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Can I cite the results from my unpublished manuscript which is included in my PhD thesis?
My PhD thesis is manuscript-based, and I have 3 manuscripts (unpublished), included as 3 chapters into the thsis. The data analysis of my 3rd manuscript is mostly based on the results of the previous two (like my main independent variable in the 3rd manuscript is the result of my 1st manuscript).
Thus, when I write the methodology, I'm actually repeating a large portion of the methodologies from the previous manuscripts, and this is just too much for one manuscript. I'm thinking if in my thesis, I can say something like "the variable is generated from the analyses performed in previous study/chapter/manuscript", so I can save more space to the analyses of my 3rd manuscript.

This is a question you should ask your advisor.

What field are you in? In some areas of research, citing an unpublished manuscript is perfectly acceptable.

Think about this from the point of view of a reader or reviewer. The reader needs all this information for your research to be clear and reproducible. Your PhD thesis and your unpublished manuscripts will not normally be easily accessible to them. Also a reviewer may not want to look for such sources in order to assess your work. For essential information like this, you should therefore not cite these manuscripts. Many journals allow online supplements for their published papers, so if you have a large amount of information that is required for reproducibility but too long to have in the actual paper, put it in an online supplement. In the journals that I know, you'd submit the online supplement together with the main paper. Reviewers can then check this material, too.
You could get away, depending on journal guidelines (that sometimes allow such references and sometimes not), with certain references to your thesis such as "in some experiments we tried out this-or-that alternative approach but results weren't any good, see (...)". But not something that is of essential importance to the material presented in your actual main paper. (I have to qualify this by saying that there may be journals who'd even allow that, but I don't think it's good practice and chances are these journals are not so good.)

"Your PhD thesis and your unpublished manuscripts will not normally be easily accessible to them." That would depend a lot on where they got their doctorate. In Germany publishing your thesis is one of the basic requirements for getting your degree.

@Maeher This doesn't necessarily mean that the thesis is then easily accessible to reviewers. Note that as a reviewer when it comes to specifics of research work that I'm expected to review, I generally don't want to be forced to look for cited literature, even if in a regular journal (of course there can be exceptions but what is explained here doesn't look like one). But fair enough, it may depend on country, field, and journal where they want to publish.

It's at least as easily accessible as any other published book. In practice many examination regulations nowadays allow the university library to act as the publisher, which means it is usually more easily accessible than your usual paywalled publication. I.e. they're freely accessible online, have assigned dois, and are indexed by the usual databases.

PhD thesis is usually counted as a publication (and in principle is accessible from the relevant university library.) Thus, the usual practice would be simply citing the thesis. More over, it is equivalent to a publication in a refereed journal, as it was reviewed by experts (PhD committee or an equivalent) prior to awarding the PhD degree.
Another option is publishing the relevant materials online (e.g., on arXive) or making them available upon request - this has less weight as a publication, but provides the necessary information to those interested in understanding your work.

I would say that you can totally go ahead and refer to the other chapters of your thesis in your situation if you are willing and able to still change the third manuscript when you are actually going to publish it, if ever (and I don't really see why you wouldn't).
If so, when preparing your manuscript for submission to a journal, simply replace the relevant citations to either references:

to the published articles, if you have managed to publish them by then (best case scenario).
to your PhD thesis if you haven't.
a combination of the two if you were able to one article, but not the other.

In my reading, this is further acceptable, because referring to a different chapters is exactly how you would go about the problem if your thesis was not prepared in a "manuscript-based" style. And given that no part of your work has, in fact, been published yet, the style/format is really all that sets your thesis apart from a monograph-style thesis. And so I don't
The other answers given so far are flawed, in my opinion:

Roger V. advises to add a fully qualified citation to your thesis. However, at the time of writing you are not able to do so, because you probably don't know the exact DOI, volume, issue or even URL where your thesis will be available. And even if you were, some people might well regard citing your own work within the same work as an abusive form of self citation, as it will increase the citation count of said work. Roger V. also suggests that a PhD thesis is equivalent to a peer-reviewed journal article. I don't necessarily agree with that, because PhD theses are frequently reviewed only by members of the thesis committee, and it could be argued that there may be a conflict of interest, as is demonstrated by the much lower rejection rates of PhD thesis compared to journal article submissions (at least in the universities I know). Finally, at least at the time of drafting your thesis and adding the citations, your thesis hasn't been reviewed at all, so that argument doesn't even apply.
HEITZ doesn't explicitly recommend anything, but their answer implicitly could be read as advice not to reference to your other chapters because (1) readers of your work would not be able to find the information you are referencing, and (2) a citation implies peer review. Both are wrong, in my opinion. Given that your entire work is contained in the same volume (the PhD thesis/dissertation) and not published elsewhere, all information will be available to any reader (assuming that they have access to the entire work and not just the chapter or a page, but we would typically make that very same or even a stronger assumption for readers of a manuscript, who we also believe to have access to the entire manuscript, plus every other published article). And merely citing "citable resources" does not imply peer review, and neither should it. You can and should cite published works and resources that are not peer reviewed, such as preprints and datasets, as long as there is no better source available to refer to (e.g., prefer to cite a peer-reviewed article over its preprint, once available).
It appearst to me that Christian Hennig misunderstood the question (or perhaps I did?), understanding that you would like to publish manuscript 3, while not having published manuscripts 1 and 2 outside of your PhD thesis. But even if that were the case, I still think it is acceptable and not unusual to cite a PhD thesis as long as it is publicly available (as it usually is). In fact, I recently saw a case where an editor of a journal specifically asked to include a citation to a "manuscript-based" PhD thesis in a manuscript that included parts of the submitted work (though, in that case, the publication of the thesis was actually predated by publication in a preprint server, which was already cited).

Note, however, that Roger V. actually gives what is probably the best advice: Try to publish all of your articles on a preprint server like arXiv, or whatever is appropriate in your field. This not only avoids your problem (just publish manuscripts 1 and 2 first, then manuscript 3 after), but also gives your thesis the feel of a more conventional manuscript-based thesis. But of course, given your timelines, this may not be possible anymore at this point, as it would still probably take a week or up to a month before you get a citable identifier / DOI to include in manuscript 3. But maybe for next time :-D

_Try to publish all of your articles on a preprint server like arXiv, or whatever is appropriate in your field. _ <--- THIS

By referencing a work you are basically telling readers two things.

where to find the referenced info. If readers cannot access referenced information due to unavailability or manuscript status, then you haven’t really provided the necessary info

if it’s published, readers infer it’s been peer reviewed.


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How to approach profs from different unis for (mini) research projects?
I am set to complete my Masters this year (in 2-3 months) from a local university in India, and I haven't done a research project yet throughout my UG or PG years. I really like Algebra and Topology and related fields, but never thought of the prospects of doing a research project. To top that, our semester exams take place exactly when other institutes in India conduct their summer research projects, so I never could apply for a summer research internship either.
Now, I get to know that to apply abroad, I have to have some decent projects to my name. It's not that I didn't think about a PhD earlier, but I never cared enough to think seriously about it, and thus plan my moves accordingly. In short, maybe I did screw up a little. Anyways, so now, with my Masters ending, I have to take things seriously and get my hands onto some projects.
I will be applying to the summer research programs here in India, but most of them accept only up to first year Masters' students. So most of the doors are closed. I am thinking of applying to colleges abroad for online research internship, not necessarily the summer research programs. I have heard from a friend from a different field that he had secured an internship through individually cold mailing profs.
How do I write to profs from different universities, India and abroad, for a research internship, online or offline(preferably online, since money is a huge factor if it is unpaid and offline), and what might the format be for a nice email to mail a prof, that might increase my chances of securing a project?

What do you exactly want the professor to do?

@MaartenBuis To assign me a project

Cold emailing will have a very low chance of success, but you never know. Using contacts of professors at your current institution likely has a somewhat higher chance. But consider why a professor would want to set up a remote project with someone they have never met.

@JonCuster I am looking for advice in general, regarding what to do

What does "assign a project" mean? I can assign you a project right now by saying "do some research" , but I guess that that is not what you mean. When you ask something from someone you need to be very precise what it is exactly you want from that person.

@MaartenBuis a guided project, preferably publishable in a journal of considerable repute.

I'm moderately shaky on the official policy, but my understanding is that expletives are generally not allowed without some compelling reason to allow them https://meta.stackexchange.com/questions/79974/whats-the-so-policy-for-swearing, so I edited the one out for a euphemism.

If you are asking for "a guided project", you are asking to receive educational services for free. Universities typically reserve those services for the students enrolled in at that university. So you are asking professors to volunteer their spare time. This means you are competing for time with their significant other, their children, parents, and friends. So I think @Buffy is correct in his answer, that you are extremely unlikely to be successful.

You are also asking for the project to be "publishable in a journal of considerable repute". This differs a bit from discipline to discipline, but in my discipline there are no more MA level projects left that are publishable, let alone publishable in a journal of considerable repute. But there are discipline where all the low hanging fruit has not been grazed away a hundred years ago. Still even in those disciplines that is a big ask. There is a reason why most people need at least an additional 4 years of specialized training (PhD) in order to publish such articles.

In short, I would encourage you to start working on a plan B: what will you do in the very likely case where you will not get such guided project. Again Buffy made some suggestions.

If all you want is to be assigned a project, then I'd suggest that you just ask one of your local professors to make a suggestion.
However, if you want guidance and a final evaluation, the problem is much harder, possibly unsolvable in most cases. I think the people that are successful in cold mailing for such things are rare and lucky.
There is little incentive for a (busy) professor to provide any guidance. They are unlikely to be paid for it, even by yourself.
And a local professor is much more likely to have a way to provide a bit of support, assuming you can meet with them occasionally.
One option is to ask one of your professors to suggest a recent paper or two for you to read. It could be one of theirs or not. Read it and enough of the supporting bibliography so that you get an understanding of a narrow field of study. This would be an essential skill in most doctoral programs. You might not get "credit" for it but you might learn something.

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Submit abstract to conference with no results yet
I am planning to go to a geoscience conference next year and therefore I would like to submit 1-2 abstracts.
Abstracts' submission has a deadline (of course) and I am not sure if I will have good results by then.
Is it acceptable to submit an abstract to a conference without having results yet?
Surely, the abstract will be very general and broad without 'making up' anything about my research's results.
Thanks

This depends very much on the conference in question. There are several conferences I submit to where it is fairly routine to outline broad strokes results, with the expectation that they will change in between the submission and the conference. There are others that expressly do not allow this, and want final-form, precise results and prohibit things like "...will be discussed."
So check the conference, and ask your advisor about the norms in your field.

@aaaaa: We can't provide info on specific conferences. You have to consult the specific guidelines of the conference for that.

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Missing Recommendation Letter
I am applying to Grad School. I have indicated three references. However, one of them has not yet completed. He has stopped responding to mails and phone calls too. Would it be wise to change him with some other reference ?
If it is of any importance, the person in the question is my undergraduate thesis advisor.
Since I don't have commenting rights I will add some more info here.
@kostia I visited his office some days back -> he disagreed to write then. Then some days after I visited, he writes to me saying he can do 5. And so I indicated him in requests. That was the last I had heard from him. I write him reminder e-mails almost every day, he doesn't reply.

Can you add another reference without removing this one? That way, in case he doesn't submit his, you can still have 3 letters.

At some places I can't

@kostia I visited his office some days back -> he disagreed to write then. Then some days after I visited, he writes to me saying he can do 5. And so I indicated him. That was the last I had heard from him. I write him (reminder) mails almost everyday, he doesnt reply.

Adding to @Kostia's answer, a negative letter from the undergraduate thesis advisor will tank your application.
He is giving all the signs of not being able to write a positive letter. He disagreed when you first asked him, then he agreed to only writing a few, now he is avoiding you.
I would absolutely not use him for any letters if at all possible. Again, a bad letter from your advisor is worse than a missing letter. Try to find a third person and have them write to as many schools as will let you change the letter writers.

A strong letter from the undergraduate thesis adviser would be very valuable, since this is the person who presumably knows your academic achievements better than others. Assuming that your adviser has agreed to write a recommendation letter (otherwise you should not have listed him as your referee), I would recommend to try your best and find him by going directly to his office, or through his colleagues or admin people.

I visited his office some days back -> he disagreed then.

I totally agree with what @RoboKaren wrote below.

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Multiple (two) undergraduate degrees in Phd application
This year I will apply to graduate school in Statistic. My situation is:
I obtained first Undergraduate degree in computer science with very bad GPA (due to not focus on study). After that I worked as software engineer for one year.
Then I returned to another university and earn a bachelor degree in Math and statistic. This time I had very good record with highest GPA among math department and many research experiences.
Now my question is: Do I need to include my first degree in CS in application or I just need to use my Math degree?

You need to follow the instructions on the application.
However, most applications will want transcripts for all prior degrees. One good thing: you may not have been successful before but you were when you tried again. So, you've shown that you can be successful. That improvement is important to be able to demonstrate (as you've done).

+1. Make sure, also, that you have some sort of explanation for anything negative in your history and can say things about how you have overcome the deficiencies. Be ready to talk about that to a professor or in an interview. People understand that change and growth is possible.

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Appeal filed -- what does it mean?
I recently submitted to a journal a manuscript that raises issues about a previous paper published before by the same journal. My submission got rejected but made no mention of our concerns about the previous paper. So I wrote to the editor to suggest that maybe they had overlooked that aspect of our paper and to ask what their policy was when claims like ours are made about a previous paper in their journal. A few days later I received an e-mail saying that an appeal had been filed and that my manuscript would be reconsidered in two weeks.
To begin with, I did not explicitly ask for an appeal to be filed (I had even prepared a submission to another journal already). What I really wanted was an acknowledgment of the issues we raised about the previous paper, and either they would look into them in more detail or they weren't convinced that our concerns are legitimate. But every e-mail I received from them was just a canned response that made no mention of the previous paper, including the one about the appeal.
So what does it mean that they filed an appeal? Is it just an automatic procedure triggered by my e-mail, with little chance of success? Or is it possible that they realized that our paper deserves a more thorough evaluation? Their generic evasive responses are driving me crazy.
Update: The journal editors discussed our manuscript and told us they would ask an external expert to evaluate it. The appeal was not just an automatic procedure.

Some journals welcome corrections to work they have published. I think many are automatically defensive. Perhaps the fact that your paper has generated an appeal (whatever that may be in this case) means they will actively pursue the questions you raise rather than just stick with the rejection.
I think you will have to wait and see what happens. In the meanwhile, try to manage the crazy making generic evasive responses.

Thank you for your response. It's easier said than done, but I'll try to be patient and wait the two weeks for the new decision. I just hope it won't be another generic rejection.

If it's a rejection then you are free to submit your prepared version elsewhere.


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Naming a library or program partially after a school
I have seen several programs and libraries partially named after a school, e.g.:

Berkeley Entity Resolution System
MIT Information Extraction
Stanford CoreNLP

To name a library or program partially after a school, what authorization(s) does one need, if any?
I am mostly interested in the United States but curious about other countries as well.

Sorry, I don't get it. Those are the people who know. You should just ask them. It's nice to have things out in the open but, unless the authorities object, you can always share the information once you have it!

My guess is no one's ever tried to name a package after a school with which they have no affiliation. People tend to like to promote their own school, not someone else's.

Berkeley and Stanford are places, not - institutes. So I guess no permission is needed (unless from the respective mayors). (However, my guess might be wildly wrong for the US law.)
See also https://perso.uclouvain.be/vincent.blondel/research/louvain.html:

is now known as the "Louvain method" because [...] the method was devised when they all were at the Université catholique de Louvain.

When one wants to use an institute's name (e.g. "MIT", as in one of your examples) - at least an informal consent may be needed. (But in some places rules may be much stricter - and it is impossible to make a general answer.)

Thanks. Who can give such informal consents?

@FranckDernoncourt I would try asking at the technology transfer office, and dean.

An university, like any other corporate entity, generally has both the inclination and legal authority to regulate the use of its name, particularly when somebody is implying that something is officially endorsed by that entity.
There is another usage, however, that is harder to regulate, which is when a name is used in a descriptive manner.  For example, the MIT Scheme implementation of the Scheme programming language was not originally named MIT Scheme: it was just Scheme, and when other implementations were created, the community started using the prefix "MIT" to distinguish it, and that ended up getting imported into the official name.  When something like this happens, it's hard (and generally pointless) to fight common usage.
So should something like the "Berkeley Entity Resolution System" be understood to be claiming the name "Berkeley," or should it be better understood as a short way of saying "the Entity Resolution System developed by Berkeley"?  Lawyers might well tussle over this, depending on the particulars of a case, but academics in many cases simply seem to proceed assuming the second and often find no objection from their institutions.


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Professor invited me to do research and I agreed, but now I am not so sure
I was invited by the professor to work with him. His area is outside of my background and I agreed because I was curious and haven't found a research area yet. After beginning to read papers and learn more, I find I'm less and less interested in the topic. I feel torn as to whether I should continue, and if I shouldn't, how to gracefully exit.
On the one hand, I feel I should develop professional relationships and skills. The topic is a valuable thing to know about. It would be almost wasteful not to take this professor up on their offered mentorship, and rude to stop now. On the other hand, I find other courses much more compelling. I can't really see myself working in this area for PhD work, so it might be a waste of both of our time to continue.
How can I decide whether or not to continue, and if not, how to politely end the relationship without making the professor feel that I've wasted their time?

Are you currently a PhD student?

Yes,  I'm a first year PhD student.

I would say the sooner, the better. Think of it this way, an unwarranted time delay is a waste of everyone's time... Better be open and frank. There is a good chance that your professor has been through a similar experience before. They will understand :)

Before you leave this professor (X), see if there is an other professor (Y) who is working in the field of your interest and he agrees to take you as his advisee.
Also check if there are any restrictions, conditions, permissions,  paperwork from the department to change the advisor.
If all clear, then talk to professor Y about the topic, way of research (theoretical or practical etc.), funding etc. Tell him that you were working with professor X and why you want to leave him.
If all talk is satisfactory and successful, then go to professor X and tell him politely and apologizingly.
I hope things will be fine.


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How to deal with professors who don't follow the text
I'm a first year math grad student. As an undergrad, all my professors followed the given text book closely, making lecture easy to prepare for and very predictable. As a grad student, my professors seem to cover material mostly in the book, but in a different order, with different notation, or different content entirely.
The result is that I have essentially no way to prepare for classes. I can only show up to lecture and hope I can keep up. If I want to review, I can only read their handwritten notes. My understanding is really suffering because I can't reinforce the content by seeing it repeatedly and clearly. I know it's unreasonable to expect professors to merely regurgitate a textbook, but this is how I'm accustomed to learning. What can I do to learn material better in these situations?
Edit: Thank you for the replies. The consensus seems to be that lectures shouldn't reinforce the text. They should provide a bigger picture, a linking of ideas from the expert's point of view, and understanding details is the job of the student on their own time. This makes total sense.
I think my issue comes from spending valuable time studying the book, then having the professor totally skip that topic and go to another, never to mention the thing I spent hours studying. My effort is wasted, and I have to expend double the effort to understand what is covered. It seems like the answer is to just learn what I can and not see that effort as wasted.

Say something about scale. How many students in a lecture? Say something about how the course is presented - zoom, slides, whiteboard, ...

This might be a dumb question but, why are you reading their handwritten notes and not yours?

This needs a country tag. "Follow the book" is (I believe) an US-American thing.

Please don’t write answers in comments. It bypasses our quality measures by not having voting (both up and down) available on comments, as well as having other problems detailed on meta. Comments are for clarifying and improving the question; please don’t use them for other purposes. Existing answers in comments and other extended discussion has been moved to chat.

If your undergraduate lectures were perfectly predictable, following the book exactly, and you showed up perfectly prepared to each one, then they were actually completely useless. You could have just stayed home and read the book yourself!
At the graduate level, the best practice is to ask the professor for good references, both at the start of the course, and whenever unfamiliar topics come up. You shouldn't expect immediate full understanding from going to lecture; graduate subjects are too deep for that. Treat lecture as an informal invitation to the subject. It's your job to turn that into understanding, by reading from references, doing problems, and asking questions.
Of course, this isn't an excuse for lazy or disorganized teaching. When a professor doesn't follow a book, they could be doing you a great service, by presenting a carefully thought out, alternative view of the subject which will complement existing books. (That's where many textbooks come from in the first place!) But in other cases, they could simply not care much about teaching, and not have any direction in mind.
I've been in classes of both types, and if you're stuck in the latter, it's absolutely essential to get good references to solidify your understanding. In these cases, don't count on the professor to supply them -- if they aren't paying much attention, they're likely to recommend books they used decades ago which are well out of date, or subpar books that they've only heard of, not read. Ask other students, and try resources like StackExchange. You can find good resources for any graduate course in any subject in this way.

I think my issue comes from spending valuable time studying the book, then having the professor totally skip that topic and go to another, never to mention the thing I spent hours studying. My effort is wasted, and I have to expend double the effort to understand what is covered.

If you're planning on doing research later, then effort spent learning core material in standard graduate-level books is never wasted. You can't know in advance what's going to be useful for your research, and often it will turn out to be the core material -- which is why it's the core in the first place. Many times, I've been stuck on a research problem only to find that the right way of thinking about it was in a book chapter I skipped long ago.

If your undergraduate lectures were perfectly predictable... then they were actually completely useless. - This is an exaggeration at best.  Things like interaction (Q&A) and presentation matter.  See Rota on Church for an extreme example: https://mathshistory.st-andrews.ac.uk/Extras/Rota_Church/

@Kimball that’s a fun (and funny) story about Church, but the sentence you say is an exaggeration is “morally” true. A lecture whose contents can be predicted in advance to a high degree of accuracy is certainly a lot less useful than a lecture that doesn’t have that property. (And knzhou’s answer is a lot more useful than other answers even though — or perhaps because — it contains such an “exaggerated” but morally true sentence.)

@DanRomik The utility of a lecture is determined by how well it serves student learning, not by how novel it is.

@ElizabethHenning I wasn't claiming lectures had to be novel, just that they shouldn't be perfectly predictable. For example, active learning works because it asks students to solve questions they have a roughly even chance of getting right. That uncertainty in outcome allows the class to both learn (when wrong) and teach each other (when right). But it's not novel at all -- you can buy books with lists of such questions.

@DanRomik I'm not critiquing the spirit of the answer, but the wording of the first paragraph rubs me the wrong way.  E.g., in my mind, I follow the text pretty closely for a course like calculus, but I don't like to think my lectures are mostly useless.  Perhaps the difference lies in knzhou and my interpretations of the phrase you showed up perfectly prepared: to me this means you showed up knowing what you need to understand the lecture in real time, and not that you understand the entire content of the lecture beforehand.

@Ezze I am from UK. The lectures did there own thing, so you had notes from the lectures that you took, possibly lecturers supplied notes and several recommended books to learn from. Hopefully one type of presentation of info would work. The worst course I had was where the lecturer had written the book and followed it exactly - I just could not get a handle on what the subject was

I am a retired lecturer, so here is my perspective.
As an undergrad, you were part of a sausage machine, taking kids from school and running them through a training process where the competent ones could earn a Degree that said they were competent to ply a given "trade".
Grad School is different. In many Unis it is a lead in to research, or if it's a coursework Postgrad, it's studying advanced materials where there may not even be a published textbook. Either way, a student has to show resourcefulness, independent thinking, and determination.
Often the lectures are led by people talking about their own research area. Sometimes the lectures are actually a selection tool. Students who do well may become preferred candidates for research places, assistant roles, and the like. If there is a tutor or assistant then they may be a student who is supervised by that member of faculty.
I think it's reasonable to request lecture notes, but don't be surprised if they consist of "Discuss Chebyshev Polynomials of the first kind, second kind, multipole expansion, and applications". It's also reasonable to request references, but again, don't be surprised if you're told to find them yourself.
After all, after this you should be able to do independent research. And publish it.
To return to the question, my advice is basic student stuff. Sit at the front. Take notes by hand in the lectures. Use a recording device to capture the words. Ask if video is available or permitted. Followup with those handwritten notes. Connect with the other students. Do any problems that are set. Attend every class.
And speak to the lecturer, asking questions about the material, not about learning issues. You may get the brush-off, but maybe you'll be rewarded by the academic seeing you as a serious and interested student. Everybody likes it when somebody is interested in their work.
[ Edit ]
Thanks to @BillNace and @ElizabethHenning for pointing out improvements to this answer.
In my experience there are two kinds of academic: those who care about teaching and those who only care about their research. I suggest the OP broach only questions on the material, so that they can get a sense of the academic's approach to students. If it seems positive then that is the time to broach these concerns.
If not, then the Faculty Office may provide a service, after that the University student support service or student union are the next ports of call. Every University that I have had anything to do with, even just to visit, has had a student support service. Student unions or associations are ubiquitous, and a good source of help, at least in finding where to go.
The final suggestion is library staff. They are generally independent sources of advice.

Agreed, I recall very few grad level classes that closely followed a book. One was left to make sense of the lecture notes by taking advantage of the text, the library, etc.

I like this answer, but just want to expand on the last paragraph.  You should also feel free to talk to the lecturer about learning issues.  Don't expect them to change their ways based on your discussion, but they may provide context and suggestions on how you can better prepare and learn the material.  After all, they have been thinking about how to learn (and how to teach) for their entire educational career (if they are good at it, that is).

Out of curiosity, whom should a grad student consult about"learning issues"? University study centers are rarely equipped to help with grad work.

Though note that - especially these days - there's often a considerable difference between finding references yourself, and finding GOOD references.  E.g. a search for "Chebyshev Polynomials of the first kind" returns some 640K hits.

I'm not sure if this matters, but in the era of remote learning, there is far less nonverbal communication in lectures. This goes both ways, including lecturers getting a feel for the understanding level of the room.

@BillNace I certainly cannot defend academics of whom I know nothing, but in my experience there are two kinds: those who care about teaching and those who only care about their research. My advice doesn't presuppose to which group the lecturer belongs. Ideally, they are good at teaching and could give advice on learning issues.

@ElizabethHenning Good point that is omitted by this answer. Every University that I have had anything to do with, even just to visit, has had a student support service. While talking to the lecturer, the OP will get a sense of the lecturer's approach to students. If it seems positive then that is the time to broach the OP's concerns. If not, then the student support service or student union are the next ports of call. I'll edit the answer to include this. Thanks.

@jamesqf Ah, it's been 45 years since I encountered them and they were text-book fare even then. Just seemed an apt case.

@qwr Ah, current reality, out of touch with, I am! Yes, if the classes are remote then the OP can simply record them. I got the impression they were in person because this is such an obvious solution and the hand written notes reference. Find ways to adapt, we must.

I'd like to offer my perspective as a second year mathematics graduate student.
I have found that the courses I learnt the most from were those in which the instructor did not follow the prescribed textbook(s) very closely. In such courses, the instructor would usually spend a large portion of the lecture hours drawing connections and nudging our intuition in the "right" direction. I found this to be very valuable. It is precisely these insights that the instructors offered that made the courses valuable, since I could easily read and follow a textbook line-by-line yet struggle to see the big picture.
Even in the courses where the instructor chose to follow the textbook closely, the standout lectures for me were those in which the instructor went off script and chose to delve a little deeper into the subject, offering their own insights into the theory.
I should add that not all of my classmates share my perception. Some of them did struggle because there was no textbook whose contents matched the lectures close enough, and not knowing exactly which topic will be covered next meant that preparing for a lecture by browsing the material beforehand was not possible. This seems very close to your experience, based on the details in your question.
Without being judgemental, I think this is because my classmates were unused to processing new material on the fly; that is, they were more used to participating in a lecture passively and wrestling with the material privately by reading and re-reading the textbooks or class notes, than wrestling with the material right then and there as the lecture is being delivered. In the former style, the instructor may come into class with well-prepared notes and the students may be expected to jot them down as the instructor delivers the lecture at the blackboard. In the latter style, the instructor may instead choose to develop the theory more organically, often speaking out loud their thoughts and intuitions, often stumbling, and may expect the students to raise questions of their own along similar lines.
Another reason the latter style works for me is that the pace of the lecture becomes slow enough that I can follow comfortably and sometimes also offer my own suggestions for how to get out of a hole. It doesn't work for others because they are unused to being taken for a bumpy ride.
While I don't have many concrete suggestions for how to handle such lectures, I would highly recommend that you try and get used to thinking and responding to the content as it is being delivered. In my experience, such a style of lecturing is closer to how research is done; at least, I see the similarities between the interactions in such lectures with the interactions I have with my guide during our weekly meetings.
One thing that you could try is to form a study group with similar students and discuss the lecture material together. Even try lecturing the same material back to each other. Some of my classmates find it easier to respond actively to a peer lecturing to them as compared to a faculty. The principles remain the same, so I expect this to help, if you can find like-minded classmates.

my classmates were unused to processing new material on the fly There's a lot to unpack here. I think you are correct that grad-level mathematics courses often advantage students who do this well, which concomitantly means disadvantaging students who don't. It is not a coincidence that those students are disproportionately from underrepresented groups, which is more complicated issue than "getting used to" it.  It's somewhat true that this is how research is done, but I would argue that's a consequence of who gets selected out of this kind of training and not the other way around.

@ElizabethHenning I completely agree! I felt that this answer was not entirely the correct place to unpack all the subtleties of that point, so I tried to leave it at that. Even if I understated the difficulties, I hope I did not come across as disparaging. I am acutely aware of how hard some of my classmates have struggled to reach where they are now, especially considering their backgrounds and how it differs from mine.

@ElizabethHenning, you are certainly correct that students who've been led to lack self-confidence can doubt themselves in coping with "live" things. This is one reason I try to emphasize my own fallibility, and the irrelevance of aiming for infallibility, during my "live performances".

Your problem isn't that the professor doesn't follow the text. Your real problem (as clarified in your edit) is an unusual aspect of your question that nobody has addressed. It is your need to "prepare for class" on your own.
In all the courses I can recall, the professor either assigns a specific reading before class, or not. Then the professor designs the lecture to be understood by a student with that specific preparation as the case may be. I've never encountered an expectation that students should guess the lecture content and prepare for it using their own unspecified resources.
It seems that your real problem is that you are struggling to follow class material in real time:

I can only show up to lecture and hope I can keep up.

Your homebrewed solution to this problem is to prepare for lecture by studying the material in advance. So you are asking us how to continue applying this strategy in a new environment. Perhaps you should ask directly about different approaches to this problem instead.
A common answer is that lecture is not guaranteed to make perfect sense the first time. After the lecture, students may need to read or think or review notes, and possibly find additional resources or presentations of the material to understand it better.
But you may have a different learning style than most of your classmates, and you may feel this common approach is not working for you. People on this site may be able to help better if you give more information about why this approach to learning (the usual/expected approach) doesn't work well for you.

It seems that your real problem is that you are struggling to follow class material in real time -- There are numerous reasons a student may want or need to prepare for class (I'm omitting your nasty sneer quotes), including sensory or processing issues, low vision or hearing, or learning disabilities. Expecting that students should follow class material in real time creates a hostile environment for those students who have difficulty doing so. It's also an expectation that has nothing to do with the actual goal of the course, which is learning the material.

@ElizabethHenning Aren't there offices in the university tasked with providing accommodations in cases as those you name? I certainly expect students to be able to follow the lecture in real time by default, and anything that interferes with that ought to be dealt with some way or the other (of course I also expect students to take copious notes to be reviewed later and try to facilitate it). If that's an unsafe assumption then the whole concept of university class needs to be reworked...

@ElizabethHenning I apologize if my post came off as nasty, which is far from my intention. You make excellent points and I think that, like mine, they suggest that Square should ask directly about whatever problems they are facing, instead of asking about one solution (X-Y problem).

@usul Sorry for being prickly about your post. It's always hard to read intentions online.

@DenisNardin OK, but what if the accommodation is to provide information (such as a structured syllabus) so that the student can prepare before attending lecture? And why should that have to be a disability accommodation instead of something that is provided by default to all students?

@ElizabethHenning I guess I don't understand what does it mean to "prepare before attending lecture". In my mind knowing the material of past lectures should be enough to follow the current lecture in real time. Moreover to understand the material of the previous lectures it should be enough to having attended them and taken notes. If this is not so, this needs to be handled in a way that's specific to whatever root problem is causing the situation. This might be a problem that affects all the students (such as the quality of the lectures) or a problem that affects a particular student (cont.)

(cont), such as hearing disabilities or lack of background knowledge (for whatever reason - not necessarily the student's fault). The correct mitigation, and whether it is appropriate to offer it to all students, is going to depend on exactly what the root problem is. I am wary of blanket solutions because I don't trust them to work.

@DenisNardin There's a lot to say about this, so I'm opening a chat if you want to discuss it. First of all, what exactly do you believe the function of class/lecture time is?

The typical professor will possess many bits of insight into their field that cannot be found in any textbook. So you are simply asking for the wrong thing. Asking for a professor who teaches only what’s in the textbook makes sense if your goal is to feel like you’ve mastered the topic of the course. If your goal is to actually master the topic at a level a graduate student needs to in order to be prepared for doing research, your best bet is a professor who will curate for you the best knowledge on the topic that they can find, not only from the primary textbook but also from other textbooks and research papers they are familiar with, and from their own personal knowledge.
Do not confuse actual mastery with the illusory feeling of it that you might get by studying in advance the content of a lecture precisely parroting a written source. The latter might feel good and can be acquired in a more systematic and less anxiety-inducing way, but the former is what you should be after.

If the problem is a lack of repetition of the material, because your lecturers are not repeating the contents of a book verbatim, then you could consider repeating the material by yourself before attending the lecture. Also consider different ways of learning the material; doing exercises, playing around with examples, and playing around with the conditions for theorems to hold.
If anything, I would say it's a good thing that the lectures are teaching you things that are not literally in the book. Be it different but related theory, or just different connections between parts of the book. Instead of 'just' dry material, you are getting some insight into how an expert views and uses the material.
Of course in order to take advantage of such lectures it is very helpful to get familiar with the material before attending the lecture. I can also recommend to let go of the idea that every detail of the lecture should be clear to you before proceeding. Instead, focus on the general ideas and how they relate, and take careful notes so you can figure out the details in your own time. Then you can always ask your classmates, or otherwise your professor, about any details that you aren't able to figure out.

I certainly grant in advance that tastes vary...
Based on my own student days' attendance in various lectures, and on my own preferences for teaching, I try to think in terms of "added value" that my lectures/classes may provide, beyond any text.
Yes, I do also try to provide my own notes that fill in details that might be tedious to discuss "live". Are more careful about all details.
My lectures, even by Zoom, are meant to be "live performances", rather than reciting notes by myself or anyone else. Live talking and typeset notes are significantly different mediums/media.
I do recall some cases of very nice people, excellent mathematicians, just silently copying their nicely written-out notes onto the blackboard... as opposed to distributing the notes. (Pre-internet, so there were complicating issues...) Worse, to my mind, were the people who thought their job was to recite a chosen text. I could read it myself, at times and at rates chosen by myself, rather than having to show up at random/inconvenient times and sit in uncomfortable chairs ...
Yes, certainly, some improvisational instructors may be a bit irresponsible, in the sense of not providing any written record of their (possibly very nice) lecture material. I myself do aim to provide more-formal typeset PDFs reflecting what I talk about "live".

I'll guess that this is fairly common, actually. Some things you can do:
Ask a lot of questions during lecture if possible. In a class of 20 or so, it is possible. In particular, ask at the very end of a lecture what will be the topic of the next lecture. This might give you a heads up to look in the text book.
But, and this is actually independent of the question, take a lot of notes. In the notes indicate where you have issues and unanswered questions. Immediately after the lecture, summarize the notes very briefly - just an index card or two. In particular, make a specific note of what the most important ideas are in that lecture.
You can then, annotate those notes with textbook page numbers for later study.
At the start of the next lecture, if possible, ask any questions that you haven't been able to answer yourself from your notes and the book.
For some topics you can use wikipedia, which is pretty reliable for many things (math, for example) and it is organized by topic, not as a course.
If in class questions are impossible, try to find a way to ask questions outside class. Do some work so that you avoid being a bother, but if you have a question, it is very likely that many other students have the same question.

This is the best, most actionable answer, of the bunch.

I know it sounds confrontional, but did you ever consider the notion that this class might be too advanced for you? Not everybody is able to deal with a grad course, nor should everyone be.
The fact that you already struggled to deal with the undergrad courses and could only cope by extensive preparation and a very predictable class, might be a good sign that the next step up could be too advanced for you.
It's never bad to discover one's limitations. If you never encounter your limits, you're not trying hard enough. And maybe, with lots of additional time and dedication, you can push your limit beyond what this grade expects of you.
But consider this a sign that you may have reached the limit of your abilities.

A perspective of an ex-student, then ex-lecturer and now a parent.
I usually taught math/physics the way I ended up understanding it. I was not a particularly brilliant student so I had to think a lot when learning, trying to keep everything more or less in a coherent state. This meant simplifications, analogies - and then understanding why the simplifications and analogies were only good to a given point.
My students usually found this useful because they had the "wandering around" part and then another approach, usually more formal, in the textbooks.
This is also how I was explaining math and physics to my children: by going with them through a journey to understand (and not only learn) what they were supposed to know.
Only in movies this works fine: they were vigorously protesting because they wanted "just the facts, and not again going through a whole story". I insisted, they protested but eventually gave up. My biggest pride was for them to ask me once to go my way because they understood that they will understand.
This was greatly helped by the fact that French mid- and high-school math textbooks are not particularly good. They love to explain to you what the derivative of a function is by starting with "Given x in the domain R ..." - at which point the children are lost. By discussing with them how to avoid a speed ticket when one sees a "50" road sign it was much easier (in other words: describe a physical context they can relate to, and then walk them through the process of though to get (in that case) to derivatives).

Depending on the technology available in your classroom, a couple of resources that might be available are video recordings of the lecture (so you can go back over the lecture later to make sense of things that weren't immediately clear) or screen capture recordings of things that the lecturer wrote on a stylus and projected on a screen during the lecture (here, you can see what was written but not hear what was said.)  The lecturer might also agree to allow you to make an audio recording of the class.  If this technology is availabe in the room but your instructor isn't making use of it, then it would be reasonable to ask the instructor to consider using it.

In my opinion, lecture is not the proper vehicle for providing direct answers or application of formulae – the kinds of things that you'd find in the textbook, and thus a "regurgitation"; rather, this would best be achieved at some recitation or office hours with TAs (who are often extremely helpful in helping students understand course content!). Rather, the purpose of the lecture sessions is to explore important ideas in the subject and link them to profound implications for society, institutions (such as public policy, law, and financial systems), technology, and the natural universe, as well as the human condition. In this way, you may find yourself mired in quite some degree of abstraction, formal proofs, and derivations of central theories, which can seem disorienting without tangible practice; this is normal. Everything may seem strangely uncorrelated or not coalescing correctly in your mind upon first sight, but most of the time there are relevant and meaningful connections that you'll discover after, say, repeated exposure from various places (the lecture, the textbook, the academic literature, slides from other university programs).
As an aside, why should we spend significant moneys or get into unreasonable levels of un-bankruptcy-able debt to hear a lecturer spout the same thing as the textbook? JUST BUY THE TEXTBOOK INSTEAD AND CALL IT A DAY, THEN! (unless your goal is to enter industry, that is, in which case the piece of paper that says you know some such stuff may be prized).
Notably, courses usually indicate how many hours you should be spending outside of lecture by the number of "units" or "course credits" in which they are advertised. Of course, this is only a suggestion. These hours should be spent, ideally, in optimized fashion reinforcing the key takeaways from lecture, and then identifying connections between these and the detailed computations and material particulars contained within the texts. This is the stage in which you should be playing around by making hypothesis about what the fundamental theorems say the output should be given certain use cases and input conditions, including edge cases or otherwise interesting or unusual scenarios, and conducting the analysis to verify that the results match your expectation. If not, what was your faulty reasoning? This practice will prepare you for any upcoming assignment.
As a personal test, determine if you can finish an assignment with little to no notes or other references. After seeing the concept multiple times at this point, it should be easier to compute answers or solve related proofs. It may take time and thought, but shouldn't require the textbook if you understand it "to a reasonable level". You don't need to know everything deeply yet, but rather a moderate comprehension, which is enough at this stage.
In going one step further than expected by the professor, you may locate the most influential publications in the field and other primary source content and read those to achieve an even deeper contextual understanding of the field. They are often free and accessible when using your .edu account, or found in the library. This isn't required, if you have time constraints, but it demonstrates initiative and you learn directly from the originators of the theories in question.
Lastly, there's often a project component, typically towards the end. This is an opportunity for you to see the content in application, and it might be the most important part, allowing you to bring together everything you've learned and use it to build something or conduct an experiment, expressing your creativity in the process. This is when I found that I learned the most, as long as I put forward significant time; if you half-ass it you won't learn anything additional, but if you focus, you may actually come away from the course realizing that you understand the core of that area much more than how well you "know" or "learned" information from a textbook for your previous classes. You'll also find that you have a new-found appreciation for the topic, beyond your initial interest during the first lecture.


text:
How can a student evaluate themself?
For background, I'm a first year PhD student in a mathematics program. Basically, I can't tell if I'm "where I should be".
As an undergrad, I read before class and lecture felt like a nice review. As a grad student, I can read before class, spend an hour or two pouring over a few pages, understanding every sentence, and the professor will breeze over it in 10 minutes. If I don't prepare, I'll be left in the dust, totally lost. Or, he will cover material with so few details it's hard to tell if I understand anything at all. Talking to classmates, I'm not unusual, but I find this very stressful because it's consistent and I'm not used to it. If it's typical to get lost and not understand the lecture, how can I tell if I understand anything at all? Is this just standard?
Reading papers or attending talks is worse. I feel like I get things only at 'handwavey' level, without details or subtlety. I know this is normal so I don't stress much, but some day I will have to be giving talks, writing papers. How can I get there if without a firm basis?
I think my fear is that I could be learning the absolute minimum and barely skating by -- which will bite me when it comes time to take prelims/do my own research -- or I could be doing perfectly fine and just stressing myself out. My question is, how can I tell? How can I gauge if I'm making typical or appropriate progress?
My grades and homework are good, but this seems meaningless. I always receive full marks, even when I find errors in my own work later, and work comes back with no comments. Talking with peers helps a lot, but is hard with distance learning. Asking a professor directly seems like it would be awkward and unprofessional, and also how could they know? They don't grade the homework and we speak for maybe 20 minutes in office hours occasionally. What else could I consider?
I've also read this post, which is relevant, but the answers are directed at the research stage of the PhD. I'm still taking courses, etc. I've also read posts on imposter syndrome and I feel like my issue is distinct. It's not that I feel like an imposter, but more that I feel like I'm untethered and in la la land as Dan writes. I'm interested in ways to feel more tethered, and in understanding how common/typical this untethered feeling is so it doesn't stress me out as much.

Yes this is standard.

To be brutally honest with you, you will know where you need to be once you take the prelim exams. The purpose of taking prelims is so that you are qualified to do research and can then stay in the program. Until then, the answer to your question is highly speculative.

However, that shouldn't stop you from asking for feedback. I suggest you start making mentor-mentee relationships with one or two of your professors. Go to them for guidance and advise, bring them (interesting) math questions. Once you've shown them your potential, they will be more open with you and give you specific feedback. Note that this is very different than showing up to office hours to ask for help with homework.

Do you have a PhD advisor?

@Jeroen, I don't have an advisor yet, no. One professor has invited me to do research with them and we are reading papers to prepare. This question was definitely influenced by reading those papers and not being sure if I really understood. I bet a better relationship with professors would help me get a read on  this.

Does this answer your question? How to effectively deal with Imposter Syndrome: "I've somehow convinced everyone that I'm actually good at this"

Student self-assessment is actually a new and cutting edge area of research, so I'd say there is no answer to the title question yet.

I think you’ve hit on a subtle point here that plagues many mathematics students up to and including the advanced graduate level: evaluating yourself without external feedback is very, very difficult.
In fact, it seems to me that the ability to evaluate your own level of understanding (in the context of studying pure math at least) and test when you understand a concept well, versus when you are just deluding yourself into thinking you understand, is a skill in its own right. And it’s a difficult skill at that, one which takes considerable time and experience to acquire. Professional mathematicians have developed all sorts of tricks and heuristics to achieve this: various sanity checks and other “unit tests” that we continuously run while working through new material to test our understanding and make sure we keep our mathematical feet planted firmly on the ground, instead of becoming untethered and flying off to some kind of la la land. At some point this becomes second nature and I would guess that most experienced mathematicians do it essentially at a subconscious level. But as I said, it takes years of practice to get to that point.
What I would suggest is that you do two things: first, put it on your todo list to develop an ability to gauge your own level of understanding and identify misconceptions about material you’re reading or hearing in lecture. It’s an extremely useful skill, and thinking of it as an explicit thing you want to work towards in a deliberate way will surely help you acquire it faster and better.
Second, until you’ve actually developed that skill and have evidence to support that, assume you don’t have it. That is, accept that there will be occasions (which become increasingly rare over time, typically) when you will absolutely have to rely on external feedback to tell you that you’re misunderstanding something, or to confirm that you’re not. I imagine people will be posting other answers here suggesting various tips and tricks for evaluating yourself. That’s all well and good, but don’t let such advice mislead you into thinking you can do without external feedback. You can’t — not yet, not at this point in your studies at least. So don’t be shy, go out and seek that feedback from your professors, peers, stack exchange or wherever else you can get it. And please get rid of the mindset that it’s “unprofessional” to seek feedback - nothing could be further from the truth in my opinion.

First, let's eliminate a couple of ways that aren't helpful to tell if you're on-track:

Don't evaluate yourself by comparing your knowledge/ability to that of your professor (e.g., worrying that you spend two hours understanding something and then he is able to breeze over it in a small fraction of that time).  Most academic staff were high achieving even by the standards of their PhD cohort, and additionally, they have several decades of additional experience since then.  It is completely normal for PhD candidates to have difficulties with problems that academic staff can solve easily (for an example, see this related question).

Don't expect to understand more from a talk than what is reasonable: By design, good talks do not usually go into heavy levels of technical detail.  Going into deep technical details requires more time, and it requires an audience having time to "digest" the material.  This is usually not possible in the timeframe allocated for a talk, so you will generally find that good speakers find ways to gloss over the technical details and present their topic in a way that gives the audience a good overarching understanding, but without the minutae.  By design, this is sometimes a bit "hand-wavey".  Usually a talk topic is backed up by an academic paper (already published, submitted, or under contruction) so if you want more technical details you can follow-up with a request for any paper the speaker has written on the topic.

Don't impose made-up impediments on asking for feedback: It may feel awkward to you, but there is nothing at all unprofessional about asking your teachers for feedback on your progress and standing.  In fact, this is literally professional --- i.e., within the direct scope of the professional duties of the academics you are dealing with.  For the lecturers of your courses, they are unlikely to be able to give much feedback beyond what your assessment results in the course tell them, but they might have some more insight on your strengths/weaknesses.  If you have a supervisor or panel at this stage of your candidature, you can ask them how you are going.

Now, here are some things that are helpful in evaluating whether you're on-track:

Other students are in the same boat: You mention that from talking to your classmates (I am assuming these are other PhD students) you are not unusual.  That suggests that the difficulties you are having are standard difficulties at this stage of the program, and are not an indication of being off-track.

Your grades are good: You mention that your coursework is progressing well and your grades are good.  That means you are learning the course material up to the required standard, which also indicates that you are on-track.  The early part of the PhD program is often devoted to coursework and "upskilling" so that you come into the research part with a solid base of technical skills.  The grades you get in your coursework are a reasonable indication of how you are doing in that part.

You are having trouble understanding papers beyond a superficial level: This is the only part of what you write that is a concern, and it is not particularly unusual at your level.  For many students, first-year of a PhD program might be the first time they ever read academic papers (as opposed to textbooks, course notes, etc.), and it takes some practice to learn how to digest this material.  Unlike textbooks or course notes, academic papers are less "self-contained" and they operate in a context of a wider literature on a topic.  These papers often rely on context and referencing of other work to point to parts of the topic, so it is not unusual that you will miss details or subtleties when you are new to reading them.  The main skill to develop here is to learn to "dig in" to the literature, read some of the papers cited by the paper you are reading, and so on, until you feel you understand the material in the paper under examination.  I recommend you dig deeper in your readings until you feel that you have understood a paper at a reasonably deep level.  That is a skill you will need to develop for your later research work.

You haven't failed any of your candidature reviews: You PhD candidature has a number of review steps where you will be formally evaluated, and these are points at which the department can identify weaker candidates.  You mention that you have some kind of preliminary examination coming up later, prior to progressing to the research phase of your candidature.  That will obviously give you some feedback on your progress.  Presumably that preliminary exam has been held before, so perhaps you can have a look at some past exams and see how hard they seem to you.  In any case, as things stand, you have not failed any candidature reviews, which means that there is no indication of being off-track.


text:
Asking University to reimburse renting a car
I'm shortly going to a conference which is held at a centre pretty much in the middle of nowhere (or, to be more precise, in the middle of a hiking region). The suggested way of reaching the destination is by taxi, and the public transportation is nearly non-existent.
Me and a group of other junior researchers (PhD's and PostDocs) have decided to hire a car to make transportation easier and to take full advantage of the attractive region. Split four ways, the cost is quite affordable.
I am wondering whether it is acceptable to ask my university for reimbursement. We have an allowance for travel expenses, so there is certainly an available source of money. However, I have two problems with making the request. First is a moral one - can I ask the university to reimburse a car which we'll partly use for our own enjoyment? Second is more practical - is the university likely to agree? Will they be able to process the kind of receipt car hire company will issue? How do I explain that I paid exactly 1/4 of the quoted price?

When you say "agree" do you mean they will reimburse the expense after the fact or they will tell you in advance that it's okay and let your reimburse it later? This is an important distinction. There's no guarantees in after-the-fact reimbursement.

@virmaior - I meant "tell me in advance that it's okay and let your reimburse it later".

You should ask your university (or department) finance office. Only they will know the answer.

@DavidRicherby - sure, I did that today. I wanted to know in advance if such request is reasonable.

Yes, this is acceptable.
At many universities, adding a few days stay at your conference location in a far-away country (using your own accommodation arrangements) is allowed and sometimes even encouraged. Especially when this allows you to take cheaper flights. This would be something similar, using the car because it's required anyway, and adding a few extra recreational km you'd pay for yourself.
Renting a car might be an issue for some European universities, as they have rules to encourage public transport usage. The 1/4 share of the car is something you'll have to discuss with your administrative staff. They might want to reimburse 1 person for the whole thing, or split it over multiple projects. Just ask to clarify, they'll also be happy to know exactly how and what they're reimbursing.

I would suggest to make sure to keep track of which expenses are for the conference and which expenses are for personal use. If the conference is for 3 days and you stay there 5, you could ask for reimbursement for 60% of the cost of the rental car. Also, you could fill-up the tank at the end of the conference and ask for reimbursement of that fuel, then pay for any fuel used in the personal time after the conference yourself.

Clearly, rules to encourage public transport usage do not apply to places not reachable by public transport.  I have managed to convince even the European Space Agency (ESA) of that, and if the bureaucracy at ESA can be convinced, anyone can.

@dimpol The standard I've seen has been more "excess cost above the alternative" rather than "fraction of personal use". That is, if the cost of a rental car is about equal to or less than that of the no-personal-use taxi fare (and it can be for remote locations), then they have no problem with reimbursing all of it, even if you had substantial personal use. It's only if your personal use made things more expensive that they care, and then only for the difference in cost. -- You just need good documentation as to what things would have cost if you didn't have any personal use.

Speak to your department in advance.  While this is a very sensible thing to do, there may be rules to follow, ignoring which would add to the cost and/or complexity.  These may include: Hire cars have to be booked through the university; the university's insurance will cover you so don't take it from the car hire company; or you must take the full insurance; or you must take the insurance abroad...
It's much easier for them to process one receipt once, so you may find it easier to use other methods to split the cost between projects (such as some projects paying for susbsistence).  Again this will be easier if the budget-holder(s) are involved up front.

Make absoloutely sure you check what your university's policy is on insurance for hire cars. Some may have the policy you describe, others have the opposite policy.

@PeterGreen maybe I should make that clearer.

As a general rule, this is acceptable and common. All universities I have had experience with consider rental cars a reimbursable form of transport-related expense. But since we don't know about your specific university's policy, the sensible thing to do would be to ask them in advance of the trip to avoid unpleasant surprises. (E.g., at my university I once discovered after a trip in which I rented a car that I was supposed to use a specific rental car company my university has a special contract with; the department's staff then had to scramble to find some clunky workaround to help me get reimbursed.)
As for splitting the cost, I am sure your department's staff are capable of dividing numbers by four and other such simple arithmetic operations related to the fact that you are splitting the expense with other travel companions and are renting the car for a mixture of personal and work days. Just explain to them what you are trying to achieve and they will help you get reimbursed for the correct amount. Again, doing this before the trip would be good to ensure everything goes smoothly.
And as for the moral issue you mentioned... I have two comments: first of all, having fun while traveling to conferences is both moral and highly recommended. (Would you offer your university to pay part of the cost of the airfare because you enjoyed looking out the window during the plane ride? And have you considered why people bother to hold conferences in the middle of a hiking region?) Second, even on the days when you are only hiking with your friends/colleagues, I'm sure you'll be discussing your academic work, and who knows what will come out of it? Indeed, I've had many fruitful scientific discussions on hikes. So depending on who you're hiking with, even from the moral point of view one may legitimately consider this a form of work as well... ;-)


text:
Associate editors status and its effect on peer-review invitations getting accepted
Associate Editors (AEs) are experts in their research fields and some of them are widely well-known to the research community. However, sometimes AEs' peer-review invitations are faced with refusal from academics, due to the lack of time, other engagements, etc. This obliges AEs sometimes to send the invitations to academics in their acquaintance to maximize the chance of getting acceptance.
Can the high status of an Associate Editor within the research community diminish the number of refused sent peer-review invitations to academics?

It is probably the other way around (which has the same net effect): It is easier to decline a review invitation if the AE asking you is someone you've never heard of, and who does not hold a position of authority in the community. That's because there are no repercussions: You'll likely never meet that person at a conference, you won't need a letter of recommendation from them, and they won't vote on your application for some major prize in your community.
I don't want to suggest that accepting or declining reviewer invitations is as transactional as I make it out above. The majority of reviewing happens because a reviewer invited to a paper finds the topic interesting and/or feels an obligation to their profession to participate in the review process.  But in a certain percentage of invitations, a potential reviewer is genuinely pressed for time or at the limit of their knowledge, and it is those cases where other considerations such as those mentioned above come into play.

Every case is different. People normally review because they want to provide a service to the profession and get early access to potentially new ideas. The star-status of the editor is probably not a consideration for almost everyone.
If a AE can pique the interest of a potential reviewer, however, it might make some difference, as can having a personal/professional relationship with a potential reviewer. I might go out of my way for a friend/AE but not otherwise.
Editors try to develop, over time, a large "stable" of potential reviewers and not to overload them, especially with marginal papers. Then, they have fallbacks for refusals.
Refusals are done for the other reasons you suggest and overloading a reviewer isn't optimal if it means the paper gets a low priority with a reviewer due to other factors, resulting in a long delayed report.
Moreover, the editor/reviewer relationship is invisible to most of the community in any case. So, not a lot of incentive to review a paper that would overload you.


text:
Can I submit a manuscript without following the recommendation of the journal regarding the use of their template?
In a Springer journal, one of the items in Authors Guidelines is :
Manuscripts should be submitted in LaTeX. We recommend using Springer Nature’s LaTeX template.
However, I have already typed the manuscript using the standard LaTeX template and I'm about to submit it.
Does the word recommend give me the freedom to choose not to use the journal's template?
Will this give a bad impression to the editor?

Why should they only recommend to use the template if is isn't mandatory? I am sure they would make it clear if only the template should be use.

Does this answer your question? Should you conform to journal formatting requirements for the initial submission?

I can speak for math - usually the editors don't care. I can imagine that if you do something silly, like setting ultra-narrow margins with small text (to decrease the page count for example) then they might object. But otherwise, just send your paper in a readable format.

Yes, you can choose not to follow their recommendation and if your template isn't too different from the recommended one, then the editor will likely pass the paper to reviewers as usual (depending on the quality, of course).
But they are unlikely to publish your paper with that template, seeking a uniform look for what they publish. At some point in the process, assuming you aren't rejected, you will be asked to reformat the paper to the recommended (now required) one. So, think about whether it is worth the effort to do it now, knowing it will probably be required later.

Usually, the publisher will reformat the manuscript themselves. (In fact many publishers don't actually use LaTeX to typeset their published articles. So there will be a conversion step for them somewhere along the way anyway.

@TimRias Not true, at least in math. Publishers will expect you to provide the article using the provided template, and then print directly from the latex sources.

@WolfgangBangerth It certainly is true for the two biggest publishers in physics the APS and IOP. In fact the IOP's latex template is so bad, I usually submit to their journals using a modified version of the APS's RevTex template.

@WolfgangBangerth: In all() my math experience, I have always provided a LaTeX file to the publisher using a standard LaTeX template, and the publisher has reformatted it themselves.  ( Only exception: Electronic Journal of Combinatorics, which doesn't do any copy editing or formatting and just puts up your LaTeX file, which has to be in their template.)

Ask the journal editor(s) about this, not us.

You asked two questions: Can you submit, and will this give a bad impression. Most likely your submission will not be rejected outright because of the template, but you might be told you need to fix this ASAP, or fix this for the galley proofs, or whatever. Or you might not - depends on the journal's policy; maybe the typeset things themselves? Again, see (1.) . About the impression - you will at most give the impression of being absent-minded, which is typical in academia...


text:
Is it normal to be given two weeks to accomplish major revisions?
I have recently received a decision on a manuscript in the field of mathematics, which I have submitted to a journal a while ago. The reviewers comments were typical: modifying the abstract, ameliorating the language and "what do you think of" type questions. The editor's decision was major revisions and I was given two weeks to resubmit the revised manuscript without mentioning any possibility of requesting an extension.
Is it normal to have this short amount of time to accomplish major revisions?.
Based on the given period, could it be that the editor thinks that the concerns of the reviewers can be addressed in a short amount of time? If that's the case, why not suggest minor revisions instead?

I've only seen/heard this type of behavior from publications that are about to appear in a book or proceedings (giving a pretty strong time limit) or from a predatory/lousy publisher like MDPI or worse.

As someone else mentions below: it could be that the editor selected "major revisions" because they were applying an overly literal definition. In the jargon of some academic journals, "major revision" is anything that requires some new mathematical content and goes beyond merely fixing typos. So authors can be asked for "major revisions" even when minor changes (in the colloquial sense) would suffice. I've been on the receiving end a couple of times

This is probably a publisher specific rule.   MDPI (crap publisher) comes to mind.  Alternatively, was it a special issue that has a specific deadline?  The reviews could have been late, but the deadline hasn't moved.

Is it normal to have this short amount of time to accomplish major revisions?

No.  In (pure) mathematics, my experience is that typically there is no set time limit on when to submit a minor or major revisions for a journal (exceptions are for special issues).  [Edit: Since I posted this, a journal gave me 8 weeks to submit minor revisions so it does happen (see also comments below), and maybe this is becoming more common now.]  In any case, 2 weeks is quite short.
I would think about how long you need to revise the paper to your satisfaction, and if you think it's more than a few days, ask the editor about whether this deadline is flexible.  Particularly, you can point out wanting time to think about questions the referees suggested.
As for why this is counted as a "major revision" rather than a "minor", I have no idea.  Possibly the editor indicated "major" to mean it would go back to the referees again. Possibly they just clicked the wrong option, or they have a different perspective on what minor versus major means.

Small data point: I currently have a paper submitted to a reputable journal where I received feedback from referees in early April and was given until the end of September to "resubmit" a revised version.

I was given a 2 week time limit for minor revisions from the last journal I published in.

(actually I don't think they used the term major/minor, we inferred that from the language

I think I've gotten a deadline for a revision before, but maybe only once, and I think it was more than 2 weeks--I can't remember where, but it wasn't too recent.  Yemon, David: has this happened often for you?

I can't explain such a short window for a journal, unlike a conference. I'd guess that the editor is thinking of a slot in a particular issue that your article would fit if you act quickly. The example would be a special issue that has a firm deadline.
Two weeks might also be reasonable for a very short paper, though you don't describe yours in that way.
But, normal journal process would make future issues a possibility.
You are the best person to accomplish this, of course, so it is probably worth accepting the challenge if you can. But if you miss the deadline but improve the paper you will have other, future, options, with that journal (most likely) or another.
If you think you must miss the deadline ask for more information and an extension, preferably with your best estimate of when you can resubmit.

I think it depends on the publication.  I can't speak for math, but in CS some expect revisions in 4 weeks, or longer, but I have seen the default be fairly rapid just like this case, especially for magazines.  Usually an extension is easily obtained unless there is a hard deadline for a special issue or something.

Focus on the changes requested. If you can do them in the time given, you can just do them and the question why the editor plumbed for the one word rather than the other will just be one of those mysteries of life that is totally moot.
If what is requested will take more than 2 weeks, months even, you clearly do need to consult with the handling editor, who will be happy give you more time.
The default time lines are short because authors favour quick turn arounds and journals try to accommodate them.


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In applying to graduate programs, what are best practices for proposing research to investigators before and during the application process?
I am a recent graduate of biochemistry from the University of Maryland, College Park and am currently working as a postbaccalaureate fellow at the NIH in Bethesda, Maryland.
For context, I work in a group studying rare inborn errors of metabolism. Our lab is transitionally oriented as we are working on the development of animal models of the disease and gene therapy.
I pursued research in a rare disease group as I am a patient of a rare congenital skin condition. I am currently enrolled in a study which is working to defined the molecular characteristics of my disease (outside of the NIH).
I would like to remain translationally oriented in my graduate pursuits. My proposal in its basic description would be to develop an animal model for my skin condition and pursue gene therapy or gene editing to correct its manifestations. This area of research (gene therapy in dermatopathology) in general is relatively underrepresented in the scientific literature (does this make my proposal stronger?). If anybody would like any more information I can absolutely elaborate.
I will be applying to graduate programs next year. How should I approach investigators (relevant to the described field) with a research proposal such as the one above before and or during applying? I would appreciate hearing your perspectives!

Graduate programs in the United States (since that is all I know) will typically have a letter you write as part of your application. It is there where you identify an area or areas you are interested in working in. My program in particular requested that I speak to this in the written letter AND identify a few professors and areas of research I want to pursue in explicit fields in my application.
Besides doing the above, you have a few options that all center around getting feedback on your proposal, which I cannot stress enough. I've lost count of the number of times I thought I had an excellent proposal or idea, when in actuality it wasn't all that great; however, having a kernel of an idea gives others a starting point to help guide you into a better direction. One option is to discuss this with your supervisor at NIH and see if there is any potential for you to either present work similar to your proposal or attend a conference to network and speak with people that work in this area. Knowing which conferences to attend could be based on your supervisor's opinion or you can find labs or people working in your field and see where they usually publish.

Good mentors want to know two things (1) what you bring to the lab; and (2) what you want to extend in the lab.

For example, are  you familiar with the techniques their group uses? While a PhD is a training opportunity, a well-qualified PhD student who already knows a lot of stuff is going to be more attractive than one who will need a year or more to catch up. That said, the second type of student can and is accepted with strong argumentation on their end. Secondly, labs are collaborative. Can you teach the lab new things?
This one sounds like the sub-part of (1), but think about it scientifically. A PI doesn't need (necessarily) a student to do something someone's already working on. With their guidance, what new directions will you go on? How can they help you achieve them? Show that you can do that.


text:
Do papers ever get published posthumously?
What is the longest discrepancy between death and publication?

19 years for A51 here

Depending on the definition of published and paper, possibly up to a century https://www.bbc.com/news/science-environment-18370797

The paper

Radcliffe, J. M. "Some properties of coherent spin states." Journal of Physics A: General Physics 4.3 (1971): 313

was submitted in 1970, published in 1971, and contains the following:

At the time of writing this post, the paper has 951 Google citations.
There is no hint as to the date of the passing of Prof. Radcliffe but it is the only publication by this author on MathSciNet; it is entirely possible that Prof. Radcliffe could have published in Journals not covered by MathSciNet.  The Mathematical Genealogy project contains references to a single John Radcliffe who graduated from University of London in 1967, but the general area of the thesis and the aforementioned work do not match very well.
Anyways, this is clearly an example of posthumous publication not done in collaboration.

Why does  your second paragraph say "D" Radcliffe?

@AzorAhai actually that what the note added in proof states, probably an error on their part.  I reproduced a screen shot of the note as is in the paper.

Yes, papers get published posthumously.
I don't know who the world record holders are, but Klaus Schulten, one of the greats of biomolecular simulation, who passed away in October 2016, has written several papers in 2019 (according to Google Scholar). These include a PNAS: https://www.pnas.org/content/116/12/5356.short

Easier with joint publications that take a while to come to completion, I guess.

Euler has several items published/presented in 1862.  This is 79 years after his death on 18 September 1783.  (Several were written in the 1740s, so the writing-publishing gap is more than a century.)


text:
Does it make sense to let a colleague know about his repeated misspelling?
I have been working on a project with a collaborator for several years. I have never met my collaborator in person but we've been a part of weekly calls and sent hundreds of emails together so I feel like at this point I know this person fairly well.
In what seems like hundreds (at least 10's) I have noticed my collaborator always misspells "a lot" as "alot". This person is my senior (he's a graduate student, I'm a pre-doc) and I am wondering if I should let him know in a polite way that he is making a common misspelling. It does not particularly bug me or anything, and I am not a particularly fantastic speller myself, but I just want to help him out in case he doesn't know already. Does it make sense to bring this up with him as a colleague or is this not my place?

I moved to chat the etymological discussion and I encourage everyone to continue there. In case, please read this FAQ before posting another comment.

Depending on your relation, pointing him to The Alot is Better Than You at Everything might help.

Alot is a small town in India. I suppose people in Alot have lots of fun with spelling checkers. Like “I come from a lot in India”

If he ever reads (instead of just writing), he already knows that it is wrong.

Nothing for you to gain and potentially something to lose. Let it slide

Let it go, while the typo is limited to emails. Emails are frequently written hastily and certain typos can be common or made on purpose to type less, or even for fun (I do sometimes this in my language, to mimic certain dialectal expressions).
If, instead, the typo appears in, for instance, a paper or other public document you're jointly writing, then correct it as you would correct any other typo in the paper.

To add-on to my question, he even makes this typo in more formal emails to people who are both of our seniors (e.g., senior professors), but your point is well taken.

@John-Henry Some people just have bad spelling, that's fine. I have bad spelling, and I know some of my co-workers and customers have bed spelling too. It happens. I doubt anyone would ever scoff at a typo in an e-Mail. I am sure most people would just read over it and not even notice.

At some point you're going to edit a joint paper and correct "alot" into "a lot". It will be a very emotional moment for both of you. "I've been spelling it wrong this whole time and you didn't tell me!!" Tell them now. Tell them the truth, which is that it's starting to become a distraction for you (proof: you wrote this Q).
This isn't your great Aunt writing "the dogs were all their" on your yearly birthday card. You're eventually going to have to tell this person about mistakes in proofs, and argue with them over ideas. There should be some comfort level, esp. after years of working together.
The one thing to watch for is the special rule that any grad student can have any lesser-rank kicked-out of any program, anywhere in the world, for not showing proper respect. To be serious, in my mind you're both grad students. I had to look up "pre-doc" and read it twice and I'm still not sure how this other person outranks you (you haven't been accepted into a PhD program?)

If you have occasion make this correction in a joint paper, you can simply attribute it to a spellchecker (which certainly should flag up "alot", for example my browser is doing it as I type).

Right haven't been accepted yet, I'm a full-time RA whereas the collaborator is a student

@EspeciallyLime Sure. But to make the lie believable you'd need to start spelling it "alot" in emails starting now, and find some plausible reason why your email editor has no spell-check. But there's always the risk they think the OP spells "alot" wrong and notice when they suddenly start spelling it correctly. Honestly, I don't see a way out. You'll have to stop working with them.

OP's colleague's spellchecker won't flag "alot" if OP's colleague has clicked "Add to Dictionary" or "Ignore All."

I would be very surprised if they had that reaction. Correcting peoples' minor mistakes in informal contexts is simply not common, and he'd never expect you to have told him.

@OwenReynolds Why? You presumably don't routinely spellcheck other people's emails, and it's plausible that both variants are acceptable.

@shoover But OP's own spellchecker will, and then they can say "I corrected it because my spellchecker told me to."

About spellcheckers, some people don't use them. They can get annoying when you write in two or more languages and half the time they think every word you type is wrong.

@Barmar Sure, but this is different in 2 ways. They've been working closely with for years. And they've seen "alot" hundreds of times to where it's gotten distracting.

@OwenReynolds I can be pretty anal, but I don't think I've ever pointed out a coworker's spelling or grammar error in informal contexts. Only when I'm reviewing documents that are going to be distributed to the public. I'll sometimes comment when someone says EST when it's currently EDT, but I've mostly given up on that windmill as well.

And if the OP actually lets these little mistakes distract them, I think the OP needs to work on their tolerance.

@EspeciallyLime The issue is that the OP has taken the time to notice 100's of "alot"s and its use with other people. "Should I say something?" is probably not going to go away, as they see it more and more times.

@Barmar as I said in the post, it doesn't really bug me, I just wanted to be a good friend and I didn't know if it was my place to say or not

@MishaLavrov - unless they are performing an academic study of auctions, for example...

I am not a native speaker and I was very happy when a colleague told me about a repeating spelling mistake of mine. If you want to do it discretly,just write him a quote were he mispelled it and say something with a lot about this quote.
Dear Mister X,
your wrote

"Alot of assumptions went into this study"

A lot of work has to been done, to make this work. We need another day in the lab

Or simply tell her.

Dear Mrs. Y, I agree with the proposed changes in your last email. I
also think I noticed a bug in your spell checker, it always says
"alot" instead of "a lot".
Kind regards
Phd Student S.

I have no clue whether "an other day" was intentional or not...

It was not. Thank you for pointing it out, I learned something today :).