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What are some efficient ways to keep a note of results of a research article in mathematics?
I learn and produce mathematics. In that process, I had to read quite a number of research articles.
Question :

What are some efficient ways to keep a note of results of a research article in mathematics?

I keep a note of definitions (in detail) and results (with out proofs) for each paper I read.
Are there any other efficient methods to keep track of what results does a paper contain?
Reading introduction or abstract of a paper does not count as they are written in cryptic manner.

This is not restricted to mathematics.. please feel free to add any general advice..

I'm a big believer in using simple index cards for this sort of thing. But there are modern alternatives also.
For the traditional approach, make a card for each paper. It contains title and author as well as publisher/source. It also contains a one or two sentence summary of the paper. What is the reason that this paper is important/interesting?
Cards are kept in a file box, perhaps in author order.
The advantage of this approach is that your card deck will still be available to you in fifty years after multiple operating systems and software systems have become extinct. Paper lasts. Another advantage of index cards is that they are small so you can only write essential things.
As a supplement, you can keep a notebook with a page or two for each paper. The index cards contain a page reference into your notebook system.
But the disadvantage is that such a paper-only system is hard to search. So you might consider an alternative. There is software for "digital index cards" that let you do the above on a computer and provide the opportunity for both searching and for updating the formats and organization of your notes. This might be a better solution for you in general, but don't overlook the permanence of paper. If you are really serious, use such a software system but also use a printer that conveniently and efficiently prints real index cards. Now you have your bomb-proof backup that you will be able to refer to in your 70's in the post-computer era.

Personal note: I have, in fact saved such things as my college course notes from deep into the previous century and have, very occasionally, gone back to refer to them. Later, I kept things on floppy disks that I can no longer access, even though I have the equipment to do so. They degrade as paper does not. Provided you use fairly good paper, of course. I found my first "paper" done back in secondary school (on paper, obviously, created when computers were made of vacuum tubes) and found it "interesting". Since it was typed (on a typewriter), I can scan it for more modern use.

Thanks. I did not knew about digital index cards...

Some software is "explicitly" digital index cards. Others are similar but can be used in that way. The only one of the first kind that I know of is for Windows 10, which I don't use, but there are also useful things for other systems.

I have come across papers which develop several 'incremental' results (usually methods / theorems), all combined to create that one interesting piece that goes into the abstract, is the highlight of the paper, and obviously goes into my 'index card' for that paper. I wonder those 'incremental' results/methods/theorems can come in use to me sometime in future as standalones separate from the interesting result they created in combination with each other. Do you face such a concern? If you do, how do you work around this?

Re index cards:  If you have access to ISO A-formatted paper (A0 with surface of 1 square metre, side length ratio 1:square root of 2) than you may fold and cut / tear them quickly from a A4 paper used for printers which may be less carry weight while on a travel. Or you cut an 8-page minibook (quickly folded, e.g., https://www.youtube.com/watch?v=21qi9ZcQVto) after returning home into index cards.

How inefficient for each reader of a given paper to do this work privately and independently! Ideally, this should be done on a common, open platform. There is no standard dedicated platform for this activity at the moment (and arXiv does not accept reader comments), here are nevertheless two suggestions:

Wikipedia: In principle this is for non-technical content, but mathematicians get away with a lot of technical stuff. In principle you should avoid primary sources (i.e. research articles) and cite secondary sources (review articles and books), but again this is not a strict rule. So long what you write is not excessively technical, subjective or personal, you may probably use Wikipedia, and benefit from its collaborative editing, wikilinks, version control, etc.
Wikiversity: a sister project of Wikipedia, with the same infrastructure, but no rules against original research, primary sources or technical content.

My own (experimental) practice is to write in Wikipedia about relatively old and well-established results, and in Wikiversity about more recent results.

Thanks for your time..

Some related posts: Is there a good site for holding online discussions of scientific papers? (Academia), Are there any good websites for hosting discussions of mathematical papers? (MathOverflow).


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What's the right time to transition from postdoc to PI?
I've been a neuroscience postdoc for the past ~2.5 years and have recently applied to Assistant Professor positions in various R1 universities within the US. I decided to apply mainly for timing reasons: there were lots of good open positions and I'd had a very productive 2018 (with many pubs from grad school coming out). Now, having received several interview invitations, I'm starting to wonder what I'd do if I got offered a job.
The reason for my hesitation is that I have changed areas in my postdoc (going from experimental work to theory/modeling and machine learning). I really like my new research area, but I feel like in the past 2.5 years I haven't learned enough about it yet, nor have I established myself as a theorist/modeler. There's so much more that I still want to explore, and I feel that as a PI I would not have the time to learn and develop new research directions, new collaborations, etc.
If I do end up getting a job offer, would I be crazy not to take it, given how competitive the market is? More generally, what's the right time to transition from postdoc to PI?

Part of a PI's job is to learn and develop new research directions, new collaborations, etc. Could you clarify why you feel that you wouldn't be able to do this?

The right time is when you get a PI-level job. Well, actually before you get the job so you can show you can do the job...

@user2768: My impression is that, as a PI, you don't have as much time for these things because you end up spending a lot of it teaching and writing grants. But even with respect to research time, you probably want to spend all your effort on areas you've already mastered since the tenure clock is ticking.

This is hard for anyone but yourself to answer as it depends on the amount and kind of risk you want to take on. You might be able to get better advice from someone who you have worked with and can judge your potential. I've voted to close, since it is, fundamentally, a personal choice.

If you do get a job offer, then yes, I think you’d be slightly crazy not to take it - more precisely, to not take it based on the concerns in your question would be a somewhat irrational decision. However, one thing you could do in that situation is negotiate a late start date that would give you time to continue your postdoc for X more years (assuming that is an option that’s available to you). I have seen this done and think this has a reasonable chance of success with X=1. For higher values of X I have never heard of anyone doing it, so I suspect the chances are not high, nor do I think it’s particularly advisable, but if it’s important to you you can still look into whether that’s a possibility.
In general, while you are somewhat correct in thinking that when you start a tenure-track position you become less “free” than a postdoc, and have more responsibilities and duties and therefore a bit less free time than a postdoc to explore and learn new areas, I think that’s beside the point. All the things you can do as a postdoc, you still can do, and in fact are still expected to do, as a PI. You also start acquiring important new skills and abilities that enable you to take your research and career to the next step. If you don’t feel ready for it, that’s probably because a lot of people don’t feel ready for it, so that’s completely normal. But regardless, the best time to do it is whenever people judge you are good enough to offer you a job that appeals to you. Good luck!

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Impact of references & quotes on essay quality
Do references and quotes improve the quality and make an essay sound better in undergraduate and graduate exams, contests, and other such situations? Could you please provide me with a book, paper, or quote that discusses this topic?

I'm pretty sure that adding references and quotes just for the sake of it is not a good idea. There are various good reasons for using them, but this will depend strongly on the subject area and even the topic of the essay.

I also believe that the major principle of writing always is to communicate with the reader, so as a rule of thumb references or quotes are good if and only if they help the reader reading and understanding your essay.  (Of course this requires thinking about who your readers are, what they want, what you want from them, and what they need.)

This depends on the nature of the essay. For creative writing, references are usually not needed. But for something intended to be authoritative and factual, they probably are. Otherwise your essay will seem like an opinion piece. And even opinion pieces may need references for context.
So, context matters.

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Forced to Leave Physics PhD Program - How to Salvage Academic Career?
I started my physics PhD program several years ago at a top-ten institute in the U.S. Recently, my supervisor informed me that he believes my talents and interests are not well-aligned with the program. As a result, the department is not allowing me to continue in the PhD program and is asking me to graduate with a master's degree instead. Finding another supervisor within the same department is not an option, as the department has made the decision to discontinue my PhD studies.
Being a scientist and studying the ultimate answers of our universe has been my lifelong goal. I've been working hard and pursuing this goal for so many years, as I set this ambition when I was young. Without a PhD degree, I'll likely be unable to stay in academia as a scientist. (I'm aware of "research scientist" positions in industry that don't necessarily require a PhD, but that's not the path I desire.)
If I decide to reapply for a PhD program elsewhere, I would need reference letters. Given my current supervisor's and department's attitude, I don't think they would write positive recommendations for me, which makes this option challenging. Alternatively, if I enter industry first and then apply for another PhD program later, I doubt my future employer would provide a supportive reference letter, as it would mean I'm planning to leave the job.
I'm reaching out to see if anyone has had a similar experience or can offer advice on how to navigate this situation. Any insights or suggestions would be greatly appreciated. Thank you for your time and advice!

Why do they think your talents and interests are not well-aligned with the program?

The most direct reason is that a specific problem continue to exist in my analysis result which does not make any sense to them. They are not able to reproduce the same problem as mine, and I failed to solved it or convince them for several months. Therefore they think my research is not going anywhere and questioned my ability to success in the field.

Is it possible to ask them what evidences can convince them? did they state it clearly? if so, are you able to do that?

Remember that a PhD is just the minimum requirement for the career you describe; getting a PhD does not mean you will have an academic career. I think your chances given your situation are very low, much lower than average, even if you do find a way to complete the PhD.

I’ve literally never heard of a PhD being kicked out that thoroughly. This sounds like you should reevaluate your lifelong goal, not throw the rest of your life at it.

What is your own assessment of the situation? You seem to worry only about the chances of turning this around, but not about whether your skills actually are suitable. People in more favourable situations had less confidence. Do you think this situation is misrepresenting your skills and you are looking for someone who will recommend/supervise/… you truthfully, or do you doubt your skills and are looking for someone who will recommend/supervise/… you regardless?

Expanding a bit on MisterMiyagi's comments, I would not characterize this as "forced to leave physics PhD". Rather, you failed the program. Letting you leave with a masters is meant as a gentler way to fail given the effort already put in, but they're not letting you continue to a PhD because you failed out of the program. From your description in a comment, it sounds like you probably had opportunities previously to avoid failing but stuck to some non-reproducible result.

It is indeed a very unusual situation if your program chooses to let you go rather than finish with a weak degree.  I've never heard of someone being asked to leave because they got stuck on a single issue: were there more issues that you did not mention, such as difficulty with courses, difficulty with presenting a coherent thesis proposal etc?

Welcome to Academia.SE. Your situation is interesting and very much the sort of thing we can help with. But, our format is strictly Q&A: you should post a single question so we can provide the answer. I recommend you [edit] your post to ask a single question. Question #1 is likely not a good fit here ("has anyone ever..." questions are not answerable, except by the trivial, "yes, someone somewhere has doubtless done this before"), but any one of questions #2-4 might be okay. Asking generally for strategies to deal with your situation, while discouraged, is often acceptable as well. Good luck.

Hi @BryanKrause, yes I agree with you that a PhD is just the minimum requirement, and that's why I am so worrying. My supervisor says that it is also probably that other fields in physics suits me, but considering the current situation he doesn't think I should spend more time in my current study so he forced me to graduate with master to save my time.

Hi @MisterMiyagi, according to my supervisor, about 10% of the grad student failed and graduate with a master degree like this, so he told me that it is still kind of normal. Although I am not 100% confident if my skills are suitable, as my supervisor has been discouraging me for some months, I still think that there are some possibility of being misrepresented or just as my supervisor say that it might only not suit this group. He doesn't think that changing to another group is a good idea as I have already spent so many years here and it would be a risk to start another research topic again.

Hi @ZeroTheHero, there are no other issues like difficulty with courses, as I have passed all of them and my supervisor told me that it is one of the reason that they can still give me a master degree as I have completed the course requirements and did have some results on my research.

Hi @cag51, thanks for pointing that out. I have edited my post, and I hope it is better now

How many years is "several years"? Some universities may have (un)official policies regarding how long they will entertain a doctoral candidate. Without significant progress after a substantial amount of time, they may have felt that you were incapable of completing the degree.

Hi @CameronWilliams, it has been four years. However I do not think there is such kind of policy in our university, and it is our supervisor that can decide if we can obtain the degree or not, at least in my case.

@pcc I think unfortunately phrases like other fields in physics would suit you are probably just kind words, plus a humble recognition by your supervisor that they cannot speak for all of physics.

@BryanKrause Yeah I agree this is a possible explanation, because if I am in his position I would probably say the same words. Only my supervisor himself would know what he actually thinks, so I don't think I can make a decision merely based on that.

@pcc did you just pass your courses, or did you pass with flying colours? Do you (honestly) view your PhD as closer to a hobby or to a job?

@NAMcMahon I passed the required courses with 3 A's and 1 B. For me I view my PhD as a job as well as a hobby.

I started my physics PhD program several years ago at a top-ten institute in the U.S. Recently, my supervisor informed me that he believes my talents and interests are not well-aligned with the program. As a result, the department is not allowing me to continue in the PhD program and is asking me to graduate with a master's degree instead.

The bad news is that you are being forced out. The good news is that you are earning a master's degree, so you have something to show for your efforts so far.

Finding another supervisor within the same department is not an option, as the department has made the decision to discontinue my PhD studies.

I rather doubt this is true. My guess is that the department does not want to fund you while you look for another advisor, nor do they want to force your current advisor to continue supporting you. They are probably also concerned that you would graduate way behind schedule if you switched advisors. So it's understandable that they are not really giving you an option to look for another advisor. But even so, my guess is that if you showed up within a week with an advisor who wanted to hire you, they would certainly allow this. Of course, finding an advisor on such a short timeline and under such circumstances may be impossible.

The most direct reason is that a specific problem continue to exist in my analysis result which does not make any sense to them. They are not able to reproduce the same problem as mine, and I failed to solved it or convince them for several months. Therefore they think my research is not going anywhere and questioned my ability to success in the field.

It's very hard to judge this from the outside. The problem here could be any combination of (a) your advisor being a jerk, or (b) this particular environment being the wrong match for you, or (c) you having behavioral issues or other limitations that will limit you no matter what you do. It's also very hard to judge yourself. So be kind to yourself. This will be a very uncertain and stressful time, and it may be a long road before you figure out where you are supposed to be. But have confidence that you are not going to spend the rest of your life in misery; you'll eventually figure it out.

Being a scientist and studying the ultimate answers of our universe has been my lifelong goal. I've been working hard and pursuing this goal for so many years, as I set this ambition when I was young. Without a PhD degree, I'll likely be unable to stay in academia as a scientist.

I'm sure you know that most PhDs feel this way, but a very small fraction of PhDs become professors. Even without this hiccup, the odds were always very much against you. In the long run, you may be very happy that you were forced off the tenure track now, rather than a decade from now.

I'm aware of "research scientist" positions in industry that don't necessarily require a PhD, but that's not the path I desire.

Do you know anything about these positions, or are you just assuming? There is a lot of propaganda about how universities solve the big mysteries while industry jobs are all about getting more clicks or selling more widgets. This is certainly partially true; there are plenty of horrible industry jobs that I would never want to do. But if you look a little deeper, you will find permanent, well-paying positions that really are R&D. On the other hand, the best positions are competitive, and your lack of a PhD may be a problem.

If I decide to reapply for a PhD program elsewhere, I would need reference letters. Given my current supervisor's and department's attitude, I don't think they would write positive recommendations for me, which makes this option challenging.

Probably true, but hopefully at least one professor likes you. You can always go back to your undergraduate professors to get the other two, but it would certainly be nice to have at least one letter from your current institution that can corroborate your version of events, even if it is somewhat mixed. Indeed, it would be strange to have a glowing letter under the circumstances, so a letter that is mixed but fair is probably okay. Of course, you will not get into another top-10 program, but I strongly suspect you'll be able to earn a PhD somewhere.

Alternatively, if I enter industry first and then apply for another PhD program later, I doubt my future employer would provide a supportive reference letter, as it would mean I'm planning to leave the job.

I do not think this is likely. While you might not want to tell your actual boss that you're thinking of leaving, most companies have plenty of principal or chief scientists who can (and do) write letters under these circumstances. The bigger problem is that as time passes, you will want to buy a house, start a family, start building wealth, etc., so very few people return to the PhD stipend after they leave.

I'm reaching out to see if...can offer advice on how to navigate this situation.

Calm down. Depending on your timeline, maybe take a few days to digest your situation. You have some tricky conversations coming up, so if you're panicking, wait a few days before launching into them if possible.
Look around for other professors in your current department who might adopt you. Preferably ones for whom you have skills / past work that is relevant, so you are not starting from zero. This is unlikely to work, but I would spend a few days trying very hard.
Talk to your advisor or others in your circle about transferring to a lower-ranked grad school and getting a letter of recommendation. Better to know now if they're willing to write and how negative it would be. If you have collaborators at another such school, you might talk to them directly.
Spend a few days deep-diving into industry jobs. You will find many that seem horrible, but keep going, there are some interesting things there. Start applying now. (As I write this, Aug 2024, my LinkedIn feed suggests that the job market for tech in the US is pretty bad...so even if this is your "backup plan," don't wait too long to start looking).
Plan to re-apply to graduate school in the next cycle.

As one data point, I have written multiple letters of recommendation for lab technologists who want to go to grad school for a PhD. All have been successful applicants. Most of them were open during the job interview of that being their plan and I was happy to have them work a few years.

Yes, I changed universities after it became impossible to advance. I actually wound up at a higher rated university and with a much more capable advisor (world class, actually). My reasons were different, but among them was an unhelpful advisor.
I was highly recommended by another faculty member at the time, though he was in a different sub-field. But he was sure that I had the ability to succeed and made the switch possible.
You may have the opportunity to find such a person also, especially in the US where you have taken courses with other professors and, perhaps, interacted with them in other ways, such as being a TA. You may have a general reputation at the current place as an able person. If so, you can try to find a way to capitalize on that in a future application process.
And, it is even possible that your advisor's opinion is narrowly focused on the project at hand, and not on you as a future academic generally. Think about whether that is true or not and consider having a frank discussion with them.
Note also that my earlier failure to advance had no effect on my career. The degree and the quality of the dissertation was the important thing.

Hi @Buffy, thanks for sharing your experience. I am going to be a TA next semester, so I will also try to take that chance. I had some discussions with my supervisor but he did not comment too much on my prospective future in academic generally, only telling me that switching to other sub-field in the future is also a possibility, but that would take me a lot of risks so he does not recommend me to do so now.


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Accepting and then declining PhD offer,
I recently got accepted into PhD programs at University A,B,C, and D.
I interviewed with Professor W at University A, Professor X at University B, Professor Y at University C, and Professor Z at University D.
I chose University B.
But now I am having doubts about B  and wish to go to University A to work with Professor W.  How do I tell Professor X that I want to change my mind and work with Professor W?
I also had additional conversations with Y and Z at C and D; they were pretty helpful and gave good guidance and tips about going to A and not going to B, so I feel even stronger about my decision to attend A over B.
University C and University D are on the east coast, while A and B are on the west coast.
How should I handle this?
Will I be burning bridges with X, Y and Z at B, C and D?
I wish to do my post-doc someday at University D or maybe C so it's important to not piss off X and Y, who both know B very well since the area of research is quite small.
W also knows X Y and Z

"I chose University B". Have you accepted verbally or written? To the professor, or you also did the administrative work as well?

Possible duplicates here and here

As you as you are professional and upfront, this shouldn't cause any hard feelings. Go with the one you like the most, after all, it is your research and time that you will be spending. You can always change your mind and email professor at A with a brief message explaining that you prefer to go to a different school. Keep in mind that you will be just starting your PhD and who knows if you will have the same opinion about going for a post doc or maybe get lucky and find a faculty job! Opportunities can rise out of no where.
One more question, why did the other professors suggested that you go to A and not B or even their university? Do they know the professor at A? Or because of the university's reputation or lab?

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Citation in lecture notes?
We do citations when we refer to someone else’s papers but what about lecture notes? If I come across someone’s lecture notes which has a different way of presentation of a theorem or some problem and I wish to expose my students to it, how do I make use of it? Can I use the other person’s diagrams or solutions and give them the credit?

@BrianTompsett-汤莱恩 and other close-voters: This question is broader because it also asks about the reuse of material from the lecture notes into new notes. I don't think it can be considered a duplicate.

There are two questions here:

how to cite?
can (and how) such materials be used?

The first question can be certainly answered. Library Guides from Victoria University has the following example in APA style:

Ooi, D. (2018). AEB1804: Young People in a Global Community, week 1, session 1 notes [Course Presentation]. Retrieved from https://vucollaborate.vu.edu.au/d2l/le/content/177492/viewContent/2217850/View

This question also deals with citing lecture notes and when to do it. Concrete example for lab manuals and lecture notes.
An important discussion on whether to use citations while preparing your lecture notes can give a perspective on why doing proper citations in lecture notes is a good idea.
However, citing lecture notes has its limitations, since lecture notes are essentially gray literature.
Now, to the second question whether and how you can use them, which is a question of copyright. This question discusses the copyright-issues-free preparation of lecture notes to get you started.
Lecture notes rarely mention a license under which they are published, so you cannot assume they are in the public domain or under a permissive license. You can contact the author of the notes (or the copyright holder, which might be university). This will raise two problems (that theoretically can be resolved):

sometimes it is actually unclear who is a copyright holder for the lecture notes
you rely on the fact that the lecture notes you are trying to use do not infringe copyrights on their own

So, I would suggest the following. Use the material from the lecture notes in a way that will constitute fair use. Citing paragraphs here and there would certainly be fair use while using images and figures might not be, as well as using entire chapters. Use appropriate citations where applicable. Also, consider asking the author of the notes for an explicit permission.
Known assumptions and limitations of this answer:

you do not intend to sell your lecture notes
copyright law is complicated and has its own peculiarities in every country
you intend a fair use (in a common, not legal, sense) and wish to be as fair and copyright-respectful as possible

For figures, one can include a figure credit in the caption, something as simple as “Figure credit: Zerothehero, unpublished lecture notes.”
The same holds for theorems:
Theorem: [Zerothehero, unpublished lecture notes] The Sun rises in the East.
Or
Theorem: The Sun rises in the East [see also Zerothehero, unpublished lecture notes]
You might also include a link or better yet the DOI if the lecture notes have been assigned one.


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Lecture Notes and Textbooks
When teaching a course based a text book, is using the proofs of theorems and examples from a text book considered reproducing the material from the textbook, while providing the study lecture notes?

Does this answer your question? How to make sure that my lecture notes do not infringe on copyrights?

What is the problem you are trying to solve?  What sort of "using"?

By using I mean, for example in the lecture course suppose I have to use the proof that the author gives in the textbook and I want to follow it, in this case the one teaching wants to incorporate the proof that the author has given, say for an established theorem.

A textbook is produced as “here is a tool to teach students or a class”, while a paper is produced as “this is the state of play of our work”.
The author of the textbook expects lecturers and students to use the material but if they quote it in lecture notes or an essay they then expect it to be correctly referenced.

+1 I generalised to lecturers and students, do revert if inappropriate

@user2768 it’s improved my answer thanks.


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How to self-advocate after rotation rejection?
I am a first year PhD student. I just finished my first rotation lab and absolutely loved it. I met with my PI every week, and I never felt like she had a problem with me. Though I never had a frank discussion with her regarding the fact that I wanted to commit to her lab (big mistake, I know), I heard from other students who spoke with her that she wanted to make sure she had enough space in the lab for me and the other rotation students had we chosen to join. She also promised us that she had enough funding so we wouldn't have to compete with one another. I really thought I had found my lab home until....
I received an email from her yesterday telling me that she couldn't keep me. The reasons she gave me seemed flimsy (i.e. I wasn't enthusiastic enough....when literally anyone else in the group can vouch for my enthusiasm!) and contradicted what she told me at the start of the rotation (ie. she said she wished I had gotten further in the project, when she explicitly said multiple times that she didn't care how far we got through our rotation projects).
I hate confrontation, but I want to be a self-advocate. My biggest regret in undergrad was not self-advocating enough. I feel like I lost a lot of wonderful opportunities because of my fear to approach professors. But this time I want to stand up for myself, try to get a chance to defend myself and ask for legitimate reasons why she suddenly rejected me. And of course, try everything I can to try to change her mind. This is my dream lab, and I want to be brave enough to fight. I know I'm stepping on some annoying lab politics by doing this, but how should I go about addressing my concerns with my PI while not offending her?

If you are in good terms with your PI and you have weekly meetings with her, it is probably best if you bring up the topic in your next meeting. If "lab politics" are really involved (which need not be the case), it is unlikely that she will provide more information through email.
If she had told you that she would have funding and space for you all, it is perfectly reasonable for you to ask what changed, so she should not be offended by the question.
Regarding how to phrase the question, I would be moderately direct but, as most "conflict management" courses suggest, prefer the use of "I-messages" instead of "you-messages". Something along the lines of:

I would have liked to be able to stay here, is it really not possible anymore? And if it is not, do you have any suggestions as to how I can do better elsewhere in the future?

I also generally like the phrasing “I expected x, what seems to have happened was Y. Could you help me understand what I missed?”

Thank you for your advice. I was afraid that perhaps I was sounding too desperate (even though I kind of am) by asking to meet with her in person to try to defend myself. But I think you're right in that it is reasonable to try to figure out exactly what went wrong. A follow up question--if she had a problem with my personality or my confidence (I have to admit there were times when I stumbled through explaining my experiments or science topics), how should I respond to this? Is it reasonable to tell her that I can (and am willing) to change?

@N.N. Offering to "change your personality" starts to sound a little more desperate... She will not tell you that she does not like your personality, that might get her in trouble. If she mentions something along those lines, your reply should focus on the work ("maybe I do not look enthusiastic or seem to hesitate sometimes but that does not mean I do not like the work, it is just my way of expressing myself"). You seem to be a little insecure about your personality/social skills. "Stumbling when explaining" was probably not the reason, don't be too hard on yourself for this.

I think the only conclusion that you can draw from the situation is that the PI perceived something that made her feel like she didn't want to commit to a multi-year relationship with you.  I don't think it does you much good to wonder if she really has the resources for more than one student or not.
There are some hints in some of the comments you've made to other answers like

there were times when I stumbled through explaining my experiments or
  science topics), how should I respond to this?

That could certainly leave the impression of "lack of enthusiasm" -- though I would go out of the way not to use that language if I were turning down an applicant.  This could mean anything.  It could mean that she didn't feel you spend adequate time preparing, it could mean she thought you didn't understand the science, it could mean she didn't like your communication skills, it could mean she thought you would need too much extra preparation before you'd be able to be productive.
That statement makes it feel like you already have some sense about what went wrong.  If I were to advise you based on what I detect, I would say that you should consider every contact during a rotation to be a job interview.  Read about the project you're involved in.  Before you start a rotation, read the profs recent papers, and contact the prof and ask if there's any reading you should do in prep for the rotation.  Read them, and read the more important papers that are cited.  Prepare for each and every meeting.  Be ready to present what you're working on, and to ask the questions you have (after you've spent effort trying to answer them on your own with literature review).  Write down the points you'd like to make.
Last, but not least, you tried and missed with this PI.  It's nothing to be ashamed of.  Move to the next, and try to use the experience to have a better experience the next time.  You should consider this the first of many such misses you'll have in an academic career.  We all have them, and we all need to move past them.


text:
How do I cite a paper that is not yet submitted for publication?
I am revising a paper which is due to be submitted today. In it, I would like to cite another paper of mine which is not yet submitted as it is still reviewed by my coauthors. How do I cite this latter paper in the former? Is it ok to say '(submitted)' when it is actually not, although it may have been when the former paper is published? Or can I say '(to submit)', although I am not sure if such is formally recognised?

You can call it a "preprint" if it is ready to circulate, or say that it is "in preparation" if you are working on it but it's not done yet.  (The difference is whether you would be willing to give interested people a copy now, or whether you would ask them to wait until it's done.)
Don't call it "submitted" if that's not actually true, even if you think it will be submitted by the time anyone sees the reference.  Getting caught in even a minor lie can hurt your reputation for honesty, and there are any number of ways something could go wrong in the process of finishing and submitting the paper.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Is it common for a publisher to offer monetary compensation for a book proposal review?
I received a book proposal review request from Elsevier. Despite some reasons to believe that it is credible, there are a few things that look suspicious to me:

A monetary compensation is offered. Is this common, and how does this work in practice?
The request is sent from a personal email account.
It says that I was suggested as an expert in the field, but in fact it is not closely related to mine.

As a security matter, you should go to Elsivier's website and look up the contact in in a corporate directory, or get in contact with the affiliated division and make contact via means you discover yourself. Or, just ignore it.

@David thanks for the suggestion. I have now contacted another editor in the corporate directory, who confirmed that the sender is a former employee who is helping with a bottleneck of proposal administration.

I was asked some time ago to review a book proposal by a leading academic publisher, and offered to choose between receiving some token monetary compensation or having them send me a few of their textbooks of my choice (I opted for the latter option and remember feeling quite happy when the "free" textbooks arrived :-) ). So yes, publishers offering payment seems not uncommon.
I do agree that the use of a personal email is suspicious and not consistent with professional email standards associated with large and respected organizations like Elsevier. It could be completely innocuous, maybe due to an employee with slightly rebellious tendencies who refuses to kowtow to his corporate culture and insists on using a gmail account, or it could be a scam, who knows. Caveat emptor - obviously do your due diligence before compromising any bank account information. (And let us know what you find!)

Thanks for the answer. Please see my comment to @David above.

Compensation for reviews is not common, but also not unheard-of. That in itself would not raise a red flag for me, and Elsevier is certainly a reputable entity in science publishing (despite their somewhat unfortunate role in the current struggle of academic publishers versus open access).
That you sometimes get invited to as an expert for fields that are not actually that closely related is also not extremely uncommon. The people that select reviewers for books are usually not experts in your field, so what appears to you as a significant difference in e.g., research approach or community may look like a mere technicality to them. You should decide for yourself whether you will be able to conduct a high-quality review despite being in a different field, and if not reject the review.
The only aspect of the request that I also find highly suspicious is that the request came from a personal email address. This alone would not be enough for me to outright discard the email as spam, but I would certainly not e.g., forward them my banking information before I don't get anything a bit more official than a mail from a GMail account that says that the person works for Elsevier.

Compensation for book reviews is quite common in my experience, although not for journal articles.


text:
Do Australian universities pay expenses to attend a faculty interview?
I have been invited for an interview for a lecturer position at a university in Australia. I am based in Europe at the moment. It is not expicitly clear, at least to me, in the invitation email that they will pay for the travelling and accommodation expenses, whether in full or in part. I thought I should ask them for clarifications, but I am not sure how to ask it, and perhaps it is better to find out more about the custom before asking.

Just ask them who makes the travel arrangements and who pays.

The short answer is 'yes'. I know some colleagues who were invited for an interview for a lecturer position at an Australian university and they were indeed reimbursed for all their travel+accommodation+food+visa procedure expenses for the trip. The reimbursement was not conditional on if they would accept the job if offered or not. It was also written clearly on their invitation letters (needed for their Australian visa application) that they would be reimbursed all these expenses.
However, you must NOT assume anything. It is going to be a good amount of money travelling from Europe to Australia, and you must clarify about your reimbursement.

Yes, always get these things "in writing". I once moved 3000 miles with a (written!) promise of moving expenses paid, but at the far end they didn't want to, by default, until I scrounged-up that piece of paper.

I have a different experience.  A colleague of mine was interviewed over Skype.  Given the current state of Australian universities, I doubt they will pay for your 'lovely' trip from Europe!

@user35582, if an Australian university goes interviewing candidates, they must have made sure to secure funding to invite candidates over! I would just get it specified (in writing, as paul garrett emphasised) to avoid any confusion.

@John, you must work for a rich university!  Usually, the university will pay for relocation if they make the offer.

hI don't work in Australia. But I have worked in a university there in the past and I know the system at least generally. They do want to hire overseas candidates. And no overseas candidate, especially an early stage academic, would go all the way to Australia on his/her own expense to finally find out they didn't get the job! So the universities do have to pay the candidates' travel expenses. As I said, the OP must confirm this in writing as a general common sense.


text:
What are the uses of an iPad for an academic staff?
As a new academic staff, I received an iPad from my department. I have never owned nor used an iPad before, so it is still in the box for the past week or so. I am a bit reluctant to open it, as I am not sure if it would be useful, and I have actually been thinking of returning it to the department. But to be sure I won't regret it, is there anything particularly good about an iPad that it would be nice for an academic staff to have it?

I do hope that your University or Department  has special softwares developed for iOS (i.e. the operating system of the iPad). If not, well, just enjoy your iPad!

Did they give you this instead of giving you a more traditional computer?  So you would use it for email, web browsing, preparing lectures/presentations, etc.?

Could you elaborate on what your job looks like? Are you teaching? Visiting conferences? Preparing or correcting exams or tests?

@clueless, I am not teaching, not preparing nor correcting exams or tests, and rarely visit conferences.

@GEdgar, it was given in addition to a more traditional computer, which I always use.

Whether a tool works for you or not depends on your work style, so general recommendations are difficult.
However, you can use it for example

to read digital articles. There are some literature management tools that work well with iOS devices, and you can read any PDF with readers like GoodReader. With the later you can, for example, highlight text and export the highlighted text (and any notes) via eMail.
You can also directly access your files if you use, e.g., Dropbox (can be helpful in meetings).
There are also apps available for classroom management, if you do a lot of teaching.
You can use it for presentations (Keynote on iOS is okay).
It's nice if you travel to conferences (for emails and the like).

In short, there are many uses, but it depends on your work style. Question I'd have would be how your colleagues use the iPad (if it's an department wide thing). Also: That's a nice problem to have. :-)

I've seen my colleague using it at the end of a meeting to take a snapshot of the whiteboard where the minutes were scribbled, and then to scribble some notes on top of the picture.

Good point, there are some note-taking apps which allow you to take notes via a pen and still have them available digitally.

In addition to this, I've had professors teach their entire course using their tablet. They would project the tablet to the screen and used the stylus to draw over their presentations (or on a separate notepad they kept up).

I don't think that an iPad does anything magically different for academic personell than for anybody else. Some of my colleagues review papers on them, some use them as a very small laptop while travelling, and (I presume) most just use it to read the news, play games, or slack off otherwise while in the train or plane.
In summary - if you have no idea what you would use it for then you probably don't need it.

But there is always a room for improvement...

An iPad connects to HDMI, so you don't need to bring your laptop to class (for slides).
With an added keyboard, and access to a remote server, you can work seamlessly from everywhere (on whatever OS you prefer). If you live in Europe you probably have, at least, 3g mobile access everywhere. Depending on your circumstances, this might even eliminate your need for a regular laptop.
A decade or more ago, everyone had papers everywhere. Then we started the  paper less office, and an iPad works well here. Save all documents in some online drive, and you have access everywhere. Put the iPad next to your desktop keyboard, and you will never have to print anything ever (mostly).
The iPad is a decent, but not perfect, replacement for taking notes on paper. Snap a picture, and start chopping away.
There are many great apps you could use, for instance for people in math there's an app that converts hand written equations to fully valid LaTeX. You can easily sketch concepts and forward by mail.
Of course all of these apply to other tablets equally.

I use a tablet (not an iPad) for reading articles when traveling, having copies of articles and open-source books available, and generally having all my course documents stored there for easy access at any time.
A new use has come in the last year: I may have a particular slide on the overhead, and students working exercises based on that slide while I circulate and give personal feedback. I have my tablet with me, both to (a) check the answer, and more importantly (b) have the same slideshow available to flip back to any prior topic if an individual student doesn't remember or was previously absent.
And finally: All my role-playing books for when I master events at gaming conventions.

It's fantastic for projecting slides while being easy to carry around.  Just put a lecture into a slideshow app, plug it into the projector, and put it down.  Control with a remote as needed.  No need to fiddle with getting it to mirror the screen.

ZotPad in combination with Zotero and Dropbox is useful to keep track of all articles you've read.

This is a little overly specific and doesn't really discuss the iPad, but rather discusses Zotero's iPad app. Do you have anything to add specific to the iPad?


text:
Offended My Professor
Last night in class we were having a discussion about how to handle an ethical dilemma in the workplace. I raised my hand said that I had read an article that said there are few times when we would have to go outside of our (law) firm to report breaches in conduct. I had found a website that provided opinions on various ethical workplace dilemmas similar to the novice employee in the scenario we were discussing. I offered that perhaps, if faced with a similar situation, writing a letter might be something we could do if our ethical rules were not clear on how to handle the situation.
The professor didn’t seem thrilled about my suggestion. He did not seem to like the website source I had chosen. Then, later in class (a class of nine) he went around the room (actually went down the list) and asked everyone for their specific opinion on an ethics video we had just watched - except me.
I think I really offended him.
Do I apologize for offering my opinion of what might help in that situation?

I really don't follow. What "firm" are you talking about? What "site that provided opinions"? In any case, this seems like a standard interpersonal issue rather than some weird quirk of academia.

-Question regarding etiquette of dealing with a professor in an academic setting, I think qualifies as acceptable topics. -Different than dealing with my mechanic or even my doctor.

To follow-up on @cag51 's comment. What firm are you talking about? Your question is unclear.

Your question is unclear: kindly attend to @cag51: firm. You indicated... Do I apologize for my overzealous participation? This tilts towards what we must tell you to do. Rather, rephrase. || Not so critical, but might be helpful: is this a graduate class.

Perhaps he assumed you had already given your opinion so didn't need to be called on. I wasn't there, of course.
If you are concerned, go visit him during office hours and work it out. Offer an apology if necessary. Ask for guidance for the future, if necessary.
But don't try to do this sort of thing by email.
If it absolutely has to be done by email, say something like the following

I seem to have offended you... I apologize for that..

But don't give a "nopology" like "Sorry if I offended you" or "Sorry you were offended."

Thank you. I understand your comment about the email. He definitely skipped over me. It was a different, specific question regarding a video we watched.

No office hours at our school. Either before class - which makes it difficult because everyone gets there early. To even bring it up might have to be by email.

I suggest using email to ask for a meeting, then.

Excellent advice. Thank you.


text:
How should I speak to a professor about extra credit that dropped my grade?
Out of kindness, my professor gave me and one other student extra credit for volunteering at an event.
The issue is that the “extra credit” actually dropped my grade. Instead of giving a 15/15 he gave us 10/15. That's a D: 66.666 It dropped my grade from a 99.066 to 98.431.
He is my favorite teacher. I don't want to seem ungrateful.
How do I broach this subject? Or, do I just leave it alone?
—————
I read all of the comments and they were very helpful. I decided not to broach the subject with him.
Final grades just came out. He must have noticed as my score was adjusted to make sure my score was accurate.

Either you or the professor is not understanding how to add extra credit to your grade. Yes he only gave you 10/15 possible credit. But in the simpliest case, that should just add 10 points to your final grade putting you at 109.066 instead of the possible 114.06 if you earned the total possible extra credit. There may be a weighting factor that makes it less than this simple case, BUT there is definitely NOT any case that extra credit would lower your grade. The simplest course of action is to just ask. At a minimum use it as a way to chat and "get to know" your professor better.

In the systems, I'm familiar with (D2L, etc.), the right way to add this kind of entry would be an assignment scored as "10/0" so it is a strict points addition. This might just be unfamiliarity with the inner workings of the scoring system,

Just out of curiosity, what is the difference between 99 and 98.5?  In the system I am most familiar with, the first is an A, and the second is an A.  Does it actually matter?

@XanderHenderson … in fact, I doubt there’s a material difference in anybody’s mind between 99 and 98, so this is really much ado about nothing.

If there is something like a subject prize for top mark, it could matter, I guess. @XanderHenderson

@AdamBurke Which is why I asked the question.  Only the original asker can answer it.

If it can drop your grade, it is not really "extra credit".  Usually when you give a student an extra credit task it is something that is capable of raising their grade (if they do it well) or is ignored if it does not raise their grade.  (In other words, the task is usually treated as if it were a "redeemable" assessment.)  For that reason, one plausible explanation here is that your teacher might just have made a mistake in how the assessment for that item was incorporated into your overall mark.
Under the circumstances, it would be reasonable for you to broach the subject with your teacher.  No particular finesse is required beyond a simple sincere enquiry that does not make demands, and shows appreciation for other aspects of the teacher's work.  I recommend you go and see your teacher and point out that your "extra credit" work dropped your overall mark, and first just check if this was intentional.  If it was intentional that it should be marked this way, it would then be reasonable for you to point out that the item being called "extra credit" work seems misnamed, and it seems unfair to you that it would drop your overall mark.
As to not wanting to seem ungrateful to your favourite teacher, it might be nice if you would preface your enquiry by telling your teacher that he is your favourite and that you appreciate what a good job he has done on his teaching.  People like to hear when others appreciate their work, especially if he has done a particularly good job with you relative to the other teachers.  However, XanderHenderson makes an excellent counter-point in the comments below where he notes that this might come across as you "buttering up" your teacher, and he might prefer not to hear this part in that context.  If after you've explained your concern, your teacher decides he wants to keep your mark as it is, and is comfortable continuing to call this type of task "extra credit" work despite its potential adverse impact on marks, then it would probably be best to thank him for considering the issue and leave it at that.  (Let him then mull it over in his own time for use with future students.)
Finally, you will have observed in the comments to the various answers that there are some academics/graduates who do not like "quibbles" over what are already high marks, and so some will take an inherently negative view of anything that involves seeking to change a 98 to a 99.  I am on the side of those who think that this part is irrelevant, and that it is still worth raising the matter to ensure that the marking is done correctly now and in future.  I think CaptainEmacs puts it well in his comments below (for another answer) when he says that "[a] student that pays attention to these things is a student that achieves near full marks.  That's the student you want to run your experiments or write your code or carry out your computations."

Thank you. I will take your advice. It was a mistake. I am not sure he understands that the possible points for an assignment and the grade earned need to match for the full score of 100 points. He has made this mistake in other classes as a matter grading for an assignment with multiple parts. In the grading app he allotted a possible grade of 25 points but only assigned enough work for 20 points which is an 80/B.  He never changed the allotted amount. So everyone’s grade was affected. I don’t think anyone caught it.

@SallyQ probably because no one has such an extremely high grade as 99 :)

@SallyQ I'm going to hope that this isn't your math professor :)

+1 I think it is likely a mistake. It sounds to me like the professor is having difficulty with whatever software they use for grading. The software might even be lacking the needed functionally to score "extra credit."

That sounds likely.  Incidentally, I have had similar difficulties with in-house online platforms (which are often not particularly user-friendly or clear) and so I always use a simple Excel spreadsheet with my own calculations as a "master sheet" for my grading.

For what it is worth, I really dislike getting emails that start with "I loved your class!  I think you were a great instructor!"  It might just be me, but those kinds of messages always come across as insincere.  If I had made a mistake like this one, I would prefer to get a short email of the kind "Xander, I think there is a mistake in how my grade was computed.  The extra credit seems to have lowered my overall score.  Is this correct?  Regards, SallyQ"  Please don't try to butter me up, even if it is sincere.

@XanderHenderson: Excellent point.  I've edited the answer to note this counterpoint.

… and for what it’s worth, I really  dislike students wasting my time in arguing they deserve 99 instead of 98.

@ZeroTheHero I'd still want to hear about it to make sure I didn't screw up anyone else's grade.

@BryanKrauseisonstrike Me, too.  "Yo, Xander.  I noticed that I seemed to lose points because of an extra credit assignment.  Not a big deal for me---I think I have earned an A in either case---but if this is a systematic error, someone else might have gotten a lower grade than they deserved.  Thanks for a great class, [Student]" (See, I can take a compliment, when it doesn't look insincere.)

Don't write "Yo Xander". Some people may actually consider that seriously acceptable writing. The fact that no honorific or polite distancing (Vous, Sie, in French and English) is used anymore does not make the student a buddy of the prof.

@ZeroTheHero I would agree with you if it was just some marking judgement. Here it is a matter of principle. It could be a small reduction or a large reduction or the step from pass to fail. Whatever it is, 'extra credit' should not penalize the student.

@CaptainEmacs I was only describing the kind of email I would be happy to accept, not what is necessarily acceptable for anyone else.  I dislike honorifics, and would prefer that students address me a little more informally.  I don't really care if students begin an email with that level of informality.  But every instructor needs to make their preferred style of communication clear to their students.  I have about a page in my syllabi on the topic.

@XanderHenderson I personally am not specifically attached to norifics. However, tolerating being addressed in "buddy-style"  will tempt the less self-restrained of students to treat the academic like a buddy, and if you have not yet experienced the downside effects of that yet, consider yourself lucky. There is a considerable number of questions on SE which deal with how to handle lack/loss of respect as a junior academic. Of course, trustworthy students/inner circle etc. can ultimately get a more informal interaction, but they have to earn the academic's trust.

@CaptainEmacs Again, it is up to the instructor to make the standard of communication clear.  At this particular moment in my career, at the particular institution at which I work, this more friendly and informal style works very well for me.  Getting students to send an email at all is a victory.  Just to be clear, I was not suggesting that precise message be copy-pasted by anyone and everyone.  Every instructor needs to clearly set expectations for their students.

@XanderHenderson Ok. With this clarification, I can accept the argument.

You are clearly on track for the highest possible letter grade in this course. No need to fuss about one half of one percent in the high nineties.
After the course has ended and you have earned your A you might consider asking your professor about a strange statistical anomaly you noticed: that less than a perfect score on what was nominally work for extra credit actually lowered your course wide average. They might want to look into that.

The fuss is not about half a percent, but losing marks on something that was supposed to be extra effort by the student. A student that pays attention to these things is a student that achieves near full marks. That's the student you want to run your experiments or write your code or carry out your computations.

@CaptainEmacs I agree. That's why I suggested calling the instructor's attention to the anomaly after grades have been assigned.

@EthanBolker Why only after? They might want to look into that before grading.

@JiK After so that there is no way to misconstrue as concerned about the miniscule change of grade. The question suggests that this applies to very few very good students. If it were general then immediate notice might be warranted.

@JiK Since the damage to the grade was totally unexpected (because it is utterly stupid, you shouldn't get worse results because you put in extra effort, and because your professor acknowledged the extra effort), nobody would have realised before grading.

Don't tell them to change your grade. Just tell that there might be a mistake in their calculation and show what happened. Do not demand any extra grade as it might be received as petty. It might be a good idea even to tell you are not after the grade. Instead tell them you are pointing this out just in case if there is a problem in the grade calculation. 99 to 98 is meaningless but if it causes someone else to drop from say A to A- due to being on the line, it could be an issue. Also there might be a deeper problem in the grade calculation which they might want to know.

But of course you are after the grade. 99 = "One of the ten best students this year", 98 = "One of the twenty best students this year". This could cost you thousands. "Sorry, you almost got the job, but we only higher the top ten students".

I don't know the department but for engineering there is 0 difference between those two. A few marks is always within the margin of error.

Your professor gave you extra credit, with the intention to give you some benefit for some valuable work that you have done. Now that good intention has backfired because of some "interesting" way someone calculated the total quality of your work. I would strongly assume that had your professor known this, he or she would have told you "you really deserve some extra credit for this work, but due to the strange ways of this university, it would actually hurt you, so I won't give it to you."
So you should tell your professor, and most likely they will make a decision so change things so that you and the other student don't suffer for this extra credit. The extra credit may be withdrawn if that is the only possibility, or it may even be improved so that your average doesn't go down.


text:
Online portfolios for college music professors?
I am returning to the academic world to pursue my teaching career.
I have been a professional musician for over 50 years, and I want to have an online portfolio using software that is generally accepted by academic decision makers.
The portfolio will include movies, MP3 files, links, professional recommendations, my artistic statement, and my teaching philosophy.
I’m curious to find out if anyone knows if there is a generally accepted format, blog, website, and so forth.

TL;DR
I am a Computer Science professor, so not an authority on this question, but my institution encourages personal websites last I checked.
Background
Several years ago when I was researching new Learning Management Systems (LMS), I interviewed various department chairs around campus to determine what their department needs would look like if we moved to a new LMS. The department chairs for Music and Performing Arts brought up concerns similar to this question. Their responses were the same:

LMS systems do not offer anything meaningful for student or faculty portfolios.
There is some software available for hosting online portfolios but it was costly; I do not remember specific software names anymore.
Personal websites were the easiest and relatively cost effective option:

Easiest being a relative term here since traditionally many music and art students/faculty have had limited tech skills to build and manage their own website.

It has been a few years since I had these conversations and there are plenty of free or relatively affordable drag-and-drop style website builders now. I am also noticing that our student body as a whole is fairly tech savvy and personal websites have become our standard for portfolios.
Dance students will often use a website or blog to share videos and playlists from YouTube. This allows visitors to their site to continue watching their performances on YouTube in a curated playlist. You can also unlist videos so only people who clicked through your website or blog can see them and they are not publicly available on YouTube.


text:
Is it ethical for a student to earn a PhD by working as a team leader?
I know several doctoral students in the field of deep learning. Their main job is to be the technical leader (full-time job, even not taking doctoral courses) in the company. They only propose research topics and write papers, and all experiments are completed by other engineers. These doctoral students will be the first authors of the papers and ultimately earn a degree based on these papers, is this behavior ethical?

I think I should describe it more clearly. These doctoral students mainly play the role of managers, who have strong management skills but limited  theoretical knowledge of related disciplines. For example, when they see that the diffusion model is very popular recently, they will ask engineers to investigate the diffusion model and explain it to them, and then they will arrange engineers to test the effect of the diffusion model on related interdisciplinary tasks. If the engineers encounter difficulties, they will arrange for other people with the knowledge and ability to assist as need.

Who will give them a PhD? And why would it not be ethical for someone to receive a PhD if a university wants to give them one and they’ve fulfilled the requirements?

This is because the experiments in the papers are conducted by others. They themselves are only familiar with the basic concepts but not the details.

Could you expatiate on ... all experiments are conducted by other engineers" ...

If a researcher or doctoral student were to be in humanities and all statistical analysis were done by others, say statisticians, would the researcher or doctoral student be ethical or unethical to lay claim to the research and research outcome?

@semmyk-research The codes and experiments are written and conducted by the engineers in the company. If positive results are obtained, these doctoral students (majoring in computer science) will write the papers.

It sounds as if you already decided the answer to your question, as you reveal more and more of the situation. You should ask what to do about it, then.

Is this in a German speaking country?

The contribution of a Ph.D. thesis needs to be attributable to the person and fulfill requirements such as significance and originality. It can depend on the work of others, even to the extent that this work is indispensable.
Proposing research topics sounds a bit weak, but we do not know the details of their importance. In my opinion, a proposal that lays procedure out such that the mythical average capable engineer of patent law following the established procedures of their field can perform the research and obtain the results is an independent, attributable contribution that derives its significance from the significance of the complete research. There is no requirement that a researcher has to do everything in the research.
Indeed, such a requirement would quickly lead to abstruse situations. If I were to use (not yet, but almost existing) AI to write simple Python scripts, the result is mine. If I ask someone to write the Python scripts for me, do the results stop being mine? Or, if I were to write the Python scripts myself, do I need to attribute the results equally to the implementers and designers of NumPy and similar modules? Similarly, would research in epidemiology only be valid for a Ph.D. if all the testing and the sample analysis involved would be done by the person aspiring to the doctorate? With other words, some collaboration and some reliance on the work by others is to be expected.
I am not sure about your experience with research, but from my experience I can assure you that some of the most difficult challenges in research is finding good research topics. Ordering a competent engineer to perform an experiment does not invalidate the contribution of the one ordering it.
Ultimately, the ethics of the situation depends on the details of the situation, most importantly the novelty and significance of the topics proposed as well as how easy it would be for someone in the field to perform these tasks.  It could well be that there is little significance in what the Ph.D. candidates are contributing, but it could also be a lot. The decision first rests with the Ph.D. committee at their universities, who presumably can read between the lines in order to assess the individual contributions. If you think yourself competent to judge that there is no significant contribution and that inferiors are asked to do the research for the superior, then you could (anonymously) inform the chair of the department, who could then raise the issue with the committee members if they deem your concern credible.

You mentioned

They {only} propose research topics and write papers, and all experiments are completed by other engineers

Depending on what all experiments are completed by other engineers is, the research is completed by them (the doctoral student).
The engineers can be seen in the same light as technicians/programmers working in (university) lab.
At times, doctoral students and postdocs get stuck in the coding, because of the search for novelty, and neglect the research. There should be balance.

I think I should describe it more clearly. These doctoral students study interdisciplinary subjects (deep learning & chemistry), and they don’t have much theoretical knowledge, but they are very familiar with popular topics in deep learning and cheminformatics. For example, when they notice that the diffusion model is very popular recently, they will ask an engineer to investigate the diffusion model and report to him, and then they will arrange for the engineer to test the effect of the diffusion model on tasks in cheminformatics.

If a PhD student does work that a university believes merits awarding them a PhD, then the student is acting ethically. The university is the one that decides what the standard is for receiving a PhD carrying its name. If they set the standard too low and award PhD degrees for too little work, or for work that doesn’t develop appropriate research skills, the university will quickly develop a reputation as little more than a diploma mill and its degrees will be seen as worthless.
The above analysis is assuming that the student is not misleading the university about the scope of the work they are doing. If the student pretends to be doing work that others are doing, obviously that is unethical behavior and constitutes serious misconduct.


text:
Better to cite github project or web page of unpublished software?
In my research, I am using several compression algorithms that do not have a related publication. For example Facebook's lzfse. Would it better to cite it's active github project (e.g., https://github.com/lzfse/lzfse) or blog or other web content introducing this utility (e.g., https://developer.apple.com/reference/compression/data_compression)?
I guess I am concerned with the amount of time this will stay active online as well as relevance.

As a reader, I would find a citation or mention of both resource types to be useful, especially in the all-too-common event of a link breaking or a github project going dormant. If you're concerned about formality then contacting the original authors to determine which citation they would prefer would be helpful. Otherwise, as long as your audience knows what you're referencing and where to find out more about it, you should be fine.


text:
How to politely describe a situation where you have no publication because both you and the advisor are inexperienced in a new research topic?
How to politely describe a situation where you have no publication because both you and the advisor are inexperienced in a new research topic?

The lab previously only did research on topic A (e.g. protein factors) and lacked the experimental conditions for conducting research on topic B (e.g. circular RNAs), which is a very hot topic recently. BTW, which word should be used? topic, subject, field or area?
The student is the first and only one that conducted the project on the new topic.
The student started from scratch and faced many difficulties. The advisor was willing to but sometimes powerless to help when the student got stuck.
However, there is no publication after several years, since both the student and the advisor lack experience in the new research topic.

I do not know how to politely describe such situation from two distinct perspectives：

From my advisor’s perspective: I requested my advisor a letter of recommendation for PhD application. He suggested that I write a draft first.
From my perspective: I need to describe it in my personal statement.

However, I do not know how to politely describe such situation and meanwhile let the reviewer understand why I have no publication on this topic. Also, I am afraid my PS and the ROL draft would make him seem inexperienced in the new field or look like that I’m blaming him, which is rude and arrogant.

Maybe it's different in my field, but I've never heard of someone being asked to provide a draft of a letter of recommendation. I can easily understand your adviser asking for a draft of your personal statement, but the LoR? That seems odd to me.

@tonysdg: See http://academia.stackexchange.com/questions/29041/what-does-it-mean-if-a-professor-asks-you-to-draft-his-reference-letter-for-you

I suspect the answer for this strongly depends on cultural context.  My answer is for applications to PhD programs in the US (and probably Canada also), but it may not hold for other countries.
In the US, it's not expected that every student going into a PhD program has written a paper.  (In some subjects, almost no students entering a PhD program has written a paper.)  Your advisor should simply not mention that you haven't written a paper, but explain what you have done successfully (and there are other notions of success than writing a paper!), and what positive character attributes you have that lead him to believe you will be a successful PhD student.  It will be necessary to go into details of your project, but no mention needs to be made about the lack of a paper coming out.
You should have a similar approach in your personal statement, emphasizing what you learned from your research project and your coursework and explaining what research you want to work on for your PhD.
The PhD program will be admitting you as a person, not your package of previous accomplishments (although of course your previous accomplishments will tell them something about you as a person).

You could ask your advisor for a "reference" as to why your publication was unsuccessful?
This may be sufficient evidence to support the fact that it "wasn't your fault" (for want of a better phrase), and the resources just simply weren't there.

This suggestion does not seem rooted in knowledge of how the academic publication system usually works


text:
Is it right to use 'X is a new research topic of interest to our lab' to indicate that the lab has not done research on 'X'?
Is it right to use 'X is a new research topic of interest to our lab' to say that the lab has not done research on X before?
I want to convey:
1.The lab only focused on  research topic 'Y'(e.g. proteins) in the past. In the future, 'Y' will still be the focus, even though 'X' will be the secondary focus.
2.The lab lacked established biological experimental conditions for conducting research on topic 'X' (e.g. miRNA) two years ago, since topic X belongs to different field. I was the first student to conduct research on topic X.
I am a student, not the PI. I want to describe the experimental conditions when I began the project in PS for PhD application. I started from scratch and encountered many difficulties.
(I hope my edits would make the problem more clear, thank you! )
Besides, Is there a more polite way to say 'our lab'?  I mean the lab I belong to.

Could you add more information about where you want to put this sentence, i.e. who is the intended reader? There are no errors in the sentence, but I think you are more interested in false implications or assumptions based on your sentence.

Vote to close as "unclear what you're asking".

I can't seem to agree completely with any answer below. But still, I think there are accepted lines on when a topic is new or not. In my understanding, this topic is now a focus in the lab, because the experimental conditions are available. So, in that case it is a new topic of interest, as there are not publications yet (if that's what you want to justify). If the PI of the lab was never interested in that topic, regardless the available conditions, then you cannot say it's a new topic. But please explain where you plan to use this sentence.

@George I added more information. Would you give me some suggestions? Thank you in advance.

@Rasituwrt I would say it depends on where you want to use it. In a motivation letter where you state your background, I would probably say something like "When the lab started working on this method, I was the first student to develop the workflow". If you are talking to someone, the way you say it doesn't sound bad.

"Our lab" is acceptable - no one will misconstrue this to mean that you own the lab as an equal partner; in this context, "our" refers to the collaborative nature of science. For the other part of your question, I am less clear; if you are applying to a PhD program and want to talk about what you did before applying to the PhD program, you should focus on your experience. If 'X' was something new to the lab, what was your role with 'X'? Were you starting experiments with 'X'? Designing experiments to look at 'X'? Reading papers to see how 'X' fit with your lab's previous work on 'Y'?

I have angst about writing this answer. When you say our lab, it potentially sounds like you are speaking for the lab in an official context and taking an ownership stake in the lab. Depending on your role, I am not sure you can talk about the lab as being yours. I am also not sure you cannot, and hence the angst.
As a PI of a lab, I have research interests that the lab has never followed through on due to a variety of reasons including a lack of funding and expertise. I would be a little upset if a student/post doc implied the lab was not interested in a topic just because the lab didn't have the expertise or equipment to do any research on the topic. Similarly, I would be a little upset if a student post doc implied that their personal interest automatically becomes an interest of the lab.

I think the question needs some clarification, as I don't think the student or post doc wants their personal interest to become a lab interest. From a different perspective, post docs, and the different levels of professors are all accomplished (in different levels) researchers. There are post docs who are PIs in projects (meaning they got the grant for it), and sometimes post docs are allowed to persue their own interests (as they are also to a degree accomplished scientists). So, don't take it personally :)

@George sort of. I think that aspect of ambiguity is why the question is important. If the OP realized all the ways the statement could be interpreted, then there would be no need for the question. To me the question is: can this relatively simple statement be interpreted in a way I do not intend.

Also, I'm not sure the aim is to take ownership. My or our lab often means belonging... It's a nicer way to express the lab you are part of, rather than saying "in the lab of the PI".

Yes, indeed. It needs clarification.

@StrongBad Thank you very much for the reminder. Is there a more polite way to say 'our lab'? I mean the lab I belong to.

No, it would be a lie. In fact, you state that X is actually not a research topic of the lab nor has it ever been. You could say that X will be a new topic, if there are plausible plans about it. This would suggest the right thing about the present and the past.

It seems to me that it's only a lie if you take an extremely pedantic reading of the sentence. If I began researching X this morning, then, this afternoon, it would take an exercise in extreme nitpicking to claim that the statement "X is a new research topic of interest to me" is a lie.

"The lab only focused on another research topic in the past" means that even this morning, research on the new topic has not been done. Which makes some sense, since the necessary equipment isn't present, too. So we talk about a future topic, not a new one.


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Misconduct report
I am teaching at the university, and I am giving Calculus 1 for first year engineering students.
I am having a problem with some students, their behavior in the class is inappropriate: making noise, speaking in the class with their classmates, not writing or even paying attention. As a consequence of such behaviors and in order to keep my class controlled, I kick them out the class.
For this, I should send a misconduct report to the director of the university. Our university has distributed a misconduct sample for all instructors, however, I have difficulty describing the misconduct.
The idea is that it is difficult for me to describe their behavior in English since it is not my native language.
Would someone help me how to start the description of the misconduct?  and what to write exactly?
I already did some researches on google, but they were useless, and as this site is concerned with Academic ideas, I think my problem can be entitled under academic problems.

Can you state what country this is, so we have some context about the culture? In the US, I would think that a formal misconduct report for such behavior would be excessive, unless the behavior is really flagrant or persistent.  And "not writing" and "not paying attention" are not generally treated as misconduct at all unless the student is disturbing others.

@NateEldredge Infact I in Lebanon, a small country in the Middle East.  As you said "not writing" and "not paying attention" is not a seriuos misconduct. But in a large class ( about 40 students), studnets that are not writinting and not paying attention they will get bored quickly and strat doing noise, speaking with each other, or do some clowning, as the lecture is about one hour and fourty minutes.

Are you required to write a report or do you choose to do it as an additional reprimand?

Voting to close...everyone is answering the (more interesting) question about whether this is a good idea, but OP's question is about the mechanics of writing such a report in English (which is not really on-topic here).

How can you teach in a language you are not quite familiar with?

@Alchimista I didnot say that I am not familiar  to English. Scientifically I am very good in English, but I find difficulty describing  such inappropriate behaviuors. In fact, these behaviuors I cannot even describe in my own language.

I see. I would try to impose your prrsonality and speak with a colleague before official moves, as others said. Good luck.

I am having a problem with some students, their behavior in the class is inappropriate: making noise, speaking in the class with their classmates, not writing or even paying attention. As a consequence of such behaviors and in order to keep my class controlled, I kick them out the class.
For this, I should send a misconduct report to the director of the university.

While it seems a little over the top to me, I am going to assume you were justified in kicking the students out and I am also going to assume that triggered a mandatory filing of a misconduct report. I would write a draft report that says exactly what you said. I would then pass that by a senior colleague and ask if it is necessary to provide more detail.

You can't find it under "academic problems". Every university might have different policies regarding how to handle students interrupting the course (there is no universal guideline).
I would ask a senior colleague "What is considered a misconduct that qualifies to be reported?".
Your colleague's answer will help you qualify the type of misconduct and you will know what to write in your report.
And for your own sake do not kick students out of the room regularly if you do not know the university culture and regulations. From your question I assume you are still getting used to the university that you are teaching at.Instead of keeping your class in control you might get a nice nickname and a headache from your head of department.

Rather than put the blame on students, you might look at what you are doing in the face to face sessions. For some reason at least some of your students don't believe that it is worth listening or participating. Likely they are bored.
One solution to such things is to force the students into a more active learning situation in which they naturally participate, rather than simply listening to a lecture. They don't seem to think that the information they are getting is worth it.
I once had a couple of teachers who thought, quite literally, that students were supposed to faithfully copy everything they wrote rather than understanding it. In one case, with only two students, we simply copied from his previously written notes. There was a lot of copying, but no learning.
It is possible that even good lectures are posed at a level that isn't appropriate for the students. It might be low, hence boring, or too high, hence frustrating.
Look to your teaching methodology. Passive learning is seldom very useful for very many students. Learning involves working with and reinforcing ideas, not just hearing ideas from another. Even marvelous lecturers can be less effective in actually teaching rather than just entertaining. It is a subtle issue.

The term "academic misconduct" usually refers to things like plagiarism or ghosting. Disturbing behaviour in class is annoying but in my opinion does not come under the same umbrella as academic misconduct. In many more traditional (old-school) universities it would be considered normal to kick disturbing students out of the class; however, I never heard on anyone filing academic misconduct report on them afterwards. In many places kicking students out is seemed as a certain weakness of a lecturer and would be grumbled upon.


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Figures in the introduction of a paper
I am preparing a paper for proceedings of a conference in the domain of engineering and physics.
Is it formally acceptable to add a figure in the introduction?
The idea is that I am explaining something that is already done/known, and I would like to keep it in the introduction as a part of the bibliographical paragraph. This idea should explain the experimental setup, and clearly this will be much clear by using an illustration.

It might be unusual, but only the conference chair (or program chair) can give you final advice.

I've seen it done in physics journals.

I think it may depend on how the figure is used. While referencing the figure in the intro may help clarify what you are interested in discussing / motivated to do, one still needs to / should actually discuss that figure in the experimental section in depth. So, a passing reference to clarify in the intro, the real meat of the discussion in the experimental part of how you are attacking the problem.

I've never heard of a rule discouraging figures in the introduction.  (Or if there is such a rule, I regularly break it.)

I would assume that there is no formal rule about figures in the introduction (at least i haven't heard of it). Still, it would be unusual because introductions tend to not get into specifics. I'd guess it depends on the context of your paper, but if you keep it very simple and brief, you should go for it.
In case of doubt: if your paper is well-structured and well-written in addition to presenting content within the scope of the conference proceedings you aim to submit in, your submission probably would not get submitted over an explanatory figure. It could be that reviewers ask for the figure to be (re)moved though.

To provide a different field's perspective: In Randy Pausch's famous Last Lecture (youtube link with specific timestamp) he actually talks about this. He said that his 1996 SIGGRAPH paper was almost a scandal since they put a large figure on the first page. It has now become a trend in that community.
Most conferences and journals probably don't have rules specifically against this. As long as you use the figure legitimately then I can't imagine it causing an issue.

tiniest linked image ever

It is pretty common in my (physics) field, where you typically need to give quite a bit of introductory material before delving into the original research. This is true both for theoretical and for experimental papers. As everywhere, a picture is worth a thousand words.
In physics, the figure may represent a picture of your experimental layout, or a visual summary of the state of the art in terms of theory papers on the subject. A picture might take similar or less space than describing it into words, and helps memorising key information faster. I have never heard of limitations on where to put a picture, and had often a figure in the introduction of my papers.

I don't see why not, unless the venue or the field has specific conventions to the contrary. I often include a map in the introduction to both journal and conference papers, to show the part of the world that the work refers to.


text:
About interviews for teaching positions in math during JMM
To what extent is attending the Joint Mathematics Meetings (JMM) important when applying for teaching jobs in mathematics, including temporary lecturer positions and faculty roles at liberal arts colleges? This question includes at least two subquestions: first, do employers, especially liberal arts colleges, care about interviews at JMM these days? Second, if they do, can candidates request Zoom interviews instead, and would this put them at a disadvantage?

I am a professor of mathematics at Denison University, a good liberal arts college in Ohio. I've been on around 10 hiring committees. Based on my experiences (detailed below), my impression is that nowadays a candidate would not be harmed (in terms of their chances of getting a great job) by skipping the JMM employment center.
When I was hired in 2014, there was an interview at JMM, followed by an on-campus interview. Back then, I think it would have been a handicap to not attend the JMM.
In 2015, the first hiring committee I served on also had interviews at JMM. We interviewed about 20 people there, then brought three to campus. I learned that the cost of the Employment Center is rather large, and I got a sense of how much it costs for the university to send a delegation for the week to the JMM to do these interviews. Fortunately, Denison has lots of money, but I got the feeling the administration would have been happier if we could have cut costs a bit here.
In 2017, the department hired a visiting assistant professor on a three-year contract and did not use JMM for this. The same thing happened in 2019. The job market keeps getting tighter and tighter, and we get hundreds of applications even for a VAP position, so JMM is not required in order to hire a great person.
In 2019, I had some friends at a strong liberal arts college running a search for a tenure track position and their search did not involve JMM, but rather something like Google video chat interviews. I knew of other good liberal arts colleges in that year who did interview of JMM but also allowed candidates to interview via video chat, and didn't bias against the latter.
In 2020, we all learned how to use Zoom. That fall, we did Zoom interviews as part of hiring in computer science and it went very well.
In 2021 we again hired a VAP and used Zoom to narrow the applicant pool to the "on campus" choices. Meanwhile, friends at an R1 university told me they were doing all interviews remotely.
In the 2022-2023 year, we hired two tenure track professors, and did not go to JMM. We used Zoom to get down to the "on campus" choices.
In 2023, we hired a VAP and again used Zoom to get down to the "on campus" choices.
My sense these days is that there's much less pressure for candidates or universities to do interviews at JMM. Most universities and colleges are happy to do Zoom interviews, as this saves a lot of money and time (e.g., transit time of the hiring committee to the conference). Additionally, many good liberal arts colleges are more aware now of issues of inclusivity and equity and are leery of requiring candidates to be at some specific conference on some specific date, as many great candidates cannot afford such a trip, or cannot spare time from family obligations during the winter break.


text:
Leaving postdoc after 6 months (or less)?
I just started a postdoc position at a prestigious institute in the US. I am one month in and the contract is for 1 year with a possibility of renewal (the project I work on received a 3-year grant). Having said that it is a prestigious institute, the lab environment is on the low standard side for me. Lab is unclean, unorganized, with instruments not working properly or very outdated. Several tools, equipment, notes are just scattered around on the benches. Moreover, it is a molecular lab but people bring their bicycles to the lab and park next to the lab bench. People touching/working on lab stuff without wearing gloves or lab coats, which is completely different from when I did my PhD in another country where none of these happened in a molecular lab.
I also didn't have a good first impression with my PI either. We seem to have different working style and can't seem to be understanding each other. I wanted to focus on a specific topic but she wanted me to do an exploratory work and also be on other people's projects. Labmates are nice though but they are on the end of their 3rd or 4th year and are planning to quit soon (I guess that is why PI wanted me to continue their work). I can feel that my mental health is going down right now.
I am one month in and keep asking myself if I should toughen it out for a year, or 6 months in case I am just homesick and still acclimatizing, or should I wait and see a few more months and if I still want to quit then just quit (with a proper notice - although my offer letter did say that I can leave with or without notice and with or without reasons).
I know I should have thought about this very hard before taking the position but because I still enjoy doing science so I just accepted it after one Zoom interview, but if this doesn't work out then I feel like it is time to explore other career options (probably industry). I don't have any financial issues as I have a secondary income.
If I am 99% determined to leave but still want to give it a chance (love the science - hate the environment), how long should I stay for? What should I do?
*Edited for typos

just checking-out: what happened then?

it is a molecular ... People touching/working on lab without wearing gloves or lab coats

You should not work in an organic chemistry lab that has bad workplace safety practices.  I know people who have been set on fire.  Don't join them.  That said, as a postdoc you should be participating in teaching the other staff to use good safety practices.

Lab is unclean, unorganized, with instruments not working properly or very outdated.

That's normal.
If you are unhappy in your job, look for a new one.