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Publishing funding issues and collaboration after PhD graduation
I managed to graduate out of a PhD program in Computer Science. But I had horrible experience with my former advisor. In addition to my dissertation related research works, I had some ideas and preliminary results with unfinished writeups. I'm now working in industry and have some free time after work and I want to continue working on them. Absolutely don't want to work with my former advisor again. I know there are significant fees to publish on a ACM/IEEE conference, e.g., registration, publishing, travelling, etc. While I cannot afford this due to financial reasons and my current employer won't support this. I've thought about two ways:

Try to find professors/researchers in other universities/institutes in my direction and collaborate with them. If the work gets accepted from a conference, is it possible to seek financial assistance from them? Are they willing to pay the fees out of their fundings to support this (assuming I'm the first author)?
Try to publish it to journals (I never published anything on journals), do ACM/IEEE journals have lesser fees? Do they have other means of supports for folks in industry?
Any other suggestions?

Seems more likely that a university partner would expect someone employed in industry to support their own travel.

@JonCuster hmm... Maybe finding an industry lab to collaborate is a better idea?

Universities could potentially support it.  It depends on the relationship.  I have PI who routinely asks me to pay for travel for all sorts of people.  But this PI does it based on relationships to these people -- they are never strangers.

@yourfriendlyresearchadmin Sounds reasonable if they established relationships. Your experience and comment give me hope :)

ACM does not charge fees to publish in their journals other than Open Access, which does require funding from authors.
I doubt that other academic contributors can contribute to your attending conferences, but they can probably cover their own participation if you are willing to have them as presenters. I see no problem with this myself and have often deferred to others.
For some, but not likely for you, conferences will defer fees. This is mostly for students and for those at small, non research, institutions not able to pay. But travel and accommodation still needs too be covered unless, just by luck, a conference is near you.
Conferences are, however, the main venue for CS publication.
The IEEE policies are similar to those of ACM, also.

Maybe journal first paper and then go to a conference could be a better idea?


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When is a math diploma thesis seriously publishable?
When is a diploma thesis in mathematics (bachelor or master thesis) actually considered good enough for a supervisor to propose publishing it in a journal? In some universities (e.g., ETH), this appears to be a prerequisite to obtain an excellent grade. What does one have to do to achieve this? Is proving a new theorem or anything equivalent necessary?
Most math theses at the bachelor or master level contain results that are already known. Therefore, there might be no point in publishing them in an academic journal I think.

Some theses, especially at the undergraduate level, are expository on existing theory rather than new contributions. There are some venues that would publish such things but they need to be at a high standard.
It is difficult for students at both the undergraduate and masters level to do research resulting in true advances, partly, at least, due to the constrained timelines for such things. It is even difficult for most students to gain sufficient insight into a small area of a field to be able to begin such explorations. Some achieve it, with the help of a good advisor and a lot of work. And some advisors are better at suggesting appropriate problems than others are.
But for research in math, as in other fields to be publishable it has to be both novel and correct. "Novel" means that it makes a valuable contribution to the literature. This is judged by reviewers and editors, however, and is known only after review. Your advisor can likely judge if what you produce is something ready for submission.
But a literal answer to your headline question is that it is "publishable" when the editor says it is publishable.

Essentially seconding @Buffy's answer: it's not easy, and not typical, for undergrad (or Master's) theses (at least in the U.S., where I've observed) to be publishable in serious journals.
Why? Well, for most even-high-end students, they've still not had enough time to really catch up to the state-of-the-art, to begin with. Further, surely it's not reasonable for absolute novices to somehow depend upon succeeding at things that much more senior people had failed to do (and would have wanted). Yes, an expert advisor can help in subtle choices of projects... and in doing the non-obvious things that might make them work ... but, still, this can't be cranked out as though on an assembly line.
(... let's not talk about increased commodification by "higher" administration...)

Ah, well, the downvote is either a random cranky one, or blaming the weather reporter for the weather... Yes, as has been discussed here before, there is an irrational inflation of apparent expectations... (which cannot literally be met, no).

Don't know about the downvote either (I upvoted). One thing that might be somewhat open to discussion, though, is the line "succeeding at things that much more senior people had failed to do", I guess. I think quite a significant fraction of the mathematical results that are published do not really prove something that others tried to prove before and failed - rather, the authors simply consider questions which nobody has (seriously) tried before, yet. This seems to be one way how, sometimes, an undergraduate student can get a result from their thesis published.

@JochenGlueck, yes, indeed, "questions which nobody has (seriously) tried before"... Still, although that criterion is good in a number of ways, it may also reflect the shallowness of the question. Hard to know...

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Question to professor one week before an exam (as a mathematician)
Assume you took a math class at the university and didn't ask any questions during the lectures. Now, during the semester break, when your exam is also taking place, you are studying from a script that the professor gradually wrote during the lectures. You relied on this script and did not take many of your own notes, especially for a certain part of the script.
Now, you realize one week before the exam that you have a question about this specific part of the script. It's more a minor question about a definition. But it has significant implications for other aspects of the material.
Is it appropriate to ask the professor a question one week before the exam?
From the professor's perspective, it might give the impression that you weren't fully attentive during the lectures. Also he is a kind of a person that gets angry if you waste his time.

What’s more important to you, clarifying the point or your fear of making a poor impression?

You could, if concerned, begin with asking the TA or your fellow students, maybe they understand the point. If they cannot help, you have a good case to upgrade to the professor.

In principle, yes, unless you know the professor's character and know they are a unreasonable or choleric type.

Why are you calling your professor's notes a "script"?

@AgnishomChattopadhyay That's a term from continental Europe. Lectures tend to be very rigid there, with the professor basically reading from their notes.

If you are afraid to make a bad impression one week before the exam, then you have an opportunity to correct that impression one week later! Clarifying a definition you don't understand may help to correct it.

@knzhou "That's a term from continental Europe. Lectures tend to be very rigid there, with the professor basically reading from their notes." [citation needed]

@knzhou I don't know where you're from, what your experience is, or how you got to that conclusion. But I've taken and given lectures in various countries in continental europe, and have seen very few professors reading from their notes. The better lectures were the ones that were prepared well, but those were also the least likely to want to read anything during lectures. I've also never heard anyone refer to "scripts".

@AgnishomChattopadhyay: "script" is likely to be a mistranslation from another language. For instance, in German the word "Skript" is quite common, which is a short form of "Vorlesungsmanuskript", which is the German word for "lecture notes".

Is it appropriate to ask the professor a question I'm surprised that you would even ask this.  It's the professor's job to help his students, yes?  Certainly asking questions is appropriate!

@knzhou That's a rather negative way of putting things. Ideally (and also in my experience, in math) these are good lectures where in addition, the professor would write things in a self-contained way on the board (so you could copy what's written on the board, without having to follow every single word they say), and in addition ideally provide lecture notes which would be close to what is written on the board. I always found this extremely helpful as a student, as compared to professors who just talk and write random bits and pieces on the board, making it extremely challenging to follow.

Yes, it is appropriate to ask the professor a question one week before the exam.
Professors and other university teachers are very well aware that students often defer exam preparation until a few days/weeks before the exam. It is part of their job to support students in their learning journey beyond just the contact hours in the lecture theatres. University teachers expect emails in the days leading up to any exam and many set aside time specifically to address these questions.
Moreover, university studies in mathematics (and I assume this is true for the majority of other fields) are very much about guided self-study. Contact hours often form just a minority proportion of the time a student is expected to spend on any module. Nobody is expected to fully grasp all concepts from just being attentive during lectures. Therefore, questions that you develop during exam preparation will not suggest that you "weren't fully attentive during the lectures".

I would also add that from the professors perspective I would count 'a week before the exam' as a student with good time planning skills. The students who send you an email the evening before the exam and expect a long answer immediatly so they can study all night through are a lot more troublesome.

I’d add: However late you are, it is always reasonable to ask.  The difference if you ask last-minute is just that you shouldn’t count on receiving an answer in time.

Just to pile on -- the timetable is fine. Heck, when I was teaching (and younger, with no children), I would often stay up somewhat late (though not as late as my students) answering last-minute emails and so on to prep. Not that it was expected. I just feel like any study is better than no study and I'm happy to help. It's why I'm there, after all.
I wouldn't stay up late to do that anymore, but I wouldn't take offense if I got an email after I went to bed; just "oops, they missed the window." But maybe they could get help from another student or etc. I would take no offense.

Perhaps also add that you might be doing the professor a service by pointing out things in the lecture notes that are maybe not completely correct, or that can in the very least be improved. I'm always grateful for that kind of feedback.

From the professor's perspective, it might give the impression that you weren't fully attentive during the lectures.
You betcha! But most students are like that... Also, the issue is not really being attentive during the lectures, but keeping up during your prep time on the evenings between the lectures, if you catch my drift.
Also he is a kind of a person that gets angry if you waste his time.
Best make sure you formulate your question in a crisp, clear, and to-the-point way. (In fact, do your utmost best to locate your point of difficulty as precisely and clearly as possible. It is dollars to doughnuts you will have answered your own question by the time you are done.)

People can be fully attentive and still have follow-up questions when they actually start working with the material.

I'm not buying this either. When following a convoluted argument (such as a delicate proof of a non-trivial result) in real time (= in class), it is perfectly normal to just try and keep up with the general outline of the argument. And then later, when trying to check all the details at the painstaking snail pace, realize that there a few subtleties you missed out while the prof talked. Those may even be intended to be details left as exercises for the reader. I think it more likely that the professor would be delighted to learn that somebody goes through the material like that.

To add to the other answers: it's possible that even if you understand the material well, you will occasionally be faced with some subtle question that you cannot immediately resolve. I'm not a mathematician, but here's an example from physics. It's been many years since I studied Newton's 3rd law and conservation of momentum, and I'd certainly say I know both of those concepts well, yet when I first encountered that question I could not immediately pinpoint the answer. (And neither could several of my friends who are also familiar with high-school level physics.)
This kind of thing can also happen at research level. You write a paper, then when you read it again five years later you might think "Wait, what about this effect? Shouldn't we have included it in the analysis?" Maybe you should have, but perhaps you just didn't think about it at the time.
So yes: ask your professor. If you're concerned that the question is simple and you're just forgetting something, then ask your classmates first, and only ask your professor if none of them know either (per Captain Emacs in the comments).

In the big picture, there's a clear dichotomy: I can either admit my ignorance now, or I can do so one week from now.
Whatever harm may befall me by admitting my ignorance now will seemingly also befall me in one week, but it will also carry with it the lasting pain of poor exam scores. The poor scores might be averted if I fix things now, though.
I do not believe that a choleric professor will view a poor exam more charitably than a question asked very late.

This is the core of the question

Based on my own experience, I'd do it, but with care.
About 40 years ago I did exactly this with a question for an enginering electrical masters degree paper. It was only one question and I felt it was reasonable to ask, despite the short time before the exam. Maybe a week or so.
To my astonishment they reacted immensely negatively and did not answer the question. They said that I had had a long time to approach them and that doing so at the last moment was inappropriate. I was very surprised at their reaction, and, 40 years on still feel that it was unreasonable.
As it happened the exam had an "answer all questions" format and it happened to suit my knowledge and style very well. A co lecturer in the subject (later the professor when the other died suddenly) remarked to me subsequently that they were surprised at how well I had done. The professor never commented subsequently.

From the professor's perspective, it might give the impression that you weren't fully attentive during the lectures.

Also he is a kind of a person that gets angry if you waste his time.

Sounds to me like the kind of teacher who wants to be effective, so put their doubts to ease by beginning your interaction with something like "Thank you for your time this semester" and some form of "I really learned a lot" or "you really opened my eyes to A and B" or to some "new connection" you were able to make between previously seemingly disparate things.
Then, "As I was reviewing everything, I ran across this one definition; at first I had thought it was straightforward, but when I later looked closer and tried X and Y I realized I don't fully understand it."
And as others advice, quickly zero-in and focus on exactly the problem part:
"I still can't get from here to there, Somehow I'm missing something important here. Perhaps it's obvious, perhaps it's subtle. *Can you help me to connect the dots? I'd really appreciate it. I just can't rest until I can bridge this gap.

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Reading takes too long (as a mathematician)
Reading a script, a book or a paper in mathematics can sometimes be so time consuming.
Sometimes it takes me hours to read a single page, because something just makes no sense.
But I find reading mathematics without going into all the details very unsatisfying.
How normal is this and how do people doing research in math deal with this problem?
Do researchers also train their basic math knowledge to become more efficient in reading?

My unscientific sampling of mathematicians (myself included) suggests we read carefully fewer papers than we write.  It's common for grad students to read more, because they have to learn the subsubsubfield they are working in (but a PhD student who is focused on learning just enough to write one dissertation can often get away with reading just one paper), but many experienced mathematicians only read a paper if they are asked to referee it (which frequetly is a full week of work) or if they actually need the detailed techniques of the paper for their own research.

I will second @AlexanderWoo's comments, and add that, yes, it can take hours to read a single page.  If I really need to grok a paper for some reason, I typically allocate 2-3 hours per page.  Sometimes I actually get through it faster than that, but that's the time I give myself.  And you should read with both a pen and scratch paper handy.

One approach: go for a general overview first, then use that to decide whether to make this paper one of the few that you actually read carefully.  This way you will have a general idea about a lot more papers than the ones you know inside-out.

Or what problem I also face is, that i.e. when making me a plan to read something, lets say one page in 2h or so, I get stuck on some point. At this point I think the best way to proceed is following the plan regardless and just making a note to come back to this problem later. But so often I don't do that and lose hours or sometimes a whole day, because of it. On the one hand this makes me understand the material thoroughly, but I feel I'm to unproductibe because of it.

@MackeyTopology I tend not to attempt to read papers straight through with the intention of understanding everything.  Typically, I start by reading the introduction, then skimming the main results (while ignoring the proofs).  If there are parts of the paper which I think are going to be useful, I'll go back and read those a lot more carefully.  For what it is worth, I think that there are three papers and one book chapter that I read very carefully while writing my PhD thesis.  My masters thesis was written after reading two papers very carefully.

http://ccr.sigcomm.org/online/files/p83-keshavA.pdf

My own experience is that if I just want to gain a basic understanding of a result, then I do not struggle to understand all the details of the paper. I read it much as a might a news story.
On the other hand, if I want to use the result, or use the approach in solving a different problem, then I'm tenacious, and sometimes very very slow. I am currently reading a paper where I have gotten stuck in my understanding half way through the second of 5 pages. It's been that way for a while despite my efforts. I understand the overall result; no problem there. But since I want to use the result and method in a piece of my own work, I really need to overcome the barrier that is confronting me ... and in my case, I suspect it will only be by enlisting the help of a colleague who can explain it to me.
Ultimately, I might have to read another paper that gives me sufficient background, before coming back to this one. I imagine, but have not evidence, that my approach is not unlike that of other people.


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Aerospace Research Paper
I am new to stack exchange so please forgive me if my question is against the guidelines. I am 16 yrs old, and am interested in rockets, jets and anything that flies really. Me and my friend wanted to study about the propulsion technologies used in our summer break. Basically just reading about the things and writing a "paper" about what we read. Although we are just doing it for fun, would this paper have any prospect of being published? (as it's not anything new it's just already known knowledge compiled for beginners)
It's about fuel types, types of engines etc.
Thank you :)

There are two (at least) interpretations of the word research.
Many people consider reading and studying a topic, using what is already known, to be (personal) research. This seems to be what you have done, along with writing up what you have learned.
However, with only minor exceptions, true research is an attempt to extend what is known to humanity and offer hypotheses about the unknown along with evidence that supports those hypotheses. This "exploration of the truly unknown" is what results in publishable research. So, in that sense, no, your work isn't publishable in a research journal.
However, there are a few venues, often supported by professional societies that do publish student work and, perhaps, even summative review of the known. You might see if some major society in physics or engineering (more likely) has such a publishing venue.
Not being publishable in a major research journal doesn't make your work any less valuable for your own development, of course.

thank you for taking the time, ill keep it in mind while writing the paper :)


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What should i do if my PhD supervisor move to another country in my third year?
My Ph.D. supervisor just informed me that he plans to move to another country after three months and I am still a Ph.D. student (not a candidate). What should I do? Is it wise to transfer to another university?

Did you ask your supervisor?

You have at least the following options:

Move along with your supervisor. This might involve getting accepted into their new university or (harder) keeping enrolled in your current one. There are also visa concerns and costs. Staying enrolled at the current university while living elsewhere also requires administrative action to enable it.

Choose a new supervisor at your current university, perhaps requiring a change in research direction.

Try to establish a co-supervisor situation with a new local supervisor and the one who is moving.

Move to a new university in your current country or another, possibly starting over.

Work remotely with the current supervisor. This is probably harder than it should be since the supervisor won't get "credit" at their new place so you might not get the help you need.

All of these involve tradeoffs of course.
Some people change universities at your stage (pre-candidacy). I did and it turned out to be a good decision.
But the first thing is to talk to your current advisor about the options. If they have a wide circle of collaborators, as some do, then they might be able to find you a place and a supervisor somewhere that will minimize the pain of a change.


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Questionable peer review practice in top-tier journal
I am a tenured professor of engineering at a major research university. Recently, I was asked to review a manuscript for a top-tier multidisciplinary scientific journal. The authors were all grad student or early career faculty, except for one who is a National Academy member (but neither first author nor last author), a well-known person in the field, and a close collaborator with the other authors and the handling editor.
The manuscript was of reasonable quality and worth publishing in a specialized journal. However, it had a couple of serious flaws that, in my opinion, made it unacceptable for a broad, high-impact journal. I legitimately felt as though I could not recommend it for acceptance, knowing that its publication in this journal would give it - and the flawed approach on which it is based - undue credibility.
The paper underwent three rounds of review. The other reviewer accepted after two rounds. I recommended rejection each time. Then the editor accepted the manuscript without even soliciting a third reviewer.
I think it is pretty obvious that the manuscript was accepted based on the reputation of the National Academy member (and their relationship with the editor), and not based on peer review. If peer review actually mattered here, then a third reviewer would have been asked or the paper would have been rejected. The fact that this did not happen makes it seem, to me at least, as though the outcome was decided before the reviewers even saw the manuscript.
So this leads to my questions.
First: Is my complaint legitimate? Is it a fair assessment that this journal seems to be using a "good ole boys" system for evaluation rather than taking reviewer reports seriously?
Second: If so, what should be done? How can I raise this concern with the journal without compromising my anonymity? What protections could I expect against retaliation from the authors, editor, or both?

https://academia.stackexchange.com/questions/135326/journal-published-a-paper-ignoring-my-objections-as-a-referee Closely related, maybe duplicate.

You are making a pretty strong assumption along with the accusation: "pretty obvious".

Related story from economics: https://statmodeling.stat.columbia.edu/2022/01/25/how-do-things-work-at-top-econ-journals-exactly-this-is-one-weird-ass-story/

"I think it is pretty obvious that the manuscript was accepted [..] not based on peer review." If so, then why did it undergo three rounds of review? Why not accept the paper after just one round?

"The manuscript was of reasonable quality and worth publishing in a specialized journal"
Enough said. The editor perceives its own journal as a publishing venue for specialized articels. It is up to them if 3 years down the line other journals will be " broad, high-impact" and their journal will just be a specialized venue... you do not have much to do with these strategic decisions.

@EarlGrey I disagree. If method A is inferior to method B because of fundamental flaws, but gets published in a top-ranking journal while method B does not, method A is given undue credibility.

Are we talking about PNAS?  This would fit with their reputation.

@mrp unless the top-ranking journal is on a downhill path because they keep on publishnig inferior methods ... "top-ranking" is not set in stone, if you are in the community, you know what really is top-ranking ...

@AnonymousPhysicist I had the exact same experience with a PNAS Invited Article indeed. Probably for good reason they discontinued this manuscript category.

This question just reeks with personal bias. There will never, EVER be a solid answer to these types of questions because it is impossible for the poster to give sensitive information required to accurately solve their problem. It also goes against the stackexchange philosophy since they are so vague for a specific problem. These questions should be flagged and closed.

I'm baffled at how the OP seems to think the paper is "worth publishing" (having novelty, relevance, no disqualifying things like serious methodological flaws etc.) but only "deserves" to be published in a lower-impact journal. The "good ol' boys club" is people like OP who are trying to deny less-senior researchers avenues for publication, not those researchers who collaborated with someone more senior supposedly as a means of getting published.

@Shidouuu It's not bias as much as inexperience and being wowed: OP doesn't know how PNAS's contribution system works (something that multiple people easily identified), and PNAS isn't top-tier, it's high-mid at best. (If you're going to blindly apply impact factors, it's 2/3 of Nature Communications and within 10% of something like Optica)

I only have one comment: in my opinion, any paper with one serious flaw is not publishable on any serious journal. Could you please explain why this seriously flawed paper is already good enough for a top field journal?

I can only speak from my own limited experience as an editor. Reviews are really just expert opinion. Just because a reviewer recommends rejection doesn't mean the editor has to act on it.
At some point, beyond a certain threshold, there is no "right" or "wrong". You can feel that there are significant issues with a paper. Someone else might disagree. It's up to the editor to decide what to do with that. Sure, inviting a third reviewer probably wouldn't hurt. But clearly at some point the editor decided that either A) your concerns were addressed or B) they were not actually as fatal as you believed. And so they didn't seek another review.
So while I suppose your complaint is legitimate in the sense that it is your opinion and no-one can tell you your opinion isn't legitimate, I wouldn't call it objectively fair. You really have no evidence that your report was ignored. There were 3 rounds of review - this is the opposite of not taking your reports seriously. And it is not obvious (to me at least) that the paper was accepted because of the reputation of an author when it should have been rejected.
Also, you're saying that maybe this would be better for a lower impact journal. But if the paper is as seriously flawed as you seem to think, it shouldn't be published anywhere. But if it isn't fatally flawed then we are right back to where we started - that it's okay for the editor to decide your concerns had been sufficiently addressed.
In any case, if you feel strongly that this paper slipped through the cracks, my only advice would be to find yourself a position as an editor so that you can make these decisions as you see fit. Going after the authors, journal, paper, or publisher at this point will not help anything. I suppose you could always write a letter to the editor detailing your concerns. These are not uncommon in my field, at least in the higher visibility journals. Though I would suspect that it would be tossed out since, essentially, an editor already decided that your concerns had been adequately addressed.

Agree with this. And, in the end, the paper should speak for itself.

If half the reviewers recommend rejection, and the editor accepts it anyway, what is the point of peer review? This "editor knows best" mentality is completely counter to the entire spirit and purpose of peer review.

@mrp The editor does not simply count votes, he/she reads the written opinions of the reviewers. So he/she might have just thought that the other reviewers had better arguments than you.

@justhalf In my experience, it is a rare occasion that a journal editor shows any sign of intelligent life.  It's worse than just counting votes.  I'm sure plenty of journal editors will reply to this comment disagreeing with me.  However, the journal editors on this site are not a representative sample of the ones I interact with, if you can count form letters as interaction.

"But if the paper is as seriously flawed as you seem to think, it shouldn't be published anywhere." This misinterprets the question.

@AnonymousPhysicist ok, point taken!

@justhalf It's not the first time I've seen this kind of thing. I've certainly been overruled before. This is just the most clear-cut time that I have seen it happen in a journal with such a strong reputation. The question has been brewing for many years.

@AnonymousPhysicist The question only makes sense in the first place if we assume that the paper is so fatally flawed that it could not have been accepted without nepotism/incompetence/whatever. But by the OP's own admission the paper would be okay for a lower impact journal. At that point, it sounds like a difference of opinion.

@sErISaNo You cannot know that without reading the journal's publication criteria.

@mrp thanks for the context that you are experiencing this multiple times and this is only based on what you consider a clear-cut case. (still, without details it's hard to judge whether this is a clear-cut case, as a top comment under your answer has said as well)

It's common practice in a lot of fields to publish rebuttals to other specific papers. E.g. "Comment on Spiderman et al.: Why two webs are better than one". The comment is also a peer reviewed paper in its own right, yet deals with highlighting perceived flaws in the original paper.
Science works best when discussions/progress happen out in the open so that the wider community learns what mistakes to avoid, or whether a widely-vaunted piece of work is actually flawed. Add your voice to the open conversation and publish your objections.

This does not address the issue in the question:  That the paper was published in the wrong kind of journal.

@AnonymousPhysicist what does it mean for it be to the "wrong kind of journal"? A specialized journal is specialized because they choose to accept specialized papers for publication, and vice versa for a broad journal. The journal's reputation is a reflection of the work that is published there, and not from decree of the Editor. If the editors start accepting specialized work to a purportedly broad journal, then perhaps the journal is not so broad after all.

@Jeff "The journal's reputation is a reflection of the work that is published there, and not from decree of the Editor."  I would expect the editor or publisher of an elitest journal would disagree with you.  They say the work published is good because they picked it.

Journals publish what they want, and they can be pretty corrupt institutions. The problem for science is that your work on the article is wasted, because the paper was not corrected, and your objections are not publicly available. One remedy is to do peer review only for journals that publish the reports, in which case you can usually remain anonymous. Or publish your objections in another venue, such as a blog or a preprint archive. Professional scientists should not retaliate again professionally written criticism.
First: You have no legitimate complaint against the journal. Dispelling your illusions on the fairness and usefulness of peer review is not an actionable offense. Making you work for no result is also fair game.
Second: Seek another venue for publishing your objections. Decline to review for that journal in the future.

This. If, after raising concerns in a review, the journal decides those concerns are not important enough for them, it makes me reconsider whether the journal is good enough for me. By reviewing for a journal, I contribute to the quality and legitimacy of that journal. If I think that my contributions are not valued enough, I'll just stop contributing to it in any way (reviewing or submitting). Granted, this is more for when I consider that the editor ignored a fatal flaw I highlight, rather than serious, but still publishable.

If we read through what you're saying the complaint isn't legitimate. The journal is obviously PNAS, so carefully read the title: Proceedings of the National Academy of Sciences.
It was founded as a place for the members of the NAS to report on their work. If you're not in the NAS, then you're secondary. In fact, prior to 1995, it was mandatory to have an author who had a NAS affiliation.

Is it a fair assessment that this journal seems to be using a "good ole boys" system for evaluation rather than taking reviewer reports seriously?

Yes, at least for consideration of novelty, and that's by design.
I would strongly suggest that you research and understand how this journal works before raising a fuss. Documentation is easily found: there is a special submission process for NAS members. Note specifically how novelty is evaluated by member-nominated reviewers.
Also observe how each published article will say whether it's "contributed" or a regular "direct submission".

How can I raise this concern with the journal without compromising my anonymity? What protections could I expect against retaliation from the authors, editor, or both?

You can't do anything. If you do, you'll look like a fool. You already may have by repeatedly bringing up novelty, which is more outside the independent reviewer's domain. If this wasn't a member-contributed article, another reviewer already looked at it for novelty.
They're completely transparent about this, so if you don't like it, then don't review for, submit to, or read PNAS. It's their journal, they can set the rules.
They're not the only ones either. For example, Cold Springs Harbor Journals are going to favor authors at Cold Springs Harbor Laboratory.

There is a lot to be said about the specific venue you are discussing (the topic is covered in this answer)
However, you are probably missing one important aspect of peer-review (as performed in many journals nowadays, please note I am not in favour or against, I just take it at the face value).
Reveiwers mmake suggestion to the editor, which then takes full responsibility of his/her/their decision. The reviewer do not decide anything. Even if three reviewers recommend rejection of a certain paper, it is still up to the editor to decide what to do.

The paper underwent three rounds of review. The other reviewer
accepted after two rounds. I recommended rejection each time. Then the
editor accepted the manuscript without even soliciting a third
reviewer.

Probably your rejection was not strongly motivated. If you suggested rejection based on what you state in your question, if I were an editor I would be thankful for your work, but I would give a very light weight to your suggestions.
I would therefore proceed with doing a weighted average of the reviews:

the two accepting it (maybe the other reviewer changed from one revision to the other, if you are 100% sure it is not the case please add this detail in your question);
your review presenting no technical flaws, just some editorial (?) flaws that make it unacceptable for an ideal broad, high-impact journal.

And you know the outcome of this decision.

Is it a fair assessment that this journal seems to be using a "good ole boys" system for evaluation rather than taking reviewer reports seriously?

It is not usually provable in any particular case.  However, I know from experience that it happens.

What should be done?

Stop hiring, promoting, and awarding grants based on low quality proxy measures.  If people were rewarded for their research, rather than their publication list, then you would not be wasting your time deciding if a paper should be published in an elitist journal or in a specialized journal.

How can I raise this concern with the journal without compromising my anonymity?

The journal already knows who you are.  You could share your concern with the editor-in-chief, but I would not expect that to benefit anyone.  You would likely get ignored.  Even in cases of blatant misconduct, journals are often very slow to react.

What protections could I expect against retaliation from the authors, editor, or both?

No "protections," but I would expect that nobody would have a desire or ability to retaliate.  Maybe if they work at your university you might have a slight grounds to be concerned.

One problem with "stop using low-quality proxy measures" is that the alternative can be lower quality. The journal something gets published in is certainly not a precise measure of how good it is, but it is (or should be) based on expert opinions. My own (in most cases) non-expert evaluation therefore is likely to be more precise but less accurate.

Embrace post-publication peer review. Write your issues on those questionable parts of the manuscript on pubpeer. People actually read it. And reputable authors respond there. This helps science evolve into more open discourse.


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College policy change after grant awarded
What recourse is there to a faculty member if the university changes its policy after a grant has been awarded?
I am a tenured professor and recently won a prestigious research grant. For years, my college within the university** has operated under policies that provide special research incentives to faculty. Specifically, faculty who win certain grants (which I have) are entitled to a reduced teaching load and a college-funded graduate research assistant position. However, I just learned that my college has abolished both of these benefits, supposedly because of budget cuts, about the same time as the start date for my project this summer.
Is there any way I can make a justification for being grandfathered into the old policy, at least for the duration of my current grants, given that they were submitted under the old policy?  And, more generally, what course of action do faculty have when their institution moves the goalposts on them like this?
** Note: my university is ranked as an R2 university (but only just). Consequently, research is not valued nearly as much as at a top-tier institution.

Did your grant proposal include the reduced teaching load, either explicitly or implicitly,  when estimating the time you would devote to the project?  And likewise the assistant as personnel?  It may play better to argue this as "we made a promise to the funding agency" than "you made a promise to me".  Otherwise it kinda sounds like you applied for the grant more to get your own personal perks, than to benefit your employer and your profession.

@NateEldredge: Good point, you should write that up as an answer.

@NateEldredge Good question. But no: writing them in would be cost sharing, which is not allowed by the sponsor. The perks are intended to provide support for other continued research (writing proposals, other projects, etc) concurrently with the funded project - not to support the funded project directly.

Taking this to the (unlikely) extreme: what happens if my university decides to change policy so my workload is 0% research, 80% teaching, and 20% service? Technically this would not change the time I spend on the project, but obviously it would limit my ability to do the work...

@mrp: If your contract prevents the university from doing this, then you have whatever recourse it provides.  Otherwise, your ultimate recourse is to quit and take your valuable grant to some other institution that is more appreciative of your skills.

Congratulations on the grant.
You can ask, politely but forcefully. One hopes with your Department Chair's strong support. If the granting agency knew about this policy when the grant was awarded that should strengthen your case.
If there is a faculty union they may take your side with the administration
I don't think you have any formal course of action.

If the reduction in other duties, to give more time to pursue the research funded by the grant was part of the proposal itself, then the university is probably obliged to either honor the reductions or give back the grant money.

@Buzz:  That seems like it should be a separate answer to the question (if NateEldredge, who made the same point on a comment to the question itself, doesn't write it up first.)

@MichaelSeifert Done.

If the granting agency knew about this policy when the grant was awarded that should strengthen your case. How so? From OP’s comments it does not sound like the university is violating any of its obligations to the granting agency by rescinding the reduced teaching load benefit. That’s all the grant agency would (and should) care about.

However, I just learned that my college has abolished both of these benefits, supposedly because of budget cuts

Budget cuts are pretty common, so that's a plausible reason.  You should probably complain, but I see little chance of getting the decision reversed.  If you get your benefit back, the administration will have to cut something else in exchange.  That is unlikely to appeal to them.

It may make a difference what you said in the grant proposal.  If the reduction in other duties, to give more time to pursue the research funded by the grant was part of the proposal itself, then the university is probably obliged to either honor the reductions or give back the grant money.
The key question is whether your proposal relied on the promise of reduced duties as one of its official selling points.  If the grant was made with the explicit understanding that your other duties would be reduced, then your institution probably has an obligation to either provide the reduced teaching load or to give up the grant.  Many external support proposals involve some commitment from the Principal Investigator's local institution.  This could be cost sharing—where the local institution offers to shoulder part of the cost of the project if the grant agency provides the remainder.  Or (and this is the case of relevance here) to institutional contribution could be releasing the PI from some other duties—to give the PI more time to concentrate on the funded research project.  This reduction in duties could a lower (or even temporarily eliminated) teaching load, reduced service commitments, or a supported sabbatical.
Grant proposal packages often involve documents explicitly stating what resources will be required to complete the funded research, and which of these resources will be provided by the PI's own institution.  If your proposal had documentation from your university that, if you received the award, you would have a lower teaching load during the funding period, then there it will not generally be possible for the institution to weasel out of that commitment.  If they want you to be able to keep the award (and I assume that they do), they will have to honor the commitments that they made as part of the grant proposal.

Unfortunately there is no binding language in the proposal. In fact, because cost sharing was not allowed, it would have been unallowable for the university to commit those resources.


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Is it a good decision to include failed/unsatisfactory result in bachelor's thesis?
I am conducting a research project under supervision of a professor for the bachelor's thesis.
Among all the tasks agreed between the professor and I, there is one task which was suggested by me. It is an attempt to solve the problem by using a completely different approach from the other one suggested by the professor (which works great). Both of them are part of the project.
It turned out that my idea did not work that marvelous. Although it somehow solved the problem with a better result, the cost (time complexity) is much higher. It is not worth the "extra effort". However, I do not want to consider any technical detail here, and for this question, the problem should be considered as (very) "unsatisfactory" result compared to current State-of-the-Art of the field.
There are theoretical frameworks that support the approach. It is just unfortunate that it does not work that well. I still think it deserves a chapter in the thesis.
It it a bad idea to still include "failed"/unsatisfactory results in the thesis?

Yes, you should include that.
In your particular case, it seems you have actually found something out, namely that the time complexity of the alternate approach is much higher. This may not be immediately useful knowledge, but it is new knowledge nonetheless. (And it could actually be useful to someone else also considering your alternative approach!)
Even if you hadn't found out anything - say you just failed to make it work in a way that doesn't mean anything to anyone else - including your attempt may make a lot of sense. As long as you have done enough to have something to write about, you should get credit for it as part of your BSc thesis grade.


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Consent for Using Scale
I am doing research on identity status. The scale which I intend to use was developed in 1995. I have attempted every possible way to reach out to the corresponding author, but haven't received any response yet. I have messaged all the email addresses of the author, the author's university as well and colleagues. Are there any alternatives to such situations where the scale dates back further in time and the consent cannot be obtained from the author directly, such as taking permission from the Journal where the original paper on the scale was published?

Why would you need consent to use a scale? What exactly is it? (software, content in a paper, etc)

In a psychological quantitative research survey, standardized scales/questionnaires/inventories are usually used. As per ethical rules, consent needs to be obtained from the author who developed the scale in the first place, before using their scale in research.

Is there any license or instructions for use of the scale included in the original publication? If the scale has been validated and used by others, there should be some information floating around. I suppose you could try looking up other authors and contacting them. I doubt the journal would have more up-to-date contact info, but you could ask there as well. I would not risk using the scale without explicit permission from the copyright holder though.
A word of warning... this makes me think of the debacle surrounding the Morisky Medication Adherence Scale (MMAS). The owner/original author of that particular scale retroactively tracked people down and demanded retraction or payment for licensing (no comment on the ethics of that). If you're interested you can read about it on retraction watch.
I bring this (admittedly extreme and unlikely) example up to say that you should be absolutely sure you have the proper permission to use a scale - the original MMAS paper, which was recently retracted for other reasons, was published in the 1980's. That fact that the scale was old did not protect anyone. One of the authors of a paper that used the MMAS scale couldn't get in contact with/never heard back from Morisky and went ahead using the scale anyway. It turned into a mess and the paper was retracted years later. If you can't get that explicit permission, consider using a more accessible tool.


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Using ChatGPT to format references in manuscript being submitted to peer-reviewed journal
I have a list of references in a pre-print article that I'm getting ready to submit to a peer-reviewed journal. I will need to change the format of the references according to the journal that I submit to. I have used citation generators in the past, but that takes a lot of time. I am wondering if people have tips on how to format references with ChatGPT. In addition, I'd appreciate advice on whether I'll need to disclose my use of ChatGPT, and if yes, whether that might lead to the manuscript being perceived less favorably.

Interesting. Many (most?) reference managers will reformat as needed, and they might solve a number of other issues now and into your journal future.

Did you manually format the citations initially? In my experience, if you have your citations stored in a reference manager or library switching formats is a non-issue.

At this point the references are in an ms word document in Vancouver format. I didn't use reference management software. I entered them manually. Thanks for the advice.

In my experience using a reference manager, this is accomplished with one click or one command assuming the format is already available in the software; if not available, it's often downloadable in a template from the journal, and if even that isn't available then there are just a few more steps to create a format. With a long reference list it can take some time to process, but we're talking a couple seconds, nothing compared to the time it would take to check for errors that ChatGPT might introduce.
My advice would be not to do it, this is a task that is already solved well by multiple dedicated software packages; even among AI aficionados, this seems like a very low-opportunity area for the technology.
If you do choose to do it, you'll need to check that no errors were introduced in the process, which likely means checking each individual reference manually, and yes, you should disclose the use of ChatGPT for this purpose.

Assuming the references are currently in a format that cannot be processed by dedicated reference managing software, I think there are two ways that GPT could be helpful in getting them there:
a) Show GPT (some of) your references and ask it if it knows of some reference management software that can read them, and how to do it. It is possible that it knows a way that you don't.
b) Show GPT your references and ask it to write a piece of Python code that will parse that format and convert it to something a suitable reference manager can use.
Obviously, in both cases you should check that the results work. For pathway (a), if you have access to GPT-4, probably the version with web browsing will yield the best results. For (b), GPT-4 with the advanced data analysis plugin can likely do it directly (i.e. it can write the conversion code, run it in a sandbox, and give you the result), but I would expect you might have to iterate, depending on how easy your references are to parse mechanically.
With GPT-3.5, (a) is still worth a shot if you do not have any other ideas, since it will be easy to see if it suggests a tool and if that tool works.
In either case, your paper would not contain text generated by AI, so you should check the applicable policies of whatever journal you are submitting to, but I would think reasonable policies would not require such tool use to be disclosed any more than we disclose that Joe from Library Services at one point showed us how to use a reference manager.

I don't think this is something that has to be disclosed. Most people in academia use LaTex that automatically formats references for your depending on your commands (e.g. APA). I never seen anyone disclosing they are using LaTex to format references even if they do and I don't see chatGPT being different in this regard.
To do it just provide chatGPT with the information about paper X and then prompt it by saying "provide citation in APA style" or whatever style you want.

I guess the difference is that a number of journals and publishers have sweeping policies dictating that use of AI tools must be disclosed; see this set of examples.


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BSc in Chemistry during PhD?
I have a BSc in Psychology with a strong focus on neuroscience and am currently studying Molecular Neuroscience. Next year I want to start my PhD in molecular Neuroscience but I am really interested in basic Chemistry. The aim for me is to get a strong foundation in chemistry and become a more independent researcher in molecular neuroscience. Thus, I am searching for a way to study Chemistry without having to delay my PhD by another 3 years. I would like to get input on what options there are and what other people have done. Thanks a lot for any help and input!

Does "currently studying" mean you are in a masters program?

In the US, your PhD program will help you take an necessary undergraduate or graduate courses to pass your prelims.

If you have time, money, and energy, go for it. Prepare to drop one program, if you feel like you can't handle both at the same time. PhD is very time consuming.

It's helpful to distinguish a degree (bachelors in chemistry in this case) from expertise in a field. A degree indicates some expertise in your major field, but it also indicates that you can manage all the requirements and expectations to achieve a degree. However, simply taking undergraduate courses (even auditing them) or self study will let you learn what you want/need to without the extraneous requirements that a degree entails (getting admitted to a program, taking courses outside your field or that you're not interested in, etc.).
If you are planning to get a PhD in neuroscience, getting a 2nd bachelors in chemistry isn't that important. You've already shown that you can earn a bachelors degree, what matters now is developing the chemistry expertise for the research you want to pursue. Get into a neuro PhD program, take some chemistry classes, establish collaborations with chemists, and learn as you go. Best of luck on your journey.

Thanks a lot that is very helpful advice!

Since you already have a bachelor's, some schools may not let you use scholarships/grants etc. to fund your next BSc in Chemistry. If this is not an issue then don't worry about it anyway.
However, it might be more worthwhile to try to find a PhD program (if you have not already chosen one) that will let you work in a strong chemistry/biochemistry research area. Many PhD programs, offer your masters degree upon completion of a year or two of your PhD program. If you can find one that lets you do this, you can design your PhD research to be both chemistry/biochemistry heavy and neuroscience heavy. This should be able to get you the chemistry background you want.
If this is not possible, during your PhD studies take as many chemistry classes as you can that even vaguely fit your project/field of study. If all else fails, there is always self-study with no degree awarded at the end.
Good luck!

Thanks for the practical advice I will certainly take that into account!


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GRE Mathematics Subject for Ph.D. of Economics
I have a bachelor degree of Engineering and a Master of Economics and next fall want to apply for Ph.D. of Economics. I have checked some universities in the US and found out linear algebra and real analysis is important for getting an admission. Although I have verifiable background in calculus I have not passed linear algebra and real analysis courses. Considering that I can't take those courses, how much taking GRE mathematics Subject exam will help me to cover that incompleteness in my resume?

My best guess is that is the wrong approach. Unless the exam has been greatly watered down you would likely do very poorly. The exam is both very broad and very difficult. As a top math student in my last year (but long ago), I felt devastated when I walked out of it, though my scores turned out well. But I had completed almost all of the normal math courses of a major.
Note, however, that for doctoral study in the US, there is usually coursework at the start, even for someone with a masters as most programs have comprehensive exams and the coursework is preparation for them. You could probably arrange to take both a course in linear algebra and in analysis during this period.
But, and this is important, don't make assumptions. See if you can talk to someone both about your chances and your options. The econ department of somewhere you'd like to apply  can probably put you in touch with someone who can give you advice.
But the math subject test is intended for mathematicians and those who wish to study it further.

My math is good. I have passed calculus with As. But my major was mechanical engineering and we did not have any course in linear algebra. Assuming I can get a really god GRE math (more than 90th percentile) is it worth it to take?

@SadeghBirjandi I took the GRE math last month. No knowledge of linear algebra, analysis, topology, algebra, or complex functions will guarantee a score well below average, not to mention 90th percentile.

To be honest, if you already have a Masters in Economics then you are probably okay. Other things such as LOR and GPA plus your general GRE score also play a big role. I'm currently a PhD student in Economics but do have a minor in Math.

My problem is that I did not pass linear algebra in masters neither and much of the universities I'm checking require linear algebra. My masters GPA is 4 but if I do not have the prerequisite of linear algebra then my application will not be considered.


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Recommendation Letter Advice and Examples
Are there examples of recommendations for first-time recommendation writers?
I've been asked to write a recommendation letter for a student applying to graduate school. I understand the general outline of what to include—my experience working with them, my assessment of their abilities—but it would be immensely helpful to see some examples to go off of and certain aspects I might want to mention, like Alex Lang's list of NSF grants.

When I first started writing letters of recommendation I would also have appreciated having examples to follow, but I think it's reasonable for people to be wary about supplying them. It's hard to write a completely generic one, and hard to justify the time spent. I recommend that you ask the people within your own department whom you consider to be good teachers and supportive advisers whether you can look at recent letters they have written for a range of students. Good letters, in my experience, are fundamentally about making fairly specific claims about the strengths of a student and backing them up with evidence that is as concrete as possible.
Here's the paragraph structure I typically use. My letters are usually 1.5 to 2 pages, depending on how strong the student is and how well I know them. Please also note that the way these letters are written will vary a lot, both by field and by country. I work at a university in the UK, and the letters I write are for students applying to postgraduate programmes in mathematics, computer science, and philosophy, mostly in the UK but also in the US and continental Europe, so YMMV.

Introduction. "I am writing to recommend X for admission to the degree Y at the University of Z. Here's who I am. I've known the student for N years in contexts C1 and C2. They are very good for reasons R1, R2, R3. They have valuable personal quality P, and I strongly recommend them to you."
Cohort ranking. This will usually be the ranking of that student within their cohort, i.e. students from the same degree course graduating in the same year. If they are very strong then I may compare them to graduates of that course over the past few years. My sense is that this is perceived as very valuable information by admissions committees.
Highlights of the transcript. In this paragraph I flag up a few courses in which the student did exceptionally well and which are relevant to the programme they are applying for. The department they're applying to will have their transcript, so I concentrate on explaining why the results are so good (e.g. difficulty of material).
Project highlight. If the student has done advanced work with me, then I often include an additional paragraph explaining what they did and how it makes them suitable for the programme they're applying for.
Contextualisation of results. Depending on where the student is applying, and their personal circumstances, I supply a range of different types of context. For example, if I am writing a letter for a student applying to a programme in a different country, I may explain some basic things about academic conventions in the UK (e.g. 75 is a very good mark [grade], not a very bad one!). This can also be the point at which to supply more personal context, like why the student has one term of bad marks (but obviously only do this with the student's consent).
Character and overall assessment. Here I write something about the student's character, interests etc. that is relevant to their future studies, e.g. motivation, dedication, focus, diligence (this should be supported by evidence, either in this paragraph or previous ones). I then sum up and recapitulate that I recommend them to the programme they are applying for.

Is there a place I can find examples of such recommendations for Engineering and Computer Science?

@Test It looks like you want a ready to copy-paste solution. I would say, if you do not want or have no time to write---it would be honest to refuse the request.

Apart from specific talking-points that surely will vary depending on the academic discipline...
... when I, as Dir Grad Studies or as any sort of Grad Admissions committee member look at letters, what I want to see is estimates/predictions for the future. That is, sure, good undergrad grades (for example) are obviously a positive thing, but only loosely correlated with success in a PhD program. That is, some people are non-conformist as undergrads, for various reasons, but/and will be energetic and decisive as grad students, finally being allowed to do what they'd wanted to do.
So, looking forward, rather than backward, is the most compelling thing to me, when I read letters of recommendation. Yes, of course, letter writers cannot predict the future, but those subtle perceptions of peoples' future potential are what I value.
Yes, if everything gets "fully objectified", so that there are "rubrics" for everything (a crude approximation to fairness?), it would become harder to explain why I'd view an application positively based on "reading between the lines". Sadly, yes, there is stunning injustice in the world, but/and, attempting to correct it by "rules" (or numerical rubrics) is insufficient, and often counterproductive. Sigh.


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Advice on class teaching as a beginner with public-speaking anxiety
I am a first year PhD student in Mathematics and I am teaching a first year undergraduate tutorial-style class. I have done lots of one-on-one tutoring before and quite enjoyed it, but I am struggling a lot more than I expected teaching a larger class.
I was painfully shy when I was younger but I thought I had overcome a lot of my shyness and anxiety around public speaking (although I'll still always get a bit nervous).
However, I have just started teaching a class of almost 30 students and I'm as anxious as I used to be; my brain shuts off and my voice shakes. I would appreciate anyone's advice on how to overcome some of the problems I'm having as a beginner teacher:

If anyone asks a question I haven't prepared to answer, my mind goes completely blank and I ramble and say things which I'm not sure are correct. As soon as the class is over I'll understand what they were asking and how I could've explained it, but it's too late. I know the problem is I'm rushing in to answering something before I've completely understood it, but I find even if I take more time my brain just won't click into gear during the class.

If I see that the students aren't understanding a concept a certain way that I'm explaining it, I can't think of any other ways of explaining it or helping them understand it. I tend to just go through a bunch of examples of the concept and hope something will click (it usually doesn't).

I would be very appreciative of any other advice for a first-time teacher, thank you!

If you aren't already, try to repeat and/or restate the question back to the student. That gives you a little time to think.

First, being shy and awkward as a beginning teacher is natural and (very) common. Many academics, in fact, are quite introverted. But practice will bring more comfort and more skill. Asking local colleagues about such things can also sometimes get good advice.
If you can't answer a question in class, don't try to fake it. It is ok to say "I need to think about that and will get back to you" and then bring it up again in the next lecture. As I said in a comment, however, if one student has a question then it is likely that others have the same question. I was once praised by my peers for asking so many questions in class. (My mom, however, thought I was a pest.)
Oh, and make a note so you don't forget to come back to it.
Your fallback on examples is a good start, but not enough as you have noted.
One trick is to ask a questioning student what their understanding is and see if you can find the flaw. Repeating the same explanation of a topic is likely to get the same result, so you need variations on a theme, which should come with practice. But it is easier to see where the student goes wrong and make corrections. Alternatively, ask them where they think they "lost you" in your explanation. You may need to encourage them to "work with you" toward a common and correct understanding.
Math, being axiomatic and relying on complex definitions, is especially difficult for students as the way we write and speak isn't typical language usage, with a lot of conditional phrases, each of which needs to be understood and melded into a whole. The definition of the limit, for example, is very difficult for novices. Assure them that this stuff is hard but can be learned with effort. The conciseness of mathematical explanations is also a difficulty for many students. Metaphor and analogy can help.
One bit of technology might work for you. I used to use a simple mailing list to which all students were subscribed members. Anyone on the list could ask a question there at any time (24/7) and anyone could answer the questions of others. Solutions to exercises were off limits, but questions about exercises were fine. I would answer those questions that others didn't, though it was most of them.
The advantage of the system was that it was always available but asynchronous, so I could think a bit before I answered. Also, everyone could see every question and every answer. For math, you might want something that could parse and display expressions: (Markdown or better). I found this mailing list one of the most important tools in my bag of tricks. Perhaps your IT department can set you up.
Note two things. If you are a doctoral student (or professor) then most of your students are not like you. They probably aren't driven to learn mathematics. They aren't as immersed in it as you are. The second thing is that people learn differently (and differently from yourself) so that variety of explanations is vital to develop. Some can handle a logic based response, some need metaphor, some need visual cues, some need it written out in detail. The all-hands mailing list is good for a lot of this.

Also note that it will help your students to learn if you give them lots of exercises but also extensive feedback on their "solutions". Grades aren't enough. I found this do-able with 30 students.
And, if you can arrange to get feedback on your teaching, perhaps by asking a faculty member to sit in and give you hints later, you will probably progress faster. Practice and feedback are important to many thing, including learning and teaching.

I am also new to teaching and I have shy personality. I got some good advice from older colleagues:

if you get question you are not prepared to answer just say: "that is interesting but complex question, we won't have time to cover it now but please send me an email with the question" or "come to my office hours with the question."
This will give you enough time to prepare and you avoid any embarrassment. Of course, not all questions can be postponed, but this advice helped me more than I can count.

When it comes to explaining concepts it always helps to somehow connect it to the real world. It does not work in every field, but mathematics is the language scientists use to describe real world so it should be possible. You can for example relate single variable optimization to hotdog stand trying to maximize profits and so on.

Your first point doesn't work. If one person has such a question there is high probability that others do also. You need to find a way to inform the entire class. Saying that you will deal with that in the next session is better.


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Should I exclude my supervisor as a reference when applying for academic jobs outside my PhD area?
I completed my PhD earlier this year and I will be applying for postdocs and faculty positions.
My thesis is quite different to the field I'm applying to. Additionally, my relationship with my advisor ended on a sour note, causing quite a bit of tension. Thus, I doubt they can give a strong reference letter which shows my research skills in this area.
However, I have published and conducted research with other academics in this field who are willing to provide reference letters. Many of them are well-known and I have more than enough to fill out the reference requirements for applications.
Do you think I should exclude my supervisor from my reference list? Why or why not?
Thank you

If you completed your PhD, then your thesis advisor probably knows you better than anyone else. If I was an employer I would want to see that letter of reference.
Since the relationship has soured, I would do my best to try and repair it. Start slow, acknowledge any shortcomings you have made, and ask to see if there are ways to meet in the middle and repair a bad situation. Approach it without asking for a letter of reference initially, and just do it as someone that wants to repair a situation.
If they still are apprehensive, at least you tried your best. If they accept, it'll help you in the short and long term. You've gotten a potential colleague, peer, friend, etc. back. And the letter of reference they write would probably be even better for you, since they could talk about your ability to try and resolve conflicts and move past previous transgressions. If I was an employer, that would be a huge perk. And if nothing else, trying to repair a relationship is often what the world could use more of. So why not try?

People will probably wonder why the advisor excluded, of course, but a bad relationship is probably more important than the change of fields.
With a good relationship the advisor can attest to a lot of things that apply across fields, such as your dedication likelihood of success.
Perhaps you can have a chat (face to face) with them to better asses what their recommendation would look like. This is the sort of thing that has to be done in person, though. Email won't do.
But if you have other strong letter writers it might not matter much and you could explain the lack of a letter based on the new field.

Whether you exclude your PhD supervisor or not, he will be asked to write you a letter of recommendation in 90% of cases. If you are applying for a fellowship, a letter from your PhD supervisor is often necessary. You have to normalize your relationship with your Ph.D. supervisor or be ready to get many surprise rejections until you become a faculty (still not guaranteeing you are safe).

In the US, at least, it would be improper for someone other than the candidate to ask the supervisor for a letter. I hope and expect that this is more generally true, though it may not be universal.


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Should I send a follow up to lab after applying for a position through university job board?
I applied for a position through a university's job board, but the lab the position it's through has a separate site with a contact name listed if I'm interested in joining or learning more about the lab. I'm wondering if I should send an email to this person, nothing long just a quick 'Hey I applied to this position, please let me know if you need anything additional'? If so, how long should I wait (I applied about a week ago), and should I CC the PI? The application is listed as being under review, idk if that changes anything.
Thanks!

I don't think there is anything wrong with a followup like that after a week. You may not get a reply and if not, just wait for something official to come to you.
If there is a listed contact, I'd leave it at that without also contacting the PI.

Sounds good, I'll wait a few more days and then reply. Thank you!


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Seeking Advice on Applying to a Competing University During Tenure Review
I am at a crucial point in my career and am in need of your collective insights. This year, I've applied for an associate professorship and tenure at my current institution, and my application has favorably passed through the necessary committees but final decision not yet made.
At the same time, I've come across an opening at a neighboring, more prestigious university that directly competes with ours. They are launching a new program in my major and are in the process of hiring faculty. While the potential role is attractive and could possibly serve as a bargaining chip for salary negotiations after my expected promotion and tenure, I am hesitant.
My reservation stems from the close proximity of the two institutions and the potential for my current colleagues to learn of my application, which could adversely affect my tenure review. Offers from the competing university will likely be made around next April, ideally after my tenure decision is finalized. Yet, the prospect of negative ramifications if my application is revealed during the tenure review is a concern.
In light of this, I seek your advice: would it be prudent to apply for this new position now? Could this move be seen as a breach of loyalty? I am weighing the potential advantages against the risks and would value your opinions on whether to proceed with the application at this stage.
Your guidance is greatly appreciated.

If they decline tenure you are out of a job. At the worst your application, if found out, can be explained as risk mitigation. Their hiring committee should be well aware of such situations.

Nothing ventured, nothing gained.
University employment isn't like citizenship where loyalty is expected.  On the other hand, it is impossible to guarantee that any advice you get will be the "right" advice since it is an attempt to predict the unknown future.
On the other other hand, it would, IMO, be unethical for anyone to make your tenure decision contingent on such a thing. But, back on the other other other hand, decisions are made by individuals who, one hopes, are rational and honest, but occasionally are not.
I think this situation isn't especially unusual, in fact. If you are considered a "great" candidate for tenure, as you seem to imply, then you will probably be looked upon favorably by another institution. But you might need to undergo an additional probationary period there. And a position at a "more prestigious" university might also imply more pressure and stress.
If I were your colleague at the current institution, I'd be happy for your advancement, either to tenure or to a better place. I certainly wouldn't try to punish you for trying to move up. Yuck.
Risky, but with potential. Life is like that. It is your willingness to accept the risks, balancing unknowns, that is key here. If you don't apply and don't get tenure all is bad. If you do get tenure then the other outcomes are all good, with some better than others.

Good response. I know, most of your responses are good, but this particularly so.

In addition to what @Buffy said, I would suggest you contact the search chair and ask that your application be kept confidential for the obvious reasons.


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High similarity index on turntin
My paper got accepted for a conference. Before submitting the paper, I used Turntin to check for any similarity and found only 6%. But after the conference reviewed my paper and sent it to me, I again checked for similarity (as I made some changes) and found that it was 95% similar! 90% of those come from a student paper at a Texas university.
Why is that? I have to submit the final version tomorrow. Is this going to be any problem?

Does this answer your question? What is the acceptable similarity in a mathematics PhD dissertation when checking by Turnitin?

In particular, as the answers to https://academia.stackexchange.com/questions/29723/what-is-the-acceptable-similarity-in-a-mathematics-phd-dissertation-when-checkin say:  Do not use Turnitin for anything important.

This is a good answer: https://academia.stackexchange.com/a/185810/13240

Did you get to see the student paper ? How much similarity between your paper and the student's paper after you read that paper yourself (not by Turntin) ? What was the publish date of the student's paper ?

If you didn't plagiarize,  you can submit the final version of the paper which was accepted. Why not ?

I don't see how any of us can say. Maybe you stole it from a student at a Texas university. Maybe they stole it from you. Maybe a glitch. Maybe the conference will use a plagiarism checker like the one you used, maybe not.
You should never need to check anything you've written yourself on a plagiarism checker, because if you wrote it yourself you don't need to check it for plagiarism: it isn't plagiarized if you didn't plagiarize it, regardless of what a computer comparison says. Focus on not plagiarizing, rather than focusing on making sure you can evade the detection system; evading the system of checks is something for guilty people to do, not honest ones.
In some cases, sending a copy of your work to a plagiarism detector may result in it showing up as plagiarism later, because the plagiarism software works by making comparisons to previous submissions.

I didn't check it myself. My teacher did. He is the co-author, and the reason I am checking now is because I added a lot of references as per the review from the conference, so I checked if they were getting caught as references or plagiarism. The similarity didn't exist before. It was after i submitted to the conference that its showing 95%

@rafraf That's not what you wrote in your post. I guess your advisor doesn't trust you? There is no reason to check if references are "getting caught as plagiarism" in your own work, unless perhaps someone is accusing you of plagiarism already based on a report like this and you're trying to refute it.

There's a plethora of reasons this could have happened but, assuming the conference did not make any mistakes in the paper that was checked and who it was reported to. It may be that turnitin added your paper to their database after you submitted it and afterwards when the conference went to scan your paper turnitin recognized your paper as previously submitted. I would bring this up to the conference and try to show them as much documentation you can (i.e. timestamps on browser history, any editing history assuming your text editor supports this).


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Citing general information about visualization in related papers
I have been reading multiple (20+) physics research articles on related topics, which use different visualizations for the same thing. I want to state that a certain visualization is used less often than others, but how do I cite this information?

how do I cite this information?

Cite? Isn't it your own observation? If someone else has made the same observation, you can cite them in the standard way, of course. If not, just make the claim and present the evidence for it. This might take the form of citing the various papers on the topic and categorizing them according to the type of visualizations they use. To produce convincing statistics, you may want to follow strategies for systematic reviews and use well-defined inclusion criteria for the papers you consider. Note that it's certainly OK to cite 20+ papers for background, but when you get to large enough numbers (e.g. several hundreds or more) it may be more appropriate to describe in detail the database search terms instead of listing all papers explicitly.

Create a data table from these papers and use it as supplementary material
It sounds like you are in a situation where the academic papers at issue are data-points for your own observation and analysis, rather than contextual academic literature for your work.  In such a case I think it would be reasonable to proceed without citing these papers.  However, you should still use good data analytics practices by keeping a clear record of your data and analysis, and including this as supplementary material for your paper.
One way you could go about this is to create a detailed data table containing all the visualisations for each paper with a set of variables that give extensive information on the visualisations in the papers.  There should be enough reference information in the table to clearly identify the papers at issue, so you should have one or more variables that give the authors, paper name, journal, etc. (ideally, this would effectively amount to full reference information).  You would also have variables giving information about the visualisations that are present in the paper, in whatever you think is the most helpful form.  Once you have created this data table, you should then be able to make the subsequent calculations of how often each different type of visualisation appears.  As good data analytics practice, there should be a reproducible analysis of this (e.g., computation script that imports the data table and then computes the output metrics) and it should also be included in your supplementary materials.
(One more tip: When creating your data table in this case, be really detailed to aid any reader that wants to check your data.  The best way would be to ensure that for each visualisation you identify and classify in the paper, you give the page number where it appears in the paper.  This will make it easy for anyone to check your data for errors.)


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Mathematical journals which accept micro-articles
A micro-article is a paper of at most six pages.
The following mathematical journals accept micro-articles:

Elemente der Mathematik,
Examples and Counterexamples and
Journal of Computational Mathematics and Data Science.

Any other example?

This is a shopping question. You may want to take the tour: https://academia.stackexchange.com/tour

Proceedings of the AMS, Bulletin of the LMS, Archiv der Mathematik, Comptes Rendus. Mathématique (all these journals specalize exclusively in short papers).

@theL Thank you!

Your question is based on a false premise. Any math journal will accept a short paper if it contains results that meet the journal’s standards for quality and significance. In other words, journals do not have a lower bound on article length. The only exception I’m aware of is Memoirs of the American Mathematical Society, which is technically a journal but publishes book-length articles as monographs. I think they won’t consider an article of less than 80 pages.


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Fellowships/Awards section in graduate application include scholarships
I am applying to Physics PhD programs at various institutions. Most applications have a section to include Fellowships and Awards. Does this only refer to funding for graduate studies (such as Fullbright or NSF GRFP) or should this include scholarships received for my undergraduate studies?

You can include fellowships, awards, and scholarships of any sort at any point that are relevant to your academic pursuits.
If you have funding for future graduate study already secured (that is, for the work you will do in the program you are applying for), you can list that here, too, but I'd also be sure to draw attention to it elsewhere in your application as this would be very important information (and something that would be very unusual for most applicants, but may be more common with programs funded by specific countries).


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Failing a class senior year undergrad - applying to grad schools
I am currently a senior during my undergraduate degree in biology. I have also just applied to do my masters in public health. However, during my junior year I suffered from a subdural hematoma, and still have concussion symptoms from it (which I have mentioned in my statement of purpose briefly) and these symptoms have impacted me and I fear that I missed up my chances of getting into grad school. Prior, to the fall my gpa was very strong and it dropped during the semester of the fall, however it has been picking back up after the fall. I took a high level biology course this semester and unfortunately was not able to do well in it due to ongoing headaches. I did very well in other lab courses I took, and my gpa is high, but I completely bombed this course and failed it. It is an upper division biology course.
My LOR's are strong, I have medical and healthcare experience (2+) years, and am also an undergraduate researcher at the moment, which I have included in my application for grad schools.
Did this one course mess up my chances of getting into grad schools since it is during my senior year and right before i go into grad school?

It is impossible to say with certainty since the course is in your major. However, you have a valid explanation for the issue and if you have mentioned the medical condition somewhere it should be ok, given that you have strong letters to support your success.
Make sure that your medical condition is fixed, however, and that you can assure people if asked that this won't be an issue in the future.
If this is for the US educational system, there is an opportunity at the start of the program to cover a deficit in the course.
I wonder, however, if you can have the grade expunged, given the medical condition. It might be worth an ask.
(A family member has just this issue applying for undergraduate and decided to delay a year to assure he won't be disadvantaged.)

Delaying a year seems too over-the-top for this issue,  imo

@DavidRaveh, Agree, unless the time is needed to recover health, as is the case I mention.


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ORI Research Misconduct rulemaking comments
I am writing comments on the Public Health Service Policies on Research Misconduct on regulations.gov. This is my first time making comments on policy making. I am curious if HHS ever censors these comments if they are embarrassing to OHRP. I openly criticize them and explain in pretty good detail why. I've tried talking to OHRP since June and they won't have a conversation with me because, as they cite, the policies they created allow them to turn a blind eye to QI/research misconduct not funded by the government even if it is at an institution the government is giving money to. I submitted my complaint twice. Both dismissed. I've experience retaliation and further misconduct by the hospital that is really alarming! Someone outside the IRB responded to part of my IRB complaint at the hospital, in an official capacity, in the most startling and ironic way they could have during this particular investigation into one of the co-authors. So I've emailed OHRP countless times and get replies with one or two sentences with no human signature. So no accountability. The institution I made my complaint about gets tens of millions in research funding annually. they have a $190 million research portfolio. There are over a thousand clinical trials going on and recruiting participants. But if you go to the IRB website and click on the link to email them a complaint, the email bounces back. This has been happening since Feb. 2023 at least. My complaint wasn't received at all when I first sent it. I had to make several calls and speak with three people to get my complaint heard and was then given an email where I sent a written complaint. But the main IRB email link is to an incorrect email that bounces back. And this is wild to me. I'm not sure where to find FWA rules about this, but someone please tell me this isn't acceptable according to FWA rules. This reading is so difficult for me and I spend day and night trying to answer my questions. It's weird because they already investigated one of these guys before. And they are still totally disinterested. Almost like they are more interested in protecting him than me. It's all very odd and troubling. Because this one guy is really famous. And my complaint is pretty extensive, backed completely by evidence, and OHRP is blatantly not answering my questions or addressing my concerns in any sort of way that resembles appropriate.
Essentially, the point I am making to Director Garrity is that HHS should not move forward with any changes to the policy to alleviate administrative and financial burdens of researchers and institutions until the consequences of the Revised Common Rule are systematically investigated. Specifically, the appropriateness of OHRPs responses to participants harmed by the Revised Common Rule, prioritizing institutions and researchers over research participants and participants whose right to informed consent were waived, should be thoroughly examined before making additional changes that could further damage research integrity.
I don't cuss in my comments. I think I'm respectful, but I am a bit of an asshat with my honesty. I am unafraid to share the most embarrassing details because (of therapy) and because I think those details make the point I am trying to make. The harm the did to me is embarrassing, to me, to the hospital, to the researchers, to the government. I want my comments public, but I call out OHRP essentially for ignoring my emails and complaints despite retaliation and misconduct after the IRB investigation has begun in several ways. I've asked so many times for guidance and they won't even respond to me at this point.
Do I have to not be an asshat at all for my comments to get posted? Does anyone have any relevant experience? I'm not really a professional here. I don't really do things very professionally. But I'm hoping I don't have to. Has anyone encountered comments that were perhaps close to crossing some line of appropriateness? Or any other thoughts anyone?
Thank you.

Government agencies are bound by laws. It seems you are upset with a law. You can't change the law by complaining to the government agency, they do not have the power to change law through rulemaking. If you think the law is bad you can ask lawmakers to change it. If you think you've been harmed you should discuss with a lawyer who can assess the legal merits of your case.

I don't think you understood my post at all. The government is asking for comments on policy. I am responding saying they should not make changes to that policy for institutions' administrative and financial burdens. I am just saying it in a very sassy way. I am so tongue in cheek. I do not know if they will actually post it. And OHRP accepts complaints about human subject research and IRBs. That is literally their job to accept complaints. It sounds like you don't understand these government agencies and rule making. I don't need a lawyer. I need the government to do their job.

I don't think this is the place for this question but if you want your comment to be taken seriously, I assume it should be professional and well thought-out.


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Can preprint withdrawals lead to retraction of articles prior to the preprint?
I was a participant in research/“quality improvement” without informed consent that was life threatening. There has been an IRB investigation going on since June. And an investigation by a publisher of a journal where two articles were published with me as a participant.
I am very unfamiliar with preprints. But on December 20, a preprint platform I made a complaint to said they are withdrawing the article and putting a notice on the preprint of patient harm from the protocol.
It says, “20 December, 2023 Research Square has withdrawn this preprint after receiving a notification of patient harm that stemmed from this protocol/study.”
I understand that articles that come from withdrawn preprints, in these circumstances, are usually retracted. But does anyone know if this impacts articles written prior to the preprint, using the same participants and intervention?
Will this possibly help the publisher of the first two articles move forward with retraction quicker? I've heard it can take years for retractions to be issued.
Do preprint platforms like Research Square communicate somehow with PubMed and Research Gate so that a notice is on their site for that preprint doi? The article is on Research Gate without the notice. But links to Research Square where the notice appears. Should there be a notice on Research Gate? There is notice already on Europe PMC.

You may want to get in touch with https://retractionwatch.com/.
They are experts in all things retraction. I think they would care about your case and they also have the experience to support you in pushing for the papers to get retracted.

Yes, I recently learned about them last month and contacted them. They wrote back quickly but they are backlogged. So I have to wait a little bit for response to everything I said to them so far.  And are already familiar with one of the researchers. I really look forward to chatting with them! I've been reading their blog non-stop since finding them! And perusing their database.

Withdrawal is a human process, performed by humans. Humans can be influenced by many things; yeah, I'd expect an editor to be somewhat influenced by knowing that other venues have retracted work for the same reason they're considering a retraction, it's difficult for a human not to be influenced by that sort of thing. But I doubt there is any direct pipeline for it, and journals may want to preserve some level of "independence".
Ultimately, it sounds like what would lead to journal article withdrawals here is a failure to adhere to protections for human research subjects. If you are trying to seek retractions of particular articles, I would focus on that specific reason. Information about other retractions is background information at most. I would not assume that any article will be retracted solely because a preprint of the same paper was retracted, I would expect the journal to have their own process.
Good for you for going after researchers abusing the "quality improvement" loophole.

what is the quality improvement loophole?

@JonasSchwarz "Quality improvement" is not research and doesn't come with the same protections for human subjects, but may involve data collection to monitor the effect of a change. That's fine when the only goal is improved patient care. It becomes sketchy when it's used to label what is actually a research project with research goals. https://www.hhs.gov/ohrp/regulations-and-policy/guidance/faq/quality-improvement-activities/index.html


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Status still “Pending decision” but date has changed
I submitted a paper to a Taylor & Francis journal. It was peer reviewed and the status has been “Pending decision” since January 30. On January 31, the status stayed the same but the date had changed. What does this most likely mean?
I read online it might mean that the handling editor has made a recommendation for the outcome of the manuscript which needs to be approved by the Editor in Chief (EIC). In this case, would that mean I’ll most likely get an accept or reject and not a Major revisions? I assume if it required major revisions then that probably wouldn’t need to be approved by the EIC.

It probably means that the date has changed and nothing more. Probably a duplicate of the canonical: https://academia.stackexchange.com/q/55665/75368

It probably means that some human has interacted with the journal's record for your manuscript. This could be a meaningful event (i.e. some step in the decision-making chain) but it could also be some administrative task (e.g. recording some additional correspondence sent by a reviewer, or changing the date by which the editor is supposed to make a decision. I do not think you can treat it as informative about the outcome. In any case, none of us can give you an answer beyond speculation.

Your mental energies are far better spent on something useful, not trying to read tea leaves. I'd suggest not checking 'progress' daily.