text:
What is the difference between bachelor's, master's and PhD?
What's the basic difference between these degrees? Who might choose one versus the other?

your title does not match your question. Did  mean masters for undergraduate  in your question?

What type of masters?  Master by research -- demonstrate that you know how to conduct research.  PhD -- know to do research + new contributions.

A bachelor's or a master's is for practitioners.  A PhD is for researchers.  For example, if you're studying computer science and your goal is a software development job at Google or Facebook, a master's would be a great choice.  But if you'd like to join their research groups or become tenure track faculty at an R1 university, you probably need a PhD.


text:
I submitted an LOR online for a student to a US school. Student claims they want a physical copy. How should I respond?
The student claims that the department contacted him asking for all letters in printed form with full contact details and signature.
Is this a common request?  How do I know it's authentic?  How should I respond?

Your question is a bit unclear.  Is the student asking you to send the letter directly to the school in a sealed envelope or is she asking you to give her the letter in a sealed envelope?  The former is quite common and shouldn't really raise any red flags.

@Brian Borchers I am wondering why they would ask for the letter in printed form, given that I have send it online?

Did they originally ask you for the recommendation letter through an online system?  If so, this is weird.  If you simply emailed it to the department, then it's not surprising that they want a copy on letterhead.  Why not contact the department and ask what their policy is?

@Brian Borchers Is the former. Thanks a lot for the help!

This is why I prepare all LORs electronically and save a copy before sending on line.  I've never gotten a request like the one mentioned, but if I did, I'd be able to print on letterhead and send exactly the same words as were submitted electronically.

I smell a rat.  If the department really wanted a paper original of your electronically submitted letter, surely they would contact you, instead of asking the student.

@JeffE  You'd hope so!  On the other hand, it's easier to contact one student than three or so referees, and I've known academic departments to, ah, take the path of less resistance.  As long as the paper letter is sent directly to the department, it should be OK.  I might even add a Post-It note saying, "the student asked me to send this."  If all is OK, there's no harm.  If something is up, you've given a clue.

It's completely possible a school might ask for an original letter on paper sent direct to them.
It's been identified as a US school but not which one.  There are perhaps 600 graduate institutions in the US.  Multiply that times the number of programs.  There simply has to be some variance in admissions policies.  At any particular school, it's completely possible they have an admissions policy of auditing LORs by asking for paper copies of all or some subsets of those submitted electronically.  There's no national standard on this kind of thing.
(I was surprised when University of Washington wanted paper originals of my own LORs for my first faculty appointment a few years ago.  So I figure there have to be schools that might want paper originals for student LORs.)
If you're unsure of the authenticity of the request, you might ask to see the communications the student received.  But once satisfied, I'd try to comply.  (I keep copies of the LORs I write so I can resend them with a new inside address when a student applies elsewhere; I assume you do, too.)
I would, of course, only accept a request for an original sent direct to the school. A request that the original be given to the student for delivery to the school would ring bells as bogus and likely end the need for any new LORs for that individual.

I'm curious about the downvote.  Was there something that seemed unhelpful?

No, it's not common.
I would guess that for some reason the department is not convinced that the letter really came from you.  Maybe there was something about the letter, or the student, that raised their suspicions; or maybe they just don't trust the security of their online system.  It's not really your concern, so I would just send the letter as they ask.

@DSVA Using digital signatures does not solve the authenticity problem, unless you have a separate channel to verify them.

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text:
Ethics: How to deal with a professor who will not accept their inaccurarcy in judging my work?
First, I am a mathematics major who is doing an REU (Research Experiences for Undergraduates) in mathematics at my school. Initially, I wanted to do an REU outside of my school because I have had this professor before, and being in his class is difficult, but not unbearable. Right now, it is unbearable. For the first project, he has asked me to prove a proposition in category theory, and his criticism is not helpful nor is it actually advice. He has went as far as to say "this is your project, not mine", even though my proof is actually correct for the problem at hand; I have seen other verified proofs and had mine verified by mathematicians. It just makes me feel stupid, and I feel depressed and stressed coming to school everyday. What are my options in this situation and what is the most ethical?

Hard to judge this from a distance. It could be a personality issue, it could be a mathematical issue, and it could be that he just thinks you missed something important and need to think deeper.

It could be the first, but it is not the last two, since I am using the sources he suggested, and his suggestions are just confusing and are misunderstandings of the structures.

What do you mean by "his criticism is not helpful nor is it actually advice"? What is the criticism? What do you mean by "had mine verified by mathematicians"?

His advice is almost always "Nope. That is wrong." with no tips on how to improve, or just bad advice. For example, in the proof you rely on certain commutative diagrams. One of them he misunderstood since a canonical isomorphism does not mean the object is mapped to the object, it just means their paths commute so the objects are isomorphic(the associativity). But that turned into an ordeal that left me with panic because that's not what the diagram means. And for the verification means that other professors who are math specialists have reviewed the proof and says that it is acceptable.

Have you asked for clarification of what is wrong? Is it possible you are not communicating the concepts in your proofs correctly or leaving assumptions unstated?

Yes, of course. I always ask, "well what is the exact problem?" or if when he gives advice, I would say "I do not understand". And legitimately, the only thing he seems to do is force me to work on it by myself with his inaccurate advice and misunderstanding of the problem. I promise, I am doing the upmost to communicate and have my proof clear for those to read. I state my assumptions, what I am using (which are all valid), and why one thing follows from another.

Are you sure you want to be asking about 'ethics' rather than say 'etiquette'?

By professors who are math specialists, do you actually mean math professors? And whether you are correct is of course impossible for me to tell from this, but your description of a canonical isomorphism is not actually comprehensible to me in the current form.

@Anyon, my guess here is that the OP is asking about the ethics of the professor - or even making a claim of unethical behavior on his part.

@Buffy The last sentence would seem to contradict that interpretation.

@Anyon, right you are.

Please expand "REU".

Your professor is not being "unethical".  It's possible he's a difficult person but ethics is not a part of this.
There's a pretty good chance that if your professor says your proof is not correct, that it really isn't.  And he may not be as unhelpful as you think.  Students sometimes think an instructor is unhelpful if they don't give them the answer any time they're stuck.  But simply giving you the answer won't make you a better mathematician.  Forcing you to keep plugging at it until you find the answer on your own will make you a better mathematician.
My advice:  Consider the possibility that he's right, you're not and that he wants you to keep working at it until you solve it on your own and go from there.

It’s really hard to understand your question.  In your questions and comments you’re using language in imprecise and confusing ways.  I’d imagine that when you try to explain math you’re probably also explaining it in imprecise and confusing ways.  My best guess is your professor genuinely doesn’t understand what your argument is.  Have you tried writing it down carefully line-by-line and thinking through whether each step is totally clear and explained precisely?  It also might help to try to explain it to another student.

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Associate Professor vs Assistant Professor vs Lecturer
I want to know the difference between associate and assistant professor in terms of contract length, status and salary. And also how both positions are published and what's the recruitment process of each one mainly in Europe and Canada?
What about lecturer positions in the US, could European PhDs land lecturer position in the US ?
Thanks

The positions are not standardised around the world, or even between institutions. Where are you asking about?

Mainly in Europe, eventhough i also want an answer covering Canada as well

This may help: List of academic ranks.

Beware that Europe is not a uniform block: each country has its own recruiting processes and the statuses can vary too. Variations are possible also within a single country.

I just want an example, do you know about Italy ?

Sam, the Italian positions are described in this answer. The RTD-B position is essentially the equivalent of assistant professor.

Many Thanks ! ! what about the second part of the question, do PhDs land Lecturer positions in the US ?

@Sam - few if any US universities I’m familiar with have a rank of ‘Lecturer’ - that seems more a British title.

yes indeed could you elaborate on the rank of Lecturer in the UK especially PhDs from the rest of Europe Thanks

@JonCuster And for those that do, I would assume it referred to an adjunct teaching-only position, not equivalent to the UK title.

@JonCuster  MANY US universities employ lecturers.  It's a teaching appointment.  That's what I have at University of Michigan.

Here in the US, an assistant professor is an entry-level tenure track appointment but does not come with tenure.  An associate professor is the next level up and does come with tenure.  Tenure track appointments virtually always require a PhD but not necessarily from a US institution.
A lecturer appointment is a teaching position, almost never comes with tenure, and does not necessarily require PhD, though it does usually require a master's at minimum.
A typical initial contract is three years.
Open positions are often but not always posted on the department website.  Contact the department you're interested in for more info.  Typically, you'll be asked to supply a CV, references, various statements describing your objectives, teaching philosophy and research interests, and possibly a teaching demonstration video.  Obviously, all of this depends on the department.

Alright, and are the assistant professor position posted somewhere ? or do you have to contact the department for them ? what comes into play for the recruitment for this type of position ? (especially if the applicant is from outside the US)

@Sam Very dependent on institution.

Also very dependent on the discipline.  In some disciplines there are is a place where nearly all academic positions in the discipline are advertised (such as www.mathjobs.org for mathematics positions.)

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Washed out from first undergraduate school, doing OK at second, thinking of applying for masters in EU
As written in the title, I'm thinking of applying for masters in Europe (I myself am from Serbia), but I made a mess of my undergraduate career, so I'm looking for advice how to present this in my CV and SOP.
Here's my background:
Back after finishing high school, I applied for a relatively well respected local electrical engineering school (University of Belgrade School of Electrical Engineering). Out of 500 students, I was 250ish. So far so good. My intent at the time was to study computer engineering.
Then came the first academic year. I passed a number of exams (mostly those I could pass with no studying at all, so as a result my grades were pretty bad, with my grade average being 7.0 out of 10, with 6 being passing grade), but I didn't have enough credits pass to the second year.
No big deal, I thought, since statistics show that the four year program there usually lasts around seven years, with first year being the most difficult. I took some exams from the second year and tried to pass first year exams again. At the end of the year, I passed none of the first year exams, but I did pass some of the second year exams. Third time's the charm I thought, got some more second year exams and tried to pass the first year again. At the end of the year, situation was the same as last time: I passed none of the problematic first year exams, but I did pass some of the second year exams.
By that time, I was pretty depressed, had gained quite a bit of weight, was having big problems with procrastination and was fed up with school politics.
At that point I decided that it was time to switch schools. I moved to a younger, less-respected school (Union University School of Computing) and got admitted (barely) into second year there due to exams I passed at my previous school. I moved to a telecommunications study program there.
In the second year, at my new school, I had around one and a half year worth of exams, but I managed to pass them. The downside was that my grades weren't all that good. They weren't bad, but nothing exceptional either. Third year went well for me. I passed all of the exams, raised my average grade to 8.0 out of 10 and became one of the best students in my (relatively small) class. In one particularly hard exam I was the only student that year to get a 9 with nobody getting a 10.
Right now, the exam season for the winter semester of my fourth year is approaching and I'm thinking of what I'm going to do next. I've spoken to few professors and they all believe that I should definitely continue my education. I wouldn't have any problems continuing my education at my current school, but I don't think that it's best equipped for the field in which I want to study further. The focus of my current school is computer science, while the telecommunications program seems to have taken a back seat.
I have read the question about getting a Ph.D. with bad transcript and fortunately for me course structure was such that just a few professors taught a large number of exams (for example six to eight hours every day for the whole semester with same professor and TA), so there are people who know me well and have a good opinion of me.
I don't think that I could do much to improve my average grade. Perhaps the best I could do would be around 8.3 out of 10.
I don't think that I would have any problems with IELTS exam and I do think that I could prepare GRE well enough. I do understand that good grades there won't help me much, but on the other hand I at least hope that they won't have a negative effect.
I'm thinking of applying for universities that aren't very highly ranked, for example some from the bottom of the top 200 from the Shanghai list, but I'm not sure if that's low enough. Also I'm thinking of applying for two-year masters, but I'm coming from a four-year undergraduate school, if that matters.
Finally my question:
What I really don't know is how to present me dropping out of my first school in my CV or SOP. I've been basically studying 6 years now, much longer than expected, with not that good grades and I really can't think of any way to present that in favorable light. I think that I matured in the meantime and my grades did improve, but on the other hand I moved a weaker school.

By the way, any tips on how to make this question a bit easier to read would be very welcome!

@user14449 Oh, yeah, I forgot... I'm from Serbia and my first school was University of Belgrade School of Electrical Engineering, while my second school is Union University School of Computing.

You appear to have two sets of choices: 1) Continue a graduate program in your current school, where you are well known and liked, and 2) Start a graduate program in an equivalent school.
I'm assuming that you will prefer the second choice. Find out which schools (e.g. on the list of 200) are equivalent of yours. Find out where the better students (the ones averaging 8.0) go to after they graduate. And last, find out which graduate schools your professors have the most clout with, especially the one who gave you the top grade.
Then apply to those schools. Use your current school as a back-up if the "equivalent" school plan doesn't work. Good luck.

I'm in the US, so take that into consideration.
If it were one of my classmates in a similar position, I would recommend searching for an internship or entry-level position with a top company in your field. With a year or two of work history, your application to an MSc would be evaluated in a totally different light, specifically there would be less focus on why you struggled initially and more on why you are returning (to continue to learn?)
In addition, this would let you gain some practical skills, perhaps save some money, and figure out whether you really enjoy working in comp sci.

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How should I prepare for an interdisciplinary interview?
I applied for a Ph.D. internship position in a protein research lab. They invited me to appear for an online interview.
My background is in IT, and the professor who will interview me is from Chemistry. How should I prepare for the interview?

What do you know of Chemistry or protein research? Would your position be one of providing software support for modeling? IT is pretty broad. What is your specialty within it?

@Buffy, What do you know of Chemistry or protein research? --- I know protein from the computational point of view. I.e., protein geometry. Would your position be one of providing software support for modeling? --- computational protein design. What is your specialty within it? --- protein modeling, and simulation.

From the comments, you seem pretty well situated already for such an interview. It is impossible to know what you will be asked, but be prepared to to discuss modeling in general. Don't be put off by questions for which you have no immediate answer. Most people will accept that you need to look into things further and that not every problem is easy.
Flexibility is your friend.


text:
I was asked to present a potential course outline for an associate prof. Position. Any advice?
I applied for an associate professor position in data science and new technologies. It was a real surprise when the committee chose me out of 16 persons to be the first among many.
After 2 weeks of the notification of me being #1, I was asked to present a potential new course in data science on data driven decision making for a master student program.
My teaching expertise is low since I have been doing a lot of research. Would you please advise me what might be helpful when asked such a request? The presentation should be 30 mins and students and staff will be invited to the seminar.
Currently, I am going to include a title, course objectives, learning outcomes, 5-6 modules, and some teaching strategies I will use.
Thank you so much for the helping out. This will be a life changing for me if accepted!

country and type of university?  (for one thing, it would tell us what 'course' means)

@AlexanderWoo It is in Europe not in the USA. The university is a public academic university. Department is information systems.

In addition to the suggestions of Wetenschaap consider adding something about student activities (exercises, projects, exams...) and about evaluation. What will student "grades" be based on. Note that the latter may be bound by local custom or rules that you might need to conform to.
Note that students learn by doing things not just (or primarily) by listening to lectures.
I don't think you need to be very detailed about exercises and such, but don't omit mentioning evaluation.


text:
Manually adding articles to Google Scholar account and linking the PDFs
Recently, I manually added a conference paper to my google scholar account. Whenever an article is added manually, google searches for it and automatically links the article location. However, in my case, the articles published by the organizer were deleted (probably unconsciously) in the meantime. My question adds clarity to this question. Is there a way to point to the article PDF somewhere in Google Scholar?
PS: I have uploaded the actual article PDF in ResearchGate recently.

Can you clarify how the answer in the linked question does not answer your question? It points to Google Scholar's help page (https://scholar.google.com/intl/en/scholar/inclusion.html), which clearly mentions what individual authors can do to get the pdf linked. If you have uploaded to ResearchGate recently, I suggest you wait for some time for it to be indexed.

@GoodDeeds: Thanks, I will wait out till the ResearchGate upload gets indexed by Google. This was the answer I was looking for.

It is also possible that when Google Scholar finds your PDF, it creates a separate entry. In that case you may need to search for it and add it to your profile explicitly, and if needed merge with your manually created entry.

Even after several months after having created a manual entry with the link to the pdf file written in the editor field (because there is no field for the pdf), the pdf is not indexed, is this normal?


text:
What degree does someone need to pursue in Germany after finishing an MBBS degree in South Asia?
After finishing an MBBS degree in South Asia (Pakistan) (a 5-year bachelor's degree plus a 1-year internship in the hospital) what kind of additional courses or degress are necessary to take (in Germany) to become a professional medical doctor in Germany?

I am assuming that the MBBS degree would qualify you to practise medicine in Pakistan. In order to practise medicine in Germany, you need the approbation. Depending on where in Germany you want to work, you would apply to a different office to get it. Your application would need to make the case that your MBBS degree is equvialent to having studied in Germany, or that any shortfalls would be compensated for by your work experience. If they aren't convinced, they can make you sit an exam (Gleichstellungspruefung). They can also approve or decline your application straight away.
The Marburger Bund (more or less the union for physicians in Germany) provides more detailed information here:
https://www.marburger-bund.de/bundesverband/service/aerztinnen-und-aerzte-mit-auslaendischer-qualifikation/foreign-trained-1-0


text:
How to organize my binder of activities for review of time as assistant professor?
I am up for review and I must compile a lot of materials from my time as an assistant professor.  Everything has to be submitted in hard copy in a binder.  I would like to make it as easy as possible for the committee to read.  I must submit the following:

A cover letter
A CV
List of all courses taught, along with syllabuses
My annual reports (about three pages per year)
Every student evaluation from every class taught
Lists of various activities that include scholarship, professional development, and service.

I thought I would organize it so that each of the categories above would get their own tab in the binder. Each of the categories in (6) will get their own tab as well. My main concern is the evaluations from (5). I teach three or four classes per semester.  So, I have dozens of classes with evaluations. If I only give a single tab to all the evaluations, it would be hard to navigate. And, each class getting its own tab seems excessive. Is there a way to have (1) through (6) have tabs that are easy to pick out, while still maintaining some kind of sub-tab system for each semester?  Or, is there a better way to organize all this stuff?  Thanks.

Use sticky notes to separate each class.

Why don't you try asking your chair if they have a preferred way to organize things?

I think that you had the right idea about having six tabs to organize each section. From there, I would have card stock paper (or something similar) to separate out your evaluations by semester. Have each semester labeled on each sheet. That will create a subtle yet efficient way of dividing out your evaluations.


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My supervisor ignores me on purpose bc I want to change the time to mark papers
I am a phd student and I am a TA for my supervisor's courses (there are two TAs in total) this term. So far I am doing well.
Recently, this course will have an exam. My supervisor asked us on Slack if we had time to go to his office at XX (time) to mark exam papers. I replied that I could at first, but after 10 minutes, I found that actually I was occupied at that time, so I immediately edited the message to ask if I could come later. He didn't reply to me before or after I edited the message.
After dozens of minutes, another TA replied that he could come, and my supervisor immediately replied to him. So I sent a new message saying that I was busy at that time. When I sent the message, I saw that my supervisor was typing in the same channel, so I was sure that he had seen my message, but he still deliberately ignored me.
In fact, I am okay if he directly says that we cannot change the time, but simply ignoring me really pisses me off.
Should I put aside my own schedule to come to mark the papers? Or should I send him an email to ask again? I am not sure if he is taming me to obey all his instructions and never dare to say no. I don't want this and I am angry with this whole meanless thing.
========= update =========
After resending an email instead of a third message on Slack, he agrees to change it to another time. I might just overthink too much.

What kind of reply were you expecting? What kind of reply did your colleague receive? So far he seems to have only asked you if you have time, not ordered you to actually come in at that time, did he?

Incredible! And after dozens of minutes you say?

@A rural reader I am not sure if you are asking my second message. It's basically the same as my first, asking if I can arrive later since I am occupied at that time.

@MisterMiyagi  He asked both of the TAs to come to his office at that time. I expect him to reply to me he can or not accept another time.

How cruel. Your advisor is obviously toxic. I suggest you contact your ombudsman ASAP and start looking for a new advisor. This type of behavior is uncalled for.

Did you suggest, in your email, a specific time when you can come in to help with the grading?

"I might just overthink too much." -- I think that is true :-) Nothing needs to be decided on the spot; give people a few hours or a day or two to figure stuff out. If you can't come one day, they might just have to figure out what other times would work for them, and that takes time. Or perhaps they just didn't have the time to figure it out right then and there. So chill out and give people the benefit of the doubt.

@Wolfgang Bangerth Thank you. I will be more patient next time. If there is no reply, I will just ask again lol.

I would suggest sending him another email.
In general I agree that not answering emails or messages is a bad practice that reflects very badly on the ignoring parties (lack of accountability, lack of basic courage, disrespect, and more). That said, many people are busy and sometimes it is hard to find the time to reply back.

Yet another email sounds like a nuisance, actually. A visit would be better.

Thanks. I will send another email and wait for his reply.

@Ashella, I'm happy to hear the email message I suggested helped at the end.

First, relax. Professors have hundred and one things demanding their attention at any given time and your assumption that you supervisor "ignores you on purpose" seems like an unlikely explanation. Perhaps he just got distracted and upon seeing that the other TA can come at a specified time, he was content that he will have enough help.
If your supervisor continues to not react to your message, I wouldn't overthink it. I would wait till I can see them face-to-face, maybe you see them in a corridor or if you can, pop into their office, and ask again if it's okay that you come to mark the exams at a different time.

Thank you for your reply. It was solved after I sent another email. I guess I indeed overthink it.


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Is it bad to ask for accommodations for disability when PhD supervisor might be in bereavement?
I'm in my 2nd year of PhD in England, with one supervisor and we are the only two people in our lab. I have two results chapters ready with a major experiment in each, and I'm in the middle of another one. About a month ago my normally absent PI first said that I'm on track, then said I have enough data but don't prioritise tasks well, now she's saying that I'm way behind on data collection (although she did not give me a deadline), she wants me glued to my office desk and to report to her whenever I'm leaving it, even if for 30 mins for lunch just outside the lab, every single day (thankfully bathroom breaks are exempt, at least for now!). Recently I asked if I could come in later (10-11am) at times when my asthma gets worse, she first agreed but the next day changed her mind, now she wants me to go to a doctor and "fix" my asthma although obviously I would have done by now it were possible. She said she's responsible and concerned for my wellbeing but generally she never listens to me or takes me seriously. I have just heard from someone that her dad might be dying which might explain her sudden change in mood. Before this she didn't seem to care where I was. She did suddenly berate me once for being too slow just before Easter last year. That was unusual for her so I thought she was stressed by something personal and ignored that.
I happily worked a 9-5 before my PhD but it was repetitive so I didn't have to think about it much, neither did I have to work evenings and weekends. My PI doesn't let me get time off after late hours/weekend work which I have to do quite often.
I fear that I may be a slow worker sometimes because I'm constantly anxious about doing things the perfect way especially when I'm new to a certain task, this may be related to my diagnosed autism. My office here is noisy and distracting, there are no physical walls between people and I feel stared at which increases my anxiety. Working in empty meeting rooms for the past half a year and coming in slightly later I found it much easier to read and write. Now my PI says she doesn't want to hear about the work I do outside of the office, she just wants me to be at my desk and that's it. The problem with this is that being underslept and not concentrating will make me a lot less productive and will end badly for me. Again, in the past I could be stuck for weeks trying to figure something out and she didn't care.
I grew up in a country with a massive stigma against neurodivergence so I'm not comfortable telling people about my autism diagnosis and I didn't declare it (or the asthma) when I started. Throughout my career so far I never had to - I graduated with a first, got prizes for best performance in my cohort, my previous PI and myself worked 11am-1am publishing four papers from my Masters together, including two with me as first author. Then I got this fully funded PhD. I do feel sorry for my current PI's situation but I don't want my career ruined at this point. Given how she reacted to my asking for health-related accommodations before, I don't feel that telling her about my anxiety will make a difference.
I'm tempted to bring proof of my diagnoses to Disability services and ask them to suggest accommodations for my PI to implement, e.g. working in a quiet space and starting later. I feel this would be forceful perhaps but I have no choice if I'm to continue with my PhD. Would there be any point in this and how would I time it to avoid upsetting my PI?
Alternatively, I could assume that even a non-autistic person would feel anxious in this situation (this is where I'd love to hear your views) and have a reason to speak to my tutor (my assigned pastoral support person) to express concern about my PI's demands. In that case should I mention that I heard they are having family problems and potentially bereavement soon, while keeping the source anonymous? I have no idea whatsoever what could happen to me or her after this.
What do you think is the politically correct way to go about this?
Also, could my PI get away with not agreeing with the accommodations or even refusing to supervise me once I declare my health problems to the university?
Edited to add this: my PI and I have had two long meetings already about this. She ignores most of what I say and goes on about what she wants. To avoid her moving the goalpost I suggested that I take unambiguous precise bullet-point notes of each decision we make on our meetings. I wrote them down in a shared document, she read and approved, but the moment I left the room she wrote her own story underneath our notes as a paragraph and in very vague terms from my point of view. She keeps adding stuff to it outside of our meetings too. This feels like a one-way conversation with a dictator and I'm giving up on trying to reason with her.

Are you objectively on track (check with a professor or graduated PhD you trust)? If so she may be having a mental health issue b/c this would seem like erratic behavior. But if you really are behind, maybe she’s just now really advising you and realizing how bad things are and so 1) her guidance changes the more she actually oversees, and 2) she’s panicking possibly partially b/c she realizes she’s screwed up but is projecting it on you. The two possibilities are wildly different so we need more info. Her treatment of your health issues is abominable though—don’t put up with that.

If you’re in the US, talk with Disability services today. Bring as much documentation as you can, and going forward document all requests for accommodation in writing so you have evidence to take to Disability services. IANAL but it sounds like she’s violating the ADA and if so Disability services can help you. It’s very unlikely your university wants a lawsuit.

I think it's appropriate to attribute some grumpiness or moodiness to bereavement and give someone a bit of the benefit of the doubt and patience as they deal with a difficult time.
However, that does not extend to everything and certainly is not a reason for you to work in unproductive conditions. From your side of the story, your supervisor seems misguided as to what makes for productive working conditions. She also sounds a bit erratic in terms of shifting feedback and expectations. It's possible the solutions she is proposing are solutions that would work for her, or have worked for a past student, even if they do not work for you.
Disability Services may be useful, but I would start by asking them for advice about how to approach the situation rather than to enforce some accommodations. I think it would be far better to come to an understanding with your advisor directly about what you need to be successful. The accommodations you are asking for do not sound to me like they are particularly unique to any disability or condition (even if that may be a valid and convincing argument for them), these are things that fit quite reasonably into general variation in preferred working habits.
Unfortunately, there is no magic formula for interacting with people to get what you want or need from them, and certainly no formula to do so without offending anyone. Personalities differ, and general guidelines that work with most people might not work with your supervisor.
My general advice would be to have a conversation starting with your shared goals for your project and to try to come up with a shared understanding of a reasonable timeline, and then move to discussing a plan to get there. I would ask specifically why her preferences for working hours are what they are, and start from those reasons when making an argument for why you think a different structure would suit you better. You could request a trial period, where you've agreed on some progress to be made by some specific time, to show that you are able to make that progress under the conditions you propose.
Another tip I commonly give here is to suggest you bring up the problem you want to solve rather than your solution. That is, start with "When it's noisy I am not able to get work done" rather than "I don't want to work in the office". This lets people feel helpful by coming up with solutions for you, rather than feeling like you're defying their own preferences.
Of course, your advisor may be entirely unreasonable about all of this and insist on a particular way forward that doesn't work for you. In that case, maybe you want disability services to impose some accommodations for your work environment. However, I do not think a supervisor/student relationship works well when it is adversarial. Mentors must be invested in their students' success; these are battles you should be fighting on the same side of. That doesn't mean there can't be disagreement or conflict, but rather that the end goals should be shared. If your mentor needs to be forced by some third party to support you, that would suggest you are not actually on the same side. If you cannot come to some agreement with this professor about working conditions that suit you, I would strongly suggest you consider finding an alternative mentor.

Right. If/when you find yourself having to (somehow) "force" your advisor to behave more reasonably, it won't be good for your relationship... For that matter, it is very hard to create effective "rules/laws" to enforce/require "positive attitudes" and/or "decent treatment of others".

First, no it is not wrong to ask for accommodations because she is grieving.
To me, though, it sounds like she is increasing her oversight of your work because she feels your progress may be too slow. If I’m right, she might not object to flexible working arrangements in principle, but feels that you haven’t demonstrated sufficient progress and thinks that this could be because you are not putting in the dedicated hours. She can’t verify hours that you say you put in at home or at night (or whether you are multitasking during those hours), so she is asking you to be where she can see you working during normal business hours. She might relax her policies once she sees you making better progress.
If I were you, I’d declare your challenges and work with her to find a way to address her concerns while also looking after your needs. Just throwing out some ideas here: Good headphones, rearrangement of furnishings or a change of desk location to reduce distractions when you are in the office? Working 10am-7pm consistently every day (rather than variable, flexible hours) so that she at least knows when to expect you to be working, even if it is non-standard hours? Doing that with a buddy who also starts at 10 and finishes later so you have some peer accountability? An agreement to check in when you start and then each hour while you are working during business hours at home? Logging your hourly activities in a spreadsheet and submitting that each week? Or perhaps some software-based solution?
Also, if you haven’t done so in the last few years, check with a specialist regarding your asthma as there have been some relatively recent improvements in allergy options that your regular doctor might not have considered (alternatives to shots for desensitisation, newer drugs that address different mechanisms of the reaction, etc) and a specialist might also be able to help you find ways to reduce your exposure better.

+1 for everything except the "software-based solution”. Sometimes a brute force search for tools and circumstances for optimal productivity simply reduces actual productivity on the task at hand.

Thank you for the suggestions. If she set a deadline for my current experiment in the first place I would've kept to it. If I didn't keep to deadlines I would've been in huge trouble long ago. Listening to music while reading/writing doesn't work for me, my office is crammed so I can't move my desk. She's strongly against starting work at 10am or wfh as I tried to express in my question. I did suggest clocking in/out or show her my lab book every day or what I did for the past month even, she said no, oddly enough. I'm up to date with ways of managing asthma but none of them improve sleep.

Headphones doesn't have to mean listening to music, you can get noise-cancelling headphones.

@grinchfly the point is to understand /why/ she is strongly against starting at 10am or wfh and try to find an alternative way forward that addresses her underlying concerns while also addressing your needs. I suspect that she is strongly against starting late or wfh because she isn’t convinced that you are working the hours you say you are, without distractions. If you can find another way to demonstrate that you are, that might be sufficient. And once she understands your challenges, she might be able to offer options from her end (such as using her influence to find a better office space).

Also, rearrangement of office furniture doesn’t have to mean moving your desk — when I shared an office, for example, I found it enormously helpful to put up some simple, light dividers to reduce visual distractions.

Bringing in the Disability services might be helpful, but you will still need to work on the project at a reasonable pace unless you plan to switch advisors completely; their requirement may not be enforced at all, because they cannot really do much about your advisor forcing you to work more.
I would suggest talking to your advisor directly regarding your problems:

Why does she suddenly think your progress is not enough? Is there a new deadline in her head? Does she want you to submit to a conference with a more recent deadline?
Your asthma is getting worse, and there is no possible "fix" except for more rest and work-from-home time (get a doctor's note available if possible). Make sure that she knows it could be life threatening for you. Don't talk about anxiety and autism because it sounds like your advisor is not so aware of mental health/neurodevelopmental problems.
You are willing to give up this earlier deadline in her head because of health reasons. You are willing to negotiate a new deadline with her and make good progress on the condition that you are not forced to go to your office in non-business hours for the sake of your health (as long as your work can be done at home, of course).

Be stern about your needs, but try to stay neutral and don't accuse her of anything, i.e. tell her that "I need to prioritize my health" instead of "you are ignoring my health", and especially don't feel guilty or be hesitant to talk to her because you heard that she is experiencing personal stress.

IANAL but if this is in the US she is likely violating the ADA by asking you to get treatment to “fix your asthma”. Pretty sure employers cannot force you to get treatment and that this isn’t a valid excuse for rejecting a reasonable accommodation which you’ve requested. You really do need to talk with your ADA office (whatever their name). Asthma isn’t something to take lightly and a PhD isn’t worth sacrificing your health (or worse).

@bob I totally agree; the advisor is quite rude in demanding that. But even in the US, the penalty is hard to enforce if it ever happens, because she can deny having said that and you will probably need to switch advisors suppose you really get into such conflicts with her. It doesn't sound like the OP is thinking of switching advisors at the moment.


text:
Given only one possible appointment for masters application interview with no possibility to renegotiate date: Is this a red flag or normal?
Background:
I applied for several masters programs this season (taking into account the advice given on this site) and have received a request for a telephone/Skype interview with one of the German universities I applied for. The response came much more quickly than I expected and I still have no replies from other universities.
The mail contained suggested date and time (ten or so days from the date the mail was sent) and asked me to confirm it. Unfortunately, at the specified time, I'll be on a highway, in a different country, traveling between two cities. In my response, I explained that I'll be on a trip and that I'm coming back two days after the suggested date and that I'll be available pretty much at any time after I return from my trip. The reply I got is that the time suggested is the only available time for the interview.
Question:
My unfortunate situation aside, I wanted to ask is it normal for universities to be this inflexible when scheduling admissions interviews? Did I go out if line by attempting to negotiate the interview date? This is the first time I'm having any sort of interview, so I really have no idea what are the cultural norms in such case.

Good thing you applied to several programs.

One possibility to consider is that they're not totally inflexible but your suggested time of interview, not less than two days after they do the rest, doesn't suit them. So they just told you "this or nothing".

@Steve Jessop Perhaps I was unclear in the question. My suggestion was two days or more after their suggested date, so I didn't fix the date to just two days after their suggested date.

@AndrejaKo: yes, but imagine there are few enough borderline candidates that they're interviewing for 2 days. Ideally they want to make all decisions while interviews are fresh in their minds, not decide some places, wait another 2 days, do more interviews, and then decide the rest. Offering to let them wait even longer doesn't help if 2 days is already too long. I guess I'm saying that maybe they'd reschedule you within their defined interview period, but that your response happens to have already ruled out the whole time they've set aside.

@Steve Jessop That could very well be the case.

German universities (in my limited experience) tend to be more rule bound than universities in other countries, so I'm less surprised by this attitude than I would be if it were in the US or UK (two countries which I'm familiar with).

Just a small update: In the end, I offered to call the university from the highway and they offered to postpone the interview, so I got a happy ending for this part of the story.

I think it was perfectly reasonable of you to ask to reschedule.  Of course, it's unfortunate that they weren't able or willing to accommodate you, but that's up to them.
You'll now have to decide what you want to do: interview while traveling, or alter your travel plans, or skip the interview altogether.  It might be worth considering whether an institution that seems so unwilling to accommodate prospective students is an institution that you'd want to attend at all!

Regarding your last sentence: an institution which is inflexible with interview scheduling can still be a fantastic place to work (as I know from personal experience).

@Tara: That's true, but all else being equal I would certainly tend to gravitate towards an institution that treated me well than one which treated me less well.  It may be that they become a lot "nicer" when their students actually arrive, but I confess that I have always found behavior to people that one can get away with treating poorly to be very telling.

At an outside-of-the-US University where I was once briefly employed, I watched a student arrive at the secretarial part of the math office and try to get information about how to apply for a graduate program.  He was treated so rudely by the secretaries that I (a postdoc) was motivated to spontaneously intervene on his behalf.  I watched a secretary glance evilly at me and calculate whether she could afford to treat me in the same way.   She couldn't quite bring herself to do it, so she became nicer to the poor guy, who was very grateful to me.

This left a very strong impression on me.  When the following year the department treated me shabbily (not for the first time), I made arrangements to do my teaching at a different university and was required to write a letter of resignation.  I am almost (but not quite) embarrassed to tell you how good it felt to write that letter.  That university had some truly first rate people, but as an institution it was not an honorable place.  I would never advise anyone to go there.

@PeteL.Clark Well said.  The poisonous meme that "Excellence justifies Arrogance" needs to be fought at every opportunity.

@PeteL.Clark:  Oh, they definitely treated me well, they just wouldn't budge on the interview date.  Luckily it was only inconvenient for me (I had a fairly important commitment in Germany the following afternoon and the interview was in Scotland) rather than impossible.  And they put me up in a nice airport hotel after the interview so that I could make the 6am flight I needed to catch.

@Tara: Based on some internet research I suspect you're talking about interviews for a job, not a master's program.  Whereas flexibility is still to be preferred, it seems like a very different thing when one is being inflexibly flown in on the occasion of future employment rather than as a routine screening for graduate admission.  (What I don't really understand is why any department would want to interview more than 100 master's candidate, as other responses seem to suggest occurs.  What critical information are they getting this way, and that is worth being so exclusionary about?)

@PeteL.Clark:  Indeed I am.  Sorry, in the original version of my comment I made that clear, but then I thought it was too long.
In the UK some universities interview 100s of candidates even for undergraduate degrees.  I don't really understand it either, except that all their applicants have fantastic grades, so I suppose they need some way to pick which ones to take.

It's fairly normal if course admission is competitive, and if one's application really hasn't stood out so far as exceptionally good. The interviewers might have many dozens of interviews to wade through, and the only way to do that is on a very tightly planned schedule.
Given it's a Skype interview, and given the prevalence of laptops, wifi and high-speed mobile data, I don't think it's that extraordinary to expect that for such a significant interview, an applicant would schedule a stop during a trip, at a place with a decent data connection to do the interview.

Two questions: (i) Are there really any European master's programs that conduct "many dozens of interviews" for their candidates?  (In the US, we conduct precisely zero dozen interviews, so the system is evidently different, but that number nevertheless sounds unreasonably high.)  (ii) If they are conducting even one dozen interviews, why can't they switch the OP with someone else?  I don't know what the cultural norms are in this situation, but I would describe the German university in question as being unaccommodating bordering on obnoxious.  I guess the question is how typical this is...

@PeteL.Clark (i) yes. Two of Masters courses have a class size of ~50, and one has ~20. That's ~120 places to allocate each year. (ii) Why should they? When the course has enough good applicants, it's up to the student to work to the university's arrangements, not the other way around. Demand and supply, innit.

(that last comment was slightly tongue-in-cheek, but we are supposed to be so market-aware these days, so ...)

"an applicant would schedule a stop during a trip, at a place with a decent data connection to do the interview". Wow. Assuming you actually want the place, that's a big chunk of your future to gamble on getting the wifi to work at some roadside cafe somewhere. Of course the same can be said wherever you plan to be for the interview. There's non-zero chance of your internet connection going down and ruining your life.

@EnergyNumbers: "Why should they?" -- for the same reason you don't cut down a large number of applicants just by randomly throwing half the applications in the bin? Because you want to select for the best candidates, not for the least busy? Of course if your program is that good you might not care about losing a few applicants who might be great but probably aren't. But clearly Pete finds it slightly surprising they don't care.

@SteveJessop exactly: our programme is that good. And for exceptional candidates, exceptions are made. For unexceptional candidates, they're not, because there's only 48 hours in the day.


text:
Design of "Members Page" for Academic Lab Website?
I am a Computational Biologist as part of an academic lab group working on the Immunogenomics of disease vectors (which may be relevant to the following).
I am designing part of a web-page that showcases the members of the group by:

Two portrait photographs
A personal statement (50 words)
Summary of their work (50 words)
Fun group photographs

Questions

What are the "Do"s and "Don't"s in designing a members page of a group such as ours?
Do you know of any exemplar members pages or group websites?

A template in wordpress so far: http://www.vigilab.org/

For each member: Name, one photo, link to personal web page. Let them do the rest.

All I know is what I want to see when I visit an academic's member page:

Their name and a picture (to confirm it's them)
Contact details
Their rank and position
How long they have been working in the group
A full list of publications with links to full-texts and a good .bib entry
A short bio / summary of work, including service and awards
Some teaching information (if applicable)
Supervision details (if applicable: whom they're supervising or they've supervised)
Project information (which projects are they funded from/P.I. of, etc.)

Keep it professional, clean and brief.
You may want to list details like publications on a separate linked page if they are too long/cumbersome.

All that's really necessary is their name, complete list of publications (with links to free full text), contact info (phone, email, and physical mail), and a link to a complete CV.

@JeffE: Indicating one's position is helpful, and a one-sentence summary of the projects one is involved with would also be beneficial. Not absolutely necessary, but definitely helpful.

Agreed. A good, recent photograph is a must, available in a decent resolution - I'd say at least 800px vertically. Also, a full name, with full middle name(s) if any. If a name change ever occurred (marriage, etc.), it should be included too, even if just to allow me to look up someone's undergrad thesis/papers. Donald Ervin Knuth got it right: doing anything less makes life unnecessarily hard for people who do research.

Designing a group web page is easy (and fun). Maintaining a group web page is hard and boring. As a consequence, most web pages (and parts of mine right now sadly) are old and out of date.
The only real solution is to keep as little information on this group page as possible, and decentralize most updates to the person whose information it actually is (and presumably who cares the most)
This is why @JeffE's statement is relevant. That information is mostly fixed, and points to where the real information is.
So unless you plan to maintain this page as a full time job (in addition to your other work), put as little information on it as is necessary. Having no web page is much better than having a web page with incomplete information and stale links.

In terms of exemplar websites, I like the style of the Ketterson Lab group, who have very basic info on their site that includes a link out to the lab members' websites--where more up-to-date info is the responsibility of the lab members.
http://www.indiana.edu/~kettlab/people.html


text:
sending good/bad rec letter without waiving my rights
Would a professor send a recommendation letter whether good or bad to the grad university or the research summer program I am applying to without my permission? if she did not like me in her lab for example, and I did not ask for her recommendation letter after I left the lab, is she allowed to send a warning to the university of the program I am applying to? I will be having other 3 good/strong recommendation letters that I have given my consent for the profs to write. I will not give my consent to her, so is it possible that she might still warn the university? or is it not possible? If so, will the university take her opinion or will refuse it since i did not waive my rights to her?

Some countries (e.g. the US) have privacy laws that would generally forbid the professor from sending a recommendation without your consent.  Or, at the very least, such a letter could not contain anything that would constitute an "educational record", which would apply to anything of substance the professor could say about your studies.

In my recent (last 10-15 years') experience, in the U.S., in mathematics, there would simply be no way for anyone to inject an unsolicited letter into your application file.
The way it works nowadays is that you list the people whose letters will support you, and they are contacted by email, with passwords, etc., to get into the relatively secure application system, and give their comments.
A person not invited by you has no good entry into the system.
Yes, they could email faculty at the other university and say negative things about you... But they could not create a "bad recommendation letter".
And, if I received a negative email about an applicant, from someone I didn't know, I would be inclined to think that they (a) did not understand how things work, and, (b) had some sort of irrational grudge...
Even if I got an email from a person I know and trust, saying negative things about an applicant, I would be (negatively) surprised that they were trying to achieve an effect outside the standard channels.

I'll focus on "bad" letters and communications.
This might depend on the country's (or other political entity) laws and regulations, but it would be highly unethical for a professor to independently subvert the application of a student. Such things as student misconduct (if that is alleged), when important, are handled within the university and (one hopes) appropriate action taken there, and settled.
It would probably also be improper for the receiving university to consider it and the processes don't normally allow such things. But it is impossible to say what sorts of communication flows between colleagues at different institutions.
It would be, in my opinion and US perspective, grounds for tenure revocation or, at least, a reprimand. It would also take an especially vindictive person to do such a thing.
I think the risk of this happening is small.

Do you mean the risk that the professor might take to send a bad rec letter without consent? like the probability that this happen is small?

Edited to clarify.


text:
Telling my professor about another professor who accused me of cheating
One of my professors accused me of cheating because it appeared to them that I opened a link on moodle. I did, but did not look at what was open. It was opened by mistake as my laptop was lagging. I tried to talk with him, but he still insisted on accusing me. I asked him to repeat the exam in front of him if that would help, but he refused. In the end, I am very sad about what happened and I went to one of my other professors to ask for advice about what to do. I do not know if that was right or wrong. I did not cheat, but I am afraid that my other professor will not trust me and might even hate me. Did I do the right thing?

The link opened itself, by accident? Well, I wouldn't believe that either.

In many cases relating to examination rules it is possible to detect a breach of the rule but it is difficult to say whether the breach was accidental or was done intentionally, with a view to gaining an advantage in the exam.  In the case you describe, it sounds like you are indeed in breach of the exam rules, insofar as you had unauthorised material available during the exam.  So no, what you have done is not right --- the right thing would have been to take proper care in clearing your browser of other tabs and clearing your environment of any other unauthorised material when setting up for the online exam.  Having failed to do this puts you in breach of the rules whether it was accidental or deliberate, though obviously the latter is worse.
A more sober professor would simply explain to you that you are in breach of examination rules, without speculating as to intention (or characterising it as "cheating"), and would then implement the relevant disciplinary procedure for breaches in a dispassionate manner.  Sometimes professors get cranky about such things, and he has probably seen many genuine attempts to cheat before, so in this case it looks like he's also sceptical of your explanation and he has given you a dressing down about the matter.  I also find your explanation strange and not fully forthright --- you initially characterise things by saying that "it appeared to [the professor]" that you had an unauthorised tab open, but then you concede that this is true.  So why characterise this professor's observation as a mere "appearance" rather than just saying that he saw the unauthorised tab?  In any case, all you can really do here is wait to see whether this professor implements the disciplinary system to report you for a breach, or decides not to.  If there is action to discipline you over the matter then you will have an opportunity to put in your explanation of events and that evidence will be taken into consideration.
As to explaining this to another professor for purposes of getting advice, all you can do is explain what happened.  If this is your first breach of rules then it is likely that people will give you the benefit of the doubt that it was not intentional.  (They might get sceptical if it happens again.)  Remain calm and put the matter in perspective, and bear in mind that academics deal with matters like this with sufficient regularity that they are fairly routine.  I've had students breach rules in my courses before (probably intentionally in some cases), and I don't hate ---or even mildly dislike--- any of them.

you initially characterise things by saying that "it appeared to [the professor]" -- This could be an ESL issue in which the idiomatic meaning was not intended. Unfortunately, arguments by defendants also often use verbiage for rhetoric purposes to minimize fault . . .

If all you mean by "is what i have done right?" is going to the other professor for advice and counsel, then, yes, you did the right thing there.
Getting advice from a trusted professor is always valuable. You didn't have to do that, potentially exploring your earlier breach of the rules, intentional or not.
I doubt that the other professor would think poorly of you for approaching them unless you took it to them as a complaint against the first professor.
I can't offer advice, though, on your relationship with the first professor. You may suffer for it, whether justly or not. But you need to be more careful about the rules in the future, as I'm sure you realize.


text:
Is conferenceindex.org a reputable source?
https://conferenceindex.org/
Is this a reputable website or a scam/predatory conference collection?

What does "authentic website" mean ? How can a website not be a website ?

This is the second question today that uses this terminology. I feel this is some "lost in translation" issue

I searched for a few good theoretical computer science conferences on that website, none of them were listed. On the other hand, the stuff they do list for computer science looks a lot like the conferences advertised via spam emails. While I can't rule out some decent conferences to be listed there, I do feel confident that being listed on this website is not at all an indication for the quality of the conference.


text:
If someone gets a PhD in Israel, can he work in the universities in Muslim-majority countries?
Are Israeli degrees recognized in Muslim-majority countries?
If someone gets a Ph.D. in Israel, can they work in universities in Muslim-majority countries?
Edit:
I give you 3 names so that you can focus on the answer:

Saudi Arabia
Pakistan
Malaysia

I think some countries prohibit people from entering their countries who entered Israel.

I think the answer would be yes, but I also think that any non-national should be very wary if they don't completely understand local custom. And not all Muslim-majority nations are tolerant of anyone breaking norms. But it isn't about religion or ethnicity. Also, a religious person would find it very difficult to practice in some places.

@Buffy, Many countries won't allow you entry if you so much as have an Israel stamp in your passport, so I suspect that declaring an Israeli degree would be a lot more serious than you think. See: https://www.highheelsandabackpack.com/understanding-the-israeli-passport-stamp-restrictions/#So_Which_Countries_Do_Not_Allow_Access_With_an_Israeli_Passport_Stamp

17% of Israelis are Muslims.  49% of Israeli Jews are secular.  The statement that "a religious person would find it very difficult to practice in some places." does not seem particularly specific to moving from Israel to a Muslim country.  Imagine being a Muslim trying to find Halal food in rural America, or Jew trying to find Kosher food in rural America.

@RayButterworth Israel stopped issuing passport stamps many years ago. They now issue a separate piece of paper that you keep with you, until you depart the country.

@Gimelist, I know that one can get the stamp on a removable page to avoid the problem.  The point is, if Iran officially refuses entry simply because you have visited Israel, they certainly aren't going to say "You spent several years in Israel getting your degree, but you didn't actually visit Israel, so come on in.".

I've always wondered about these kinds of questions. Similarly, are Taiwanese degrees unrecognized in the PRC and vice versa? Similarly, if I get a PhD in Crimea, am I going to have a great deal of difficulty getting a postdoc in Kiev or are universities there pretty much live-and-let-live?

Similarly, how are citations to Israeli books and journals typically done in countries that boycott Israel? Are scholars expected to change "Israeli Journal of Advanced Advances in Amazing Stuff" to "Occupied State of Palestine Journal of Advanced Advances in Amazing Stuff" or is academia above such political statements?

This question is vague and poorly written.  It would be a lot more clear if it said “countries that ban travel from Israel” instead of “Muslim-majority.”

Echoing/reiterating @NoahSnyder's comment: this surely isn't really/literally about "Muslim-majority" countries, but about "countries that do not recognize Israel as a legitimate state".

Conversely if this is a concrete question about one country, ask about that country.  There’s no reason to expect that an answer for one of those countries is the same as the others. (Malaysia allows Israeli stamps, Saudi Arabia is in the middle of rapprochement with Israel).

Your question confuses two things: 1. passports 2. the degree itself. You do not need to be physically present in a country to get a degree from a university there, particularly during pandemic times. You also may update your passport or have it re-issued at any point, therefore removing any physical signs on it of having entered Israel. Many Muslim countries do joint research with Israel in respect to academia. The only places this may be an issue is where there are severe ongoing hostilities such as Iran (although even they had join research at a time).

"Islamic-majority countries" are a fairly heterogenous group and the answer is unlikely to be the same across all of them.
Turkey and Albania, both Islamic-majority countries, are signatory to the Lisbon Recognition Convention which would seem to imply a default recognition of Israeli degrees.

And there are certainly examples of people who got their PhD in Israel (e.g. Tel Aviv), and then a university job in Turkey.

Kazakhstan, Tajikistan, and Kyrgyzstan, also are Muslim majority signatories.

@NoahSnyder: That is not correct. These are majority secular countries with  large Russian part of population.

@MarkSapir: Kazakhstan used to have a Russian majority, but hasn’t since shortly after the end of the Soviet era.  They all have clear Muslim majorities according to recent census results.  They may well be “more secular” than Muslims in some other countries, but they do identify as Muslim.  (Also while I’m at it, Bosnia’s at a hair over 50%.)

I believe that for the countries you mention, the answer would be no. (To the best of my knowledge,) These countries do not allow people whose passport is stamped with an Israeli stamp to enter their country (check, e.g., here). I believe studying in Israel would be a red flag that would not to be overlooked by these countries.
However, other (Muslim/Arab) countries have peace-agreements with Israel, e.g., Jordan, Egypt, and UAE. I know of some academic relations between Israeli universities and UAE universities and I believe student exchange between these two countries are only a matter of time. Also, countries relationships do evolve and peace agreements might extend to many other countries in the short/long term, possibly including Saudi-Arabia and others (I'm less optimistic about Pakistan or Iran, but who knows).
To the best of my knowledge, students from any country are very welcomed in Israeli universities. However, getting the legal permissions (VISA, etc.) and going back to the home-countries might be a big issue. (I heard of people who arrive into Israel without official papers, e.g., with a "travel authorization" instead of a passport, but these cases are very rare).

I do not see the relevance of the passport stamp rule; countries that do not let people with an Israeli stamp in know that Israel does not require visitors to get a stamp.  This is a deliberate loophole.

@AnonymousPhysicist This loophole can be used as long as the officials have a graceful way to look to the other direction. As said in my reply, it is my option that staying several years in Israel, and having a PHD from an Israeli institute will be too much to be overlooked.  I don't think previous such cases exist and this is possibly another (weak) indication.

Maybe Muslim majority is not the right classification here. I know that there are visa issues between some Arab majority nations and Israel. A friend couldn't enter an arabic country (maybe Egypt? not sure though) for a business reason because he had an Isreal stamp on his passport. There is some information online about this. (needs fact checking)

While the state of Israel is a member of the United Nations, and has been at peace with both Jordan and Egypt for four decades now (and travel between these three is no problem), several Muslim-majority and Arab nations do not recognize the existence of the state of Israel and deny admission to anybody who is Israeli or shows any evidence of having been to Israel (e.g. visa (stamps) in a passport). On the reverse, travel to Israel with evidence in your passport of travel to one of the countries mentioned below is usually no problem, but you may be selected for especially intense questioning or scrutiny at the border or airport. Source

Since Turkey is mentioned anecdotally perhaps its nuances should be adressed. As far as I am aware, a significant portion of universities in Turkey are public with massive government control over them. Erdogan has been a big critic of Isreal for a long time. Erdogan also is acused with academic purges 1 2 3 4. Mind you that if you look closely these purges were done under a state of emergency and people's jobs were suspended or lost without even a criminal indictment. Time has shown as an overwhelming majority of these suspensions were baseless. Long story short, I can't say with confidence that this would never cause an issue in Turkey.

can you reflect on those 3 specific countries I pointed out?

@user366312 I can't. I would guess it would be less of a problem in Saudi Arabia but other than that I have nothing.


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Peer-review: Reference to unpublished work
Paper I am reviewing
I am reviewing a paper from authors Xs. In their paper, they assume that a function f was equal to g. In my opinion (see below paragraph), the particular choice of the function f can have important impact on the end results. I would note that most people in the field assume that f is equal to g (without good justification for this assumption).
Unpublished work from a colleague
A colleague of mine (let's call him Y) had the idea that depending on the field of application the choice of f might be important. He worked on it and we recently talked about his first results which suggest that he was right; if f equals to h for example, the results of interest might differ. He has not published his work yet.
Issue
I would like to suggest to authors Xs to comment on the potential importance of the f they chose. However, by doing so I would give author Xs the credit of being the firsts to recognize the importance of the choice of f while it is Y who first came up with this idea. I obviously want to avoid that. If the work of Y were published, I would just suggest Xs to cite this work but it is not published.
Should I just remain silent?

It seems highly unethical to disclose the work of Y. If no previous literature questions f=g, I don't see your role as the reviewer to question this. Hold your horses, review this in view of past literature, and wait until the work of Y is public.


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Efficient method to receive alerts for new publications
I am currently using Google Scholar to receive alerts (emails) for new publications in my field. However, to my understanding (I might be wrong) Google Scholar doesn't allow to:

Use regular expression

might very useful for looking at variants (noun, adjective, adverb) of the word of interest

Indicate the field where the matching pattern should be found

author name: if you write the name of an author, you just get all the paper that (s)he publish and all the papers that cite him/her. Also, if the author has a short and common name such as Do then, Google Scholar will basically send tons of articles.
title: If I am looking for a concept that is used in a whole lot of different papers but only few papers really work on it such as the word evolution for example, then it would be useful to be able to ask for publications that contain the word evolution in the title only.
Journal: Well... because we all have our favourite journals.

Use AND and OR statements

Such as for example: Give me all new publications which author is John Smith AND where the word action potential is present in the title OR the article has neurophysiology as a keyword. Something like  author: John Smith AND (title: action potential OR keyword: neurophysiology)

There are probably various algorithms that can be found online that would allow one to receive alerts for new publications. Can you give me recommendations of what (and why) is best to use for receiving alerts?

FYI: My field is evolutionary biology and more precisely theoretical population genetics. I am particularly bothered by the fact that I am working on the concept of robustness in evolutionary developmental biology but the word robustness has meaning in so many different sciences and I just receive tons of alerts that are no relevant to my work.

There are a few things Google Scholar can handle, for example here is a query that can be made into an alert and is similar to what you gave as an example:
author:"John Smith" (intitle:"action potential" OR neurophysiology)
To get all the results from a particular author (with or without articles that cite their work) you can search the author, click on his/her name in one of the results and there will be a "Follow" button on the profile page to get email alerts.
If you click the drop-down in the search box you can fill out the advanced search form to make complicated queries and at the bottom of the search results there is a "create an alert" link, but this option seems to disappear if you specify a journal.
As for using regular expressions, hopefully most of your queries can be solved by using OR, e.g. (color OR colour)

Oh does it work? You just right that in the field called alert query? Are you aware of a help page that explains the notations that scholar understand? Here is the only thing I could find. +1

I found most of this by using the advanced search and looking at the generated query, using some of the google search operators, and reading the about scholar page you linked.

The two large commercial bibliographic services come pretty close:
Web of Science can handle alerts with boolean searching - it couldn't exactly replicate this as it can't search keywords only, however. (It has a generalised "topic" which searches title/abstract/keywords). Leaving off the author element, there's about 1050 results for 2014.
Scopus can run this exact search. It has a somewhat broader scope than Web of Science - so 1930 hits for 2014.
Both are, unfortunately, (expensive) subscription services. But your institution may well pay for them ...

edit - UBC does indeed pay for Web of Science, so give it a shot and see if you like it! You probably want, in advanced search, something like TI=(action potential) OR TS=(neurophysiology)

Thanks a lot for your help. Yes, indeed UBC pays for WebOfKnowledge (thks for making your answer so specific to my needs). I thought we could not receive alerts from WebOfKnowledge but seeking a bit more I see that it actually works (click on My Tools) +1. However, I think we can only receive alerts for selected papers that get cited but not for papers that match some pattern. Or can we?

You can get alerts on saved searches, but only (for some reason) if the search is on a specific WoK database rather than "all databases". Run your search on 'Web of Science Core Collection', then at the left you'll have a bell icon and "Create Alert". This then runs either monthly or weekly.

One caveat to be aware of: WoK only includes papers when they're finally & formally 'published', so it won't pick up any which are "early online", "in press" etc on the journal website. Given that some journals, naming no names, can leave things "in press" for more than a year when waiting for a special issue, this may produce odd gaps...


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Best practices for organizing digital and physical articles
As a thirsty graduate student, I've amassed a burgeoning collection of research articles in both paper and digital formats. Right now I manage PDFs and references with Zotero, but I'm still searching for an organization logic for paper documents that allows rapid access and prevents redundant printing and storage. Some have suggested organizing by topic, while another approach is to sort by author name. Topical organization has not worked well for me in the past because my research is highly interdisciplinary, confounding my categorization efforts. For a coupled digital-physical organization system I'm considering the following:

Digital documents and references stored and tagged in Zotero
Indicator in Zotero whether or not I've printed in the file
Physical documents stored in manila file folders labelled alphabetically

What is the most effective way that you've found to maintain both paper and digital document repositories?

Scan them, recycle the paper, and then use Zotero.  Print only when you have to.

For the digital part, see also this question.

I use essentially the system you suggest (with Bibdesk instead of Zotero and I don't take the time to indicate whether I've printed the file).

Related for tagging documents in your bibliography, How do I effectively use tags to organize my bibliography?

I have them organized similarly to the blog post you linked. I'm not sure it is the optimal way, but it works quite well.

The central search key for me is (First)AuthorYEAR. By now I know my way around in my field so that the author names are meaningful. And easier to remember exactly than title abbreviations.
I try to have almost all papers also digitally, and organize them with jabref. I started using jabref before Mendeley, Zotero & Co came up and didn't change.
jabref allows to assign the papers to topics/groups, which can be hierarchically organized, but a paper can also belong to several of them.
This is important for me, because one paper may be about an application (e.g. tumor diagnostics -> group with tumour or cell type), use specific measurement technique (group that), and maybe use or invent an interesting data analysis technique (group there).
Jabref stores its information in a .bib file (with a few non-standard fields and some more info in comments at the end). But essentially I can work with this file as with any other .bib file.
.bib and digital versions are in a git repo which basically solved the mess of having lots of copies that go out of sync while I'm still able to work completely offline. As .bib is a text format, version control works fine with that. Papers usually do not change, so it doesn't really matter for the version control that they are binary data.
When looking for a paper, I usually search for it in jabref, and then look whether I do have a printed copy (I'm too lazy to keep track of printed status).
physical copies I keep in two drawers with a suspension filing system. One has collections of important papers on topics I'm interested in. The other keeps other physical copies alphabetically by author name (one folder for each letter so far, some will be split soon).
I tried before with normal lever arch files, but was too lazy to put papers away into their proper place.
For a while I had the luxury of working with dual monitors. During that time I printed considerably less papers. Now I have to work with only a single (and not too big) monitor again, and again print most papers.

I always store the references in zotero before printing them. I don't print all of the references, therefore I always use zotero to find the references before searching for the printed paper.
In this context what I did is:

When I print the paper I write in one corner the date and time when it was added to zotero (always the same corner).
When I search for a paper I check that identifier (date-time) and perform binary search on the big pile of printed papers.

I only print papers that are very complex on formulas, though. This could not scale well for hundreds of papers, but it's a handy identifier. One advantage is that papers are usually added to one side of the pile, so old papers can be stored somewhere and I don't use to need to insert a new paper between old papers, if you use folders (or similar) some of them could overflow by doing that.

I always create a collection in Zotero for each of my projects and papers. That places a paper into a proper context. As was already mentioned above, the nice option of Zotero (and jabref) is that you may put a bibliographic record into infinite number of collections.

I hope, you know of and use zotfile and better bibtex extensions for Zotero. Zotfile makes sure the PDFs are stored and named properly; and better bibtex creates a .bib file for your library, just like jabref (that happens to be useful dealing with TeX).


text:
Am I allowed to share a final copy of my published paper privately?
Suppose I published a paper in a journal with no open-access policy, but with the usual constraints regarding copyright.
A researcher that I do not know in person has asked me for a copy of a this paper I coauthored. Am I allowed to share the final-version PDF file with them (by e-mail)?  I mean,  does it make any difference with sharing it publicly (which I do know I am not allowed to)?
If not, what would be a polite way to tell them so?

Am I allowed to share the final-version PDF file with him/her (by e-mail)?

From a (US) legal perspective, that depends entirely on the publishing agreement. Some journals do allow this; if so, it will be stated explicitly in the agreement. For example, the APS copyright transfer agreement includes the text

The author(s)...shall have the following rights (the “Author Rights”):
3. The right...to make copies of all or part of the Article, including the APS-prepared version without revision or modification, for the author(s)’ and/or the employer’s use for educational or research purposes.

Without something like this in the agreement, whether you're allowed to share the paper depends on whether it can legally be considered fair use. No copyright agreement can prohibit something which falls under fair use, but on the other hand you don't really know what falls under fair use until a court tells you. I'm not sure if there's any precedent on whether sharing copies of an article for private research use qualifies as fair.
I won't address this from a moral perspective since you asked whether it's allowed, but as some of the other answers show, it's possible to reach a different conclusion that way.

I mean, does it make any difference with sharing it publicly (which I do know I am not allowed to)?

Well, this also depends on the publishing agreement. By default, if the agreement doesn't say anything otherwise, there is no difference between sharing the article publicly and sharing it privately; both qualify as unauthorized distribution, and both are similarly illegal. But the publishing agreement may allow for some forms of public sharing. Going back to the APS agreement, it includes several clauses allowing various forms of public sharing (under "Authors' Rights"):

2. The nonexclusive right, after publication by APS, to give permission to third parties to republish print versions of the Article or a translation thereof, or excerpts therefrom, without obtaining permission from APS, provided the APS-prepared version is not used for this purpose, the Article is not republished in another journal, and the third party does not charge a fee. If the APS version is used, or the third party republishes in a publication or product charging a fee for use, permission from APS must be obtained.
3. The right to use all or part of the Article, including the APS-prepared version without revision or modification, on the author(s)’ web home page or employer’s website and to make copies of all or part of the Article, including the APS-prepared version without revision or modification, for the author(s)’ and/or the employer’s use for educational or research purposes.
4. The right to post and update the Article on free-access e-print servers as long as files prepared and/or formatted by APS or its vendors are not used for that purpose. Any such posting made or updated after acceptance of the Article for publication shall include a link to the online abstract in the APS journal or to the entry page of the journal. If the author wishes the APS-prepared version to be used for an online posting other than on the author(s)’ or employer’s website, APS permission is required; if permission is granted, APS will provide the Article as it was published in the journal, and use will be subject to APS terms and conditions.

So under this agreement, you (the author) can post the final journal version of the article on your own personal website, and you can post preprints (i.e. versions you prepared prior to submitting to the journal) on a site like arXiv or grant permission to third parties to distribute these versions.

I believe that it is a moral obligation of scientists to make their work available to colleagues, except when larger considerations such as safety intervene.  Most publication agreements allow for some form of sharing, even if only a preprint---you might or might not be able to post it for free online, but you can at least share via email.  There's a decent fair use argument for it as well, which is likely to cover ambiguous agreements.
I also believe that if you discover that a publication agreement explicitly prohibits sharing a pre-print via email, then it is appropriate and ethical to commit civil disobedience and share a pre-print of the article.  I believe this because I think that a publication agreement that prohibits individual exchange of pre-print scientific documents is itself unethical.  Don't share the final version, though: the moral obligation of scientific openness is served well enough by a pre-print, and the final version does often clearly incorporate real work and value added by the publisher, which you have no moral right to.
Do note, however, that if you choose to share when you are prohibited from doing so, that you should realize that you are committing civil disobedience and that there is a chance (however unlikely) that you may have to take the legal consequences for doing so.

Fantastic answer, but it is inaccurate to refer to "civil disobedience", which is defined by Wikipedia as "the active, professed refusal to obey certain laws, demands, and commands of a government, or of an occupying international power." I understand you are advocating a kind of rebellion against "the system", which is conceptually kind of similar, but calling it civil disobedience makes this act sound both more glamorous and more far-reaching than the (at worst) microscopic copyright infringement that it actually is.

@DanRomik Please read the article you link more carefully, and you will note that the definition is not quite so clear-cut, and some definitions cover the type of action I'm recommending as well.  Note also that I make no claim that the action is not microscopic, only that it is a reasonable choice.

@jakebeal okay, I concede that some people are interpreting "civil disobedience" to include actions taken against corporations. It still seems like a strange use of the term to me, and I wish there was a better term to describe this sort of thing. I completely agree with your answer aside from this minor semantic quibble

-1 Honestly, if you sell your copyright of the preprint version as well then it's no microscopic copyright infringement when you share the paper with colleagues. If anything is unethical (I don't think so) it's not such a prohibition or the company asking for such a thing, but a scientist deciding to sell his copyright under such terms. Like honestly, as the author and a scientist you're the one who decides where you publish and once you decide you should just abide by the terms of your agreement.

IEEE says you are allowed to publish the article on your personal website. Looks like it depends on the publisher.

@DavidMulder Given that there is a near-monopoly of certain companies (exacerbated by several recent mergers) on high-esteem journals in certain topics, the choices to publish away from them are limited. "Selling copyright" is not a life-and-death duress situation, but there is an element of lack of options which is out of the control of the individual scientist. Publication is a very lucrative market where the public pays for the work of research, writing, reviewing, and then also has to pay for accessing the work paid for by the public. It's not quite a balanced agreement, is it?

In the old days, one received 25 or 50 paper reprints gratis, and could order more, each time one published a paper. These would be sent out in response to requests such as the one you describe.
These days, I believe some publishers have provisions for the same kind of on-request personal sharing of single copies of a paper. I'm sure this varies from publisher to publisher, however.
I also suspect that there may be a strong fair use argument for sharing a final pdf upon request but I do not have the legal expertise to say for certain.
Finally, I'll note that many, many researchers post final pdfs of their work openly on the web. Irrespective of whether you support this (as I do) or consider it unethical, if the publishers are unwilling to target these people they will certainly not be interested in someone who privately emails a pdf of his or her own work to a colleague upon request.

There are publishers (e.g. IOP) which, still nowadays, send free offprints of published papers.

It could easily be a violation of the publishing agreement you signed unless it specifically outlines how you might share the article (which many agreements do). You are unlikely to get hauled into court by your publisher unless you or whoever you send it to informs them of your transgression and you refuse to correct it. That being said, it's unethical in my opinion to purposefully violate your publishing agreement (which is a contract that you signed), so I wouldn't advocate it. Reread it, and follow its terms.

You are unlikely to get hauled into court by your publisher unless you or whoever you send it to informs them of your transgression. - Even then I would be very surprised if the publisher actually sued. In general, I expect that they have more to lose by alienating authors than they gain from single-article sales.

@Mangara, yeah, I thought better of that and softened the language a bit in my edit. I know of no cases where a publisher has sued an author over a violation of the publishing agreement of a scientific journal article. There are other cases where a publisher has sued authors over failing to deliver promised manuscripts after having been given an advance, but that's almost standard publishing fare.

I strongly disagree re: "unethical". It's not unethical to violate an "agreement" that you're basically compelled into accepting as part of participating in academic research. Things would be different if this were an agreement you specifically negotiated with the publisher where it was your choice to relinquish your moral right to share your research for specific financial benefits, but everyone knows that's not how it actually works.

@R.., I clearly disagree. I don't like our current publishing model and question much of its ethical boundaries and parameters, but signing a legal contract with the intention of violating it is definitely unethical in my book. If we all say that violating a contract because you don't like its terms is ethical because OP (or yourself or myself) was compelled to sign up for it in the first place, I think that's a bit disingenuous. Yes we all want to publish in the best journals which are run by big corps that treat us badly, but we do have the choice not to publish with them.

Most academics are not sufficiently prestigious to have a genuine choice which journals they publish in. The "choice" is just "agree" to despicable terms or abandon their careers.

@R.., lots of people signed up for the Elsevier boycott, though I can't tell what's become of that. What might matter more would be if departments and their tenure committees would come out and say that they weren't counting certain journals published by the publishers with the worst policies any more than the lower tier ones. Some high-powered people resigning from editorial boards (e.g. Topology) might also do some good. A bunch of tenure track profs boycotting the best journals isn't going to do much, I agree.

@BillBarth I find the ethical (rather than legalistic) argument problematic, they should not be equated. If indenture were legal, does it make unethical to battle it? High-profile publications are critical for esp. young scientists, and the large publishers have a very powerful stake in it. I would have agreed with your argument had you stayed on the legalistic level. I strongly disagree with the ethical argument. The public pays for almost everything in an article except the final edit and the availability. How is it ethical to demand extortionate fees for the public to see an article?

@BillBarth I might revise my opinion if an article would just cost 2-3 dollars, but paying ten times as much for something paid, developed, written and reviewed by the scientific public, and I may not even end up using, that's inappropriate. I would not even bring up ethics here, it's just not the right category to discuss this in.


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What are 'Article Influence' and 'CNCI' and how to obtain them?
I've been asked about my Article Influence and my Category Normalized Citation Impact (CNCI). I have several doubts regarding this:

Are they metrics that can be calculated for each article, or, on the contrary, do they refer to a single value per each researcher?

I haven't been able to determine what the 'Article Influence' actually refers to, or how to calculate it. Any clue?

Regarding the CNCI, I have found out that it is calculated and published by Clarivate (specifically, in InCites). But, as far as I have been able to understand, there is NOT a CNCI for each article published by a researcher, but a CNCI for each category in which a certain author has published some work (in a certain period of time); and a global CNCI can also be calculated for a researcher (in a certain period of time). Is that so?

Does Article Influence Score refer to this? If so, it's a score calculated for journals and what you were asked seems akin to being asked about your individual impact factor. Perhaps it would be best to ask for clarification.

There is some info on article influence https://incites.help.clarivate.com/Content/Indicators-Handbook/ih-article-influence.htm and eigenfactor https://incites.help.clarivate.com/Content/Indicators-Handbook/ih-eigenfactor.htm?Highlight=eigenfactor, but both are only a metric on journal level, not for single articles, so I am unsure how that would matter for a person.

this might be usefull: https://mylibrary.sutd.edu.sg/sites/default/files/Research%20Guides/CNCI_SOP_20210218.pdf