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Should recommendation letters mention a candidate's weaknesses?
Even the best candidates have weaknesses and areas for development. When writing a (generally positive) letter of recommendation, is it appropriate/helpful to mention these, or will this count against the applicant?
Does the answer change depending on the candidate's career stage (i.e. whether the letter supports an application for a PhD, Postdoc or Faculty position) or by geographic region?

The case of letters for PhD applications was addressed in this question.

My understanding is that the answer is different in the US and Europe, say, and it may also depend on the situation (e.g., to explain a gap in a publication record).  What situation do your really want to know about?

See the last section of the appendix of this article

Even the best candidates have weaknesses and areas for development. When writing a (generally positive) letter of recommendation, is it appropriate/helpful to mention these, or will this count against the applicant?
Does the answer change depending on the candidate's career stage (i.e. whether the letter supports an application for a PhD, Postdoc or Faculty position) or by geographic region?

Rather than listing weakness, describe how the person would grow in the position.
For example, let's say you are writing a letter of recommendation for your recent graduate student, J. Doe.
Rather than saying:

Dr. Doe lacks experience running large research programs and programming in Shiny new language.

Write something like:

Dr. Doe's experiences with my research group showed their ability to run experiments and projects. Your project would be a great opportunity for them to expand their skills for managing larger projects. Furthermore, Dr. Doe did a great job analyzing data with old rusty program and I am confident in their ability to apply similar methods in Shiny new language as part of your program.

Or, something along these lines that are true.
Also, this answer is US specific. A US letter would almost never include a negative statement for a positive letter. I have heard that other countries are different.

If you don't feel you can write a good letter say no.  If you feel you need to mention a weakness say no.
Your letter should be positive.  If you cannot whole heartedly recommend someone because of weakness in an area, then don't recommend them.  I very rarely see any negatives in recommendation letters.
When I do, I wonder if the student/applicant knows what one of their references is saying this about them, and could find a better letter writer if they knew.  It's as likely to make the reader wonder about you than the candidate.
There is also a difference in a weakness and room to grow.  You can phrase room to grow positively.  "This person is ready to lead a lab/write more grants/etc."  Especially if this is the next logical step in their career, it's a positive they're ready to step up to the plate so to speak.
The is primarily an American based answer.

Need to agree - absolutely don't write about weaknesses unless they are minor in the overall context of an outstanding ref. I won't agree to write a letter of recommendation unless I'm going to write a glowing ref - in the US, all of the letters of reference I see are glowing. I recall turning down one person's request for a ref because it wouldn't have been really positive. Just focus on the positive.

On the other hand, that's how systems break down over time: by not having honest feedback.

@Zeus - it’s not a failed system.  It just means that people on the fence probably won’t be able to get recommendations.

Yes, but that's not granular enough. There are plenty of people, especially in academia, who might deserve a glowing recommendation but have a major weakness - which may or may not be relevant, and the reviewer doesn't know if it's the case. Say, an absolutely brilliant researcher who cannot work in a team.

Your recommendation letter should, above all, provide a truthful picture of the candidate. But you of course also know that other candidates will receive recommendation letters written by people who might shy away from mentioning weaknesses, so you don't want to exaggerate. The difficulty is not whether to include weaknesses or not, but to find the balance.
This means: if you have to write a recommendation letter for a good student, who at some point made a mistake, or have some minor disadvantage, then don't mention it.
On the other hand, if this student never kept a deadline and always had to have things repeated 4 times, it would be silly to write a stellar letter. Also: if you give that student top recommendations, what are you going to write for students who are truly great?
A good exercise (also backed by science, see eg Kahneman: "Noise") is to perform a mental ranking of this student vs other students, and make your letter reflect that raking. Say you rank this student in top 20%, you could write that, give your reasons, and also state what it would take for this student to be top 10%. Then it also does not come across as you "slamming" a particular student.
When I am asked to write a letter for a student I cannot give good recommendation, I usually tell the student this, and recommend them to find someone else who can write them a better one. They usually appreciate the honesty.

I'm not sure about "ranking": it's too one-dimensional. Emphasise the strengths: if someone isn't a top researcher, but is great at explaining the work of the research group externally, find a way to bring that out without being negative.

I have seen several universities that mention you should not talk about your weaknesses in a statement of purpose. I think the same rule applies to recommendation letters. If the weakness you want to write about is critical and you don't feel good recommending someone because of it, then don't write a recommendation letter for that person. Otherwise, if it's not that important and you still want to recommend the person, don't mention the weakness and instead just don't give credit to that person for that weakness. For example, if someone is really talented and hard-working but can't work very well in a group, don't mention their working ability in a group and only talk about their talent, etc.
Everyone has a weakness, and since no one else is writing about others' weaknesses, you writing about that weakness makes the person look bad. In fact, the name of the letter is the recommendation letter; I suppose that means why you recommend this person to us, not why you don't recommend them, so talk about all the good things that make you recommend them and leave the weaknesses.

TLDR: Always ask about geographic-specific format and content expectations  in the region you are about to send your recommendation letter to. Careers can depend on it.
What I have heard is that the expectations around reference letters vary heavily by geographic region and that the differing cultures and the unintentional "clashes" between the cultures can significantly impact academic careers. The example that I heard (from a reliable source) was the difference between letters in the US and the UK (in STEM). Apparently, it is traditionally expected in the UK that letters include comments about a candidate's weaknesses. Traditionally in the US, however, anything other than a very positive letter is viewed as a red flag. Any comment about a weakness would destroy the chances of obtaining a position and could be perceived by the candidate as back-stabbing them (if they found out about the negative comment).
Thus, there were apparently significant problems at one point about obtaining recommendation letters from professors in the UK for US positions and vice versa. Fortunately, however, there has now been enough cultural exchange happening over the past many years that professors in the UK and the US better understand the cultural expectations and practises in the two geographic regions, such that fewer problems occur (but it is by no means perfect).
Given such a situation between two countries that have a significant cultural connection already, it is important to always ask about the geographic-specific expectations regarding reference letters if you are not absolutely sure. I commend you for asking about what to do on this site and further recommend that you reach out to people who know the geographic-specific expectations before you send any letters.

A recommendation letter should generally be positive and reveal the student's best qualities and lay out where the student can further develop and gain from the new challenge they are applying for. However, you should also always be truthful as you will not help your student if they obatin a position that is above their abilities because of a dishonest application.
If you feel you really cannot write a very positive letter for someone, it might be better to decline the letter rather than hurting the student's chances to make the next step in their career.


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How do you advise an early career researcher who has an unrealistic opinion of their prospects?
One often reads stories along the lines of "I was told I wasn't suited to a career in academia; now I'm a professor at < Big Name University >". At the same time, given the structure of the academic job market, many people who desire an academic job will never get one. I am sure many of us can think of individuals who made big sacrifices in an unsuccessful pursuit of an academic career, despite never really being a competitive candidate. Equally, we can probably also think of people who succeeded, against our prior expectations.
Given all the above, what should an advisor do/say when confronted with an early career researcher (graduating PhD student/junior postdoc) whose career goals appear incompatible with their current trajectory? How do you support and encourage your advisee, while also being realistic?

Incompatible how, exactly? You've described two separate issues: the chanciness of the job market and the quality of this person's CV. No one has any control over the first, but they do over the second.

Honestly, without putting down.
Explain the weaknesses of their approach or profile, explain what they would have to change in your opinion to get where they want and explain what they can do if it does not work this way. The point is not discouragement, but letting them understand what their options are. Some people are able to rise far above their original level, just as some never exploit their possibilities.
Whatever you do, you can not go wrong if you understand that the choice remains theirs and yours is only to show them the map.

This is the optimistic positive answer but I fear the advice OP feels would be needed is 'you need to do much stronger research and produce more and better papers in order to have a chance' which is not really useful as advice.

@quarague Actually it is, if OP explains in which respect the papers have to be better. The answer is also not so optimistic (I do not consider painting the future in bright colours) as attempting to be a fair assessment of the possibilities.

I might be seeing this way to negative, but I was more thinking in the 'I don't believe you are good / smart enough to ever become a professor' direction than something like 'change these two bits in the paper to make it better'. In analogy, if I asked for advice how to become a world champion marathon runner, telling me to practice and train is correct but no matter how much I do it, it will probably not b e sufficient.

@quarague My life experience is that I have seen multiple people going up so many levels of mastery through sheer willforce that I would never say anything like "don't believe you are good enough". I do not see why one should outright discourage people. If you do not want them as project or PhD students, that's fine, as it is your resources you have to consider here, but it is not the teacher's job to decide how OP wishes to invest theirs, especially if they are still young.

Advise the researcher of their options beyond their current trajectory, discuss the differences between trajectories, and establish what they really want. (Just because a research says they, want a permanent academic position in five years and professorship ten years after, doesn't mean they've thoroughly considered and understood what this will entail!) The advisee may themselves favour a different trajectory once they better understand their options.

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Revised manuscript sent to a new referee after editor hearing back from one referee: What's the possible reason?
Early this year, we submitted a manuscript to a journal and heard the revision suggestions back very quickly from two referees. Both the two referees suggest some revision while remaining generally positive about our idea. Last month, we resubmitted our revised manuscript and the editor sent it to the two original referees.
As suggested in the submission system, one of the referees sent the report back yesterday while the other referee has not yet. Then the editor sent our revised manuscript to a third referee today, which is a bit out of my understanding: I know sometimes the editors may send a revised manuscript to a new referee to hear some new voice about a manuscript. However, in my case, the editor didn't seek a new referee right after they received our revised manuscript, but until they heard back from an original referee about the revised manuscript.
I am trying to decipher the underlying meaning of this action: The editor may hear something terrible from the newly-arrived report yesterday so they wanna make use of another referee to see if the bad words make sense. Or the editor just forgot to send the revised manuscript to a new referee, and they remembered to do so just now.
Could anyone also provide some thoughts about the editor's action here?

You're asking us to divine from tea leaves... that's all one can say for sure.

This happens (not so infrequently) when one of the referees indicates she or he is not available or otherwise unwilling to review the revised version.
As many take vacations at this time of year, it could well be that one referee is on holidays and cannot submit a report within the recommended timelines.  Of course there are lots of other reasons: an obvious one these days is that one referee needs to isolate or rest because of some illness.

There are a million possible reasons one could try to enumerate, but at the end of the day it comes down to this:
There is nothing you can do about it at this stage.
As a consequence, here is my advice:
Move your brain power to other projects and wait till the editor sends your paper back with any feedback. You won't find out the precise reasons for all of the moves behind the screen, and nor is there any use to you if you did know the reasons. So, stop spending time and emotional energy on the issue. The time will come when you will learn, and in the meantime work on something else productive, such as your next manuscript.

Indeed. Clarity of process is great, but it was easier to not obsess about it when there was no information available…

Here's an example I remember.

Journal policy is to get two reviews per paper.
During the initial stage of invitations, two reviewers agreed to do it, but only one submitted a review.
We decide to send the manuscript for revision anyway, because the alternative is to invite another reviewer from square one, which at least doubles the review time.
After the manuscript is revised, we invite a second reviewer.

Your description reminds me of another paper, which went like normal except the reviewer said "I'm an expert on [this part of the manuscript], but not really on [another part of the manuscript]" - although in this case I would imagine it's more likely that the editors will invite a new reviewer prior to revision, and the paper simply takes longer to review.

The only way to be sure is to ask the editor. There are a ton of possible reasons. The one that comes first to mind is that the referee expressed some doubt both about the paper and about their own ability to review it properly (expertise, time constraints, ...). So, the editor wanted more advice.
But the editor gonna do what the editor gonna do. They want some consensus that the paper meets the journal's standards and they probably don't have it yet.
There are about a million pathways through the review system and since there are some loops in the process it is not easy to answer these questions from afar.
Ask the editor or have patience that something is happening and you haven't been rejected. And asking might not get you an answer also. Be prepared for that. Patience is suggested.

One likely scenario is that the referee that hasn't answered has told the editor there will be further delay, so they are bypassing them...

Surely I understand what I am doing now is purely guessing, and I don't think bothering the editor before they prepared a decision for us is a good idea. But thanks for your answer anyway.

@JonCuster This is definitely a very probable case. Thanks a lot for sharing this point!

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Timeline to ask postdoc interview outcome
I was interviewed for a postdoc position and I was so nervous but tried to respond to the question the best I can. I think the interview was OK but not to the best of my expectation. They asked me when can I start though. It was a 15 min presentation and 15 min Q&A. At the end I asked them questions but didn't ask when will I hear back from them and they didn't tell me either. Is it polite if I ask them a week after the interview (if there is no news sooner)? Or should I wait, say, at least 2 weeks after interview?

It is fine to ask for an update now, or to wait. But, unless there is some other option that makes early notice necessary, I'd suggest waiting for a bit.
In any request, however, it might be good to express, again, your interest (strong interest) in the position.
If you don't get a quick answer, don't fret over it. These things can take time.

Thanks Buffy, at the moment I don't have any other options, so maybe I will wait until next week. Just curious about how long is on average applicants heard back from the PI. Is early news tend to be good news for example?


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In IEEE, after the article undergoes the major revision and accepted, do I have a chance to correct a small error and submit the final version?
I have a journal paper submitted to the IEEE, and I have submitted the revised version for the major revision recently.
However, I have found a small mistake today, and this small error will not influence the main contributions of my paper, but this may mislead the readers.
I wonder if the revised manuscript is accepted by the IEEE, can I still have a chance to correct this small mistake?
Here I do not mean that the reviewers' work is not good, but this error is too cryptic to be detected.

Yes, you can make changes.  When submitting the final source, I often proofread a paper once more and fix any minor errors.  I have also carried out relatively major changes.  For example, I've even broken up a long mathematical expression that runs across the column boundary into multiple parts.


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How to cite the correct page number from the IEEE Access Journal?
I want to cite the IEEE Access journal including the page number.
For instance the following article has page numbers, but they are in the six figure range (i.e 198912 for the first page).
Surely this magazine cannot have that many pages in a single edition, can it?
Is there some encoding scheme of page numbers with this magazine, or can I just use these long numbers?
Apologies if this is super obvious, but I just want to make sure I am doing everything correctly.

Yes, the page numbers are correct.   It started counting from the first issue and IEEE Access publishes loads of papers, many have questionable quality.

Just use these numbers. They are correct.
IEEE Access is 100% digital. There is no print version. The page numbers are there solely for orientation (or perhaps because of outdated metadata-schemes, who knows).

Thank you very much!


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I want to do a research project in Mathematics. But I am getting rejected due to no research experience. How should I proceed?
I completed my undergraduate in Mathematics in 2018 and masters degree in 2020. After that, I taught in a college for two years. I was not satisfied with my masters degree, and also was getting rejected from a lot of institutes for Ph.D. due to my masters college. So, 2022, I joined a good reputed institute to do Master's again. I completed my SEM I, with good marks. I am way more serious than I was before, regarding my career and my studies. Although I have good teachers here, there is a lack of guidance in some other things. I want to do a research project in during this course. I have applied to some good institutes for that, but they ask for research experience in the form, and since I have none, I get rejected. Also, maybe because I am doing my master's for the second time. I don't know what to do. How do I convince people I am focused and passionate about research in pure mathematics? So far, I have only studied and taught college courses, so I get empty headed when asked to write the statement of purpose. I have no one to ask to, friends or family. My teachers are not particularly from the field I wish to apply. They only suggest to read more books.
Can anyone please guide me as to how to overcome this block? How can I get a summer research project without having any experience? What should I specifically mention in my statement of purpose?
P.S. My aim is to do research in cosmic topology. The subjects I want to do a project is Abstract Algebra, Topology, and Geometry.

Do I understand it correctly that your current Masters degree is not finished yet (I don't know what a SEM is)? Do I understand correctly that you are looking for research internships at the moment, before having finished the degree, rather than for doing a PhD once more? It may help to say in which country you are, and where you look.

Your teachers’ advice is good — you should read more books. Mathematics research is not something you typically jump into early. There is a lot of background knowledge to learn before you are at the stage where you can contribute to active research. You can do this no matter what program / institute you’re at. So it’s generally good advice, especially from someone who otherwise isn’t involved in the fields you’re interested in so can’t give more specifics.

@ChristianHennig Yes, my current master's degree is ongoing. SEM is semester...so as of now my second semester is going on and after this we have a 2.5 month break. During that break, I wish to work on a research project. Many institutes offer such programmes, and I have applied for those. But rejections are making me question my decisions as what exactly am I doing wrong and where can I improve so I can get selected. I am from India, btw

@Eric I do take that advice seriously. But I do want to proceed to the next step. I want to work on a 2-3 month project and since I have no prior experience, my statement of purpose feels empty. Also, I am having a hard time writing about the content I read in my SOP.

@user519535 Please add relevant information to your question rather than just posting it as comment.

@AnonymousM For students who have completed their first year of masters, many institutes offer 2-3 month visiting programmes. Here, if selected, the student goes and does a project work under a faculty of that institute. It's a common thing here...in India....and preferred by many who want to pursue Ph.D.

@user519535 My impression is that there is far more interest in research internships than the number of places on offer. The problem with these is that there is quite some risk that there is far more effort required to get the student up to what should be done than the amount of work that the supervisor "wins" because it's delegated, so supervisors shy away from students they don't know and who have little experience. This can explain your experience, it doesn't mean you do anything wrong. You'll be in a better position even for a PhD if you finish your current degree well.

I don’t know what you should write in your statement of purpose. However, you could consider asking your current faculty to reach out to their peers and help you secure a summer position if you think they believe in you and your potential to do a PhD. I am in a totally different field, but my masters faculty would have been more than happy to send some emails on my behalf when I was a student. I would do something similar for my students if I thought they were highly competent.

Coming from Physics, my impression is that you need a lot more training before you can begin to do meaningful research into mathematics than you have to do for physics. When I did my honours (master's equivalent) me and all the other physics students did some basis research, while the maths honours students basically did a lit review. So maybe you should change your goal from doing research to doing a guided review of a topic/review a paper and learn how everything in the paper works and how it fits together (which is what I think the maths honours students did).
I also noticed a master's thesis from university of Helsinki on your topic of interest: https://arxiv.org/pdf/1612.04157.pdf which I noticed described itself as a comprehensive review.
The other thing to keep in mind is if you go to a mathematician and say you want to do cosmic topology, then they are going to wonder why you are coming to them to do a physics research project (its really mathematical physics but I've noticed pure mathematicians call it physics, and physicists call it mathematics). So that might also be leading to rejections.
Another thing to do would be to find out if there are any weekly mathematics seminars or reading groups on a topic you might be interested in at your university (or possibly if there are any that run virtually/hybrid) and ask if you can join. You probably won't understand most of what's going on but you may be able to build relations with other mathematicians and perhaps then they'd be more likely to take you on as a research student since they already know you.


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How to add bibliographic data to a Google Scholar article?
A recent article of mine has just been successfully crawled by the Google Scholar robots; however, since the article is quite large (>40 MB), only the abstract and some basic journal metadata was extracted, and not the article's PDF itself. This has meant that none of the article's bibliographic information has been processed (and, as such, none of the articles cited by my article have had those citations recorded within Scholar).
Is there anything I can do to attach that missing bibliographic data to the article on Scholar manually? Would it help for me to upload the article (or its bibliography) somewhere else entirely and wait for Scholar to crawl that? I notice that some other services (such as ResearchGate) have successfully extracted the article's bibliography - will that make any difference?
Ultimately, what I'm asking is: is there anything I can do to make it possible/easier for the Scholar robots to extract the citation data correctly from this paper?
Any help would be greatly appreciated.

On your Google Scholar profile page, you have two 'tools'

the + to add article (preselected and manually)
the edit option when you click on one of your articles.

Is there anything I can do to attach that missing bibliographic data to the article on Scholar manually?

Click on the article, select edit, input missing bibliographic entries.
NB: GS is missing key metadata fields. You can input the minimum to make your article citable/searchable!
Wonder why DOI is not available!!

PDF

Under "Public Access", you might be able to upload a copy of your article (if it's open access or has a mandate).
I must acknowledge this doesn't work well at times.

Would it help for me to upload the article (or its bibliography) somewhere else entirely and wait for Scholar to crawl that?

It should help. Ensure, it's 'available'. Upload to well known repository (subject to articles right).
You may also want to take a look at indexing of websites with scholarly articles in Google Scholar


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Coauthor copying text - is it plagiarism, and what should I do?
Someone I coauthored a paper with a couple of years ago has recently posted a new preprint (with some new authors) in which several paragraphs have been copied from this earlier paper; at least two paragraphs have been copied verbatim, with several others copied with only trivial modifications made to certain words. The new paper does cite the old paper, but only in the introduction (i.e. not within any of the relevant sections in which text has been copied), and in particular does not give any indication that any of the text has been copied from elsewhere (e.g. there are no quotation marks, no "as first described in...", etc.).
Here's where it gets slightly more subtle: I actually have proof (in the form of records from our collaborative Overleaf document) that all of this text was written by me, and not by my coauthor. However, despite writing this text, I am not credited anywhere within this new paper, except for the aforementioned citation to our collaborative paper in the introduction (my name does not even appear in the acknowledgements).
A couple of questions, then:
(1) Does this constitute plagiarism?
(2) Irrespective of whether this formally constitutes plagiarism or not, what can/should I do about it (if anything)?
Many thanks!

In what field are you? Since you mention overleaf, is it Math or Computer Science? What does "two paragraphs have been copied verbatim, with several others copied with only trivial modifications made to certain words" mean? Do they concern the context, notations, etc? Are those paragraphs the main core of their paper?
Do you consider you should be acknowledged for your work in the previous paper? Just ask yourself these questions before making waves.
Verbatim copying is sloppy from their part, but I guess the paper does more than just those plagiarized paragraphs.

With or without citation, this sounds like plagiarism. I can't imagine a scenario where copying entire chunks of published text (outside of a direct quote) would be acceptable. And as @Buffy mentioned, there could be some legal/copyright issues on top of the ethical concerns.
You should absolutely contact your former collaborator as well as the other authors. This sounds too egregious be be an innocent mistake but, in any case, the easiest solution would be to get them to fix it before they submit it anywhere. A side note, assuming they want to submit the manuscript somewhere remotely reputable, this would probably be caught by even the most basic plagiarism checkers...

If done without citation it is plagiarism an/or self-plagiarism. But, it might also be copyright infringement if they aren't the copyright holder. If you haven't given up copyright to the earlier paper then you likely still have a copyright interest.
You should just inform them (all authors) of the problem and ask for a fix. Don't just inform your previous collaborator.
It may have been just sloppy work and not an intent to infringe.

Apparently, rampant plagiarism happens in Stackoverflow answers too.

It is plagiarism, specifically self-plagiarism if submitted to a journal.
You need not worry about it as this will be caught by plagiarism detection softwares immediately after submission.
Other than that, you can contact the author directly as request them to rectify it by citing your joint paper and rewriting the section or add you as a coauthor, so that you could rewrite for them.
Beyond that you have no rights as of now unless its published by a journal (unlikely), then you could contact the new  journal as well the original journal where it was published.
I would contact the author and if they do not agree to suggested changes, would leave it the journals to sort it out.


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Choosing between very different presentation topics for PhD application
I have an interview for a theoretical physics PhD position next week. I have been requested to prepare a 10 minute presentation of some of my recent work for the interview. Herein lies my dilemma: my Masters thesis, which I am very proud of, contains original results and showcases my abilities well, but lies in a different field than the field that I have applied for (think hep-th vs cmt). Some theoretical skills may be transferable to this new position.
However, last summer, I performed research at a different lab in a similar field to the one I am applying for. The research was much less organized, a combination of various experimental and computational projects - not theoretical. One of those projects led to co-authorship on an upcoming publication, but I don't believe it showcases my abilities as well as my Masters thesis and I am a bit less familiar with the topic and slightly less confident in my methods. Since I only have 10 minutes, I assume that I should limit myself to one research project only. Which one should I chose?

I see two options. One is to choose the one you think best, maybe the first, but add a sentence or two at the end pointing out the other. Less than one minute here, though there may be questions after you finish.
The other is to ask whomever you are communicating with which they might rather see. Explain the options as you do here.
Good luck.


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How should I balance risk when choosing between two PhD offers?
I recently completed a Masters in theoretical physics. I was fortunate enough to receive two fully funded PhD offers in Europe with very good groups in their respective fields, and am having difficulties choosing between them. They both pay the same, are in comparable cities with similar commute times, have enthusiastic advisors, etc.
The first would take 4-5 years, is in an experimental condensed matter physics group but with very very strong connections to a theoretical physics group at the same institute, with opportunities for co-mentorship with them. The funding for research is virtually unlimited. I spoke to some people in the know, who told me "the group is very prestigious and strong in technique, you will publish amazing papers, and the group's PhD and postdoc record is unbelievable." However, the group leader is very focused on certain topics and does not allow too much freedom outside of them. I am indeed quite interested in the theoretical aspects of the research there, but am afraid that if my interests drift too much outside of there, I might end up unhappy, since my current interests already lean on the less applicable side.
The second offer would take 3-4 years, is in a relatively applicable field of high-energy theory (but not particle physics, which I would not be interested in doing) that has a larger community in Europe than in the US. I wrote my thesis on a topic closely related to this, and I could jump right into some very exciting work. However, it is a small community and career prospects would likely be worse than in the previous case.
The bottom line is that I can choose to either 1) be risky with interests now, guarantee academic career 2) guarantee interests now, risk academic career. The difficulty lies in that judging the risk levels involved with either is very difficult. Are there any crucial factors that I may have missed that I should take into account? Does anyone have a personal experience similar to mine? Did you end up happy with your choice?

This is a decision only you can make...

Indeed. I am really only asking for insights that would come more naturally from people in these fields and for which I do not have the knowledge or experience to know off the top of my head.

I am not familiar with your field, but in general, I think the biggest risk here is calculating with any guarantees.
Say you pick option A. Even if you work on something you are not happy with for 6 years, there is NO guarantee whatsoever that there is an academic career at the end of the line. So, it is up to you whether you want to work on topics that you don't prefer (are you sure that you might not learn/grow to care about them if your advisor really is so amazing and the surroundings are inspiring? can you still switch fields after or will you be working this for the rest of your life?) to best prepare you for an academic career (assuming this is true with said advisor and group).
Say you pick option B - can you guarantee that your interests are met? How important is field size in Europe and US (unclear to me, but you mention something about it so maybe important to you?) If it is a smaller community, that might also mean less competition? Or a faster way to build a network with key people?
Go about this the scientific way: list all possible parameters and pros and cons you can come up with, do the math (i.e. score all of them). Ask advise from mentors/friends etc. And then follow your now well informed gut.


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How can I convince the universities that I am applying to for Ph.D. program for accepting the reference letters given to me by my referees?
I am in the process of applying to overseas institutions for the phd programme. For this purpose, my referees have already provided me with the reference letters as I am applying to the multiple institutions. So, they are unable to find time for filling the reference request forms. Unfortunately, most of the universities are asking for online reference request which I know my supervisors won't be able to fill it due to the time constraints. So, I fear on losing out on the applications of interest. Please guide me through this.

Does this answer your question? How frequently can you ask for a personal reference without being disrespectful?

There is nothing you can do but politely ask of your referees that they understand your situation and fill the online form.
There is simply no way my school will accept reference letters supplied through the applicant, and no amount of convincing will change this: there is just too much fraud with LoRs supplied by students.
Even if your referees fill the form online, expect (depending on the country) that they may be randomly contacted via their university or institutional email address to confirm the contents of the LoRs.  Again, there is just too much fraud with applicants (or sometimes their agents) creating or controlling false emails.  Be advised that our school logs the IP address of people filling out reference forms.  I suspect other schools have similar policies.
Regrettably, we have seen (international) applicants arriving under false pretences, leading to absolutely horrible situations.
Finally I would personally automatically dismiss as not fully frank any LoR that is not confidential and has been seen by the applicant.

This really depends on the country, you're not very specific. But my gut instinct is that, if your referees really wouldn't find the five minutes it takes to fill out one of these online forms, they wouldn't actually want to support you.
But my guess is that your referees will be happy to support you, you're just too shy to ask them to fill out the online forms! Can't say I don't understand you.

I am not sure I agree. Yes, it's probably only 5 minutes for one graduate school for one student. But, if the professor has 20 students applying for graduate schools, each student applies 10 schools, then the professor has to spend 20 x 10 x 5 minutes to fill out online forms. That's 1000 minutes, more than 16 hours. It's quite a lot of time for a busy professor.

@Nobody it is then incumbent to the professor not to agree to write so many letters of support.

I think it is just rude by the institutions not to provide an upload option for a fixed reference letter. That's what I am usually encountering: the possibility of filling a form or else upload my own written reference letter. The latter can be done a number of times without undue burden.


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PhD rejections from schools of similar tier and telling potential advisor about it
I am an international applicant and I applied to several schools in the US as well as the UK (and one in the EU) for PhD in this cycle. I got accepted with funding from one of my top preferences in the UK after a (really good) interview with a potential advisor (a global top 5 university), and I am looking forward to it (I have not accepted the offer, not received a formal letter, and I am waiting for some other results). I have received rejections from some of my preferred departments in the US (and I understand and respect that), but one of my applications did not even make it to the committee because it was "filtered out by postdocs" (found upon inquiry). I am feeling a loss of confidence, mainly because of the last part. I am posting this question here for the following point:

Of course, I will be honest with my potential advisor if asked (she has also shown interest in my applications and is in general very understanding). Will this make me look bad to her or make her lose faith in the decision? I think I will be a good fit for the group, but this makes me look bad on the competitive scale. I don't want her to think that she made a mistake by accepting me, when other programs of similar tier have rejected me. This may come up because I am scheduled to meet with her soon, before I give my decision to the admissions office.
How should I take in these decisions myself? I do think I should ideally be happy with such a result, but this still bothers me.

You are basically asking: "someone else thought I was not good enough for their programme, will my potential advisor think less of me because of this?" If she has no confidence in her own judgment and needs other people to tell her what to think, yes. Otherwise, no. So, probably/hopefully, no.

Admissions are a numbers game. If there are 10 great candidates for 3 spots, well, 7 have to be rejected.

It's very rare for people (even highly competent people) to be accepted everywhere they apply. This is even truer when applying for a real job rather than a PhD (e.g. you could be rejected 30 times before acceptance), so get used to it and don't let it destroy your confidence!

On the face of it it seems like you respect the rejections more than you do the acceptance. Why?

Was your potential advisor ever turned down for a job?  If so I'm sure she'll understand.  If so, would that change your view of her?  To the point: this is not as big of a deal as you are making it.

She'll be happy you were rejected at the other places, so she doesn't have to worry about you picking a different place to do your PhD at.

From my point of view your question shows a somewhat unhealthy obsession with notions such as "global top 5", "similar tier", "competitive scale", and "look bad".
I think the advice that you need at the moment is simply: Relax!
It's very unlikely that your future advisor will "lose faith in the decision". Most professors are very confident to form their opinions on their own, also if other people make different decisions.
You got accepted into a good PhD program, you say your're looking forward to it, and as far as one can tell from the question you seem to have a decent future advisor. Now it's time to enjoy the journey. Life is not (only) a competition.

Indeed when I look back at my question I understand I care about those notions more than I should, perhaps rooted to the 'educational surroundings' I grew up in, thanks for pointing that out. I understand why it can be unhealthy, It's something I need to work on for sure.  It's definitely good to think that other rejections won't waiver the confidence of my Potential Advisor, thanks for that remark.

@Mathaddict I would highly recommend watching the video Is Success Luck or Hard Work? by Veritasium. Provides a different perspective that I think you will benefit from.

@Mathaddict when competing with the best on paper, being number 1 everywhere is statistically impossible. Someone will dislike your nose, your courses, your papers, your aura or whatever.

If I thought a student was good and I then learned that their application to another university had been filtered out by some postdocs, I'd probably think "Well, that other university made a mistake by having postdocs filter the applications." That's certainly more likely than "I must have made a mistake in evaluating this student."

Congratulations, you are an exceptional student that got into a top program. I am so sorry that you have to live with the fact that while you are exceptional, you may not be the most exceptional (read that with sarcasm).
If it comes up, be honest. Your advisor is well aware of your strengths and weaknesses as an applicant/candidate and chose to hire you. Now focus on doing well so she does not regret her decision.
In academia acceptance and rejection after a certain point becomes about fit. Obviously, your future advisor thought you were a good enough fit to support you. That's fantastic.

I think I will be a good fit for the group, but this makes me look bad on the competitive scale.

You're past that stage now.  The competition is over and you have won. Congratulations!  Your task now is to figure out how you can best achieve your academic goals and contribute to the work of this group.

This may come up because I am scheduled to meet with her soon, before I give my decision to the admissions office.

Actually, I doubt that it will come up.  There's no need for you to proactively bring up the other schools you applied to.  This doesn't have anything to do with being "honest" or not, it's simply irrelevant and none of her business.  Likewise, it's unlikely that she will ask you about your other applications; it would be tactless.
The focus for the meeting should be on the future: what would it be like to do your PhD at this university and/or in this group?  Is it a good mutual fit in terms of research interests, skills, expectations, workload, standard of living, etc?  The meeting will go fast; use the time on stuff that matters now.

It may be unusual to ask where the student applied, but in my experience it appears common to ask what other offers the student is considering.

In addition to the above, different universities have different priorities and criteria. Even those that are considered of similar 'tier', age or are otherwise grouped together.
These different priorities/criteria are effectively one large experiment to try and get the best candidates, that unfortunately has very real impacts on people like you. [1]
Don't take it to mean you are a worse candidate than those who got offers to the ones you didn't, the fact that both you (and obviously your potential advisor, given they gave you an offer) think you are a good fit for that team means that their methodology works.
It is a lot better to be with an advisor you can work well with, and in a group you are happy with, than be in one you hate, simply because it was ranked marginally higher by a quite arbitrary ranking system 2 years ago.
Also, Universities and in particular potential advisors, will likely have different opinions of your uni, especially as it is an international one, they may have had limited interaction with other graduates, so limited positive or negative experience can drastically shape their attitudes towards the quality of education for the uni as a whole.  If this is a factor, it's not your fault and there is not much you can do. [2]
Finally, you might not have got into your absolute dream uni, but you still got into a program you consider one of the best, and you should be proud of that.
[1] My universities current entrance criteria for my program has been the subject of continuous study, adjustments and experimentation for over 20 years. It is entirely possible that the uni that rejected you bluntly was simply trying something a bit drastic that they thought would improve candidate quality, whether it was the 'right' choice, I couldn't say.
[2] Slightly different, but there is a local uni that is generally considered '2nd tier'. Not bad, just not the best. However, I know a number of people that will hire people far more leniently from there than the so-called 'top' unis, as the consider that the quality of education is drastically better in their fields. They are only basing it off their own anecdotal evidence, but they are only human, much like those in charge of phd programs, so previous bias can have a large effect. 1 of these people even graduated from one of the 'top' unis, but now (admittedly quite a few decades later) strongly recommends the lower ranked uni to prospective students, and favours it amongst graduates.


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Not included as an author in 2 publications
Tldr: I was not included as one of the authors of 2 papers. What to do?
History: Around 2.5 years ago I started a PhD. I was producing very good results and my supervisor was very happy because there was a lot of data that could be published.
We did not have a good relationship, however. The relationship became very toxic, to the point that I had to look for psychological help. My therapist recommended I leave my PhD position. I put myself and my mental health first and took that recommendation.
Before leaving I talked with the Dean about my situation and the details of what happened. He recommended I put a formal complaint against my supervisor. After thinking about it, I didn’t file a complaint because I had a new job and didn’t want to think more about it.
When I left, my advisor and I did not end up on good terms because he “felt I was putting him in a difficult position and I was not appreciative of the opportunity he gave me”.
The other day I randomly found 2 papers that were published by my former supervisor, both on my research. My name was nowhere on the papers. Some experiments were copy-pasted, some were polished (but used a strategy I developed), and some were new.
What should I do?
Is there any chance to get my name added as a co-author? Should I escalate this?
Personally: I feel his decision not to add me was intentional as a punishment. The job I do now is not related to academia and I would not “need” the publications. However, I worked a lot and got those results during a time that was very difficult for my mental health. I subsequently feel my work should be acknowledged.

I know one such case. It happened to one of my former students. After he left his first postdoctoral position, his former supervisor "punished" him like that. Fortunately for the guy, he had on his hands a considerable volume of proof of his participation in the disputed research: e-mails, computer programs. So he complained to the university authorities. After the university refused to act, he filed a lawsuit.
This endeavour lasted for several years. Eventually, the university hired a top lawyer who examined the case -- and recommended to the university to settle. As a part of the settlement, the university was obliged either to retract the publication or to ensure that the postdoc's name be added to it. The university also paid to him an undisclosed sum of money. The postdoc, on his part, agreed not to disclose the story.
Amazingly, the guy managed to defeat the university without hiring a lawyer. He himself was representing his interests in the court and in the subsequent negotiations. This does not mean that his victory came free of charge. He paid for it by his time, energies, health. Also, by the end of this saga he got so tired and strained that his relations with his wife deteriorated badly.
Now, questions.
(1) Do you have in your possession a formidable volume of proof to produce to the university authorities or in the court of law?
(2) Do you have enough time and health to allocate for this battle? Or enough dollars to hire a good lawyer? ('Good' means: having not only legal but also academic experience, and knowing the university realities.)
(3) If your answers to both questions above are affirmative, would the win be worth the trouble? Would it not be better to allocate your resources for activities more productive than litigation?
The old rule "pick your battles" is still in force.

+1 for pick your battles. Apart from or in addition to contacting the university, you can contact the editor. The paper would either have to be retracted or you are added as author. You may want to give COPE and Retractwatch a reading


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Should I inform the graduate school about the notation of academic dishonesty on my transcript?
I got a notation of academic dishonesty on my BSc’s transcript after I received the conditional offer from a top graduate school. I submitted the application very early before the notation was added to my transcript. Now I received a conditional offer from the school. They’ll give me the official offer after I get the final transcript and degree certification, which is in June. Will the school withdraw my offer because of this notation? Do I still have a chance to get matriculated after I send the official transcript?
Should I inform the school in advance about this notation on the transcript? Or I should wait until they check my transcript? I’m not sure if the admission team will look very carefully at my transcript. (Since they have no requirements on my cumulative GPA.) I am worried that if I tell them right now, my offer will be withdrawn. Since the top school has lots of competitive students on the waiting list, they’ll probably reject me. Maybe I should wait until later in May, maybe there are some extra positions left, and although there’s a notation on my transcript, I’ll probably have a chance. But I also worry if I wait until they find out, I’ll be regarded as not honest and transparent to them.
I don’t know how should I do currently. Since the incident happen, I lived under regret and self-accusation every day. I’ve really learned from this and I’ll never let this happen in my future study. Now the offer from my dream school is just in front of me. But I may be going to lose it.
Does anyone know what is the right thing I should do currently? I am very hesitant to send the school an email to tell them in advance.

Can you please clarify what the notation will mean for your BSc degree?

It is disastrous for me to have notation due to academic dishonesty in my BSc degree, it occurs because I have some similarities in some questions with another student in a take-home exam.

I assume that the disciplinary action for the dishonesty was already carried out in the past by your BSc university. I don't seem to understand why they would want to add a notation in the transcript. Is it possible to meet with the top people (registrar, chancellor or dean, whoever) of your Bsc University and try to explain - why you truly regret the act  and how this hampers your future, how you already bore the consequences, etc, etc and if they can issue a new transcript without the notation.

The whole incident happened after I submitted the graduate school application. It’s a course I took in the last semester. I tried to submit an appeal but was unsuccessful. Since the evidence was clear, it was totally my fault, I shouldn’t talk with another student even if it was a take-home exam. My school didn’t give me any chance. I am trying to contact the dean's office (I wrote an email last week but haven’t got any reply yet.) I think there is very little probability of removing the notation.

Most importantly, please do not (once again, DO NOT) live "under regret and self-accusation every day". This will not change things, but may be damaging to your psychological and perhaps even physical condition. No matter how important your academic attainments are to you, please rest assured that your health is infinitely more important. Set your priorities right.
Regarding your notation. I am not in a position to advise, but I wish to ask this question: what does it exactly mean to inform the graduate school about the notation? Won't you be informing them of it by simply submitting your transcript? Won't that, by itself, be a disclosure of the existence of that notation? You are not going to hide anything. If they look attentively through the transcript, they will find the notation. If they do not find the notation -- then good for you. One way or another, no one will be able to accuse you in hiding something.
Or is there any special regulation at that school, requiring you explicitly to inform them by a separate letter about any major development?  I doubt this.

Inform the graduate school means I will tell them in advance before sending the final transcript. Since I have not yet finished all the courses, I need to wait until May to get the final transcript. I am unsure if it is better to inform them now or wait for them to review the transcript.

The only requirement that the school gives me is to submit the final transcript and degree certification before July. I asked an advisor (not a professional), and he suggested I do not inform them in advance, wait to send them the final transcript, and if the school has doubts about this notation, they will probably let me write an explanation separately.

@Betty I would be acting strictly by the rules. If the rules require you just to send them your transcript -- then so you do. No additional moves that are not explicitly required.

I think the dilemma is that when Betty sends her transcript, they'll see the notation and could potentially revoke her admission, at which point it will be too late to make other plans. Whereas if she discloses this incident proactively and gets an answer now, she'll have more time to make other arrangements if necessary. And the odds that they do revoke her acceptance may be different in the two cases, though this will likely be impossible to predict.

It seems by what you have written that you looked to what is required by the application standards in terms of what you need to divulge. As many have pointed out, you are not hiding anything, though that could be considered a technicality . In an adversarial setting such as a court of law, this fine line might be just the thing to win a case.
Is that on an ethical level enough?
What does honest mean at this school?
Have you looked to academic dishonesty policy for students at this university? Could these rules inform you of the level of honesty expected at this particular university?


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Is it appropriate for a teacher to make a sex analogy related to physics?
My physics professor was talking about the companion forces that act on an object with molecules interacting with one another and Newton's 3rd law canceling out the internal forces. Then he said something like “do you have to put all the little forces? No it’s not necessary, but you can. This will be a bit unsettling but your parents may tell you “don’t have sex” or else you may have to deal with a child and other stuff. But it’s like you can, but you’ll have to consider the consequences. So it’s not like “don’t do it” but you can, but consider the consequences” (it was much longer than this but this is the jist)
It felt like an analogy that could've easily been replaced for something more appropriate. It kind of threw me off center and felt irrelevant. Was this comment appropriate for him to make?

I don't know that I'd characterize this as a "sex analogy" per se but it doesn't seem to be either useful nor particularly vulgar, it seems like a poor attempt at humor and the reference is really to prohibitions by authority rather than about sexual activity, besides acknowledging the mechanism by which humans reproduce and the tendency of parents to want their kids to plan their reproduction.
If you were the instructor asking, I'd say drop it: risk that it's taken the wrong way for little to no benefit.
As the student asking, I'd recommend just forgetting about it. If you have an opportunity for anonymous feedback you could mention it made you feel uncomfortable.

It probably was a poor attempt at humour. I agree with your answer, BTW, and upvoted. One needs to be very careful these days with jokes. They say the only safe jokes to make these days is about oneself and about lawyers. And I wait for the moment when the latter will be the matter of lawsuits, too. And, when that happens, of course, there is not a chance of a snowflake in Death Valley to win that one.


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What to do if you've organised a conference at current institution but been offered a job elsewhere?
Asking a slightly unusual logistics question about changing academic jobs with future plans in place. I have organised a conference which is due to take place at my current institution next year, but I have just been offered a new job elsewhere (and therefore would no longer be employed where the conference is due to be held). Is this normal? What do people tend to do in this situation? The options I can think of are:

Ask very nicely to still host the conference at my former institution, even if I no longer work there
Try to move the conference to the new institution (problematic as the call for papers has already been released and I don't want to make life difficult for participants)
Turn down or ask to postpone the new job (but that would be a 7-month delay, which is almost definitely pushing it!).

Does anyone have any advice?
Thank you :)

I'd suspect this depends on the institution, your former and new contract, the current state of organisation, and maybe some other details. If your job offer and your willingness to take it isn't a secret, talk to everyone affected at your current instituion like head of department, room administration etc. to find out what your position is and what your options are. Also, are there local collaborators in the conference organisation who will stay at the current institution?

I am not sure I completely understand your question: is the solution to hand over to someone else in your current institution off the table? (i.e. you absolutely want to organize this conference for some reason)

What would the fallback arrangements have been if you had fallen ill and been unable to host?

Moving the conference seems like the worst choice. You disrupt the plans of too many people since it has already been advertised.
Turning down the job seems also to be a bad choice if that job would enhance your career. And, it shouldn't really be necessary.
If your current department head knows of your plan to move (and they should, once you accept), then work with them to make the conference happen just as if you were still there. You don't actually need to be on the faculty of that institution to take a lead role in the conference.
But, I also suggest that you convince one of the current faculty to join you in leading the conference. This should allay any discomfort at this institution and also provide backup for things that occur along the way.

The last paragraph seems key. If it's hosted using university facilities you're highly likely to need an insider to deal with booking venues and catering.

Hopefully the conference organization does not depend on your work only. It can of course also be an option to pass on all conference related duties to somebody else as soon as possible, just like most other tasks when transitioning from one place to another. Organizing a conference is a lot of work, but not incredibly difficult, so somebody else should be able to pick up where you leave. There is nothing fundamentally wrong with handing over tasks, and you are free when starting your new position.

Asker didn't indicate willingness to not host it, but how to host it given the situation.  Or, that's how I interpret his list of ideas so far, anyway.

@RubelliteFae, OP asked for options what to do in the given situation. I found it surprising that the obvious option in my answer is not in OP's list, so decided to write it down. Depending on where in the world OP is and what kind of contract OP signs with the new employer, OP might also have to discuss this with the future employer. And they might just not be happy with OP working on tasks for a past employer. Then letting somebody else take over OP's role could be the only option.

In a perfect collegiate world, your new employer would be fine with you organising the conference, and your old employer would keep you on as an (unpaid) adjunct in order to give you staff-only access to the university to organise staff-only type things.
I would go for option 1. It is a win for your old institution to host the conference; they get all the glory for it, and someone else is paying your salary!


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Found error in my journal paper, correct preprints?
I found an error in one of my journal papers several months after publication.  The error doesn't affect my results, but I mistook the prior state of the art.
I misreported a feature of a prior work. I said it has a feature that it does not actually have and therefore improperly credited it as holding the previous record for best performance for products with that feature. As a result, I credited the wrong prior work for setting the prior state of the art. My paper boasts a 2x improvement over prior work but it should be 4x because the performance of the real prior record holder isn't as good.
I've already emailed the journal editor and waiting for a response about whether I can/should issue an erratum.
My question to the community is: Should I fix the preprints that I uploaded to various repositories (techRxiv, research gate, etc), regardless of what the editor decides? Is this a common way to address publication errors? Would it create confusion if the latest preprint upload date is several months newer than the published paper?

I have not had this exact experience, but I do not think that fixing the preprint would cause confusion. You could add a note highlighting the change and indicating that it is not yet reflected in the published version.
If you're concerned about running afoul of some fine print from the publisher, you can always wait. Since this doesn't affect your results, there is probably no harm in being cautious. But as long as you are complying with the journal's requirements for preprints, updating it to reflect a minor correction should not be an issue. You've already taken the step of informing the journal for an "official" correction and will change the preprint eventually anyway. You should double check that there are no rules about modifying the preprint after publication though.


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Why can the same person sit on the boards of trustees of multiple schools? Has this caused problems?
I was reading this dude's Wikipedia page and it caught my attention that he seems to have served on the boards of both Chapman University and Caltech. Although his status on Chapman's board of trustees has turned "emeritus chair"1 there seems to be significant overlaps between his roles. He chaired the Chapman board from 1976 till 20012, and has been a Caltech trustee since 1992, a life trustee since 2008.3
I'm assuming this practice isn't unheard of or even uncommon. Has it never become a conflict-of-interest issue? Why isn't it one considering universities are vying largely in the same pool or pools with significant overlap for potential donations, resources, federal and state fundings, local investment opportunities, and even land when those schools are in geographical proximity as is the case for these two schools.
In the corporate world people can sit on multiple boards as long as the companies they serve on the boards of aren't competitors. Another fact is that higher education has been compared to the corporate world a lot and a lot of university administrators in the U.S. are paid corporate level salaries.

Chapman and Caltech are not exactly competing for the same students or grants.

@JonCuster They both claim to be the top-tier private research institution...

They're not private companies.  They are not really in competition?

Caltech and Chapman are separated by 40 miles of SoCal sprawl.  I'd hardly call that "geographical proximity" and I highly doubt there is any competition between them for land.

Such conflicts are often handled with disclosure and recusal.  I'm sure both universities were well aware that he was also on the board of the other, and in the unlikely event of an issue where his duties to them really were in conflict, he could recuse himself.  That would surely be so rare that it wouldn't significantly reduce his effectiveness as a board member.

@NateEldredge Urban universities can hardly continue their expansion contiguously. Most urban universities have to invest in land that sometimes doesn't situate in its immediate adjacency but rather a ways away. More famous among possible examples is NYU's expansion in Brooklyn and on Governor’s Island. There are also countless cases where universities purchase campuses or carry out mergers in a different city, or even across the continent (Mills, Monterey, and so on and so forth). So in that context, I'd consider the Chapman and Caltech in geographical proximity.

Trustees of private, charitable institutions are usually expected to give substantial amounts of money, eg, 6 or 7 figures a year. Is this person wealthy enough to contribute to both universities?


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What tools exist for organizing the most recent papers covering a specific topic?
Inspired by the recent post, How can I be up-to-date on recent papers, practically?, I want to know what tools exist for finding recent papers (pre-print and published) on specific topics.
The recent post focused on how to stay up-to-date on a field, in general. Many of these answers provide helpful tools when trying to stay up-to-date on a broad field. (For example, benty-fields provides a nice daily arXiv display, but can only filter by broad, pre-defined terms). I am interested in a tool (like a website) that can organize papers published on topics that I can specify with a search term. I am not looking for email alerts.
The best thing I have found has been a Google Scholar search with custom keywords, filtered by most recent. If this is the best tool for my specific case, I can work with it. However, it would be ideal to not have to redo this search every day or deal with Google Scholar's slow indexing. Additionally, if the tool has more features, like saving to a "read later" list, that would also be great.
Does anyone have any tips?

Is there a particular reason why you do not want to use email alerts? You can request email updates based on defined searches in many of the aggregate search engines. It would be easy to automatically separate these emails into a dedicated folder and peruse them at your leisure. You may consider using RSS feeds in conjunction with a reader program. Many journals and databases still provide RSS feeds that summarize recent publications (though this a bit of a dated method and likely even less convenient and flexible than email).

I'm having a hard time understanding what you're looking for, since you hav exlcuded email alerts and you acknowledge that a database (e.g., Google Scholar) search with a set of custom search terms does the job. When you say, "it would be ideal to not have to redo this search every day", what's the difference between than and an email alert? And I don't understand what you mean by "Google Scholar's slow indexing". I don't think you will find any source that updates the most recently published work faster than Google Scholar. Please rewrite your question to clarify what you are looking for.

Perhaps you could rewrite your question by describing what exactly this tool you are looking for would do and clarifying in detail how Google Scholar's email alerts do not do what you want.


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In that scenario, how will the editor handle my academic paper (a revision)?
I submitted a paper to the Elsevier journal and got positive feedback from the editor and two referees with only 8 comments. However, after I submitted the revision, one of the referees declined (or ignored) and another accepted the invitation to the second round but didn't upload any review report. So, how will the editor handle this paper???

What happens if, after revision ...

A reviewer declines to review the revision (or does not respond). The editor has several options. They can 1) check the revision themselves, might not be possible if they lack the subject expertise; 2) invite another reviewer; 3) make a decision anyway.

Accepts the review invitation but then goes incommunicado. Same as previous, with an extra option 4: wait.

Thank you for your kind answers. The editorial board has withdrawn the review invitation and hasn't sent extra invitations. Perhaps, they might check the revision themselves.


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PhD advisor keeps insisting I define commonly used terms (terms of art)
I work in an NLP-adjacent area and while my advisor is pretty familiar with NLP in general, she isn't super familiar with the specific sub-domain I'm working in. While editing my paper, she strongly asks me to explicitly define some utterly obvious terms that would be extremely out of place in a typical paper for this venue (think having to define what "force" is in a physics paper).
I completely realize that there are times when even seemingly obvious terms can be ambiguous, but trust me when I say that this is NOT one of those cases.
When I point this out to her (even with evidence of other papers in the field), she gets super defensive and says something to the effect of "You are effectively saying that I don't know this field. Do you realize how problematic it is?" I wish she was at least open to the idea that NLP is such a fast-paced field that there might be something she doesn't know (and honestly, even reading one or two papers in my field will clear up things for her).
This may seem like a minor thing, but arguing about defining every small term that SHE doesn't understand makes me feel VERY frustrated, because I would either like constructive feedback on the ACTUAL IDEA OR I would at least like to be left alone in confidence that I know what I'm doing. Instead, I get nit-picked.
This was a bit of a rant, but any advice would help!

Could you define NLP for us here?

What is your question?

I think it's "utterly obvious" that the OP is talking about neuro-linguistic programming /s

Given the quotation marks around "utterly obvious", I assume that there is some kind of ironic joke here ... but since I assumed that neuro-linguistic programming was the subject being discussed,, the joke has passed me by. Enlightenment please!

@CrimsonDark: There're a few things commonly abbreviated as "NLP", including "non-linear programming", "natural language processing", and "natural language programming".  The joke presumably has another layer to it that we might not say.

I think you need to clarify what your specific question is.

Communication is difficult. Jargon and acronyms can make the message difficult to understand. It is easy to assume the reader knows what do you mean, but it is the purpose of writing to communicate properly.
As an example, I was once compiling results from many papers on the same topic, but written by authors coming from different scientific communities. One of the key parameters of the study can be defined in 5 different ways. Each of these 5 ways is very logical, and convenient in various situations, but they are incompatible. Some papers didn't bother to mention which way was used, which rendered the results useless for me. Possibly those authors didn't think of the other 4 ways to define the parameter.
It is not uncommon for good papers to start by explaining context of the study before progressing to details. This demonstrates a good understanding of the topic, as well as helps the reader to follow.

I wish she was at least open to the idea that (...) there might be something she doesn't know

Most scientists are well aware they don't know everything. This only supports the need for effective communication.
It is impossible for us to say what's going on in your papers, and between you and your advisor. However, if you are failing to explain to her what you are doing, it is not a good sign.

[W]hile my advisor is pretty familiar with NLP in general, she isn't
super familiar with the specific sub-domain I'm working in.

Do you only want your paper to be comprehensible to experts in the specific subdomain (as opposed to e.g. your advisor) who are intimately familiar with the jargon of the field as of 2023 (as opposed to 2018, or 2028)? Then by all means omit the definitions. But this of course means that you are saying that your advisor (and by extension, other experts in NLP who are not experts in your specific subdomain) is not part of the intended audience of the paper and that it does not matter if she can understand the paper easily or not.
Now, if it's your paper, it's your choice. On the other hand, unless you run up against a page limit, there is no downside to putting in the effort to make your paper accessible to a broader audience. The more accessible a paper is, the more useful it is to the scientific community. Isn't that the goal? Your advisor is simply pushing you to make your paper more accessible to a larger number of people, which is certainly what you should want.
Note that it is, in fact, entirely possible that you do know more about a specific subdomain of NLP than your advisor does, but this is very different from knowing more about how to write a good paper than your advisor does. The latter skill in particular involves learning how to write papers that are easily digestible by the actual reader, rather than the imagined reader who is familiar with all the "utterly obvious" terms.
It is common for Ph.D. students who have only really focused on one specific topic and interacted with one specific scientific subcommunity to falsely imagine that the definitions and notions they are using are common knowledge. In reality, scientists even from the neighboring subdiscipline might not be familiar with what you consider to be the most basic results and definitions from your subdiscipline.
Finally (assuming that you are correctly relaying what your advisor said), trying to browbeat you by claiming that you are doing something "problematic" if you imply that there are things she does not know about your specific subdomain is, in my book at least, not great behavior. Of course, a certain amount of intellectual humility from the student is expected, but certainly there is nothing "problematic" (in the sense of "morally questionable" or "potentially offensive") in disagreeing with your supervisor's advice.
P.S.:

and honestly, even reading one or two papers in my field will clear up things for her

Perhaps. Or perhaps the authors of those two papers decided to follow your logic too and did not bother to clarify their "utterly obvious" terminology either.

I would either like constructive feedback on the ACTUAL IDEA

She is giving you feedback on how to best present that idea. That is part of her job as an advisor, and it is part of your job as a PhD student to learn how to present your ideas well.

I don’t know anything about NLP, or what it even stands for, so this is more of a general point.
As a frame challenge, you should perhaps just for a moment consider that your supervisor knows better than you do about what’s an appropriate amount of detail to write in a paper. As a PhD student, you are at the beginning of your journey and there might be a lot of things that you don’t know and aren’t aware of. Being humble and listening to senior people is the best way to learn the unwritten rules of your field. You don’t need to bow down to authority, but you do need to have the maturity to when and who to argue with.
Take a moment to reflect on how she, as an experienced academic, might feel when a relatively inexperienced PhD student tells them that they know the right way to do things and she doesn’t. I think a lot of people would get defensive in such a situation.
My advice - just write the definitions. No harm can come from including them if they really are necessary and a lot of harm and ill feeling can come from acting like you know more than your supervisor does. Knowing which battles to fight is one of the most important skills you need to learn in academia.

+1 on "knowing which battles to fight" this is very important advice more generally too. Learning where to put effort and where to put up a fight, and to not take losses personally. You can really been yourself by fighting the wrong fight. I've burned myself many times fighting the wrong fights. I eventually learned better though!


text:
When Masters advisor said she will not gonna write a favorable rec letter to ph.d
I graduated from a Master's program in the US a couple of years ago.
I had a conflict with my toxic advisor.
It was a really really hard time for me.
I came back to my own country
and currently, I am working as a full-time worker.
However, I really want to apply for the Ph.D. program.
I talked about this with my master's advisor,
and she said I should get a good rec letter from my current supervisor in my workplace
so that it can cancel out her negative rec letter.
I am thinking about not getting a rec letter from her.
Actually, it traumatizes me a lot, I can hear her emotional voice in my head vividly
every time I think of her, even until now.
I don't know what to do....
Is that a big red flag if I don't get a rec letter from her?
Is it good to write about the conflict in my personal statement or anywhere?

There are many questions and answers already on this site that pertain to this very question.

@WolfgangBangerth yea... I've looked over it. However, I could not find a discussion on ideas to present in the essay for admission...

Is the rec letter from your master advisor compulsory?

@Tube that is probably the case because this is not a discussion site#

@EarlGrey no it is not systematically  required

I'm sorry to hear about the difficult experience you had with your Master's advisor. It's understandable that such a situation can have a lasting impact on you. When it comes to applying for a Ph.D. program, there are a few things to consider:
Recommendation Letters:
While recommendation letters can play a crucial role in your application, it's not mandatory to get one from every past advisor. Admissions committees understand that conflicts can arise, and they may consider other letters, especially if you have strong recommendations from other sources.
If your current supervisor can provide a positive recommendation that highlights your skills, work ethic, and potential for success in a Ph.D. program, that would be valuable.
Personal Statement:
You have the opportunity to address any gaps or potential concerns in your application in your personal statement. If you choose to discuss the conflict, it's essential to approach it diplomatically and focus on what you learned from the experience and how it has shaped your goals and resilience.
Focus on Positive Aspects:
Emphasize your achievements, skills, and experiences that make you a strong candidate for the Ph.D. program. Discuss your passion for the field and your commitment to contributing to research.
Alternative Recommenders:
If possible, consider seeking recommendations from other professors, colleagues, or professionals who can provide insights into your academic and research abilities.
Ultimately, the goal is to present a well-rounded and positive image of yourself in your application. If the conflict is a significant aspect of your journey and has shaped your decision to pursue a Ph.D., it may be worth mentioning, but do so in a way that highlights your growth and determination rather than dwelling on the negative aspects of the past.
Before making any decisions, you may also want to consult with mentors, colleagues, or career advisors who can provide personalized advice based on your specific situation and the dynamics of your field.


text:
Need help advising my life-science / biochem daughter on choice of major, career, and internships
My daughter will be starting her senior year of high school and plans to study a biochemistry related field in college. (Makes me wonder if biophysics might be up her alley.) She participates in the school robotics team as the "human player" and doesn't code or engineer, but may be the best human player in the state due to her attention to detail. She is very academically talented, artistic, and will have a large amount of AP credit transfers. As a bookworm, I see her mostly headed towards the researcher type roles.
As a computer science major, my knowledge of life sciences is practically nonexistent as well as professional networks of the same.
I am looking for some pointers for what kinds kinds of jobs various life science / biochem majors kinds of majors at a school like OSU (https://catalog.oregonstate.edu/college-departments/science/school-life-sciences/) translate to, so that she can make an appropriate choice of major.  We've been on a couple of tours already, but they spend most of the time talking about the facilities and don't get have the knowledge and experience to talk about anything too deep.
I am also looking for some recommendations of life science / biochemistry professional societies that she might be able to join to get her some broad exposure to the field.
Lastly, I am also looking to make some local contacts in the Portland, Oregon metro area that might be able to find her a high school internship in the life sciences area.  There are lots of chem majors here, but most of them make integrated circuits. :-(

Those tours are so annoying! Glad to hear a confirmation of their usefulness from a participant. Especially, when they come to our building and there is no way I can get to the conference room on time... I'm not a biochem student, but we had a panel a couple of days ago focusing on career opportunities in biotech industry. The panelists were: Oregon bioscience association (https://www.oregonbio.org/), Twist Bioscience, Seran BioScience (from Bend), Lazarus 3D (from Albany), Absci (from Vancouver), MSE (from Lake Oswego). Maybe this list of employers and one association can be of help to you.

And if you haven't tried it yet, check out national labs for an internship. They do K-12 through Ph.D.. But it's not that straightforward to find one. You'll have to go through their websites manually. I don't recall we have any biochem here at Albany's NETL, but PNNL should have it, I suspect. A resume with a national lab record gives an incredible career boost. They have a variety of internship options.

Your daughter should try to find out where graduates go--what percentage to grad school or industry and if so which ones. I had one parent in medicine and one in entomology. I did physics as an undergraduate and pivoted to a different 'hard' science as a graduate. They didn't worry about giving me any career advice. Don't panic! She's got plenty of time to change/tweak a major.


text:
truncated educational history on a PhD thesis Vita
My PhD thesis includes a required "Vita" section that includes educational background.  I'd like some feedback on omitting work completed prior to my most recent bachelor's degree, in an effort to avoid any hiring bias regarding my age or any perceived 'lack of direction'.  Please see below for details.
I have two bachelor's degrees, the second was completed immediately prior to my PhD, and closely-related.  The first was completed quite a while ago (I left academia for a while and did other stuff).  However, I do have a couple peer-reviewed publications in my previous area of study which were published following the completion of the first bachelors degree, but I've been omitting them from my CV.

I don't think anyone ever reads the vita included in a thesis.  Frankly, I don't know why institutions require it.  The more pertinent question is what to put on the CVs that you submit to potential employers when you apply for jobs.


text:
Declining (?) MSCA (Marie Curie) Postdoctoral Fellowships (IF)
I applied last year for a MSCA individual fellowship and was waitlisted. Last week my proposal was moved from the waitlist into the grant preparation phase. Due to this delay I have committed myself to a different position and would defer the MSCA fellowship start date by 1 year. The grant preparation phase including the final signatures of all parties is not affected by this shift and ideally would proceed in the next weeks. This is well over a year before the start date of the fellowship.
This is all a great success, however, if possible, I would still want to apply to a select number of positions in the coming year. One reasons for this is mostly to secure a postdoc of length 3 years or more. The MSCA fellowship is capped at 2 years. I will not be able to complete these applications before the date set for finalization of the MSCA fellowship.
What are the consequences of accepting and fully finalizing an MSCA fellowship and then withdrawing in favor of a different academic position? Is it (legally) possible? Does it make a difference if this position is a postdoc or faculty position?

We can read the fine print of MSCA  for you, but it is in the best of your interest if you do read them and come back with a more precise question.

MSCA postdocs can be terminated during or before the fellowship even after the final signature in the grant agreement process by the researcher. There is no administrative obstruction and it usually occurs when researchers are offered a better, for example permanent, position. In particular when the fellowship is deferred by a year, I encourage to continue applying to positions leading up to and throughout the fellowship.

I don’t want to sound blunt, but what do you think your chances are of securing three year funding? There are very few guarantees, so with a Marie Curie fellowship you are very well set and also well positioned for future up funding at this point in your career.
As you undoubtedly know many postdoc fellowships will not allow you to be in your new host lab for more than a year, so I can see that you would want to apply for them asap. But don’t burn a bridge you cannot afford to burn yet. In the wonderful case where you do get another 3 year fellowship you might even defer that one so you can finish the Marie curie first or at least half way. Pretty sure you are not the first to do that with postdoc fellowships.

Thanks, BioBrains! This is good advice.

Ill leave others to discuss if its a good idea or not, but of course you can accept a fellowship and then not end up taking it.
In the end, a fellowship is just a contract. We don't have bonded labour in the modern age, and so of course these is no legal obligation to work for someone with the possibility of escape.
just about possible people involved could sue for breach of contract,but this is highly unlikely, as their costs for sueing would be higher than any damages they might be awarded by at least one order of magnitude. And that is only if the contact doesnt contain a break clause, which it almost certainly does.

Thanks for your response, Ian! I need to understand the break clause.

Important point: a PostDoc position is a transition from what is often the most stable position in research (PhD) to something even more stable (professorship or moving outside of academia).
There are exceptions to this (i.e. postdoc staying so long in one institution that they become really needed and therefore will be employed as full-time technicians or researchers) but they are statistically negligible, so do not count on them.
After a 2-year MSCA you have much higher chances to land a professorship of some sort, somewhere.
A postdoc time of 3 years Postdoc does not help more than that. And 2 years postdoc are enough to make up your mind if you want to stay in the academia or go away from it.

I did not downvote, but I disagree with this interpretation. The extra year certainly helps in that you have more time to apply for positions and more time to build your CV. Moreover, at least in some disciplines more than one postdoc is the norm, whereas your answer seems to assume that the path is PhD > one postdoc > stable position (otherwise I cannot make sense of your last paragraph).

I agree in general with your interpretation, but in this specific case 2 years of MSCA are the best of the best, in those 2 years you must surely make up your mind about staying in the academia (and living some years with the related uncertainty, maybe going through other 3 postdocs) or leave it for good.
But picking 3 years postdoc instead of 2 of MSCA brings nothing. Even that additional year is in my view, detrimental (it may make you think you are "safe").

Thanks for your response, EarlGrey! I didn't downvote, but I agree with Adam. Perhaps I should have given more details. Due to crowdedness in my field this will be the second of (expected) three (if unlucky four) post-PhD but pre-Prof positions. My first position was 3 years and I believe it made a massive difference to my mental. Fundamentally the question I'm asking is: is there a way I can keep my options open?

@MEH no. Every year that passes, the more options are closing. You can open more options open with quality in research, or "quality" in research, where the brackets means quality = your own fundings.
So MSCA is the best option, to keep (and possibly even bring new) options open.
By the way, since you already spent 2-year as a postdoc, you already confirmed my last point  (you made up your mind and you want to stay in the academia).
Unfortunately the system is  "go up or go out". If you make clear you want to be a postdoc to stay postdoc ... they will prefer someone with the ambition of

@MEH going up. Because even the 5 years postdocs are given with the knowledge that the Postdoc is unlikely to stay there for 5 years (and rationally so). Usually it is some rigid funding that force such opening, but no one is expecting a person to stay postdoc for 5 years (although they will be happy to have such a long time worker)

Thanks for your input!


text:
Should I add a color calibration target to some figures in a scientific paper?
I have to say first that I am not very familiar with the world of color rendering in computer graphics, I am more closer to a physical approach of the phenomenon.
My problem is that I am writing a scientific paper in which we are recreating the perceived colours of some materials, and in which of course we are showing our results in some figures... But as always in this kind of things, how can I be sure that the colours of the figure that I am creating on my laptop will look the same on the screen of readers of my article, or on printed papers?
I know that this is impossible, but my idea was to add next to the figure a color calibration, such as a simple black-yellow-magenta-cyan square, or a ColorChecker figure... I do not know what is the convention for this kind of problems, or if one of my solutions is better than the other.
If someone has an advice, I'll take it!
ColorChecker Example
CMYK Example

FWIW, I don't think I've ever seen a color calibration target as part of a figure, nor would I know what to do with it if I found one. That said, I don't work in a field that deals with color and have only ever needed self-consistent coloring between figures and legends, rather than faithful representation of particular shades. Do you expect your readers will actually use it?

General rule for these sorts of questions: What do people do in the papers you cite?

" that I am creating on my laptop " well, unless your laptop is a professional laptop for photographers, you are embarking in a nightmarish task (see here for a brief overview how to do that https://www.adobe.com/creativecloud/video/discover/how-to-calibrate-monitor.html ).
Why do not you use standarized RGB colors and let the numbers behind it work for you?

With the possible exception of specific fields, I think you should expect most readers to read the paper on non-professional displays that lack color-calibration or full bit depth, or on a color-inaccurate printout. I've also seen publishers end up affecting color balances when compressing figures for publication in the form of .pdf files. The case of actual print journals is rare enough these days that you can probably neglect it, but if it applies you should ask them how to prepare figures for accurate color reproduction with their printing processes.
If the precise color information really matters for your paper, I think including a calibration target in generated graphics or a color rendition chart in photographs would be reasonable. Whether you include one or not, however, it would also seem worth supplying the figures either in the form of supplemental material deposited with the paper, or in a data archive cited in the paper. (If you go the data archive route, you may need to clear it with the publisher beforehand depending on how the figures are copyrighted.) That is a more robust way of communicating the exact color information, and more convenient to readers that would make use of it. Alternative ways of communicating the colors, such as including color codes in an appendix, might be workable too.
Of course, in the majority of cases good enough is... good enough. Certainly for plots and illustrations you should design them such that they're easy to read (also for color blind readers!) and don't require ideal color reproduction.

In general the advice is: Assume people print out your paper in black-and-white. They should not lose any information.
However it seems your specific paper concerns color in a direct way so this doesn't really apply. Here I would recommend to specify the exact colors you mean through one of the standardized notations like RGB or Hex or something like that. RGB (123, 23, 43) is a precise specific color. A given computer screen or printer might not render it correctly but that is on the device not on you. It is uniquely specified which color you mean.