meet or who got a degree from their institution (or one they trust). In the country where I got my PhD (EU), supervisors often selected international students fresh from the uni's MSc programme. We had 4 Indian students in my year, 3 stayed for PhD. Maybe you could try to find a 1-year scholarship to a country/uni you like to get your foot in the door?

@FourierFlux $400 mail back to India is possible. But, you'll have to suffer a lot. I know a Taiwan student saved around $500 a month in a midwest college town. What he did is, $300 housing (6 people living in a house,$300 food (he cooked himself) $300 for other expenses, like textbooks, cell phone etc. I forgot to mention around $250 for health insurance.

Back to 50 years ago, many (if not most) Taiwan students had TA/RA around $200 a month. Their parents borrowed quite a bit money for the airline ticket for their children to go to US. So, they had to pay back the debt. The way they did was, spend @100 -150 a month after a year they paid the debt. During that year, they sleep on the floor, pay very little rent, eat dog food. Many of them are emeritus  professors now (meaning they are retired). (One of them is a good friend of mine, so I know)

@scaaahu 200$ of the 60s are roughly 1.8k of today. I am quite sure they were sleeping on the floor (not many people were renting to asians), quite sure about the huge debts taken by their families, I am not quite sure about dog food (canned meat can have an ugly aspect) and I have some ideas what rural people with bright minds and poverty background were doing with so much cash (it starts with g, it ends with ambling). I am quite sure that many of those emeritus professors overblow the hardness they encountered, promoting the enduring-hardness style "PhD only for those who will not die".

@EarlGrey I assure you dog food is a real story, although I did not actually see them opening the can and eating them. I did see the opened cans in the trash and they did not have dogs. I did not ask them if they bought wrong can food or they simply bought it because of cheaper price. I did know they were having financial problem. They had to borrow $20 from me (I only had that much in my wallet) for the food that night. when I visited them for an assignment. Sorry I cannot continue. It's so much memory I don't want to remember.

I can't speak much for the US, mainly Europe.
From my understanding the professors are frequently not too much interested in your grades (particularly in maths/CS). It is more important that you show that you looked at that professor's research. That you are interested in the research ideas conducted at that chair, that you understand the implications of that research.
Let's say you are interested in machine learning approaches, but apply at a chair for analysis - that will not fit!


text:
Professor not replying after agreeing for internship
A professor had agreed to an internship and asked me to remind her again before the start of August.
She has not responded to the reminder email I sent 10 days ago. Should I mail her again? Is it impolite to call her in her office?
I was very eagerly looking forward to work with her, so yes, I’m slightly desperate.

It is very likely that she just overlooked the mail. You definitely should send her a mail again. It's totally reasonable to keep asking until you get the response, even if she suddenly changed her mind about hiring you.
BTW, it's summer now. Many professors would go on vacation at this moment. If this is the case, I am afraid you have to wait until she gets back to work.

Sorry that this comes so late, but others may benefit.
In such situations it is advisable to contact the professor's department, usually via a public phone number or email address. A staff member in the department might be able to put you in contact if you explain the situation. Or, they might be able to explain to you why communication is impossible at the moment.
Don't make it a complaint against the professor, just an inquiry about how best to communicate. The staff member might have a lot of options for such things, including contacting the professor on your behalf or asking the department head for advice.
But this is for time-sensitive inquiries, such as the one in the question here. If waiting is reasonable, then wait until it is closer to deadlines that can't be missed.

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text:
Mentioning a scholarship at the end of an article
So I finished my first degree and immediatly hoped onto my next (Master's). The issue was that when my supervisor asked me to write the article that contained my diploma thesis I was not able to manage it before I changed universities.
In my new school, I actually managed to obtain a scholarship from a company and I am still writing the article. So my question is, in the scholarship contract that I signed it says that I should mention the scholarship in every paper I ever write. Of course one could say that the work has all been done while I was at my first university.
With that being true, I have grown a lot in my Master's programm and changed because of that. So I  deem it appropriate to refer to that scholarship since my Master's really helped me mature  and change my way of writing and seeing things.
Is it considered appropriate by scientific standards to include the scholarship at the end of the article?
Edit: I forgot to mention that my supervisor is ok with my including it since I seem to have a valid reason. I don't know if others would view it that way.

If I  correctly understand the situation, the scholarship did not support the research for your diploma thesis but did support writing it up as an article. In a similar situation, I've used an acknowlegement of the form "Much of this paper was written while the author was a visiting scientist at ...."

so it did not exactly supported in a direct way, but I think I benefitied by the scholarship in the end so I consider it proper to refer to it. Thank you for the suggestion, I will implement something similar!!

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

Do scholarship rules really about every paper you write, ever?  This seems absurd, as it could apply to a paper you write thirty years in the future.  Perhaps you can clarify with what the rule actually states?

they mention for as long as I am under the scholarship whatever i public, i should mention them, at first I wasnt gonna include them, but my master did help and now  my conscience says me to do it, of course stating clearly what their contribution was

Actually, I think that their request to mention them in every paper you ever write was inappropriate. I would eventually ignore it unless I had an actual contractual obligation.
But in the short term it is fine to mention them, though whether you say they actually enabled the work or not depends on whether that would be true or not.
I hope they haven't given you a specific formulation. But "I want to thank X for a scholarship that helped fund my early education." is probably honest and without issue.

Yeah , I was planning to focus on the fact that they funded my Master Studies without mentioning their involvment on the paper  because they didnt. I dont  know exactly what's the correct way and my professor was ok with me mentioning them because from my country the company is really strong in my field and it would only benefit us in a way. I think also that what i signed is  quite uncertain and I could simply ignore because the publication is reffereing to my work before the scholarship and not with my current institution. However as I am planning to affiliate myself with both institutions

and I am working through it during my stidies that I am also being paid- I find more proper to mention them, reffering to their actual role. I dont think anybody will think that they funded the project since my professor urged me to thank a specific national grant for the project. So i think the liines are pretty much drawn

I also want to add that I would ahve preffered not to add them but I might too honest of a person and want to write things as they are and not  try to be sneaky. I guess it also is up to the other participating professor and if he agrees.

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Interview for postdoc position in mathematics
I have an interview for a postdoc position in Mathematics at a very good university in the UK. The interview committee comprises a maths professor (not in my field, which is analysis of PDEs) and three other professors from other scientific disciplines.
I do not expect any technical questions since they are not in my field. But I am worried they will ask me: "why is your work important/useful/relevant?" in the context of applications to real-life. What can I say in such a situation? Also does anyone have any general advice to what such a panel might ask me?

Is it an applied postdoc?  If you're working in PDEs then "real life" applications (as though maths isn't real life!) shouldn't be too tough to come up with?  I don't think the panel is necessarily looking for killer answers here, they just want to see that you've thought about how your work fits in the "bigger picture".

please slap them if they use the phrase "real life" :D

Also, is the postdoc for a specific project (e.g. on an EPSRC grant) or will you be doing independent research?

@P.Windridge Thanks for the advice. Basically the university awards x number of maths postdocs in a year, and those are awarded by this committee. Essentially I can do what I want if I get the postdoc.

For specific postdoc positions in the UK the panel is required to ask all interviewees the same set of technical questions. I mention this because you say you don't expect this kind of question, just in case.

@JackPasl  Then I suspect one of their concerns is that you can be productive without much supervision.

Why should you be worried? This is a pretty standard postdoc position interview question and you should be prepared to answer it.
I echo P.Windridge's comment:- your specific answer may be less important than a clear indication that you've considered how your research fits in, extends, challenges, tests the current state of the art in your field.
You've set the problem of answering this question in the context of "real life", whatever that is. For your specific case, I would have thought the "real life" applications of PDEs is easily referenced.

Well I work in existence of solutions to PDEs. So I can say eg. "this PDE comes from heat diffusion across a rod" though my work has nothing to do with the physical motivation of it. I just feel "cheap" for saying something like that but I guess I have to.

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Optimize lab report grading rubric to minimize grading time
I will be teaching a new course with a new grading rubric. All of my students will write a lab report at the end of each 3 hour lab session. Each lab report will have an abstract, introduction, data, results, and conclusion sections. How can I prepare my grading rubric to minimize grading time for all lab reports I will grade at the end of each week?

Not clear what is happening... are you going to "receive" the rubric or are you going to "prepare" the rubric?

Handed in = Pass. Not handed in = Fail.

Even easier: Pass.

The more that grading is turned into a box ticking exercise, the quicker you are going to be able to do the grading. The more easily you can determine if students have ticked a box, the quicker you will be able to grade. In many ways using a box ticking rubric approach may transform the lab reports into an exercise of gaming the rubric instead of learning the concepts and material.
My biggest problem when marking lab reports with a rubric are the good reports that have gone in a different direction. The rubric says they should do bad, but the report seems good. I think by showing the students the rubric you can transform the lab report into a true box ticking exercise. It might be best to even reformat the lab report to not use traditional sections, but only require "short answers" to the key components.
Potentially the introduction could be 6 (12, 24 depending on the level) references and one sentence stating why it is relevant. The results could be the relevant numbers (with units) and any statistical tests. The conclusion could be bullet points. The less the students write, the quicker you will be able to mark the reports.

When I was teaching physics classes in grad, grading got easier after creating a key (or rubric) that was really concrete. By creating a specific set of things to look for, grading took less time and students were happier with their grades.
Here is what worked for me.

Explaining figure etiquette: axis labels, include units, have the data points take the majority of the graph area.
Communicating the expected details: clarity of answers, showing work, including the data sheet, etc.
Giving examples of deducting points for poor quality.

I found same-day grading took less time (since the material was fresh in my mind) and created a great deadline for late work. I accepted work for full credit until I grading was finished; afterwards, I awarded late labs 50% (without grading).

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Which software can check on false references and incorrect citation on student papers?
I'm a TA at a medium-sized university in Asia, and as part of my routine, I randomly review student papers before using Turnitin for plagiarism checks. During these reviews, I've come across numerous errors related to citation formatting, including instances where references contain non-existent links. I suspect some students may be using AI writing tools like ChatGPT to generate their papers. To address this issue, I first need to assess the extent of the problem. However, considering the large class size of over 50 students, I'm wondering if there's a tool available that can automatically detect and flag false references or incorrect citations in their papers.

I think I have found the solution after researching for a while, I will suggest this to my professor and the Chair of the department.
https://www.scribbr.com/citation/checker/

I would require students to provide a list of DOIs and URLs.  DOIs can be checked with these instructions: https://dx.doi.org/
For books, students can provide an ISBN.  Those are a bit trickier to validate, but could help.

In machine learning DOIs are not universally assigned at very relevant venues like NeurIPS: link. This might make it hard to demand DOIs universally.

@MarkusLange-Hegermann Which is why I did not recommend that.  NeurIPS has both URLs and an ISBN for their most recent proceedings.

That might help with the false references, but it will be a daunting task if students write papers with 20 pages with 50 references and above. Also, will you ignore the miscitation? Probably I will ignore a few, but not about 25 miscitations and above

@throwawayta From experience, DOIs are massively easier to use in writing than traditional citations.


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Overcoming the burden of calculations in undergrad Math
TL;DR:
I’m going thru some ups and downs, struggling with some (math-adjacent or bag-of-tricks types of) classes, and looking for advice on balancing grades and passion.
For the sake of TL;DR, here are the questions that I listed below:

Is it necessary to maintain good grades in all subjects to be accepted into a PhD program, or can I focus on excelling in math-related courses?
Do PhD programs expect only max grades, or is there some acceptable lower bound?
Is it acceptable to have low grades in subjects that are not related to my academic goals?

First, for your to be able to answer the question(s), let me briefly describe what I love about math
Why math:

TL;DR of how I got into it: coding → theoretical computer science → pure math.
Discovered coding as a kid, but eventually realized I’m more passionate about the theoretical aspects – which led to CS.
And then naturally fell in love with math, since for me, it had all there was in Theoretical CS but the ideas were deeper, the connections were more intricate and so on.
In stark contrast, I find myself absolutely hating the mundane tasks that software engineers often face in their jobs; it feels like nothing more than grunt work. I want to avoid that at all costs.

Current Situation:

Important note:
Our university (EU) has this system where we have oral and written exams covering theory and practice/calculations respectively, for every class. You can’t pass if you fail either one, which is really tough for me, since I absolutely hate dull computations

Disclaimer: I definitely do not think I'm gifted at math, but I genuinely love it and want to pursue it for life.

For context, here are my current grades:

Class
Grade

Linear Algebra
4.0

Real Analysis I
4.0

Data Structures
4.0

Coding
4.0

Wolfram Mathematica
4.0

Econ
4.0 (even tho got max points hated it for life)

Analytic Geometry
3.0 (absolutely hated it)

As common in EU math programs:

the load is pretty demanding
drop-out rates are over 40%.
classes are proof-based from day one (which is awesome!)

I really dislike the practical, calculation-heavy parts of my courses, especially in subjects where we don’t even touch on the underlying theory.

It feels like all we are doing in classes like Differential Equations, Macroeconomics, and Mathematical Modeling is just memorizing tricks

While yes, the above mentioned subjects consist entirely of computations (or at least that's how they are taught), there's also another category of classes. For example:

Mathematical Analysis [i.e. Lebesgue measure, Stoke's Theorem...]
Discrete Math [ZFC, Combinatorics, Automata theory]
Abstract Algebra
Complex Analysis

I absolutely love their 'theoretical' part

But I hate the stuff that we learn at workshops and have on written exams, because those are just dull computations... It almost literally makes me sick.

reminder:
in my university written exams cover 'practice'

Let me give you some examples so we are on the same page:

What we learn at lectures
What we learn at workshops

Proof of Schröder–Bernstein theorem
Find bijection btw N and NxN

Proof of Fubini's theorem
Calculate volume of a 3D shape, defined as:

.
x_1<=x<=x, f_1(x)<=y<=f_2(x), g_2(x,y)<=z<=g_2(x,y)

Proof of Liouville's theorem
Simplify sum_(k=1)^n cos^2 (k•a)

Prove [...]
Calculate [...]

...
...

And I can't just skip the computations :(

Because the final grade is (almost always) an average of {writtem exam grade} and {oral exam grade}

So if I do poorly in one part, my overall grade will be very low :(

I feel overwhelmed and miserable studying for these classes

(remark: In case of classes like Analysis and alike I only dread studying for written exams / taking workshops, not for theoretical part)

And I really want to do well, but I’m starting to question if I need to ace every subject, especially the ones that don’t align with my interests.

I'd rather aim on doing a PhD and diving into some "cool" math than just chasing high grades for nothing.

Questions:

Is it necessary to maintain good grades in all subjects to be accepted into a PhD program, or can I focus on excelling in math-related courses?
Do PhD programs expect only max grades, or is there some acceptable lower bound?
Is it acceptable to have low grades in subjects that are not related to my academic goals?

Because of this possibly flawed (?) belief that I need to crush even unrelated classes, I ended up taking (still on it atm) a year off just to pass my exams.

It wasn’t that the classes were hard; I just dreaded studying for those calculation-heavy ones.

Also, the answer is not necessary clear to me, since for example, in EU we do Masters before PhD.

So maybe my undergrad grades won't even matter much?

To summarize

I took that year off to focus on passing my exams, but I’m still unsure if that was the right decision.
I want to make the most of my education without feeling sick of the classes I can’t stand.
I’d really appreciate any insights or advice from anyone who’s been through similar challenges.
Also, some tips for managing coursework that feels less relevant to your goals would be extremely valuable

Thanks for reading to the end [:

Too long, even if nicely structured, and the TL;DR lacks clear question.

@CaptainEmacs, thanks for feedback!
Three questions are listed under «Questions» section. I will add them under the TL;DR as well

What is desired here is one question at a time.

"It feels like all we are doing in classes like Differential Equations [...] is just memorizing tricks" Shame on the person who taught your course in differential equations!

Yes, one question per post, much shorter, and we absolutely don’t need your transcript. The idea behind this site is that others could have the same question in the future; your post is way too specific-to-you and is therefore likely to be closed.

@cag51, Even though there are technically 3 of them, they are definitely in the same vain. I could've probably compressed it to only one, but instead optimized for readability over length

@cag51, Also, regarding too specific-to-you. I definitely think other users might benefit from it as well. It's just that the subjects in question will be different, but the idea is the same

Then rephrase it in way that doesn’t give a ton of details about the subject, and certainly doesn’t state your exact grades in a bunch of math courses. You can do it or not, but no point arguing with me, I’m just letting you know that questions with this many details tend to be closed (by community vote).  I think your question could be salvaged with some editing.

How are your peers handling the same situation?

As a frame challenge, I would question the belief that there is a sharp dividing line between dull calculation and cool math. In my experience, the work that precedes finding something cool and new is often either dull calculation or something similar to it, and the difference between someone succeeding with an idea and someone who has the same idea but fails to execute it is often the willingness of the former to do the dull parts of the potential project.
Sometimes the dull parts can be handed off to a computer, but there is unavoidable dull manual calculation even when the calculation in question can be done by a computer, because doing things manually can build intuition in a way that handing the details off to a machine doesn't (the reverse is also possible in some cases, due to scale).
That said, the field one works in does influence what types of relatively dull work are necessary to ultimately get results. Also, "dull" work can feel exciting if one has had prior experience of it being a first painful but absolutely necessary stage of a larger project that ends with some success!

My question concerns the undergrad experience tho.
It's a fair point to make that 'theoretical/cool' results often stem from concrete examples or calculations. I don't mind that at all(!), as it differs from what undergrad students typically face.
For instance, in my experience, math students are often required to memorize algorithms and just execute them in their heads during exams (in my case – written ones).
This is quite different from the process you describe, which can be rephrased as 'playing with [X]' to gain intuition. Imho, those are fundamentally different things.

@quasicat: math students are often required to memorize algorithms and just execute them in their heads during exams --- Aside from philosophy, I don't know any academic area one can study in a university that requires less memorization than math. See my comments to this Mathematics SE question and my comment to this Mathematics Educators SE question.

@DaveLRenfro, thanks for your input!
I agree with your point, but it seems to focus on the theoretical side. In the linked post, it was suggested that one should understand theorems instead of memorizing them, which is indeed what I enjoy doing and what I am doing.
Let me illustrate with an example what I mean. During lectures, we might prove how to find the antiderivative of rational functions, which is cool. However, during workshops and exams, solving these problems often relies more on memorizing the identities favored by the TA than on understanding the proofs.

Regarding antiderivatives of rational functions, the vast majority are learning these techniques and identities for their further courses in engineering, physics, chemistry, etc. (whatever their major is), and also it's very difficult to design "theory problems" at this level that students can be reasonably expected to solve. That said, I always thought calculus texts were a bit unclear about the "big picture", at least those written after roughly the 1980s. See this 15 Apr 2006 sci.math post for how I gave the big picture.

@DaveLRenfro, in EU we don't have calculus tho. And moreover, we don't share our workshops/lectures with other majors

As for good marks, having them will improve your PhD options. These marks will fade into oblivion as your career progresses, but at the current phase of your studies, you will profit from having better ones.
Concerning the mechanical work: Sometimes, you have to go through the slog to hammer out the gold. In fact, it may be unavoidable. Even you made us go through the slog of your post to understand what you are actually asking (the TL;DR is not actually at the core of the question) ;-)
Being able to be disciplined and do things you do not like is a skill very worth training. You will encounter phases in your scientific life where this will be crucial.
The teaching of facts without understanding is a different issue and here I sympathize, as I found that a major issue in how science education is done.
Sometimes it's a matter of time. The teacher does not have either:

the time to prepare
the time to deliver with all the context linked up.

This is not easily resolvable. You need is a good mentor who can explain context; and also you should search through books and literature until you find those pieces which actually help you creating this web of meaning. I personally estimate that in my area, 5% of literature actually gives real insight, by the way it links up with other work, is meaningful and not just incremental etc.
That being said, and closing the loop, sometimes you have to work hard to have a full mastery of the low-level skill and then the higher-level insights will emerge with time. So, your perceived waste of time may not be a waste of time after all.

(+1) especially for . . . well, for almost everything!

@DaveLRenfro That's very kind! If you say where I could improve, I am happy to do so.


text:
One of the multiple submitted paper is published and others are withdrawn
I have written one paper on mathematics and submitted it to 5 journals concurrently. Four of them accepted the paper and one asked to send the paper in their required format.
The paper contains one theorem and two applications. There was two argument gaps in the proof of the theorem. Only one journal caught that.
I have communicated with that journal and updated the paper throughout as below:

Changed the proof of the theorem entirely ,i.e. an alternative proof is provided, there is no similarity between the two proofs of the theorem.
Remove one of the applications and add a new application of that theorem.
Changed the way of applying of the theorem for the other application i.e firstly there was case distinction for the application, but later I removed the case distinction.

this paper is published in that journal and I have transferred the copyright agreement form to them and withdrawn the paper from other journals stating personal reasons. I am an amateur mathematician and I'm not pursuing any Phd degree.
Now my question is that what are the impacts may fall on the published paper in that journal as I have withdrawn all other manuscripts and they don't have the copy right agreement also, so is there any chances to claim the published article by them or they can force the editor of the journal which published the paper to retract the paper ?

I do not fully understand the question is the last line but: Since you did not adhere to the journal's policies (which, almost surely, state you shall not submit something that is submitted elsewhere), they may well retract your paper. Multiple submission are a serious academic felony.

By the was: I did not downvote. I think it is a legitimate question and one shall not downvote it to express "what you did way wrong". This can be done by upvoting the respective answer.

"I have written one paper on mathematics and submitted it to 5 journals concurrently". Very naughty.

It sounds from the edited question like you are worried that the other journals might be able to force the publisher to retract the article.  They can't, but the worry instead is that the publisher might want to retract it if they knew the facts.

I'm also puzzled by the timing of the four acceptances.  Usually, there's a lot of delay and randomness in how long it takes to referee a paper.  If you kept the article in submission for a substantial period of time as the acceptances gradually came in, then that will upset the publishers/editors even more.  (On the other hand, if all four were quick, then either you got really lucky, your paper is exceptionally easy to referee, or you didn't choose respectable journals and they didn't referee it seriously.)

Whatever you do in the future: do not submit the same manuscript to multiple (not even two) journals.
If you have managed to get the manuscript accepted in one journal you need to immediately withdraw all others. You state you have given "personal reasons" whereas in reality you should have provided a serious excuse to the journals for wasting their time.
If you have withdrawn all other manuscripts there should not be any further impact on the one accepted for publication. You should learn from the experience and perhaps acquaint yourself better with the publication process so as to avoid mistakes such as these again. If repeated, it may affect you adversely by gaining a bad reputation or possibly being "banned" from certain journals by their editors. So most negative impacts, if any, will fall on you.

Thank you for providing valuable information. I have withdrawn all other manuscripts and they don't have the copy right agreement also, so is there any chances to claim the published article or they can force the editor of the journal which published the paper to retract the paper ? This journal which published this paper has the copy right agreement form.

@SureshSharma they certainly cannot claim the published article, but they still might publish it, depending on how trustworthy the are; and they certainly cannot force an editor of a different journal to retract the paper, but those might still do that - see my answer.

First, a related question is How is it in my best interest not to submit a paper to two journals simultaneously?
Second, if any double publication occurs, you are screwed. I would agree that since the other journals do not have a signed copyright agreement from you, they should not be allowed to publish the paper, even though they accepted it for publication. However, this has happened in the past, and it led to the duplicate submission being retracted:

The two corresponding authors of the two published articles claimed that the problem arose from a mistake: the Scholarly Journal of Biological Science had asked for a publication fee that the authors could not pay. Believing that the journal would therefore return their manuscript, they submitted the manuscript to our journal. [...] We therefore decided to retract the article from our journal on the grounds of duplicate publication, informed the Editor of Scholarly Journal of Biological Science of the situation, told the authors about our decision to retract the article, and—considering their actions—reported the misconduct to their institutions.

(Journal runs retraction, editorial over duplicate submission of pathology paper, https://retractionwatch.com/2015/02/17/journal-runs-retraction-editorial-duplicate-submission/)
In some cases, both papers are retracted, which I feel should be the standard for double submissions.
https://retractionwatch.com/2013/06/18/double-submission-leads-to-retraction-of-probability-paper-and-a-publishing-ban/
So keep your fingers crossed that all the other journals honor your withdrawal "for personal reasons".
Third, assuming no double publication will ever take place, the issue of double submission: they still can take action against you, and maybe your paper. It certainly depends (well, not so much - see below) on what you the journals asked you during submission and what you told them.
Many journals nowadays expect an implicit or explicit confirmation by the author(s) that their work not been submitted (well, meaning it is not under consideration) elsewhere at the same time. Some expect you to include that confirmation in the cover letter and/or the manuscript, and if you did not add it there, you may be fine. But some may also have a mandatory checkbox in the submission system; some may have it in their author instructions or ethical guidelines, which you implicitly accept by submitting your manuscript. Either way, chances are very high that at least one of your five journals has such a requirement, which you failed to adhere to.
Thus, assuming you have made any such false statement, you may be in danger of being banned from these journals - this has happened in the past:

One week after it was published, the editors of journal B contacted our journal stating that this work, with the exact same title, authors and content, had been submitted to journal B and, after receiving an acceptance letter, the author withdrew the paper, informing them that it had been accepted by a different journal.
When the editor of journal B asked the author for an explanation, the author did not provide a satisfactory response. Journal B, in consultation with their editorial board, banned the author from submitting to the journal in the future.

(COPE case 17-20, ongoing; from https://publicationethics.org/case/consequence-dual-submission)
[While you see some going back and forth about submission dates in the above link: these are very often printed in the published paper, so any editor of your four other journals will be able to determine that you submitted concurrently.]
Also, an expression of concern might be published next to your published paper:

The Forum agreed this is still a case of duplicate submission and that there has been possible misconduct on the part of the authors. Although there is only one copy of the paper in the literature, the Forum advised the editor to consider publishing an expression of concern to alert readers to this.

(COPE case 12-30, ongoing; from https://publicationethics.org/case/retraction-first-article-case-duplicate-publication)
(very similar: COPE case 15-40; https://publicationethics.org/case/duplicate-publication-and-removal-article)
I have yet to find a case of a singly-published paper being retracted for dual submission, although I would not be surprised if that happened, given that both papers of a dual publication can be retracted (see above). However, one of the links above (I would have to find that passage again) says that retractions should be made to correct the literature, not to punish" - and if there is no literature correction to be made on the grounds of double publications, my guess is that your paper is safe.


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What are the chances in getting a PhD in a sepcific Professor, when I barely passed his elective?
This might look similar to other questions, but I considered mine is more specific.
I basically messed up, my grades in the whole Masters degree are completely average to  higher than average (not my take - have asked for evaluation) and there is this elective that I even retook to improve my grade and still got the same! The professor that teaches this course has also accepted me for a Master Thesis and I was planning to ask for a PhD after I finish my Master's next year, but now I don't know if this is going to be possible. I know that he accepted students that haven't even taken the course, but I got myself into the situation of getting a low grade twice and he knows that!
Has anybody been in this situation either as a student or a professor? How did it go?

Even if someone had a similar situation, it will always depend on the individual situation. So ask your prof and make a good case for yourself.

How is your master's thesis going? Is there time to do good work there before a decision has to be made about your PhD application?

To answer to the first question, I know that probably is the best solution, but knowing about othe people's experiences might help me.

For the second I have barely started, so there is still time to salvage, but i don't know how to approach the situation, as I wanted to ask for a most difficult and heavy workload in order to show my capabilities as a researcher and I am not sure how it will look like. Also I am in Europe so the deadlines are still far away. I was even considering going first to industry - research after uni to improve my chances with gaining experience.

Instead of asking for the "most difficult and heavy workload" (not a good idea!) just talk to them about your future plans. When I supervise a master's thesis, the information if someone wants to pursue an academic career or simply wants to get their degree done is very important for the whole (supervision) process etc. That way, you could e. g. see how you can structure the thesis to have a good chance to get a paper in a peer-reviewed journal out of it.

Ok thank you! Yeah , i will avoid addressing it like i said and take more of your approach.

I agree with the above: it's best to talk to your professor. Tell him now that you want to do a PhD and should orient your master's toward that. Then when the time comes to choose a PhD advisor, you can have that conversation then. Coursework and research are only loosely connected, so I don't think you are disqualified. In any case, for future reference, our site only takes "answerable" questions; we don't really do poll questions or speculation/"what are the odds" questions. We're a little different than most other sites; you can learn more in our [help]. Good luck!


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Checking Plagiarism among student's work (PDF documents)
I want to check the plagiarism among the students work. I have student's assignments and looking forward if I can make some settings in Turnitin to test the plagiarism only among student's work. I have simple PDF documents. I am okay to check plagiarism both ways i.e. with the internet sources and among the student's work. But the latter is most important. Also, I do not want to submit the work to the repository. How is this possible?

Is the scale so impossible that you can't just read their work?

Its not about that. I want to get a report out of this to see the level of plagiarism. Also, what if there is a large number of students?

Scale is a problem. But plagiarism can be more sophisticated than an AI can catch. Simple copying, yes, but not misattribution of ideas. Artificial Intelligence is certainly artificial. The other, not so much. You are likely to get both false positives and false negatives.

That's okay. So can I achieve my goal using Turnitin? I know it will analyze the documents with the internet sources but what about among the students?

@DanielHatton, my worry is that, by conflating plagiarism and copying in the minds of students, they will emerge with a flawed view of what is allowable. Many (many) questions here seem to imply that an OP believes that by paraphrasing they avoid plagiarism. I've tried to dispel that in many (many) posts. Most, but not all, student work is "common knowledge" and not subject to plagiarism rules, or, more correctly, it is obvious if someone misattributes common knowledge to themselves. But they need to know that the "essence" of plagiarism isn't copying a particular  expression. ...

While specific citations don't need to be given for common knowledge, it is still possible to misattribute idea to the author. People would laugh if I try to plagiarize Einstein, but they would still recognize it as plagiarism. Assuming, of course, that they don't have too narrow an idea of the essence of it.

What is the easiest way to check for plagiarism in student essay papers?


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When looking for a PhD advisor, will it matter if I send them an updated version of my masters thesis?
I am about to finish my masters degree, and I want to apply for a PhD in the near future. I know that when contacting a potential advisor, they will ask you to send your CV and your previous research. The issue is that, according to my current advisor, my masters thesis will have no issues on being approved and my grades are good. Due to the pandemic, though, I was not able to be in the country my university is located in; communication and feedback with my advisor was very complicated. In my opinion, my thesis could be improved in some ways, but now I am lacking the time to do so.
My question is:
When a potential advisor asks me for my masters thesis or my previous research, it is compulsory to send the document I submitted for graduation? Can I send an updated version of it (I know I will be able to improve it, because I will work on it at my job)? Is this wrong?

Always send the best version.   We know that a thesis may not be 'perfect', especially if there is a time constraint.  If you have an improved version, I would want to see that.

There are no strict rules about this, so you should do what is in your own best interest: send them the best version you have available.
However, you should consider that your potential PhD supervisor may talk to your the supervisor of your master's thesis. It is possible they will discuss the thesis, and it could cause lots of confusion if they unknowingly are talking about different versions. Therefore I would recommend to let your prospective PhD supervisor know that you have sent them a version you updated after your graduation.

I think you could send either version, correctly labelled. But you can also indicate that the other version is available "on request".
For example, if you send the official version, say that you have updated the work since and can make the newer work available if requested. This makes it clear and also indicates that you haven't been inactive in the interim.
The opposite is also possible, sending the latest (as suggested by Louic), but saying that the original will be sent on request.
But, I wouldn't send both at once.

and what if he/she asks me for the repository link? should I send the link and also the latest version specifying that this is my last version so please consider this more? thanks for your response

@JPgiq You are overthinking this. Your best option is to send the latest version. If they ask about the older version (highly unlikely), send them the older version as requested. I do not understand why you see a problem here.


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Can I still get accepted to a PhD program if I did mediocre in my second master's program?
I recently completed my second master's degree, but unfortunately, I did not perform as well as I had hoped. Despite receiving a distinction in my first degree, I struggled to find motivation in my second master's program (started during COVID) and ended up with an average grade and a mediocre thesis.
While my committee criticized my poor time planning they did not have that strong opinion on my research work , I have to say that I also received little help from my supervisor, which left me feeling unmotivated and ended up being underperforming during the writing process. As a result, I now want to switch back to the field of my previous master thesis and pursue a PhD. However, I am concerned that my mediocre performance will negatively impact my chances of being accepted, and I am not confident that my professor will be willing to provide a strong recommendation letter or any at all.
Is it possible for me to get accepted into a PhD program based on my first degree's dissertation field? I excelled in that area and enjoyed it. I realised that I prefer simulations over experiments.

"I have to say that I also received little help from my supervisor, which left me feeling unmotivated and ended up being underperforming during the writing process."
Your milege may vary, but the median person that cannot find the motivation during their master thesis should run away from a PhD.

the thing is that I mostly was passing some mental health issues due to covid and I hated my thesis which I selected based on a very bad anxious mode, disregarding my personal likes I went the experimental path that I apparently now hate, I would love going back to computational where things are to my mind pretty straightforwarrd

Sorry being blunt: no one cares about your feelings, you are applying for positions, not for mental support. Your mental health is at first your responsibility, not of your future employer/tutor/advisor.
Said this, see my answer...

yes I understand, I want to mjust pintpoint that this second degree is a small personal obstacle that I stumbled upon and nothing that I personally- not expecting any supervisor to care -  cannot eventually overcome, i want to know how my chances look and maybe some suggestions how to deal, overcoming now this dark period and looking forward to do something I enjoy

You have now a (kind of) strong point: experience in two fields, A and B. It is what you are, so either you cancel two years from your CV, or you make the best out of what you have.
It depends therefore on how you present your experience.
Please keep in mind the difference from the receiving side, in reading

"I like A but I hate B"
"I enjoyed and I was extremely productive in A, while
in B I could complete the work but it was not completely suited to
me and I had to overcome difficulties in B1-B2-B3".

If I am a practitioner in B looking for someone with expertise and skills in A for a PhD, to test some new path or new research ideas, I would straight reject your cv in the first case, but I would consider you a serious candidate in the second case. All other things being equal.

Thanks for the insightful comment! I will take it into consideration!

Yes, you can still get accepted. What's more, your experience might even help if you frame it the right way. Having done two masters and realizing that your strengths lie in field A and not B tells prospective advisors that you know what you are getting into, and that you are unlikely to have second thoughts once immersed in the PhD.
Make sure not to say things like "I hated field A", because they make you sound like a teenager complaining about a flavor of ice cream. Nothing wrong with saying that you prefer one field over another: everyone does.
Also beware that a PhD can require a lot of sustained, unsupervised work, so if you are looking for a lot of supervision, prospective advisors might see it as requiring lots of hand holding, and that's always seen as a negative.

Thanks for the reply!  Yes I understand  now that saying hate etc looks bad. I am really looking forward to do the unsupervised work but only in the domain of my interest. Reading these comments I understand that I have a lot of work to do still to become more self dependant in research. Regarding the supervision thing, I was under a PhD and exxpected to be given an initial compass, a little help and was left from the first day, I don't know much about that ask others...


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Can I study remotely in a USA university as a foreigner (Covid-19)? What are the prerequisites?
I thought because of COVID-19 and remote education plans, maybe some universities are providing a remote plan for international students. My goal is a PhD in machine learning, maybe I can start as a remote student and afterwards (after the pandemic) maybe immigrate to USA and complete the studies. The question is are there universities that are providing these kind of remote plans? If yes, what are the conditions?

Sorry, but this seems to be a "shopping question". I think what you look for would be rare and you would need to ask a few universities specifically about their policies. I doubt that many would consider this to be an ideal plan. Most US doctoral programs start with course work and most universities are wanting to go back to face to face instruction. But you might find something. "Going remote" after passing comprehensive exams might be viable, but less so to start out.

@Buffy Well, I know that my university in Australia allows for remote learning by international students for its coursework Master's Degree. Not sure about PhDs, though I do know they require a completed Master's Degree for admission into the PhD program.  It seems plausible that at least some universities would allow for the coursework portion of a 5-year PhD to be completed remotely.


text:
Is it appropriate to ask for an opinion about a preprint from researchers I don't personally know before submission?
I'm writing a paper as a Ph.D. student, and I'm starting to feel a little bit unsure about the general approach and results. My supervisor isn't a great help here, and I thought to maybe send a preprint to a couple of authors with more expertise than me, whom I cited a lot, and ask their opinion and if they would find it of interest.
Is this appropriate? I wonder if it would look like I ask them to work as my reviewer or supervisor for free, or I would even look like one of these crazy persons sending researchers their huge manuscripts with fringe theories. On the other hand, I would get feedback during peer review anyway, so I'm further unsure about it.

In my field (mathematics) it is somewhat common to send out preprints like this, especially for junior researchers like yourself.
In my experience, the most common way is to send a copy of the paper as an attachment, briefly introduce yourself and the paper, and say something like "I would welcome any comments if you have any. Thank you very much."
In particular I would not recommend asking questions, at least not in an initial email. I would especially avoid questions such as "would you find this of interest", which can be very awkward to answer. As you said, you want to avoid looking like you're asking them to serve as a reviewer or supervisor.
That said, in my opinion, sending a paper and indicating that you'd welcome feedback is a perfectly fine thing to do. I've got some interesting feedback this way as a grad student, and more recently I've responded to similar emails coming from students.
Good luck!

How long would you recommend a person should wait for a response from the person they emailed until contacting the person again?

@A-LevelStudent infinitely long. If they answer your original email, great, if they don't, do not insist.

@MarcGlisse Thanks. What if they agree to take a look at it, you email it to them and then they don't get back to you?

@A-LevelStudent If they promise to "take a look at it", you generally shouldn't write again until/unless they respond. If they promise something more specific, then depending on the circumstances it may be okay.

@MorganRodgers Goodness, I was completely unaware of that, thank you!

@MorganRodgers Six months is a very long time ... I could have gotten the paper reviewed and published in that time ...

You can do this, but a blind email with a large attachment isn't the way to do it. Instead, you could send an introductory email, introducing yourself and briefly describing your work, perhaps with any notable contributions/results. Then ask them if they would be willing to give you feedback on the paper itself.
Don't neglect to tell them the length and any time constraints you might have.
Even better if this intro email is from your advisor. Or, if that is impossible, copying your advisor (with permission) on the mail. It is harder to turn down a request from a colleague/peer than from a student.
But, in addition to getting feedback it is a way to expand your circle of contacts which can be valuable in the future.

If you are suggesting to omit the PDF in the first email, that looks like a bad idea to me. If I receive a PDF (or a link to a PDF, preferably on arxiv or some other server where you are unlikely to have access to the logs), I may take a quick look at it, which may motivate me to give feedback. If I receive a request to blindly commit to spend time giving feedback about a paper I can't take a look at first, I am very likely to ignore it.

I think the third paragraph is quite important: your advisor may help the OP by sending the first rounds of emails, and their style may be better. An introduction by a better known academic can also help the email not fall through the cracks. The OP can then learn from the first few iterations, and later in the final years do this themselves.

If the author you send it to is close enough that you cite her/his work, then it might be ok. Make sure that the person is still active in the area.
If your field puts papers on arxiv, sending a link after putting it there is ok (but also, I have gotten emails where the intention is to put it on arxiv in the upcoming week).

It might be field dependent. To me, the most critical aspect isn't the reaction of the contacted expert but rather that of your supervisor.
Sending your ms out without knowledge on the part of your supervisor seems a bit uncommon.
Obviously all this depends on the "supervising style" of your supervisor and eventually on the relationship between groups etc.
This is to say that you should frankly discuss your idea with your supervisor instead of asking here, because we don't know the scenario and its details.


text:
How do I deal with colleagues/advisers who aren't responsive to e-mails?
I've had some frustrating situations with a colleague who will say that they will do something but then never do it. Is there a way to "encourage" them to respond more promptly? I take it as a sign of incompetence. I do sometimes follow up with a reminder but this colleague is not somebody I can rely on.

Try knocking on their office door (when in the office), calling their phone (when working remotely), or just stop relying on the colleague, work with someone else

I suspect the only real way to deal with this is get used to it. The majority of senior people in academia are unresponsive. If its really important, then as user2768 says go knock on their door, or call their phone, and wait with them til the thing you want done is done. But it had better genuinely be that important.

Colleague or advisor? Makes a big difference.

@henning: former PhD adviser (I got my PhD but I still need to talk to this person)

I don't think this question is specific to academia. The world is full of people who are difficult to work with.


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Keeping the same supervisor/thesis topic upon transferring to MSc
I am currently a second year PhD student going on to a third year. I have made the decision to transfer my candidature to masters instead. I would like to ask the following:

Do people usually switch advisors/thesis topics upon transferring from PhD to masters? As with many stories shared here, I too, am losing interest in my current research area (which is one of the main reasons of me deciding to drop to masters degree).

But for those who decided to change their advisors/ topics, what are your reasons behind doing so? I am open to learning new areas but the maximum duration of candidature for masters in my university is up to 3 years. So I only have a year left to write my masters thesis. I will have to spend a lot of extra time and effort into reading up on a new area if I do decide to switch.

Even if one decides to continue doing the current topic they are on, how vastly different is the aim of your master thesis as compared to say the initial goal of your PhD research? Most PhD research topics aim to resolve some open research problems. However, when one decides to transfer to master, they may not have the time or resources to give a positive answer to the problem at the end. In such cases, how would one change the approach to writing their thesis?

I am asking this because while I have made some progress on my reading and research with my supervisor, I feel that I will not be able to provide a full positive solution to my current topic at the end of the year. Granted, I could probably press on with my current topic and just write whatever progress I have and call it my masters thesis.
I would to love to hear your inputs and comments. Thank you!


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Is it a good idea to apply for another position at the same university while awaiting tenure review?
I am a faculty member in the Science School. I have recently submitted my materials for a tenure review. During this waiting period, I've become aware of an attractive position opening in the Business School for a role, which I believe aligns well with my skills and interests. The potential salary increase is also quite substantial.
My dilemma arises from the overlapping timelines of the tenure review process and the application for the new position. Both processes, if pursued, would eventually reach the desk of the same decision-makers, including the Provost and the University President, almost simultaneously. I am concerned about the implications this might have on my tenure review.
Is there a risk that my tenure application might be jeopardized if I apply for the other position? How is such a situation perceived in academia, especially when one is applying for a position within the same institution but in a different department?

This is an extremely thorny issue, complicated further by the fact that you will very likely know people on the hiring committee for the other open position. It may be worth pursuing a joint position over switching colleges, risking having your tenure revoked or tenure process halted, and not getting the other position with a tenure clock started at 0.

@CameronWilliams That's an answer.

Okay, I'll convert it into one. It seemed more like thoughts than actual advice.

If your user name is your real name, you should probably change it to something anonymous, given the private-decision-making nature of the question.

This is an extremely thorny issue, complicated further by the fact that you will very likely know people on the hiring committee for the other open position. It may be worth pursuing a joint position over switching colleges, risking having your tenure revoked or tenure process halted, and not getting the other position with a tenure clock started at 0.

"Revoking" tenure, once granted, would be entirely improper in such a situation. Restarting the clock at 0 is, in my experience, unlikely, but some probationary period would be typical.

Applying for the different job at the university makes sense if you would be willing to give up tenure (that you do not yet have) for the new position. Someone in a decision making role would appreciate that the new position is much better remunerated and more prestigious. The department at this point has probably already voted (it is November) and they and maybe the dean are the only one who would feel bad if you jump ship to another school at the same university.
If you were to not get tenured, then the reasons for this decision would probably prejudice against your new appointment as well, but you would not loose by applying.
As always, local conditions and culture might make this bad advice. If you have a mentor in the department or in the dean's office, talk to them. Maybe you can even talk to the dean, but remember, that deans are sometimes prevented from telling you the truth.


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Consequences of publishing work using text from millions of Sci-Hub articles
I have a project that involves large-scale text embedding of biological literature. In this case, each biology article would be given a set of numbers (embedding) based on the text in the article. We would then analyze these embeddings exclusively.
Ideally I would use full-text articles rather than being limited to abstracts. However, only a small subset of PubMed has full text freely available (PubMed Central). I have found that I can access and torrent millions of full-text PubMed articles through Sci-Hub.
What are the potential implications of using these Sci-Hub articles when it comes to publishing my work? Would this be considered a major red flag by the journal editor (especially from larger, older journals, e.g. Cell, Nature, Science)? Is it even necessary to specify where I got the full-text articles from, barring a peer reviewer requesting it?

One option would be to do your initial studies with whatever material you can easily obtain, and then negotiate some kind of arrangement with e.g. PubMed for research purposes before the publication.

What exactly are you doing with the articles? How much information from each processed article is retained in the final result?

Have you considered trying the analysis with just the abstracts? It is likely that, unless your embedding dimension is extremely large, you are going to get similar results with abstract-based embedding. The whole dataset of fulltexts is going to be colossal

https://twitter.com/sgrodriques/status/1733193844110557432

It is standard practice to detail in the methods of a paper how any large literature review was undertaken. Often people specify the search terms they used and the database they accessed. In your case I don't see how you can avoid specifying the sources of your papers.
Since Sci-Hub exists almost in protest to most major publishers, it is unlikely any of them would publish work based on exploiting it as a resource. If there are independent journals in your field who are taking an ethical stance on publishing then perhaps they would consider it. There are some journals run entirely by academics who are probably much more sympathetic.

-1 since Since Sci-Hub exists almost in protest to most major publishers, it is unlikely any of them would publish work based on exploiting it as a resource is not true, there are many pure OA publishers, although I am not sure any of them would publish work based on illegally acquired data.

@DanielHatton I was thinking more "we used search term X and Y in Scopus which returned 371 results. These are the papers we've used as the basis for our review". As far as I can tell the rough equivalent here would be "we scraped all of biology SciHub to get the papers we review here".

it is unlikely any of them would publish work based on exploiting it as a resource. - since the only way the "publishers" are involved in the publishing process is collecting money, they will not even know such a paper has been submitted. The decision to accept is done by voluntary editorial board, which could not care less about publisher's political interests.

The data collection you describe probably violates copyright laws. The specific legality of downloading articles from SciHub depends on the jurisdiction and on other circumstances; e.g., personal use is legal, but scientific research is not in Switzerland, and your proposed scraping of millions of articles will probably rather fall in the latter category. Typically, no publisher will come after you for downloading a few articles, but you are proposing to download millions of articles, and then to advertise to the world what you did by publishing an article about it.
First, most publishers will not accept a paper based on questionable-to-illegal data collection. (You might be able to argue that your particular approach was indeed legal in your jurisdiction, but then things become hairy if the jurisdiction of the publisher is also relevant, and nobody really wants to get their legal team involved in the publishing decision.) Commercial publishers won't like it because you are... demonstrating your contempt for their business model. (I toyed with other metaphors.) And even if "nonstandard" publishers might like it, e.g., journals run entirely by open science aficionado academics whose philosophy and ethics this very much resonates with, if they have any sense at all, they will not publish something like your paper, because it opens them up to serious litigation. And they know full well that the commercial publishers will absolutely love having an opening like this to put them out of business, and at the same time send a clear message to all the other academics that might consider intruding on their turf.
Because, second, make no mistake: if you plan on doing something this (probably) illegal, and publishing a paper about it, then litigation may well be coming your way. There have been high profile cases about people breaking copyright in similar ways, and publishers have enough legal experts to drag you through courts for years. (Edit - Franck Dernoncourt asks the obvious follow-up question here: Has any researcher been sued for using Sci-Hub data in their research?) And at the same time, your internet service provider will get wind of this and may start litigating as well, because you very probably broke your service agreement in multiple ways. (Did you read all the fine print you accepted?) If you are doing this from a university account, the least that can happen is that your IT department could close your account, then you may be expelled if you are a student, and terminated if you are an employee.
If you write a paper that actually gets published and nobody reads, so the legal s***shorm does not arrive immediately, you are now living with a huge problem on your hands that could explode into your face at absolutely any time in the rest of your life. You do not know whether someone will dig this up in ten years and make your life miserable in the ways described above, even if the legal aspects are under a statute of limitations. You don't know how copyright laws and court decisions will develop in the coming decades, but doing something like this now is not a good starting point for the rest of your life.
And all of these may well happen even if you have a case that your method was legal in the first place. If your school expels you over this and you win a case against it in court in five years, then yes, you did win, but was the legal hassle worth it?

Sometimes civil disobedience is worth the risk.

Downvote reasons: Your unsupported claim that someone would get sued for this seems unlikely to me. People have publicly done this before; I don't know if they published in journals about it, but they have openly published it on the web and haven't been sued yet. You can find these projects by googling; they're still up. And your boldfaced instruction not to do this is opinion-based, condescending, and not responsive to the question as asked.

@GlennWillen: thank you for giving your reasons. I stand by my post.

I have not downvoted you and agree with most of what you say, but the statement at the very beginning ("Downloading articles from SciHub is illegal.") seems problematic. This likely depends on where you are.

Has any researcher been sued for using Sci-Hub data in their research?

@Glenn Willen "People have publicly done this before" People have, under their own name, written scientific papers analyzing millions of SciHub articles? If you don't want to link to them, can you at least tell us what to google for?

@Nick can you name a jurisdiction where downloading articles from SciHub is not illegal? I'm curious if any exist.

@Nick Is downloading articles from SciHub legal in some jurisdictions?

@Allure Switzerland, for instance.

@FedericoPoloni curiously, I remembered that question, and interpreted the answer as saying it is illegal, in particular: "Downloading a book or article from Sci-hub for scientific research is illegal".

@Allure And, a few lines above: "Downloading a book for personal use is legal", irrespective of the source. That answer makes many distinctions and subtle points; one of them is "for scientific research" vs. "for private use". In particular, though, the blanket statement in this answer "Downloading articles from SciHub is illegal" is false.

@FedericoPoloni Presumably we are interpreting the context differently. In the other perspective, the OP is not downloading articles for personal use; he/she is downloading papers for scientific research.

It would help to add qualifiers then, so that the ambiguity is resolved; for instance "downloading articles from Sci-Hub is illegal in some cases."

@FedericoPoloni: after the ongoing discussion, I have toned down my answer. I would still argue strongly against this whole idea, but you are right that the legal aspects are less clear-cut than I thought originally.

Is it even necessary to specify where I got the full-text articles from, barring a peer reviewer requesting it?

Authors are generally encouraged to give full details of their work, such that other researchers can duplicate them. So: yes.

What are the potential implications of using these Sci-Hub articles when it comes to publishing my work?

Opinions on Sci-Hub tend to be very polarizing, and there's a significant number of people who split both ways. Which means that if they ever find out you used Sci-Hub, some large number of people will strongly disapprove.
On the legal side, you might be liable for copyright infringement, although there are so many people using Sci-Hub that it's improbable you yourself will be sued.

Would this be considered a major red flag by the journal editor (especially from larger, older journals, e.g. Cell, Nature, Science)?

As mentioned, opinions on Sci-Hub tend to be very polarizing. For people who dislike Sci-Hub, this would surely be a major red flag and maybe sufficient for automatic desk rejection.
It's possible you'll hit sympathetic editors all the way and the paper ends up accepted, but it's still possible in this case that the publisher will override the editor and refuse to publish the paper. One might think reputable publishers never do this, but it's emphatically the case that they can and do, e.g.:

If the authors cannot pay the APC
If sanctions prohibit the publisher from publishing the paper

Similar legal objections could also apply to your paper (although this Law.SE question suggests that the journal would be in the legal clear, they might not want to take the risk, even if it is legal).

"On the legal side, you might be liable for copyright infringement, although there are so many people using Sci-Hub that it's improbable you yourself will be sued." Does that probability remain small even in cases where there exists an admission in writing of very large-scale infringement from a named author?

@Anyon don't remember where I read it, but I definitely read somewhere that the optics of a publisher suing researchers would look very bad for the publisher, so publishers are unlikely to do it.

@Allure that sounds like the opinion of a single person. It makes sense but is far from a guarantee. It may not apply so much to a large-scale infringement.

You are concerned with the wrong question, namely whether you have to disclose how you obtained these articles.
The question you should be asking is whether it is ethical and legal to use what Sci-Hub offers. Regardless of one's position on the commercial publishing model used in the sciences today, the legal answer is that these journals own the copyright to these articles, and that they make them available for a fee to universities and others willing to pay. Sci-Hub do not own the copyright, and violate copyright laws by making articles available for free. It is likely not legal (perhaps depending on the country you're in) to download all of these articles.
So what you propose is to use a data set you cannot legally own when downloaded from Sci-Hub. This is no different from analyzing the painting technique on a Picasso a friend of yours stole: It is certainly not ethical to attempt to publish data obtained from this data set. Whether you can conceal this fact from reviewers should not be your first thought.

"not ethical" - yes; "no different from stealing" - no; it is different. The word "stealing" does not really suit the situation (I know it is a popular term). The data remain available to other, legally paying users. This type of copyright violation is more like fare evasion. Getting a service without paying for it. The service does not disappear for others, but it gets a tad more expensive. That being said, it is not clear whether the prices charged for many journal articles based on free authorship/editorship/reviews by government-funded scientists should not be called highway robbery.

My previous comment notwithstanding, you are of course right that OP should ask the ethical question first and foremost.

@CaptainEmacs Fair point. I edited to say that you're publishing on a painting someone else stole. That's still unethical. As for highway robbery: I don't disagree. But that's a separate question. You're not allowed to steal from Elon Musk either, even though he's rich and perhaps unethically so.

This answer conflates ethical and legal. You separate them at the start and then conclude that because it's illegal it's also unethical. The two often do not overlap. Many would argue that SciHub is the ethical response to an unethical system. Assuming the OP is doing good science, they're even showing how that science wouldn't have been possible within the publishing industry's current boundaries.

@thosphor I would disagree on the overlap. I cannot think of cases where it is illegal to publish something (short of revealing national security secrets). But I can think of many research topics where the data was obtained illegally (say, by infecting people with syphilis) and where publishing the data would be unethical. Today, of course, IRBs would not give you ethical clearance for such experiments, and journals will not publish such papers because publishing without IRB approval is unethical.

As for whether the publishing system is unethical or not: I agree with you that it is not. But I do not think that scientists should mete out vigilante justice.

Just because something is “illegal”, not necessarily “unethical”. OP may break a contract term, but not all contracts are automatically fair or moral. Also, text analysis and scrapping is kind of forbidden even when one is subscribed to a journal, so the publisher is not missing any fees if someone scrapes SciHub version of papers.

@WolfgangBangerth Breaking criminal law may be vigilantism, but breaking civil contract law is not. Also, researchers are enablers and one of the main cause of the deeply flowed publishing system, and it is questionable if following the present practices itself is any more moral behavior.

@WolfgangBangerth Of course there are many areas where the law and ethics overlap. But that doesn't mean they are equivalent. There are many areas where they don't overlap. Obviously ethics are up to debate, but I don't think anyone would argue that ethics follow from legality. Your example of national security secrets illustrates my point: whistleblowing laws are necessary to prevent the law being used to suppress ethical behaviour.

In a country with a highly repressive, punitive and undemocratic system of government, basic research into topics considered forbidden may be illegal. That doesn't make conducting and even publishing such research unethical. The copyright laws in the United States are highly repressive, punitive and undemocratic...draw your own conclusions.

"But I can think of many research topics where the data was obtained illegally (say, by infecting people with syphilis)" Are you under the impression that actually happened?

Folks, all I'm trying to say is that there is an ethical question to answer that is bigger than the question "Am I going to get caught".

Maybe a better analogy is "entering a museum without paying the ticket, and analyzing the painting techniques on the Picasso in it".

This is true. But the "fruit of a poisoned tree" doctrine doesn't necessarily apply here. AI LLM are trained on content not legally available for reproduction, yet courts have ruled that their output is copyright-free, rather than copyright-infringing. If OP's project is similarly transformative, that may apply.

What are the potential implications of using these Sci-Hub articles when it comes to publishing my work?

The most important implication is that you are contributing to science by using one of the best datasets for scientific text mining. While this may cause the paper to be rejected by many venues, the goal of a researcher is to contribute to scientific progress. You can still upload the paper to arXiv or similar venues.

Is it even necessary to specify where I got the full-text articles from, barring a peer reviewer requesting it?

No. What matters is describing the dataset. The way you obtained doesn't have to be disclosed if you think this may cause issues.
When you publish your article, please consider thanking Alexandra Elbakyan in the acknowledgement section, as Nemo reports it is increasingly common.

Some of the answers seem to assume that you don't have any legal access to the papers and your only motive for using sh is to acquire them. This baffles me: if you have a university affiliation, you most likely have access to most of all of them through your uni library.
So while I'm not an expert in law, I don't think technically you're stealing something you already have access to and your library has paid for. The premise of stealing is that you are using something without paying that you should have/would have and the seller loses money because of this. But in your case it's already paid for by your employer (university). Unless you are unemployed and without access to a library that offers the papers. In such a case it is baffling to consider using sci hub unethical but maybe that's just me...
By the way, the usual practice in such cases or cases of lack of access is to email the authors and ask for the paper. Is that unethical? Who here hasn't done it? Everyone I've known has been on both ends of these emails. We're then all criminals and bad people for not telling our colleagues to spend the 40bucks and buy the article from the publisher, of which we as authors get of course 0 royalty because we (and the reviewers) donated our labor to benefit multi billion corporations lol.
Anyway, in the end you have simply chosen to access the information you anyway have access to in a way that's more convenient to you. There's no material loss to the publisher.
I guess alternatively you could ask your library to do that for you and prepare/deliver you a package of the papers you need.
Nor should reporting some consolidated data based on an idiosyncratic numeric ratings of these papers be illegal. If that doesn't fly then how do systematic reviews, which disclose much more data from the individual studies?!?
Finally, I've never heard of a requirement to disclose how you accessed the papers you used. This sounds even more baffling than the rest. Do I have to say "these 20 were OA, these 10 were preprints, these 5 were through interlibrary loan, these 30 were through the library and these 10 I emailed the authors". I've never seen a paper reporting such info but who knows maybe it's different in biology!?! Are you then supposed to attach also the library receipt and the emails from colleagues as evidence?
On a final note, sounds like preparing the bibliography for your paper is going to be a pain in the derriere  that alone would make the feasibility of the study questionable

"So while I'm not an expert in law, I don't think technically you're stealing something you already have access to and your library has paid for" Incorrect. ToS may prevent anything beyond regular reading. There are special licenses for text mining e.g. see the Elsevier Text and Data Mining (TDM) License. "On a final note, sounds like preparing the bibliography for your paper is going to be a pain in the derriere": you have no idea what OP meant by embeddings and/or are unfamiliar with AI publications.

If your search terms are for the articles on pubmed, how you got the full text doesn't matter at all. All that matters is how you found the articles with your search terms with respect to what you would report. No need to mention sci-hub as such in this context.


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Being in "1 Reviewer(s) invited" state for 4 months, What should I do?
I have submitted an article in a math journal, the status has remained at "1 Reviewer(s) invited" for the past 4 months. In an attempt to understand the reasons behind this delay and seek an update, I reached out to the journal's editorial team. Their response was as follows:
"We have received your submission in good order. It has been assigned to an Editor who has invited reviewers. You are able to follow the status of your manuscript from your author dashboard."
This response didn't answer my question or provide any assistance.
Is it recommended to wait further for the review process to complete? What are the steps I can take?

Does this answer your question? What does the typical workflow of a journal look like? How should I interpret a particular submission status? see "Peer review" section of the answer

Also see this question
https://academia.stackexchange.com/questions/88355/is-my-paper-under-review-or-similar-for-too-long-and-if-yes-how-should-i-reac

Additional details which may be needed: could you give more details on the subject you are working on/type of paper you submitted/the type of journal.

@JackRed I am working on Nevanlinna theory (value distribution theory) and have submitted my article to the Mediterranean Journal of Mathematics


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Master thesis opportunities in High Energy Physics in Germany for Indian/International Students
My final year will start in coming August, and our department allows us to go anywhere in the world for an MSc thesis. I wish to do a one-year (min. 8 months) thesis in Germany in high energy physics theory with a stipend. The maximum I can afford is a visa and a plane ticket. I don't know where to apply and where my chances are high to get selected. I've tried contacting professors here, in India, but positive replies were 4%, and I could not contact those under whom I really wish to do my thesis.
Is there a way to get selected for reputed institutes in Germany with a stipend? My Gate rank is under 150, and my grade point average is also under the top 5 in the class. Any suggestions would be greatly appreciated.

The stipend is going to be the critical point here. You might want to put that into the title, as it is absolutely not the standard for MSc in Germany.

Supervising MA students is work. The university hires a professor to do that work for students enrolled in that university. This makes sense: the university only gets money from/for its own students. This is what all the bureaucracy around exchange programmes is all about. Exchange agreements between universities look something like: university A promises to take care of x students from university B if university B also takes care of x students from university A.
Some governments also reserve some money for students who want to participate but come from a university that is not attractive enough to sign such an exchange agreement.
So, your first step is to figure out if your university or country has signed exchange agreements. If not you can look for aid. In Germany a big part is organized through the DAAD.


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Risking declining a postdoc offer for a potentially better one
I have an offer of a good postdoc that I have until the end of tomorrow to accept or decline. It's a 2 year post at a decent UK institution, working on interesting applied interdisciplinary work. I know some people involved -- the PI and people they've worked with, and the previous research fellow who had the job is a friend (and I'd be working a % with them).
On the other hand, I have applied for another postdoc at a more exciting EU institution, doing more exciting theoretical work that is a very natural extension of my PhD. The PI there has commended my work, added an article of mine to the project's pre-launch bibliography, and said in a phonecall that I could be optimistic of my chances, based on my application. They also asked me not to accept the other one(!). The deadline for this is end October, so interviews would only take place in November. I also don't have any personal connections with the PI or other researchers (although I know the literature of course). The project starts next year, so the group is being built from scratch.
My dilemma is this: do I take the safe, good option, which is guaranteed but which involves an overlap with the PhD timeline, or do I risk "reaching for the stars" with the more exciting option which, because of its high profile, is likely to attract applications that may in the end be better than mine? If I decline the first one, but the applications for the second are stellar, I might end up with nothing.
My gut tells me to reach for the stars. But my wallet, in the months since my scholarship ended, says otherwise. I'm really torn!
Edit: some more detail -- the UK position is in a generic English midlands city that I am not inspired by at all, while the EU position is in a capital (indeed, the capital), and has a lot of draw because of that. I can't deny that the location is a big factor for me, not least because of Brexit.
Outcome: In the end I declined it to go with my gut instinct, which is to try for the other one. Time will tell if that was the right choice -- I may come out with neither, but for whatever reason that prospect doesn't frighten me (I will find something ultimately).
Outcome v2: I was offered the more exciting postdoc and will start there in 2019, so my instinct was correct

I should clarify -- the suggestion was for me not to accept yet, i.e. delay my response so I can interview for the second one, although in reality it seems unlikely an institution would realistically wait a period of a month for my answer. So perhaps they're in effect the same thing!

"A bird in the hand is worth two in the bush" so take your decision and live with it...

You may ask if you can defer the offer for one year, if the postdoc offer is an one year offer. That's common in us

When does the offered postdoc start?

Accept the "good postdoc" position, get paid whilst you finish your PhD (during evenings/at weekends) and benefit from the position. Apply for the "reaching for the stars" postdoc. Should you be successful, quit the "good postdoc," optionally after negotiating a delayed start date to allow more time in that position.

The OP has declined their other, so this answer is for other readers.

I'm not sure that taking the first position as a stop-gap is the right choice. Aside from the moral aspects, the OP would also be potentially burning bridges with people in their field.

@JamesWilson Why do you think that?


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Hypothesis formulation
Can hypothesis for doctoral dissertation be formulated as "to demonstrate that approach X can be used effeciently/successfully to model Y"?
I'm trying to use novel approach X that has been rarely used in my field to model Y in my country where X has not been used at all.
The problem is I don't have anything to compare it with Y to validate my results. I can only compare Y with Z which has been modeled using different approach and aggregates several other factors that are not the subject of my research. They are not directly comparable but both Y and Z should have similar trend. Nevertheless, I will compare these two to check external validity of my results.
In addition, there are some previous predictions about Y which I will also use for testing/proving validity of my results.

Sure, why not?  But maybe you could be a little clearer about what you're actually asking...

What does your adviser say?

@jakebeal I have edited my question. Hopefully it's a little bit clearer now.

@Cape Code I will talk to my advisor after I make a draft version of the hypothesis.

Are you saying that you are modelling something that is unobservable and untestable? And therefore you've got no way to validate the model?

@EnergyNumbers Yes, you could say that.

Are you required to write down a specific, formal hypothesis by your departmental or university dissertation requirements? Much of science is done without this level of formalism. If you are required to do such a thing, it might be better to write something like:

Using approach X to model Y will lead to quantifiable improvement in Z.

Where Z is the error in approximation, efficiency of the method, or some other quantifiable measure of the performance of the approach. You probably don't need to know what level of improvement will obtained before you start the work, but you're better off stating a quantifiable improvement in some specific aspect rather than a vague statement that X is better for modeling Y.

Thanky you for your help. However, I don't think I will be able to use something like Z. Please see my edited question.


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What is baseline funding?
What is baseline funding in academia? What does it mean for professors to have individual baselines and where does the money come from?
Edit:
My professor says he is paying for my travelling expenses from his baseline. I am doing undergraduate research under his supervision. This is in the Middle East.

Would you please provide more context? Baseline funding for whom and what? Graduate student? Postdoc? Tenured Track professor? Research? Non-research activity?

Funding differs hugely from country to country, so for what country do you want to know this?

Why don't you ask him?

While the details and availability vary radically from institution to institution, some professors are given a certain budget to spend on whatever they deem appropriate (within limits).
In the United States, this is most commonly associated with more senior positions (e.g., endowed chairs). It is typically not a very large amount, but often enough to support some travel or undergraduate researchers.
In other countries, it may be structured differently.  In particular, I have heard that some universities in the Middle East have been giving extremely attractive funding packages to professors as part of their program to attract foreign talent.  My guess is that this may be the case with your professor, though it is impossible to know for certain without more information.


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What if a call for application does not mention a letter of motivation?
I will apply for a fixed-term position (max. 6 years contract) at a German university and the part on the necessary documents and information that should be send to the university reads as following:

Please send all required documents (curriculum vitae, copies of
certificates, lists of publications and courses taught, details of
third-party funding and cooperation arrangements; also include
teaching evaluations and plans for future teaching and research) along
with a completed application form (see link above)

Hence, it does not mention a letter of motivation. The 'completed application form' is basically a short CV.
Now, I am wondering whether such a letter might not be even necessary, but because I am not very experienced with such applications, I was wondering whether others have seen similar job application descriptions or experiences with such (unmentioned) requirements.

Likely you should say something about motivation in your plans for future teaching and research. It would be pretty natural there.

What Buffy says. I never got what you would write into such a separate letter of motivation anyway. Nobody wants to read your well thought-out version of the story about why you wanted to become a professor ever since you were ten. And your current motivation is much better shown along with the details of your plans, a separate letter calls for redundancy.

Can you please [edit] your question to clarify what kind of position you are applying to? Also, does fixed position mean permanent position (there are not many such positions below professor) or fixed-term position (though I do not think it matters that much for this question)?

Required documents vary widely by position even within fields.

Plans for future teaching and research can be quite personal and informative. As a commission member I'd be far more interested in what the applicant is planning to do than what their "motivation" is. I tend to find motivation letters rather pointless when it comes to assessing the applicant. So I'd assume that if they don't explicitly ask for a motivation letter, they think that they can well do without.

Most likely you merely need to provide exactly what is mentioned in the published application requirements, but if in doubt, ask. When asking, just be polite and make it clear that you've already read all the rules but still feel that something might not be mentioned there. Then, unless you are dealing with some really evil minded secretary, you'll quickly receive a response eliminating all doubts. Also think of everything you want to clarify before sending your inquiry so that the person on the other end will not have to engage into a long e-mail exchange with you.

Provide what is asked for. Adding additional documents won't help much as they are hard to evaluate and integrate into a process when not required. If you have a cover letter to accompany your application and it isn't too space limited you could give a very short version of something like a Statement of Purpose within it, saying a bit about long term goals and how the position would contribute to that.
And, as I wrote in a comment, your "plans" documents can contribute a few positive ideas as well, especially if they don't have rigid space limitations.
It is a matter of how you organize the important messages you wish to convey.


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Attitudes towards External/ Political Motivations for Technical PhD
How would potential research advisors view someone entering graduate school because of interest in particular "real-world" problems, with the ultimate hope of leaving or changing fields if these particular issues are resolved?
I can come up with a few examples. Perhaps someone is very passionate about a particular disease for personal or family reasons, and 15-20 years later therapies have progressed to the extent that they feel the problem no longer needs their attention. Maybe someone is passionate about climate change, environmental protection or missile defense because of the challenges of their hometown, and 20 years later political circumstances change (e.g., in the last case, the Cold War ends) such that they no longer feel these issues threaten their communities.
This model of thinking about one's career, "If society is successful the problem will be solved and we can all quit our job" contrasts the life-long academic model. At the same time, I feel that's how many people are motivated to enter research, not from the perspective of "I'm interested in X technology" but "I want to help solve Y problem".
My concern is, if I interview with potential future advisors with this kind of story, even if the political problem I'm focused on has a long, 1-2 decades timeline for resolution, a future advisor might find this kind of attitude "disloyal" to a field. When advisors ask about my interests, I feel that they're looking for a response that describes intrinsic academic interest in a topic, "I think X is really interesting", rather than a framing of research as "I'm concerned about Y political problem that you might not necessarily care about or may even disagree with, it's unlikely to go away in a 10 year time-frame, and I think getting a PhD in Z is the best way for me help my community in working through this problem". Especially for a pure-academic, "I'm primarily motivated by recent, specific political circumstances" may not sound very dedicated coming from a student entering a new field for them, even if all signs point to this problem staying around for decades. And for certain issues, like defense/ security, advisors may object to training students with this motivation because of their ethical views.
What concerns would such an advisor have, and how can I respond to them?
I'm in a technical field, for reference, but am interested in answers oriented towards humanities-oriented fields as well.

You’re overthinking. While a noble consideration, there are plenty of challenges getting an academic position in the first place, no need to put yourself at further disadvantage.