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In-line APA reference for webpage from an institution
Insofar as I can see the following is a valid APA reference to a website I'm referencing in a school paper:

American Academy of Pediatrics. (2021, October 19). Aap-AACAP-Cha Declaration of a national emergency in child and Adolescent Mental Health. https://www.aap.org/en/advocacy/child-and-adolescent-healthy-mental-development/aap-aacap-cha-declaration-of-a-national-emergency-in-child-and-adolescent-mental-health

When referencing this inline should I write "(American Academy of Pediatrics, 2021)", or could I write "(AAP, 2021)", since AAP is a well-known acronym for that organization? The first option seems a bit ... wordy ...

This is what APA says:

If the group name first appears in a narrative citation, include the abbreviation before the year in parentheses, separated with a comma.

The American Psychological Association (APA, 2017) provided information on overcoming opioid abuse.

If the group name first appears in a parenthetical citation, include the abbreviation in square brackets, followed by a comma and the year.

People can overcome opioid abuse through residential treatment (American Psychological Association [APA], 2017).

In other words, use (American Academy of Pediatrics [AAP], 20xx) on first reference, and (AAP, 20xx) thereafter.


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What's the best way to inform a supervisor of collaboration on papers with a different professor?
A professor in the same department has asked my friend to collaborate with him in writing a paper which is close to his area of research. My friend is not sure what to tell the professor since he is afraid that his supervisor will not be happy that he is publishing papers without letting him know or without adding his name.
Should he ignore the invitation of this professor or let his supervisor know about this? What should he do in this situation?

What is keeping him from asking his supervisor about this? Easiest way to find the supervisor's opinion...

Do the faculty in your friend's department not talk to each other? The idea of a PI inviting a student to collaborate with them without any discussion with the student's PI seems utterly bizarre to me.

@MJeffryes: I have written several papers with graduate students in my department who are not my PhD students.  In no case did I ask the student's advisor (if they had an advisor at the time, which some but not all of them did) first.  So something which seems utterly bizarre to you seems pretty routine to me...

...  I will comment that most of these collaborations took place in the context of a course I was teaching; the exception started with a problem proposed in an email sent to my entire department, and the student was the one who answered it.  Whenever I thought that a project with a student would take a substantial portion of their research time I did encourage them to talk to their advisor about it...and in most cases the student decided not to pursue the project further.

In some cases, a supervisor will be happy to have a student work on independent projects as well.  In other cases, the supervisor will be happy for the project to happen but want to be involved themselves as well.  In yet other cases, the supervisor will feel the project is a distraction or problematic for some other reason and strongly advise the student not to take part in it.
Which case you are dealing with depends critically on the details of the people and projects involved, and the best thing to do is for the student and supervisor to talk.  Don't make it a big scary deal, just let the supervisor know about the opportunity, say you're interested, and ask what their opinion is.

Your friend should consult his supervisior for sure, explain situation and ask him to work on that paper as a side project. There is no reason for supervisor/mentor to have bad reaction to this. On the other hand, paper is public thing, if he goes behind his back sooner or later his supervisor will find out and that will seriously affect their relationship.

Your friend should consult with his supervisor for sure, this seems like a pretty trivial matter to me.
Just make sure the friend wants to do this themselves, and isn't just being pressured or motivated just because some professor asked them too. I mention this because a student afraid to mention something so trivial to a PI might be one who thinks they have to say "yes" to anything someone with a PhD tells them.
If your friend wants to do this then he should tell his PI. I'd tend towards informing the PI what you plan on doing, and asking what they think rather than asking permission. You do not, and should not, need permission from anyone to write a paper about whatever you want, especially if they're not really involved.
If the PI is very against this, for some reason, then your friend should feel free to try and be persuasive. Sure, it's going to take some time, but if it's not going to tank his primary research then he should do it. Having more publications is very much in his interest, even if it's not in his PI's interest. Many grad students are too timid with their PIs. They forget that they have rights as students/scholars/employees, and often PIs will give you their opinion expecting you to push back if you disagree, and timid people won't. In fact, students who do the latter will often find their PI confused when this kind of thing is discussed. For example:
PI: "Do this by Friday."
Student: "It will take longer than that."
PI: "Oh ok next week then."
If the PI commands this student "YOU MAY NOT WRITE THIS PAPER." Then he should consider getting a new PI (if possible) because this one is terrible. If he doesn't want to do that, then consider just doing it anyway or not doing it.
I have found that many times when a PI tells you "Don't waste your time on that" and you do it anyways, they often won't seem to remember they told you not to, plus if it ends up being useful they'll be happy you did it. I often did things I was told to not waste my time on. If it turned out being a waste of time, they never found out about it, and if it didn't he'd often just remember it as his idea anyway.

In an ideal world, research collaborations with others would be none of his advisor's business. As long as your friend does not neglect his responsibilities that pertain to his thesis work, there should be no reason for his advisor to even care, maybe except for appreciating that they have a prolific student. As for adding his name, the advisor should certainly not get credit for work that he did not contribute to.
In the real world, things are more complicated. The answer, more than anything else, will most certainly be determined by his advisor's personal preferences. Some professors will be happy that their advisee is pursuing research on their own time, and some will be very upset. Your friend himself is probably in the best position to know the answer in this specific case. That said, most disciplines have conventions around matters of credit and authorship, which may influence the advisor's outlook. My understanding is that when the advisor is responsible for providing facilities (lab, office, equipment...) to their students, they will justifiably expect to receive credit for the work done by the student, even when they are not directly involved. If your friend is using resources provided by their advisor for this project in any way, he should definitely not act without consulting them. A similar code may apply if the work relates to a method etc. that the advisor is known for. Otherwise it is almost entirely a matter of personal preferences.
In addition, (as a commenter points out) it is interesting that the professor has come to the advisee rather than the advisor with the invitation. In a situation like this, most professors I know would ask the advisor if they could 'borrow' the student first.

"In a situation like this, most professors I know would ask the advisor if they could 'borrow' the student first." Students are not "owned" by their advisors.  In my opinion, an advisor who objects to a side project the student is doing on his own time with none of the advisor's resources is being completely unreasonable.  When dealing with colleagues, I try to assume that they will be at least somewhat reasonable unless I have a good reason to think otherwise.  If a colleague approached me in this way, I would say: "It sounds interesting, but you should really take it up with [the student]."

@PeteL.Clark In certain countries a PhD student is considered an employee: so, it might not be "owned" by their advisor, but, like any other workplace, the employer has all the rights to tell what the student can do or not. And, at least, the advisor should be informed. And even where the student is not considered an employee, the advisor might be the one who secured the student's funding.

@Massimo: What they can do in the workplace, perhaps.  But not what extra work they want to do on their own time!  (By the way, I am certainly considered an employee by my university.  I would be outraged if anyone at my university told me "You can't work on this...")  I think it is probably a good idea for the student to discuss it with their advisor...because that's what their advisor is for.  I don't think this discussion should be about permission, but whether it's in the student's best interests.

@PeteL.Clark Certain students work on projects that might have tight deadlines, especially in countries where the duration of the PhD is not as flexible as in the US: if a student underestimates the time or the commitment needed for a side project, and then they are too tired to fully work at their main project and miss the main deadlines, as advisor, I could get angry. And the programme committee might ask at the end of the year: why this student didn't make sufficient progress on his project during this year? Should we admit them to the next year or should we fail them?

So, yes, I want to be informed of any side project: it doesn't mean that I intend to forbid the participation of the student to a side project, but I want to know what will be the impact on their main project.

@Massimo: I don't disagree with anything you said, but your worries about a student badly allocating their time are certainly something to discuss with the student, not with the other faculty member.  On the other hand, if a student is sure that she can complete a modest project without it interfering with her main project, and if she is right about that: no problem.  So it is most often the case that asking your supervisor is the right idea, but...there are some capable, independent students out there, right?

@PeteL.Clark For the first part: yes, sure, I agree. For your last point: uh, well, I wish I could find more of them :-(

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How to convince a journal editor that my paper is not a duplicate?
Recently, I submitted two manuscripts in two different journals. The papers are related, but their contents and purposes are different; and they also made use of different data sets.  One of these manuscripts got accepted for publication, but one of the reviewers for the second manuscript informed the editor the paper was a duplicated paper that he or she recently reviewed.  Evidently, that the same reviewer has reviewed my both manuscripts. However, the editor has asked me to clarify and provide evidence that my paper is not a duplicate. So how should I respond to convince the editor and reviewer that this paper is a legitimately separate work?

did they specifically say that it was the duplicate of your own paper? Otherwise, just do that: highlight the points that are different. However, it might be that the papers are overlapping too much and the second paper doesn't justify to be published as it is or at least in the journal you had submitted it.

Yes, the editor has specified that this is a duplicate of my own paper as per reviewers comment.

Just enumerate in which ways the two papers actually differ. As you already do in your question above: they differ in (i) contents, (ii) purposes, (iii) data sets.
The reviewer may of course still think that these differences are not large enough to warrant a second paper. In that case, you need to reconsider whether you actually think that the second paper can stand alone. But your first step is articulating how you think the two papers are different.

Providing the editor with a copy of the other paper would make the differences very clear.

Indeed! This way the editor can see the differences herself.

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Determining the appropriate research design
I am currently working on my master's thesis. My primary task is to perform qualitative research on the development of a purpose-built software application.
I realise that I am now doing things in a rather backwards fashion, as I have already decided how I will do my research -- now I am trying to find an established research design to back it up.
My research approach is as follows:
I will first do a literature review of the current research in the field and develop a proof-of-concept mockup based on this and my own initial ideas. I will then conduct interviews (5 or so) with professionals from the field, and improve the mockup. Then I will arrange an iterative series (well, only two actually) of workshops with acutal users to determine their impression of the current design and content. The plan is to improve the mockup after each workshop. The final result will be a conceptual design of the software application and perhaps a suggestive software requirements specfication.
I have looked into different research strategies, such as "grounded theory" and "design science", but they both seem to be too time consuming. My time limit is 20 weeks in total.
Are there any developed research strategies that would fit my methodology?

20 weeks for initial mockup building and three iterations of setting up interviews and workshops, getting feedback, analizing it and redoing the mockup, and the summarizing results, sounds awfully short.

Welcome to Academia SE. I am by no far expert on this matter, but your question seems to be only borderline on-topic here, as it is about the content of research (software development) and not about researching itself. I’ll leave that decision to others, but I suggest to consider taking a look at [programmers.se], [pm.se] or even [ux.se] as to whether your question may fit and receive better answers there.

In this instance, I respectfully disagree with @Wrzlprmft's comment. The core of this question is clearly focused on the research design / methodology and, thus, fits the scope of Academia.SE very well. Software development in this case simply represents the context of the applied research.
In regard to the essence of the question, I can offer the following insights and recommendations.

In my opinion, grounded theory (GT) is not a good fit for your study, as GT is typically used for designing general theories, rather than applied ones.
Design science seems like a pretty good fit, so you might read up and consider strategies for compressing research, performed, using this approach, to fit your time frame.
You might also consider other qualitative research designs and approaches, such as content analysis, narrative analysis and others (see more details, for example, at Qualitative Research Guidelines Project).
I would especially recommend you to pay attention to action research, as this research approach seems to fit quite well with your planned study. For more details on action research and other qualitative approaches, as well as likely the most popular qualitative research software ATLAS.ti, see this page.

Finally, I would urge you to pay attention to your terminology, as it might be very confusing not only to potential readers, but to the authors themselves. For example, your phrase "theoretical design of the software application" sounds... quite strange and reduces the clarity of your work and, thus, potentially, can hurt readers' impressions from it. I think that "conceptual design of a software application" sounds and reads much clearer. Hope this helps. Good luck with your thesis!


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How to deal with a nosy fellow graduate student?
There is another graduate student at my school working in the same area as me that is extremely nosy about my work. His curiosity definitely goes beyond the normal amount of "What are you working on?" chit-chat that I have with other graduate students. He frequently asks me to list exactly (his words) which papers I'm reading. If I walk past him in the hallway holding a book or a paper under my arm, he'll (very obviously) contort his neck to see what it is. If I'm working somewhere public, he'll walk up to the table and start reading what I'm working on.
This may sound silly, but I really feel like my privacy is being violated. I think this guy's behavior is creepy and rude. I could never imagine doing any of the things I listed above. What I do with my time is my business and no one else’s, and what other people do with their time is not my business. How can I deal with this guy without appearing unfriendly?
I don't want to appear unfriendly because this other graduate student works in the same area as me and I don't want to burn any bridges. In my very short time in academia, I have also never witnessed anyone acting unfriendly. I have no idea what is appropriate or how to calibrate my response. It is also difficult because the other student is not the same nationality as me, so maybe there are cultural things that I don't understand.
I can't merge my accounts to comment. I am indeed a woman.

Why don't you want to appear unfriendly?

Follow the instructions here to merge your accounts so that you will be able to edit and comment on your post.

What your fellow student does is unfriendly, so you have witnessed it. You can't have your cake and eat it; either you accept rude behavior, or learn to stand up for yourself.

May I ask if you are male? This seems at least a little bit relevant to your question. Sorry if this (ironically) seems like a nosy thing to ask, and of course if you prefer not to answer that's absolutely fine.

@DanRomik I really think that question is inappropriate. The gender of either party should not be relevant to polite work conduct. If a person is uncomfortable with the behaviour of a colleague it should be dealt with fairly irrespective of gender.

I have not had this problem at uni.You can always say MYOB to the offender and if the hint is not taken then start asking nosey questions to put the boot on the other foot.

@FJC: I have only my guesses to go on, but what the asker describes matches exactly how some guys (especially those from western cultures) would go about trying to get the attention of someone they are interested in. If I'm right, the asker should explicitly tell him if she is not interested.

I agree, gender is important because flirtation is implied by the OP, but it is still fairly ambiguous. Also the OP specified the "creeps" gender but not their own. To answer the question, we really need to know if the other student is interested in their studies for academic/professional reasons, or unprofessional reasons.

Also would be pertinent to ask the OP if the other student is from the same cultural background as them.

@FJC of course the behavior "should be dealt with fairly irrespective of gender", I never said or implied anything else. However, precisely how it should be dealt with (and precisely what other advice I will offer OP) may legitimately depend on the genders involved. I can tell you I'm not planning to write two separate answers addressing both scenarios. But as I said, OP is under no obligation to answer. Besides, I hardly think asking such a detail from a person posting anonymously, in an attempt to provide them with the most relevant advice, is inappropriate, but you are free to disagree.

I'm voting to close this question as off-topic because it's about social interactions not specific to academia.

@JJ To be fair, OP specified the "creep"'s gender but not their own because that is how English grammar works. It is complicated to refer to a third person in English without spending several bits of information to specify explicitly which set of genitalia they have.

Possibly he's simply desperate to do something right and feels that imitating you in what you read is his only hope of succeeding.

Confront him head on. Tell him how his behavior is perceived by you. You should also talk to your advisor...this might not be the first time he's done this. OTOH, you could just create fake title/cover pages for papers you print out and carry around to send him into a frenzy when he can't find them anywhere.

Story of my life. I had just produced a table summarizing all the important recent work in my field. Fellow graduate student literally took the table from my desk and copied it without my permission or anything. He has done this before and each time it happened, no credit was given to the source material. He is in the same department as I am under the same supervisor, what can I do?

@StackexchangeHouseNinja Talk to him, if that doesn't help, talk to your supervisors. However, better open your own question here on SE instead of asking in comments of another question. Yours is not a duplicate.

In my experience, when it comes to dealing with people with boundary problems, you have to talk to them (in private).
This isn't nice (it might come off as unfriendly), this isn't fair (you just want to do your work, not deal with this issue), but it's the best course of action -- both for your job satisfaction and (in the long run) for the other person (if he can learn from feedback).
Framing the conversation is going to be difficult -- I'd suggest "I" statements ("I notice that you look at my material ...") and framing the issue as your perception ("I perceive this as nosy. I'd like to talk about my work, but I see this behavior as an intrusion of my privacy."). Given that probably most people would consider his behavior as "nosy", you might even point out that other people might regard this kind of behavior badly too. Hmm, just stick to describing the behavior and avoid making judgments about the person. You can change behavior, you can't (easily) change the person.
(Note: I might be biased here. I recently tried to solve a boundary problem via non-verbal communication, only to notice -- again -- that people with boundary problems don't notice non-verbal cues (correctly or at all). If they did, they would not have crossed boundaries in the first place. So non-verbal "cues" are either overlooked, ignored, or they react in the opposite direction of the desired effect. For example, they notice that a person is distancing himself from them, so they move in even closer. Addressing the issue verbally is anything but easy but I think it's the way to go.)

+1, especially for people with boundary problems don't notice non-verbal cues.

@JeffE from what I hear, sometimes they do and they simply don't care.

@DavidZ That's functionally equivalent to not noticing.

@DavidRicherby the difference is that when you point it out explicitly to someone who didn't notice, they try to change their behavior. When you point it out to someone who noticed but didn't care, they don't change.

This is true everywhere, but especially so in academia: your life dramatically improves when you learn to say "no" to unreasonable requests.  Consider this an opportunity to start learning this important skill.

-1 While I agree 100% with you, the answer doesn't address the question, which restated according to your premise would sound like: how to appropriately say no to unreasonable requests.

+1. I agree 100% with you. The answer pretty much satisfies the question. Simply saying "no" to a question like "can I check out what you're working on" would send a solid message to the nosy fellow.

@ThreeDiag the answer is implied.  When a nosy grad student asks you to list the papers you're reading, exactly what you've had for lunch, or anything else you don't to share, you should (politely) tell him "no."

Implied answer? If you don't handle your cohort with tact, you risk losing a potentially valuable resource that your competition in the field may not have risked. If anything the brevity and offhandedness of this answer implies no tact whatsoever.

@AaronHall I think you are taking it a little too literally. He doesn't mean to literally just say "no". There are ways of saying "no" with tact.

@luke thanks, of course you are right.  Politely saying "no" means saying something like: "Sorry, I don't feel comfortable sharing my work to such detail."  Again, I thought this was implied.  I guess academia.se is the one place where I should be least surprised at being taken too literally :)

@LevReyzin: You might add to your answer that it must be an unconditional no. Not "No, I don't have time right now" or any other excuse. And a consistent no. Excuses just encourage the asker to ask again, trying to overcome the excuses. Lying is worse, if the asker enquires and finds out about the lie. Occassional "Yes" also encourages them to try harder. Just "No".

@Luke: Tact can be counter productive.

@gnasher729 lack of tact can also be counter productive. If, for example, the OP had been rude to this nosy person and yet later wanted to ask them for help then they may be more reluctant to give it. I don't think that potential, hypothetical productivity gains or losses are a good enough reason to not conduct oneself with tact.

You are not being silly; this person is crossing the line and you should feel free to say "no" to his requests.
However, there's often a middle ground between saying "no" (and probably feeling undeservedly guilty about it, because you sound like a considerate person) and letting someone walk all over you. You can try to address the person's underlying needs instead of what they're asking for.
Consider why this person is behaving this way. I can think of two possibilities: (1) he is intimidated by the process of doing a literature search, and is worried that he is missing important papers, or (2) he has no idea what to do for his research, and is hoping to grab one of your ideas. I would go with the first assumption, but bear the second one in mind to be on the safe side.
Next time he asks what you're reading, you might do one or more of these:

Ask if he's having trouble finding appropriate literature. Ask what search terms he's using and suggest a few that you have found useful.
Suggest he request a one-on-one session with the librarian to learn how to do a literature search.
Ask what area he's focussing on in his research and offer to pass along any papers that you think might be of use to him, asking him to do the same for you.
Suggest that he ask his advisor or the PI for suggestions of articles to read.

If he continues to try to leech off of your hard work by asking you to provide him with a reading list, etc., then at least you know you will have done all you can.

Option 3: this person is really bad at social interactions.

@Davidmh my thoughts exactly. Maybe OP can apply Hanlon's Razor here.

I disagree (but not enough to downvote). The OP is under no obligation to address the annoying person's "underlying needs". It may even be imprudent. If the person is seeking unwanted attention or doesn't know how to observe personal borders, helping them out would only encourage more of the same behavior.

It's hard to tell what his motives here are, and other answers have addressed several possibilities already. I just wanted to add my perspective as a fellow woman (FWIW, CS department in US) who's had to deal with awkward peers before. My suggestions, in escalating order:
Avoidance.
This means you doing work to minimize his opportunities for creating uncomfortable situations. Carry your papers in a plain folder so he can't see them, work in your office or with your back against a wall so he can't read over your shoulder. If he corners you in the hallway, make up an excuse to exit the conversation. (I used this one a lot when students would try to keep me after office hours...)
As an example, I have a rather large "personal space" radius, and I realize that's really my problem rather than anyone else's. So my tactic was to position myself across the table, in a single chair rather than bench, etc., to provide a natural barrier without having to ask someone else to change their (reasonable) behavior.
Redirection.
He is acting inappropriately, so make him do the work. Possible motives for his behavior can be categorized as, roughly, real academic interest but poor social skills, or just wants to bother you (for whatever reason).
To handle the first, make him show that he is seriously interested in your work. For example: "What are each of the papers you are reading?" "Right now, X. Say, you seem to be awfully interested in what I'm doing, maybe you should talk to your PI about collaborating with my group?" or "You know, there's a reading group for X, maybe you'd be interested in joining.", etc. This gives him a way to keep up on the research, without you being the unwilling mediator.
For the second, take control of the conversation. When he tries to read over your shoulder, close your laptop lid and say "Can I help you?" (or the milder, "Hey X, what's up."). Throw in an "I'm really swamped right now" to signal that you're not interested in an extended chat. If you're feeling nice, invite him to email you his questions and you'll respond later when you have time. Hopefully he will get the idea. Again, this leaves him an avenue for collaboration, without you getting cornered in a conversation you don't want to have.
Confrontation.
Some people have very poor social skills and do not pick up on hints, verbal or otherwise. If he still doesn't get it, be blunt. It will feel uncomfortable and like you're being terribly rude but... behaviors like craning his neck to see what you're carrying around or reading over your shoulder are rude. (Here's a quick sanity check: do you see other people in your department acting like this? No? Then his cultural background is not an excuse, and he shouldn't be doing it either.) It is okay to be blunt in response, especially if he is ignoring what you think are obvious signals. I think Daniel Wessel's answer has some good advice on what to say if it gets to this point, so I won't repeat it here.

Although I never had to put words to it like that, this is just what I usually do. "Avoidance" may at first seem stupid if you're already angry and have a point to make, but in the end, what you want is studying in peace, and avoidance is most efficient in that regard. I had to learn this bit myself, but it's proven valuable for me. Also, Hanlon's Razor http://academia.stackexchange.com/questions/63086/how-to-deal-with-a-nosy-fellow-graduate-student#comment150503_63093 fits this spirit nicely.

Some people don't pick up on hints - those people are glad if you say literally what you mean ("blunt" but not in a way that can be misinterpreted). Example: "Do you have a problem with your neck?" - very wrong if someone doesn't get hints. "I don't want you to stare at my papers" - perfect for that person. They hear exactly what you say and won't think of you as rude, but as a person who doesn't want anyone to stare at their papers. If they did get the hints and ignored them, that reply is fine as well.

This is an unpleasant situation, and there are a million variations of how you can respond, half a million of which were already proposed in other answers, so I'll stick with a high-level answer.

How can I deal with this guy without appearing unfriendly?

I will throw a wild guess out there based on the little information you've given, namely that you are a person who values friendliness perhaps a little more than is good for you. In my experience, this is a very common phenomenon: many people in the U.S. (my guess of where you're from) and certain other western countries are educated to be polite, friendly, courteous, and non-confrontational, even when the situation gets very awkward. I will also venture to speculate that women in those societies are socially conditioned to value friendliness and politeness more (perhaps a lot more) than men.
However, the sad truth is that this is precisely a situation that calls for an unfriendly response. The guy you're describing is, quite simply, a jerk. We can spend weeks analyzing his behavior and constructing elaborate explanations for why he's behaving the way he is, as some of the answers and comments here do, but after all this analysis, he will still remain a jerk. There is only one kind of response that will make him back off, and that's an unfriendly, confrontational response. (Examples: "none of your business", "butt out", "sorry, I'm not willing to discuss this", etc. I'm guessing you've seen enough movies and TV shows to have at least a theoretical idea of how to construct such a response, so I won't bother going into unnecessary detail.)
To summarize: my feeling is that when you talk about "not wanting to burn bridges", this is code for "I've been conditioned by society to maintain a friendly demeanor in all situations, even at the cost of suffering extreme discomfort for myself." Well, this incident shows that you can't have it both ways: you can sacrifice your own comfort to appear friendly and accommodating; you can assert yourself and protect your space and privacy at the possible cost of antagonizing someone else; but you can't simultaneously enjoy the benefits of both approaches and not suffer the drawbacks of either.
In any case, if the guy is an unredeemable jerk then a "bridge" with him is one bridge you should have absolutely no hesitation burning, since it's pretty clear that you will never derive any benefit from having any relationship with him. And if on the other hand he is not a total jerk and there is some hope that he will improve his behavior, then quite possibly by asserting yourself and sending him a clear signal that he should respect your space and privacy, then with an unfriendly response you have a much better chance of eventually developing a healthy and friendly relationship with him. Good luck!

I half agree. It's true that this seems to be just the kind of situation that calls for politeness to be dropped in favor of delivering the message. But I think she means the professional bridges here, no purely social ones. Picking up on your first paragraph, it's possible that rude behaviour might reflect more stigma onto a woman, which in turn burns or at least scorches her bridge to a potential colleague.

You need to be somewhat careful here. Many of the answers assume that he is trying to work with you. In which case the suggestions about formalising a collaboration are sensible (assuming you want to work with him). However, if you pursue that path and this is actually an attempt to be friendly, then any offer to collaborate or to talk about the paper with him later or other such responses will actually encourage him and possibly make his behaviour worse.
I would suggest a direct question, which can be done in a nonconfrontational way. Perhaps something like "which particular aspect of my work are you interested in?" If he is able to give a sensible answer then you could (if you wish) pursue that further with "Does that relate to your work in some way" and then go down the collaboration path.
If he is not able to give a sensible answer, then you possibly need to get out of having one-to-one conversations with him about your work and definitely need to actively discourage him. The easiest way to do this is to deflect to some public discussion. Do you have lab meetings or progress seminars? If so, you can say that you will be talking about it in the next meeting. If you don't have something like this, then you might have to confront him with something like "Since there's nothing in my work that's of interest to you, why do you keep asking about it?"

IMO, this is a good answer, professional and directly addressing the issue.

If this person is bothering you, learn to avoid, sidestep, and leave the area when they are around.  Do not feel obliged to answer their questions, do not feel obliged to let them read your work, and do not feel obliged to 'be polite' just because this person happens to be working in the same academic area as you.
This person is allowed to be curious, but you are definitely allowed to have your privacy, and you are definitely not required to socialize with him just because you share a public space.
it is also important to let this person know that they are impeding upon your privacy.  Not only because they might not know, but because of plausible deniability - let them know, firmly but politely, that their behavior has been bothering you, and that you do not wish it to continue.  Be specific, and don't be overly concerned with 'being rude', just get your point across as clearly as possible.
If this behavior continues after you've told them that it has been bothering you, consider taking actions to avoid incidental encounters with the person.  And if they're constantly impeding upon that privacy to the point of impeding your academic career, consider filing for harassment.

This might not be relevant if that person is too creepy, but:
Have you considered turning this problem on its head?
What I mean is, you're two graduate students working in the same area at the same place. But from your description it looks like you're not actually collaborating at all. S/he might be going about it in a very misguided way, but -
Why not try to arrange for actual proper collaboration? - working   together on something that's interesting for both of you or for your wider research group / area overall?
It might just be that in this context you could develop a better rapport. I'm not saying that's sure to happen, but why not give it a shot?

Firstly, excellent question.
Secondly, I experienced a similar issue during my doctoral study. Another PhD student (call him S) requested to see my paper work while work in progress prior to paper submission. To be frank - he was neither humble when talking with other people nor an amicable person.
My strategy was avoidance. We worked on the same institute.
Because I assumed that he would go the advising professor and/or me posterior to reading my draft paper. And he would say something like 'Let's give me an author credit because I did a paper review'.
Worth to mention - he was not aware about the details of my work --- he was not aware about the domain of my study (neither the paper nor the thesis).
He did not use LaTeX in contrast to me. (No need for a Word vs LaTeX discussion with this guy.)
We worked on different topics. Thus, he was not able (from my perspective) to give me a proper feedback concerning paper details.
Concerning my ability to write an adequate English grammar - That's not the best but paper reviewers gave me always much feedback concerning improvements for the applied grammar (apart of various hints regarding the content itself). All the time during my doctoral study - confidants (1 person with doctoral degree & 2 persons without doctoral degree) were available who reviewed my paper work. They got an author credit or a reference within the acknowledgment section.
There was no need to show S my paper work prior to an acceptance.
I was listening his words and my chain of thought was 'no way --- nope'.
Fortunately, this issue was never requested by him. (But some other stuff, which are another issues.)
Finally, as far as I know, S (last seen in 2011) did not finished his PhD in contrast to me. :-)
Hence, some problems are temporarily.
Please differ carefully which strategy you are using --- avoidance is one option.
But you have also the option of confrontation or redirection as mentioned by whrrgarbl.
Perhaps, you wanna escalate the issue. But then you should write down the history of all events, which are happened - only facts without any animosity.
Wish you all the best.

The following is a personal perspective, tries to answer the question, what would have I done in the mentioned situation.

He frequently asks me to list exactly (his words) which papers I'm
  reading

I find nothing annoying in this statement, rather I feel the other person is extremely interested in my work and methods. I would be happy to give him the literature but not when I am working. I would say something like
Why don't we discuss about it while we have coffee tomorrow. I will send you some of the important works in the field tonight. By the way, I propose you to read P1 to have a preliminary understanding of what we would be talking about, of course if you haven't read already.

If I walk past him in the hallway holding a book or a paper under my arm, he'll (very obviously) contort his neck to see what it is

I would show him happily. It doesn't bother me if I am not holding something inappropriate.

If I'm working somewhere public, he'll walk up to the table and start reading what I'm working on.

Okay, now the line is crossed. If it bothers me, I would say something like
If you'd excuse me, I am reading something important, we will talk later.
I find it useless to waste your time thinking what would be the exact motivation behind his apparent nosiness, rather I would treat the problem objectively irrespective of gender or culture.
A side note.
 I find some very good ideas emerge out during the informal coffee break discussions, as a researcher I welcome such discussions, it is also a good way to judge if the person is genuinely interested in your work or not. Also, if possible invite one of your fellow graduate student in your group into the above mentioned discussion.

While you might not find his behavior annoying, the asker clearly does, as made evident in their question, so while I understand where you are coming from, I feel like it's not pertinent to the question to say how you would react.

I see two strategies here: "discuss tomorrow", "propose to read P1": increases the cost of his behaviour. If he is really willing to invest the time, the OP might find a collaborator. Otherwise, the OP can just ask him whether he has done X yet when he approaches. "send you some of the important works": gives too much information to be useful, e.g. a long list of books and papers

Based on my personal experience, I would not recommend inviting the person to coffee to discuss unless you really want to, as this would encourage him to continue (especially if he is being flirtatious as has been suggested in other comments). Including other graduate students could temper this a bit, perhaps by suggesting a reading group or that he sit in on your research group meetings. This would allow him to learn more about such topics if he is truly interested, while keeping OP's interaction with him clearly professional.

@whrrgarbl A reading group is a huge amount of work. You shouldn't have to go to that much effort to get somebody to quit bugging you.

@DavidRicherby Very true! I meant suggesting he go to an existing reading group, not suggesting that OP organizes one with him. I tried to be more clear in my answer but I guess it got lost when trying to fit in the comment limit.

In graduate school, there are times for collaboration, and times for establishing independence from a peer. These are personal choices based on the nature of the work and also your personal instinct. Based on the way you've asked the question, I assume that you simply want your space respected without drama and without burning any bridges. I think it's important to speculate about his motivation, but it's not necessary. In any case it's your choice. If it makes you uncomfortable, then be professional, but be very direct so there is no confusion. Establish your boundaries as you see fit. If that doesn't work for you, then you've given him a chance and it's time to discuss it with someone of authority in your area. You might as well get used to establishing your boundaries now, there will be more opportunities going forward.

Sometimes we come across someone whose behavior is a little off.  There are a number of possible explanations.  One possibility is that he is on the autism spectrum, but what's often called "high functioning."
The "off" behavior can be disconcerting or annoying -- until we understand the reason for the odd behavior.  Then our empathy kicks in, we're able to divert his attention away from something he's fixating on, and we're able to ignore, without confrontation, and seek the aspects of the individual that we can connect with and enjoy.
Who knows exactly why this person's behavior is slightly bizarre.  We don't need to know precisely.  All we need to do is operate on a working hypothesis that this person is wired differently from most other people, and realize that confronting him is unlikely to change his behavior.
Once you start thinking about the person this way, you'll be able to use some simple preventive measures, such as
(1) keeping papers stowed in a manila folder while you're walking from Point A to Point B
(2) diverting his attention to something else, to help him get out of a groove if he's a bit stuck
(3) using some gentle humor (but not at his expense)
Note that all three will be easier to carry out, and more successful, if you've taken the time to build a bit of a relationship with him, around things that have nothing to do with what you have hidden in your manila folders.  See what common ground you can find.  For example, maybe you both like dogs.

Many of the answers here involve trying to speculate on the person's motives, or to categorize his behavior.  I suggest you take a course of actions that doesn't do that.  I suggest that the next time he asks you what you are reading that you reply with something like "I'll be glad to answer that if you'll answer a question for me first."  Then you proceed to say something like "I notice that you ask me what I'm reading very often, and I wanted to ask why you are so curious about it."
Listen carefully to what he says and the way he says it.  Let him talk as long as he will, even if there is a long pause in the conversation (perhaps up to a minute).  If he gives you a very short, non-responsive answer you need to ask for more information about why he is so curious.  It's possible that his answer may reveal his true intention, and it's possible that it may not.  This conversation should be casual, and should not be confrontational in any way on your part.  It's just an honest question seeking an honest answer.
If the answer he give you does not cause you to feel comfortable with the questions he asks (and I expect that it won't) then you could end the conversation by offering an alternative solution.  I'm not saying this is the only option, but you could end the conversation by saying something like.  "It tends to be distracting to me to always answer the questions about what I'm reading.  What I'd like to do is email you once a month with the names of the two or three best papers that I read in the last month.  Would that be OK?"
This way you are trying to handle things politely, and to determine what he says his needs are.  If his behavior should persist after this conversation, you should probably discuss it with one of your professors.
I also encourage you to talk with your fellow grad students to see if he behaves this way toward anyone else.  Also, have you considered that this might be his way of flirting with you?

What if you don't care about what he's reading?  Then you have to sit through his long explanation just to be polite?  If a person asks you to do something you don't want to do, simply and politely saying "no" should be the first course of action you consider.  This not only has the same upside of not speculating on his motives,  but also saves you time!

@Lev, I think you misunderstood what I said.  I didn't say ask him what he is reading.  I said ask him why he wants to know what I am reading.

What I'd like to do is email you once a month with the names of the two or three best papers that I read in the last month. — No, no, no.  Absolutely not.  There is absolutely no reason for OP to make this kind of promise, especially as a response to someone repeatedly violating their boundaries.

this answer is ridiculous. OP doesn't owe this other person anything. and if it is flirting, it should not be welcomed just because it's flirting.

What you don't seem to be understanding is that I am trying to propose a workable solution to a real problem. In an ideal world she doesn't owe the person anything.  The poster of the question doesn't live in an ideal world, she lives in the real world.  In the real world social interactions are messy and often complicated.  I'm suggesting that she make an attempt to understand why the person is behaving the way they are so SHE CAN ATTEMPT TO FIND A WORKABLE SOLUTION TO THE PROBLEM.

@sgroves.  Please tell me anything that I said that suggests that flirting would be welcome.  I am suggesting that if she knew it was flirting she might deal with it differently than if she thought it was academic competition.  Please tell me where I suggesting it would be welcomed.  Think about it this way;  If you go to the doctor with a headache, it helps for the doctor to know if you went out drinking last night, or if you accidently drove a nail into your head.  Same symptoms, different solutions.  She knows the symptoms.  Knowing the cause might lead to a better solution here.


text:
Is it acceptable to compare your experimental results with the claimed results from another paper?
Consider a scenario where one (say Mr. X) has implemented a method for solving a problem, experimented it on a dataset D and obtained significant results. The obtained results seem to be better than a set of results published in a paper P in a reputable journal J which solves the same problem experimented on D by some another author.
Mr. X decides to cite P and directly compare the claimed results published in it with his own.
The question is how much necessary (in the perspective of a reviewer) is it for Mr. X to reproduce the results published in P by himself if he is to publish in

a) the same publisher as journal J?
b) a totally different journal publisher?

Most importantly, what would be the case if J is an IEEE journal?

In theory, if a result is published you can use it as is.
In practice, it is better to replicate it yourself. That way you can really make certain you are comparing like with like. Research often involves a very long chain of decisions that cannot all be published in an article. Good research documents that somewhere else, but it is easy for honest mistakes or omissions to seep in. So that way it could easily happen that Mr. X's design is subtly different from the design used in paper P, and the difference in result are due to that difference in design rather than the difference in method. You can rule that out by replicating the results in paper P yourself.

And (to make this relevant for the last three questions), while in practice there could be one, in theory there should not be a difference based on the fact if the journal the person cited and the person citing published in match.

Thanks for answering. I understand the practical implications and the need to replicate. I was concerned about how will it affect the publishability per se if the results were not self-replicated (in an IEEE journal).

In general, good research is more publishable. In your particular case, if you are improving on a given method, then chances are that someone involved in the original method will be a reviewer, and know in detail what they did, and find what you did is different and thus uncomparable.


text:
How to Ask via email for supervision of professor for Japan Graduate program admission
I would like to apply for graduate programs in Japan, and I have sent email to several professors in Japan (e.g., Todai, Tohoku) using this format (I only change the name of the professor and university, since the research topic is always the same):

Dear Prof Name,
I would like to introduce myself, I am Ahmad Zahi Ulul Azmi, Graduate of Engineering Physics from Bandung Institute of Technology (ITB) with specialization in robotics, medical instrumentation, and control. My Undergraduate thesis is about assistive exoskeleton robot for upper-limb stroke recovery therapy. Moreover, i have developed several robot such as unmanned ground vehicle controlled by smartphone, autonomous underwater robot (Champion of autonomous underwater robot category in Singapore Robotic Games 2016), remote operated underwater robot, quadcopter, and wall-climbing robot.
I would like to pursue Graduate Program in Toyohashi Univeresity of Technology for Fall Semester next year with MEXT university recommendation scheme scholarship. I am looking for possibilities for conducting research in your laboratory. I will be glad and feel honored if i can be accepted as graduate student in this university and have you as my supervisor. For the fundamental asset, i am familiar with CAD especially SolidWorks, i have done several projects with it. Also, i have a good basic knowledge about mechanics, calculus, control system, signal processing, computer vision, and programming in Python, C, and C++. I think it will be really useful for my research at Toyohashi Univeresity of Technology . Apart of it, i am ready to learn something new and develop more advanced robot.
If my study field is not well suited with your laboratory, i would be truly grateful if i could get a recommendation of another laboratory or professor.
With this email i attach my CV, please contact me if you require any further details or documents. I hope to hear from you in the near future.
Thank you

But I don't get any responses. Is there anything wrong with my email? How can I enhance it?

Your English could use a bit of work. In particular, the personal pronoun "I" should always be capitalised. However, I doubt that's a reason for getting no responses.

You need ti customize each letter to the professor and his or her lab. Find their papers or papers of lab members and tie your experience or skills what the professor and lab group are working on.

What kind of response do you expect to your e-mail? You're not asking any question.

It needs to be much snappier. Consider something like this:

Dear Professor Name,
Do you have any positions available for graduate students in the Fall? I have a lot of experience with CAD, control systems, and signal processing (i.e., my autonomous underwater robot won the 2018 Singapore competition), and have published a few well-received papers [1,2]. This seems well aligned with your past work on similar topics [3,4], so I would be pleased to discuss opportunities working for you (or your colleagues) as a PhD student. Please let me know.
Name
[1] https://arxiv.org:blah.pdf
[2] etc.

where [1] and [2] are references to papers, links, codebases -- anything they can dive into to understand you more, and [3] and [4] are references to their work, so they see that you took the time to research them.
For me personally, I almost never respond to generic e-mails.
Note, I know nothing about the Japanese system; I'm only commenting on how your e-mail could be generally improved. (In particular, I'm wondering if this mail should be written in Japanese -- I know a lot of science is done in English, but if you speak Japanese, and the language of the university is Japanese, it might be better to write in Japanese or at least provide a translation).

hello, thank you for your reply, I really appreciate it. I used this subject "Asking the possibility to enroll as TUT graduate student in your laboratory", is it appropriate? TUT is the name of the university

No. The grammar is wrong, but worse, it is wordy and sycophantic. How about a subject like "PhD candidate - dynamic control" or even "grad school position"

I've worked for Japanese universities that are considered prestigious, both national and private. I am going to base this answer on my experiences with professors and administrative staff. I should note that while I did do a little bit of teaching, a good chunk of my duties at both universities was administrative support, especially communications between faculty and students both Japanese and international.
Bottom line is that there is a chance your email is not going to get looked at, but there are things you should take in to account, and things you can do, to increase your chances of actually finding a grad position while still staying sane.

You are going in with a disadvantage in that your email is in English. It depends on how comfortable the individual professor is with English, but I know plenty of professors who either just trash English emails from people they don't know or have students/staff (i.e. Myself) look at it, and then just blow it off when they hear it's a foreigner looking for a grad position. Keep this in mind so that you don't feel too disappointed when a professor doesn't get back to you.
The email is too long and difficult to read. Again, keep in mind that it's more likely than not that the person who ends up reading your email is not proficient in English, at least not to your level. Keep it concise and to the point. I would also recommend making the title something short and clear, for example, "Supervisor for G30 Ph.D".
You're probably not going to get a normal graduate position meant for domestic applicants, unless you are proficient in Japanese enough for academic purposes. Programs for non-Japanese speakers do actually exist, but randomly emailing professors won't get you a response. You need to actually look for those programs and apply accordingly. If you want information on such opportunities, you are better off emailing the university's admissions office, or at least the department office. Emailing professors asking about grad position openings will only result in them deleting your email, or if you are lucky they may forward it to the admissions office but I doubt it.
You need to check that the professor is actually accepting students, especially international students. If they are not taking students that year, they will simply discard your email and forget about it. This information is usually available on the department's website as part of the admissions page, or at least it will be included in the admissions information packet.

Right now, MEXT is putting incredible pressure on universities to increase the number of international students and to promote diversity, so many universities are creating internal quotas for non-Japanese students. I have talked to admissions officers from other universities over drinks and heard them complain about having to accept international students who do not meet the standards normally applied to domestic applicants because they need to fulfill the quotas, especially programs that are funded by the government and need to have the numbers to continue being funded. If you can find the right programs, they will be hungry for international students, especially those who have already proven themselves as talented.
Here's one well-known example: G30 Program

In this respect, (Japanese) researchers in CS are much better: they actually read and reply to my English language emails...

Thanks for the write up. One thing caught my attention..."..I have talked to admissions officers from other universities over drinks and heard them complain about having to accept international students who do not meet the standards normally applied to domestic applicants..". I have seen a lot of people who struggle to cope up with studies abroad although they had quite a sound academic record at home. I wonder, why well deserved students are denied a position for the sake of diversity!

I've worked with researchers at both Tohoku and Tokyo University, among others. Their English is typically excellent and have better writing skills than spoken English. This is not your problem. Contacting by email is the norm.
These are among the top schools in the country (especially in your field) with many applicants each year. It is common in Japan to ignore emails they're not interested in and not to respond to unsuccessful applicants. Sorry, no news is usually bad news.
There are a few things to bear in mind to support your case. Sorry, these are not really related to your specific field of interest but are more general concerns. You need to show that you have independence and ambition to be successful in Japan. Both living abroad and the research environment are very demanding. If you can suggest a specific research interest or reason for seeking a career specifically in Japan that will help to show you are serious about it. Having a common connection such as a recommendation from their collaborators will also help them to trust you. Be proactive and offer apply for funds yourself, ask only their support and feedback. If you are able to, offer to visit their laboratory or Skype them and their lab members. Anyone serious about applying should also be looking for if it's the right research environment for them as well. Whether an international student can handle the language and cultural barriers is a real concern in Japan and they will prefer candidates that have realistic expectations, ideally those that have visited Japan before and have some language skills.
English is still very challenging for them (it's vastly different to their native language). Be clear and concise. They're busy and you need to get to your point quickly. Leave the details for your resume, it can be assumed that a candidate proposing research in a particular field would only do so if they had the technical skills to carry it out. State clearly if there is a technique that their laboratory is good at that you are interested to learn with them. It is much more convenient for them to take domestic students so while international students can bring new skills into the lab, they are more of an administrative headache and more of a burden to mentor entirely in English.
Depending on the lab, they may not be willing to consider this. They should only respond to you if they are prepared to guide you. This a big commitment for them, it will demand their time to train you and their research funds to provide equipment for you. They have the right not to do so. It's better for you if you end up in a lab that is able to give you the support that you need. They also may have funds to support you or fund a visit to their institute (do not ask for this but bear in mind that they could offer it to you).
Please be polite and respectful, especially for senior academics in Japan. Once you meet them, they may understand that foreign cultures are not so hierarchical but until then, you cannot know whether they will be offended. Addressing them by "Surname sensei" is typical for a professor. Be polite to their students and administrators as well, they will pay attention to how well you treat them. Overall, the entire tone needs to be more polite and formal for someone you've never met before (even if they aren't from such as respectful culture as Japan).

Remember that professors receive hundreds of such an email every day and they don't have time to read all of them -if not any one of them-. To increase the chances that your email get noticed by at least one professor, you will need to send a lot of these emails. However, be careful and do not send standard emails to several professors because it is easy to be recognised and it gives a very bad idea about you and your working attitudes. Actually, this way is not really prefered by most of the professors -I would say- because your email would be considered annoying if the professor is busy and he/she does not aim to supervise new students, regardless of their qualities.
The other option is to check their websites and whether they announce offers (scholarship or job). In this case, you can contact the professor on this basis and of course very high chance to be contacted if your cv and skills fulfil the requirements.

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text:
Is it necessary to cite all publications with erroneous interpretations in a PhD thesis?
In my PhD thesis, the main topic is to justify that a philosopher P claims that x = a, but a (very) large number of publications assert that x = b, even though their research doesn’t directly deal with the question of "what x means for P". My question is: Do I need to cite all these publications that adopt the x = b interpretation, even if they only do so indirectly?
Or would it be enough to cite the most relevant works that engage with this issue more directly?

For my own curiosity, is there some reason you believe you might even consider referencing all such publications rather than a representative handful? I doubt that that would have ever crossed my mind.

@Aruralreader Well, I want to armor myself in the defense of the thesis. I do not want to be told that I “forgot” to cite this and that publication, especially when the “most representative” can be a somewhat subjective term.

@Ian Are you claiming to cite the "most representative" paper? Why not just go for something like "a number of publications assert that x=b, for example (list of maybe 3 references)"?

@Ian, in that case I think this is a great learning experience for you. If someone says ‘You forgot to include ABC,’ you simply thank him or her and acknowledge you carefully selected representatives of the ‘x = b’ camp. Diplomacy.

@Anyon Question: Would that be sufficient for the purposes of the thesis? Would it be enough to cite some of those publications for the thesis to be justified?

@Ian What does your advisor think? This is what they are there for.

@Aruralreader Fair enough!

@BryanKrause As I don't have the availability to talk to him and her (they are two) continuously, this doubt hasn't been resolved yet, and I want to have it somewhat outlined before submitting the chapter for correction.

You need to cite what you use in general. However, for a doctoral thesis, it is probably better to cite, in some way, perhaps with a specialized bibliography the papers you are concerned with. This is just to convince those judging the thesis that you have completely covered the ground. Over citation (within reason) is probably better than under citation.
That would be my advice as your advisor, but your advisers opinion is the one that should be followed for a question like this.
And citing "all" such papers may be impossible as you would find it hard to make that claim that you have found them "all".

Thanks, what you answered is kind of what I have in mind, so it makes perfect sense.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Are the peer reviewers of a journal article allowed to voice surprise to the editor at a "minor revision" decision?
Are reviewers allowed to express surprise to an editor? I was shocked by the ‘minor revision’ decision for an article I reviewed.   Reviewer 1 was positive and listed a few minor points.
My review and Reviewer 3 included extensive comments that would require ‘major revision.’
The number of words for my review and that of reviewer 3 came to 1800 words.  Reviewer 3's review had two opening paragraphs, and then 11 numbered action items.
My own review opened with a positive sentence about the value of the topic.  But my very next sentence (in its own paragraph) was: "I remain unconvinced that substantial new knowledge has been produced.”  I then spent 700 words defending this, including four practical ideas for providing value to readers.  The implication of my points is, if implemented, providing this value could make the article be worth publishing.
I worry I should have opened with a criticism, because the editor may have been skimming the review and the editor's takeaway was then my positive comment?
With this, I am a first-time academia.stack exchange poster.  I have been reviewing manuscripts for 35 years and I have never seen a minor revision determination when reviewers had this much to say.
Not only that, there was no substantial points in the decision letter.
The "Dear Reviewers" letter from the editor contained:

Thank you for reviewing the manuscript XXX.  We greatly appreciate the
voluntary contribution that each reviewer gives to the Journal and
hope that we may continue to seek your assistance with the refereeing
process for XXX
The decision that we arrived at for this article was:  Minor Revision,
basing the decision on your review and those of the other referees.
A copy of your comments to the author, along with those of any other
referees, follows at the end of this letter for your information. Any
files that referees uploaded for the attention of the author are
attached as a PDF proof.

Is ‘allowed’ the word you meant?

Not in any meaningful way, but you maintain full s3lf determination for what editors you're willing to review for.

Just noting that this is a common practice of predatory journals (to get reviews but send every paper for only minor revisions regardless of the recommendations).

I am not nearly as experienced as you, but the decision letters I've seen rarely contain much more than a fluffy statement about the changes you need to make. Is this a journal in a field you regularly review and work in?

In many fields, there is no clear differentiation between "minor" and "major revision". It's simply an indication to the authors how much work they should expect to put into the revision, but in reality there is a spectrum in between. What is it in your field? Do authors have to do something specifically different between the two categories?

I'm not the OP, but in my field, "major revisions" means that it is definitely going back for a second round of review (and maybe more than one more round). "Minor revisions" means that it is unlikely to have a substantial re-review. The editor might run the revision past the reviewers as a courtesy or might just make a decision on the revision without further review.

This exactly has happened to me with MDPI as a reviewer and while technically allowed, was the last straw for me to avoid the publisher like the plague. Some editors may disagree with you, but ignoring/not acknowledging your reviews in the response smells predatory, and would suggest you refuse to review and publish in this journal.

I think there can be different in the definition of 'major' and 'minor' between you and the editor, and you could definitely express your opinion. As some fields had a tradition that minor revision may not send back to the reviewer again, you may even want to voice it out, if you really want to read the revision.
For example, you may think the number of items that required changes are large so it is 'major'. But the editor may think that overall the paper is methodologically sound, just need some edits, and changes on the interpretation of results. Therefore it is 'minor'.
I agree with Buffy that unless your comments are ignored, there are not much to concern.

Since it is typical for the journal to send reviewer comments to the author(s) and there is no suggestion here that it hasn't been done in this case, "Minor Review" might be nothing more than noise, or encouragement to the author. They might disagree on impact, of course, and the revisions suggested might be easy to make. You haven't indicated otherwise. And, you are making an assumption on how they came to that characterization. Your disagreement is fine, but don't be so sure you know how they arrived at it.  But the characterization itself has no actual impact on future decisions.
I would only be concerned if the editor allowed the authors to ignore reviewer comments, whether the characterization was major or minor revision. You won't know that unless and until you see the next version.
Yes, you can express your "surprise" or even disappointment in the characterization, though I think that the characterization, as such, is largely meaningless without knowing more. You can also refuse to review for this journal in the future. Neither of those is a problem.

Although they're often interpreted differently, 'minor revision' and 'major revision' are functionally the same. In both cases the manuscript is returned to the author, and revisions are expected. If there is a difference at all, it is that the automated deadline when the manuscript is expected back is generally shorter for 'minor revision'.
A 'minor revision' decision is not a sign that the manuscript will be accepted. In other words, 'minor revision' and 'major revision' is arguably just a difference in semantics and personal definition of what is major or minor; what ultimately matters is whether the authors incorporated the changes you requested.

Are the peer reviewers of a journal article allowed to voice surprise to the editor at a "minor revision" decision?

Yes, you are allowed to do this (I've certainly seen similar things before). Just put it in the confidential-to-editor box, since it's got nothing to do with the author.

Your field must work differently than mine.  For me, Minor Revisions and Major Revisions are both signs that the paper is very likely to be accepted, and the difference is that Major Revisions require another look by reviewers and Minor Revisions don't (though sometimes they are sent to reviewers anyway).  If the editor is not sure the author(s) can make the changes necessary for the paper to be accepted, then the verdict is Reject, sometimes with Encouragement to Resubmit.

HI Everyone.  Thanks for sharing your opinion.  I appreciated this point (similar to what a number of peolpe wrote):  " would only be concerned if the editor allowed the authors to ignore reviewer comments, whether the characterization was major or minor revision. You won't know that unless and until you see the next version."  Agree.   But my fear is what some of you noted, that the authors think think the understaking is minor, and that the reviewer might accept without sending the ms back to the reviewers.   If my comments and reviewer 3's are not fully addressed, I will complain.


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How to deal with mistakes or embarrassing moments in front of peers?
I am a post-doc (just finished PhD) and today my advisor asked me a question in a meeting. And I answered wrong. He laughed at me and asked me "Who taught you that subject??" in front of the
PhD students.
I was embarrassed and I realized I never really learned about it before. My university in my home country is very poor with zero government support and our education system was so bad.
I graduated with a master's and a PhD because I tried so hard and basically I had learned by myself throughout the graduate study years from online and books. I know I am lacking in many areas. But after today,  I really depressed and lack of self confidence. I feel like no matter how hard I try, I will never be it.

This doesn’t seem to have anything to do with academia, other than that it happened to you in academia. The interpersonal SE may be more appropriate for this.

Is this your PhD advisor? Is it possible they meant to be self-deprecating since they are the one who taught you?

Are you certain this remark was meant as a criticism or a "put-down" rather than simply an off-hand jest meant in a jovial light-hearted manner? Hard to tell from your description.

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion or containing answers will be removed.

First, the put-down from the PI was unkind and shouldn't have been said.
Second, it is natural to feel dumb when something like this happens. And it probably happens to just about everyone in some context.
Third, you don't, and can't, know everything and you can admit it to yourself and to others. Apparently nobody taught you that and you probably didn't think about it previously, leading to an error. But it is also possible that somebody taught you wrong and misled you. I had a student once who had serious misconceptions about how math works in computing and in simple equations. It was the fault of an earlier teacher who drilled in the error, but was trusted.
Finally, you are very probably competent in your field, having earned a doctorate. Don't let "imposter syndrome" develop in your self perception. But when you find a gap that is important to fill, fill it.

He is usually a very cool person, so I was so shocked today when he reacted like that. But anyway I will improve myself more, what else can I do, I just started this position. I’ll try to move on and be a better person.

Just focusing on the situation, I think it is really rather common, particularly in a group in which there are mixed backgrounds and somebody is the only one from one particular background, that there are a few things where one person is alone in not knowing something that the others know and kind of take for granted. I think most if not all of us have found ourselves in a situation in which we didn't know something that people around us knew and had difficulties understanding why we wouldn't know it. People tend to forget how heterogeneous experiences and backgrounds can be, and what this implies.
If such a thing happens just once or very rarely, I wouldn't worry much about that, but of course if you feel there is something important for you that you should know, you should make an effort to learn it (as apparently you have made many times before).
It may even be that the advisor didn't mean it all too seriously and would be surprised if he knew that you are now depressed because of it. As I wrote, such situations are rather common and most people are at the receiving end of ridicule because they don't know something that some others know once in a while.
Of course there is no way for us here to assess your general competence based on this story.

Thank you for your answer. I feel more positive now. There may be a cultural difference between my advisor and me (I am Asian, and he is Western). I completed my graduate studies in Thailand; I moved there right after finishing my bachelor’s degree in my home country. Everything was quite serious back there. I also just started this position two weeks ago. With a new country, new environment, and new employer, I may not have adapted well yet.

@Purplehour I (European) know a number of people who would make remarks like your advisor did in an entirely humourous way, even to their friends and family. Of course it would be better to be careful with this kind of humour with people who come from a background of which one has limited understanding, but in my view it is very possible that the remark wasn't meant in a serious way.

One more remark I want to make here is that advisors (professors, group leaders, etc.) are rarely good experts in psychology or mentoring. Very often they just have been "promoted out of their field of expertise". They were good scientists who were then promoted until their duties encompass everything except science. Usually they have little or no training in psychology, management, accounting, acting in public, intercultural relationships, etc. but have to do that most of the time. That's why their jokes can be dull or inappropriate. Good if they have enough self-reflection to realize that.

As an example, about 10 years ago I attended a PhD defence of my friend in Paris who then applied for a position in a company (in industry), and a person from that company's HR was present at her defence. The advisor made an inappropriate joke about her performance without thinking too much, which possibly cost her the job.

Perspective: A Healthy Environment
I'm over 50 with long stretches in both academia and industry.  That's long enough for me to have acquired a thick portfolio labeled Stupid Things I've Said In Public. Some of those have garnered similar reactions to what you describe-- not the exact words, but the sense of, "What the heck did you just say?"
In a normal US-based environment, that can be (but isn't necessarily) a sign that people are comfortable with each other to say things like that.  It can still sting.
One thing that helps is perspective:  If I pointedly asked, I'm sure a few co-workers remember the time I thought gold was more conductive than copper.
But I am quite certain that this is not the first thing that comes to mind when they see me, and therefore, it's unimportant and in the past.  Also, everyone does things like that from time to time.
Perspective: An Unhealthy Environment
Not all working environments are healthy, and sometimes, jerks will take advantage of a healthy environment.
It's not always easy to tell which you're in, though.  One sign of an unhealthy environment is if this sort of thing happens constantly.  Another is if it's always the same person catching the criticism.
A third, more subtle, is how people react when you ask for help/clarification.  This is a little more tricky when you have a PhD and are firmly in the "go teach yourself" part of your career.  (And I note that you did, which is good!)  But if you or another member of your group-- especially a more junior one-- are in a position where help is needed, the way in which that help is delivered (or not) can speak volumes.

Wow, today I learned gold is not more conductive than copper! Gold coatings are used for their chemical inertness rather than for their conductivity.

@BasilBourque ...and it's something I really should have known, at the time and place I said it.  Totally unforced error.

The way how you reacted to this situation by searching the right answer and learning from it means you are on the right way. Such embarassing moments are common, but thanks to them you learn things you will never forget, which at the end makes you an expert in your field. Don't be discouraged by that but see it as an opportunity.

This is not a question about academia, but about interacting in a professional group of people.
What happened to you will happen again and there are two components to your reaction: your natural character and experience.
Best case: an extrovert, assertive person with a lot of experience. They will turn this to their advantage (either earning "what a nice guy" badge, or by even pushing their position by ridiculing the ones who laughed (aka hardcore politics)
Worst case: an introvert with a sentiment of "inferiority" to whom this happened fo the first time. This looks like the end of the world, your career and your social life.
The thing is that this is not. After the round of laugh everyone will forget that. The smoother you let go, the less drag there will be.
It is very easy to say this for someone who is rather in the first category (in the sense that I do not care and I will play this cool) but this is something that you ought to try to learn.
We have in France a saying: l'esprit d'escalier. This is the situation when you have a hundred excellent answers and behaviors, an hour or a day too late. Face them. Think about them. Replay them in your head. Put yourself again (in your head) in that situation and say loud, louder than you would do it normally, the responses (preferably when there is no one around :)). With time this will become second nature. In some countries this is a must because of the culture (it does not have to be toxic at all, it may just be how people react and how they do not hold on afterward)
TL;DR: this is normal, happens to everyone, get over it, and learn to react. Improvise. Adapt. Overcome.

Respond with humility. See yourself as a life-long student; do not expect yourself to know the right answer to a question when it is asked, and be eager to learn it.
When your advisor responds to your ignorance with something like the cruelty you describe, @camden_kid's comment is spot on - that is your advisor's embarrassing moment. The humble response then is to try and help your advisor save face, by responding as though he meant it as a joke. Don't let it be about you. ;)

Researchers become good by discussing a lot with other researchers, in particular asking questions, proposing ideas, trying to give answers, ... Unavoidably, because we are all humans, sometimes questions are naive or silly, sometimes answers are just plain wrong... It may hurt one's feelings a bit, but the mistake would be to protect oneself by reducing interactions with others. On the contrary, good researchers move on and keep talking to others in order to learn and improve.
Take it as badge of honour: we're here to learn, and mistakes are part of this process of learning.

When I was studying for my MSc, I asked one of the lecturers about an unfamiliar mathematical symbol. He laughed at me and said if I didn't know that I shouldn't be studying his course, and then told me several times I had to drop his module because I didn't know enough maths. I ignored him and eventually got just over 70% in his module (in the UK this is the cutoff for the highest grade boundary). I was never particularly concerned about this, I just mentally wrote him off as a jerk and a bad teacher.
I have also made people feel stupid in the way I reacted to something they said. Either by laughing in surprise, or sounding overly incredulous when asking why they think that. Some of the times I've reacted in this way, I was the one who had the facts wrong! I recognise that this is a flaw in how I talk to people and is something I'm working on changing, because that's not how I want to make people feel when I talk to them. When I react in that way, however, it's definitely not because I think they're stupid, and when I first found out that this was how I was making people feel I was really upset.
How people react to you making a mistake or not knowing something says more about them than it does about you. If you make a mistake and someone responds mockingly, try to treat the conversation as a collaborative exercise in making sure everyone is on the same page. Treat it as a learning opportunity even if they're being a jerk about it. If they're not intending to be rude it will diffuse the situation, and if they are intending to be rude it makes you look like the more mature person. For example, you could have responded "I'm mostly self taught in that subject, could you explain where I've gone wrong?".
As a final example of how this kind of conversation can go positively, I remember asking a question of one lecturer during my MSc - something along the lines of "you said A earlier and B just now, but they seem to contradict each other, have I misunderstood something?". He laughed and said "you've got me there", and explained the mistake he'd made in thing A earlier. Nobody thought less of him for making the mistake, and I still remember it years later as an example of someone graciously handling a mistake being pointed out in front of a room full of people.

I agree with the other answers that your advisor's behavior was rude and inappropriate.
In addition to those answers, some perspective may be useful.
What happened to you -- not knowing the answer to a basic question in a certain area (if it is indeed a basic question) is completely normal, not just for students, but also for professors!
Indeed, everyone is a novice in most fields other than their own.
For example, a PI who works in a very applied field may be completely unaware of basic questions and concepts in theoretical areas, and vice versa.
In fact, this is the point of academia, that we are always learning more! No one person can understand every subject, and the point of research is to learn and to understand more.
In the future, when you receive such questions, you can always respond honestly, for example:

I actually did not take that class as an undergraduate so I am a bit rusty on the details, so I would have to brush up on that. Can you recommend a good textbook?

or:

It's a bit embarrassing but it has been a long time since I studied as an undergraduate! I'll have to review that definition.

It is never a shame to not know; it is only a shame to stop learning more.


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Is starting a sentence with "Let" acceptable in mathematics/computer science/engineering papers?
I received a comment from a colleague that starting a sentence with "let" is not good practice. I know that starting a sentence with "let" is grammatically correct, so that is not the question. My question is if starting a sentence with "let" is good practice and acceptable in technical writing.
Here are a couple examples:

Let scalars be denoted by lower case letters.
Let x be a real number greater than zero.
Let the set of real numbers be denoted by R.

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These are all acceptable. My personal preference would be to reserve "let" for statements that are (essentially) assignments, like the second one in the question. The other two establish notation conventions. I might say something like

We use lower case letters for scalar variables.

or

Lower case letters represent scalar variables.

and

We write R for the set of real numbers.

Me too. The first and the third sound distinctly non-English.

@TonyK both are fairly standard in scientific papers

When you get right down to it, those are all notational conventions, and all are also assignments. I don't see any reason other than personal preference to treat them differently.

I could be splitting hairs, but OP's second example strikes me as an assignment (as it presumably introduces a previously unused quantity in a proof) rather than a notational convention. Ethan makes a good point; starting with "let" is something of a technical term within proofs so outside uses might detract from ease of reading.

Agree. In mathematics, sentences like "Let x be a real number greater than zero" or shorter "Let $x>0$" are very common. For notation, like the first and third sentences, there might be better ways that using "let", e.g. "Scalar variables will be denoted with lower case letter: $a,b,c,x,y,z$."

@NiharKarve. They don't sound standard to me;  they're certainly not good English.

These sentences will appear normal to anyone educated in mathematics in the English language.
They could, perhaps, be made more concise if written without "Let" but I would not think too hard about it.
For such trivial issues, it is often wise to give your colleague what they want.

How could it be more concise without the word "let"? What's the more concise phrasing? I would've thought the "let" phrasing is the most concise way to phrase this

@vrijox Active verbs: "Lower case letters denote scalars. R denotes the set of real numbers."

@eric_kernfeld Putting the first in active voice changes the meaning. But you can avoid "let" simply by getting rid of the "let": "Scalars are denoted by lower case letters."

Yes, the meanings are different.  "Lower case letters denote scalars" implies that all lower case letters denote scalars, not other mathematical objects, and it allows for some scalars to be written in other ways. Though this is not exactly the same meaning,  both statements will likely hold in this use case (mathematicians declaring conventions to the reader). And it's more useful to the reader to have a map from what they see (a lower case letter) to what it means (a scalar) than the reverse. This is a great example of how improving concision also improves clarity.

Yes, this is common in math writing. It is hard to imagine a book or long paper that doesn't use the convention to some extent.
But, I would only add that too much repetition of a phrase become tedious and even annoying to your readers. So while

Let x denote a real number.

is perfectly fine,

Assume x is a real number.

is an alternative.
Make the writing lively if possible. But clarity in math is the more important thing.

To me, "Let x be a real number" and "Assume x is a real number" have distinct logical meanings. The first is a type declaration, the second is part of a case distinction. In the statement of a theorem it wouldn't be wrong to use "assume" instead of "let", but "let" seems cleaner (at least if you dislike untyped variables).

A better synonym for "let" would be "suppose", or a construction like "If x is a real number, then (something)". IMO "assume" should be reserved for making an assumption about the properties of some object which will later be proved either true or false.

@alephzero, there are a lot of possibilities, but I doubt that any working mathematician would be misled by any of them. The message here is "lively writing" not the specifics. And if you want to use "Let" and "Assume" and "Suppose"  etc. in some narrow technical sense, you should explain your usage.

I would interpret "assume x is a real number" as meaning "We already know that x is a complex number, now for the duration of this [sentence/paragraph/section], assume it's also a real number."

In your first example I would actually agree that the "let" construction is not such great style. I wasn't sure why at first. But as Kimball pointed out in his comment, "let" is for definitions. You aren't really saying "let a, ..., z be 26 scalars", since you'll use those letters to stand for different scalars in different places. Besides you could just say "lower case letters denote scalars" or something like that.
The other two examples are certainly typical mathematical English.

The first example is not of the form "Let X be [definition]" because you are not defining scalars but just your notation for them.  A cleaner way to say this with let, though certainly more old-fashioned would be "Let it be known that scalars are denoted by lower case letters."

@Kimball, +1 and question updated to agree with you!

The immediate, facile answer is that "yes, it's fine, since so many people have done it already"... and, also, since your audience will certainly understand the content.
A secondary point is that quite often a more effective-and-efficient sentence structure is available, as exampled in other answers and comments. In some ways, these secondary things don't truly matter, but they can distract the reader, as well as allowing a critical reader to wonder about what you think is happening... which is probably not good.
An exaggerated case is "Let the real numbers be complete." What? Well, yes, they are, but what is the point of saying this? Or "Assume $x$ is a real number." Wait, what? What if it's not? Does one mean "here let $x$ be a real number..."? Probably. And, yes, experienced readers can decrypt the weird syntax, but there's no point in making them do so.
Alternatives to "Let $x$ be a real number..." are, for example, "For real numbers $x$, ..." and such.

"An exaggerated case is "Let the real numbers be complete." What? Well, yes, they are, but what is the point of saying this?" Well, presumably you're making a mathematical argument that's based on that premise - possibly involving producing a result that shows that the real numbers aren't complete, thereby producing a proof by contradiction of whatever the main thrust of your proof is.

@nick012000, for the example you mention, I'd be inclinced to say "assume" or "suppose" [thing to be shown false], rather than "let". But, once again, perhaps language drifts even over a few decades...

One of the most lauded writers in mathematics in Jean-Pierre Serre. The first sentence of his book A Course in Arithmetic is "Let K be a field".  The first sentence of André Weil's book Basic Number Theory begins "Let F be a finite field..." The first sentence of Section 1 of Chapter 1 of Wiles' proof of Fermat's Last Theorem is "Let p be an odd prime."
Conclusion: it is perfectly fine to start a sentence with "Let" when you are talking about fields or odd prime numbers. Maybe you can generalize this observation.

I see no problem with saying, for example, "Let x be a real number", but I often say "Choose a real number x", as well as "Take" or "Consider".
I don't really have a reason for saying it one way versus another way, but I like to mimic the language that my math professors use when going over proofs during class. They know better than me.

Obviously a matter of opinion.  LGTM.

Expand a bit, please?

@jakebeal Google says that's "looks good to me". Who knew.

Sorry. My co-instructors and especially my student staff use it all the time in Slack messages and I've picked it up as well.

I really don't think this should be an answer (no offence intended, of course).

@YiFan Several of the longer (and upvoted) answers really don't say more than this.

@jpaugh I disagree with that interpretation of those answers.