Is it plagiarism to submit the same work in a course after withdrawing from the course on a previous occasion?

Whether or not this is a problem probably depends more on the goal of the assignment for the purpose of this course rather than plagiarism as a general academic concept, because in both cases the work is your own sole work for a course assignment (the same course even), and is not owned by anyone else, published, etc.

The only thing you can do is to ask your instructor for guidance. Depending on their goals for the assignment, they may be okay with a re-submission of the previous work or they may want you to complete a new assignment; they may even want you to pick a new topic if the assignment allows for a broader interpretation.


How to prevent desk rejection when trying to publish papers which are counter to the prevailing view (but still legitimate)?

I wonder if there exists, at least in plans, a centralized system that examines editors' decisions in journals, a kind of "appellate court" in peer-review publishing.

In cases of unethical behavior, professional societies can investigate a journal, but your description includes nothing that appears unethical.

  In most of those trials the paper was rejected without going to peer-review, but editors didn't point out specific flaws. Instead, they used general statements like "your paper is certainly interesting, but we get so many even more interesting papers, so unfortunately we cannot publish yours".

This may be frustrating and reflect genuine bias against your ideas, but it's a reasonable and standard way to run a journal.  Some sorts of bias are unethical (for example, discrimination based on the author's race, ethnicity, gender, etc.), but intellectual bias is almost unavoidable.  There are a few journals, like PLOS ONE, with the mission of publishing anything that's new and not clearly defective, but most journals try to filter based on interest and importance.  That necessarily involves judgment calls by the editors regarding what is likely to be satisfy these criteria.  In particular, part of running a prestigious journal is favoring some topics and approaches over others, and the community judges the editors based on how well they manage to select interesting and important papers.  To reject a paper without review, there's no need to identify a flaw.  Instead, the editors can simply decide that it's not interesting or promising enough to justify the effort of formal reviewing, or that the chances of acceptance are low enough that sending it out for review would just waste the reviewers' and authors' time.

  In one journal the editor simply replied that the paper is out of the journal's scope, which is plain-out false (the paper deals exactly with one of the major topics of the journal).

Scope can include both subject matter and approach.  Some journals like to publish controversial papers that may well turn out to be wrong or misleading but will at least lead to interesting discussion and follow-up work.  Other journals are more conservative and have no interest in going out on a limb with a risky theory that reexamines what the editors consider to be well-settled science.  I don't think the editor in your case was lying to you about the subject matter scope, but rather indicating that your paper is outside the scope of the type of work they want to publish.

  In another journal the editor passed the paper to peer review. In two months it was rejected "in view of reviewers' comments". But - amazingly! - all reviewers recommended publication, with certain revisions.

This is an awkward issue, and it would have been helpful if the editor had clarified.  (E.g., "While the reviewers' comments were largely positive, the editorial board felt that they did not make a strong enough case for publication in comparison with other recent submissions.")  But I can appreciate the editor's position.  Sometimes you get a submission that is unusual and unconventional, one you know a lot of the community won't like.  Who do you choose as reviewers?  You can predict many people's opinions in advance, which introduces an intrinsically political aspect (if you want to kill the paper, it's easy to choose conservative reviewers, and vice versa).  One approach is to ask sympathetic, open-minded reviewers but hold them to a high standard by seeing whether they can convince you to accept.  The question isn't whether they recommend acceptance, and in fact the editor may know in advance that they have a soft spot for this topic.  Instead, the question is how compelling and forceful a case they are able to make for this specific paper.

Of course I have no proof that this is what was going on here, but I'd bet it was.  If the editors were determined to kill the submission, they would have rejected it without review or deliberately assigned unsympathetic reviewers.  Instead, I think this journal gave you more of a chance than any of the other six.

  Could anyone give any recommendations as to how to safeguard oneself against unethical situations like those described above?

As I explained above, I don't think these situations are unethical, but they are still worth avoiding.  One factor to consider is how often a journal publishes unorthodox or unconventional work (even if it's not on your exact topic).  If they sometimes do, then they are likely to give your paper a fair hearing.  If they rarely or never do, then that's probably because they are reluctant to do so.


Is it acceptable to include a paper in the reference list but not cite it in text?

There are lots of situations where this type of citation naturally emerges:

You want to cite a paper that you have gotten inspiration from, but you cannot pinpoint any specific objective relation between that paper and yours. For example, some equalities appearing in that paper look similar to some equalities in yours (even though they involve completely different objects), and you have built some parallels in your mind without ever making them rigorous. You may try to be open and mention these parallels in your paper, but they will be so vague and subjective that readers will tap their foreheads and referees will ask you to remove the sentences.
You have cited a paper whose results you used in one of your proofs, but then you find a better/simpler proof and no longer had any use for the citation. But you never bothered to remove the citation, since you might well need it again for something different. It's much easier to keep it in and only remove it at the very end of the process, when the paper is about to get published.
You have written a long paper and then split it into two. Each of them still has the full bibliography of the original paper, because removing references is thankless and boring work and you may need them again (see the previous point).
You have pre-emptively added the citation to the bibliography since you know you will want to cite it in a forthcoming section of your paper. That section never gets written.


You need to include the introduction to your paper because it might be the first paper in that field the reader is about to read.


Should I put my papers which are not written in English on my social-media profile?

Yes, it is. English is a lingua franca, but that doesn't mean that all scholarly literature must be in English. Make sure your paper is in a institutional or disciplinary repository, if you like the idea of your paper to be open access. Translate it, as Davidmh suggests, to make it even more available.

Regarding indexing in Google Scholar, that depends by the site you archive your paper into. You can make some arrangements to be indexed, but in my experience even if you suggest resources to GS you cannot be sure you'll be.


Applying for postdocs and for Postdoctoral fellowships at the same time

A postdoc is not usually considered a permanent academic position. It is the most temporary of temp academia positions. The rule on not holding a "permanent" position likely means that you cannot be working as a (tenure-track) professor and then take the fellowship. This would be a question you would need to ask directly to the sponsors of the fellowship.
I also am not clear on how a postdoc and a Postdoctoral fellowship are different. These usually would be the same type of position in my mind. If so, the position at U of B versus the position with Prof X are really the same sort of thing. It would just come down to interests and pay at that point.


How to politely enquire how serious someone is when they say "work for me as a postdoc"

I would follow up the verbal conversation with an email.  For example

  Thanks for the encouraging words the other day about a possible postdoc.  I wanted to check, were you talking about a funded position?  Where would I find instructions for submitting an application?

Depending on the vibes you got, you might want to start with something less formal, for example

  Thanks for the encouraging words the other day about a possible postdoc. I was wondering whether the position might be available for the upcoming semester.


I am currently a postdoc in the UK. My situation is similar to yours: in my thirties, have a family and little children. This is my first postdoc, which I took in my thirties. I also wish to pursue a career in academia. But unlike yours, I have no industrial experience and I am not from the EU. Cost wise, if you and your family are non-EU nationals, you will need to pay a lot more so that your family can stay in the UK with you. Still, regardless of your nationality, it can be a bit hard to support the family if you are the sole breadwinner, but it is not impossible.

Do you intend to continue living in the UK, or are you open to moving to another country at the end of your postdoc? Your experience of living in different countries plus your industrial experience are an advantage should you find that there are no suitable academic opportunities in the UK after your postdoc.

What I would think is more important is to have an understanding and support from your wife. As a postdoc, you might have more freedom and flexibility over how you manage your time at work, but the pressure to publish may be high. It is important to know your limitations now that you have a family. It is likewise important for your wife to know what to expect. Having said this, considering you experienced Japanese working culture, what I have just said might not be a problem for you.

All in all, it looks to me that there is nothing for you to worry about going back to do a postdoc in the UK at 35, at least not from the technical aspects above. The deciding factors could be something more practical or personal, but it could be that I have said this from my own limited perspective.


Common scenario and situation leading to similar questionnaire -- Is it plagiarism?

tried to obtain some ideas from other examples for the questions

That has the hallmark signs of plagiarism, although without seeing the original sources and your questionnaire it is hard to give a definitive answer. It is okay to look at other sources for ideas. Paraphrasing is okay also. Copying, or even changing a few words, is not okay without proper attribution. In general it is okay, and often desirable, to reuse an existing questionnaire, or parts of an existing questionnaire, in a new study, but you need to provide attribution to the original questionnaire.

As to the similarity between you and the other student, this depends on if you used her questionnaire for ideas. If you never saw her questionnaire, then you clearly did not plagiarize from her. It is possible that both of you got ideas from the same source, in which case you both plagiarized someone else.

You need to determine if you plagiarized and if you did plagiarize, who you plagiarized from. If you plagiarized from the student, you need to tell her and your supervisor. If you plagiarized from a third party, you need to tell your supervisor. You should also inform the student that your questionnaire contains plagiarism, but that you did not plagiarize her. You should also tell her that you are telling your supervisor.


What training is appropriate to get to help students deal with stress?

It is admirable that you are trying to address this on your own, but I would recommend not trying to solve it yourself by trying to find resources. There are complex ethical and legal (like FERPA in the US) issue.

There are likely other faculty, staff, other students who find themselves in the same situation -- wanting to know what to do but not knowing where to go to learn. Graduate students also often find themselves in this position when teaching undergraduates

So why not try to address that issue for all of these groups? You say that your university has a counseling service. So why not ask that service if they would put on a one-day or half-day training course for any university member who desires to learn how to respond appropriately to students in need. My university does this, and it has been extremely successful. They even have separate sessions depending on the context in which you interact with students.


Will low grades for a minor on my trascript affect my chances of getting into grad school?

If I understand you correctly, you have been doing rather poorly in your current major but will change to another where you expect to do better. Assuming that you do, in fact, do very well in psychology and all of your later grades are better than your earlier ones, you may be ok. You can explain that you were ill suited to your first choice of study and changed, and now you are doing fine.

That would be a winning position for some, but not all, institutions, but you have what you have in your background. Make the most of your future, of course, and work harder, if necessary, to be a success.

Short story: Not a great position, but not necessarily a losing one. Make the future count as you can't change the past.


Can I collect meta information on papers and put this online?

With the hopefully obvious caveat that I'm not a lawyer and this is not legal advice: at least in the US, this is probably fine. Copyright law (17 USC § 102) applies to "original works of authorship," not to ideas, and I think everyone would agree the metadata of an article's publication (including journal name, author, and date) fall in the latter category, not the former. Otherwise the whole system of academic citation would be untenable!

The title and abstract, on the other hand, are content created by the articles' authors and are protected by copyright law, but I think it's quite likely that fair use (17 USC § 107) protects you from being held liable for using them in the manner you describe. With reference to the four conditions to be considered when determining fair use:

  (1) the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes;

You say it's a free, noncommercial endeavor, so that works in your favor

  (2) the nature of the copyrighted work;

It's an academic article; the whole purpose of its existence is to be widely disseminated

  (3) the amount and substantiality of the portion used in relation to the copyrighted work as a whole

The title and abstract are a small part of the work

  (4) the effect of the use upon the potential market for or value of the copyrighted work

Using the title and abstract in a database like this will more likely increase the market for the original paper than decrease it (which is in fact the entire point of having an abstract)

In fact, you would hardly be the first person to do something like this. In high energy physics, INSPIRE already aggregates abstracts and metadata from nearly all published papers.


Applying to a Math PhD program which doesn't require GRE as a physics/math major

I don't think it will prevent you getting accepted.  I followed a similar path (Physics + Math BS, Physics GRE only -> Applied math PhD).

But I recommend that you decide who you would like to work with in the places you'll apply to, and write them a very polite, short e-mail explaining your qualifications and interest.  If a faculty member is interested in you, GREs won't matter at all.


Is the level of difficulty of the Physics GRE on a par with the Math GRE?

This is subjective and not a complete answer, but too long for a comment.

I doubled-majored in math and physics as an undergrad, took the physics GRE, and got a PhD in physics 25 years ago. Since then I've mostly been teaching physics, plus a little math, at a community college. In other words, I have a background in both subjects, but my physics is stronger.

I recently participated in an online discussion initiated by a physics student preparing to take the physics GRE. This student felt that studying for the physics GRE would be a big project, because there would be a lot of formulas to memorize and so on. I tried the sample test, and I didn't really feel that it required any significant amount of memorization. There were almost no questions where I felt like I needed some obscure fact that I'd forgotten long ago. I said this, and the student said that of course it was easier for me, since I have a PhD and have been teaching the subject for a long time. There is some truth to that argument, but because I teach at a community college, I actually don't get a frequent workout on any of the material covered in upper-division courses. It really seemed to me that the test did a good job of testing fundamental understanding, and was not something you could cram for or pass by memorizing formulas.

Out of curiosity, I also took the sample math GRE. I think my score was somewhere around the 75th percentile, which was considerably lower than what I'd gotten when I retook the physics GRE. There were some pretty broad areas where I drew a blank, because I hadn't done anything in those areas since I was an undergrad.

Based on all of this, my impression is that the math and physics tests are about equally hard, and both of them do a good job of testing fundamental understanding rather than short-term memorization.


Can reviewers ask questions of or communicate with the author outside of the formal review process?

In general, I would consider it unethical for a reviewer to deliberately communicate with an author outside of the formal review communication channels.
The reason for this is that the person ultimately in charge of the decision is not the reviewer but the editor who is managing the process. The communications in the reviewing system are thus the record that they have available to work with and that form the basis for their judgement not only of the paper but of the quality of each review and the weight that should be given to each reviewer's opinion. Moreover, if there are questions that arise later around the paper, that is what will be used to audit the process that was used to approve the paper.
If a reviewer takes their communications outside of these channels, then they are essentially choosing to hide their communications from the editor and the scientific record (even if it's a normally confidential portion of that record). That can have bad effects in both directions, causing a good paper to appear less supported (because they wrote a weak summary review based on a complex communication) or a bad paper to appear more supported (because information was communicated that weren't actually in the paper).
So what if a reviewer has already been communicating with the authors and then is asked to review? Well, first of all, they should let the editor know; the editor might or might not see this as a conflict of interest and wish to choose another reviewed. If the editor doesn't have an issue, then the reviewer should at that point stop having out-of-band communications and communicate about the paper through the review system---where they might be able to turn around a review extremely quickly if they already have a well-formed opinion of the paper!
But should any of this affect your choices as an author? I don't think so. Ultimately, the reviewers are just some of your first readers, and the impact of your article will be determined by the many more opportunities that people have to read it after that. If people are contacting you to talk about your work, that is already a great sign---even if they don't like it, they were interested enough to engage with it!


What is minimum GPA for getting PhD in Germany?

As flo said, it totally depends on the university.

In principle, you can become PhD student at any German university if you

Have someone eligible (normally a professor in the department) who declares that she/he will supervise you, and
You meet the requirements from the examination regulations for the PhD.

In the majority of cases, the examination regulations can be found on the web. Many departments do not list a formal "grade" requirements, but some do. Typically, the grades are only given in German style, so there is room for interpretation when translating foreign grades. GPAs are pretty much unknown in Germany. Admission officers will look at the grades (e.g., A-F, where F means fail) and if the institution where the grade has been awarded is "OK". Summary grades are expressed in the same system as the individual grades. To make this part of the answer complete, as you are probably aware, it is normally a requirement to have a Masters degree before you can start with a PhD.

Structured programs, such as graduate schools, typically have their own rules on top of these. Again, standard vary, and you should be able to find some information on the home page of the respective graduate school.


Authorship of an article based on semester project

What is considered normal, hence ethical, varies by field. In mathematics, this would be a highly unusual situation. But in some lab sciences, the PI is normally included on all publications since the lab itself exists only by their efforts.

I suspect you are in some such field and would then suggest that the senior professor should probably get his way. It may even be advantageous to have him as "corresponding" author as it may ease publication. In such fields readers understand these things and know who does the actual work. Thus it isn't considered to be a problem in those fields.

If you are a co-author it is probably as much as you can expect here. And maybe even that is impossible. But work to get an acknowledgement in the work, at least - especially if it says that the original idea came from you. You actually say that the student did the work of developing the idea, of course. If the student is "first author" it is a good outcome. The rest is just a bit of an arcane dance.

I think that if you don't press to hard for what might be considered in the field to be an unusual outcome that the relationship between the student and the senior professor will settle down sufficiently.


Is it OK to put a paper on the arXiv after it has been published online?

This will depend on the terms and conditions that the journal published the paper under (and theoretically on the legal systems of the US and whichever country the journal publisher operates from). These conditions could range anywhere from "the publisher now owns the copyright, and you can't publish the paper anywhere in any form without their say so", to "put their typeset version up online anywhere you like". These terms should have been included or linked to when you signed for the final publication.

On average though, provided the publisher is willing for you to put out preprints, they typically want it to be your last version, not their typeset version, in which case there isn't likely to be any additional issue with the kind of differences you appear to be talking about.


Assistant professor vs Associate professor

In a typical university in the United States:

An assistant professor is an entry-level faculty member.  They are generally on the tenure track (although the term "assistant professor" does not guarantee this) but do not have tenure yet.  Typically, within about seven years an assistant professor will either be promoted to associate professor or will leave the university, although the timing can vary a little and it's theoretically possible to remain an assistant professor forever.

An associate professor is one step up from an assistant professor.  This promotion is usually the same as getting tenure, but not always.  (Some universities, like MIT, frequently have non-tenured associate professors.)  The final step for most faculty is a full professorship.

As for what an associate professor can do that an assistant professor can't, that varies even more than the terminology.  In many US universities, the only additional power an associate professor has is voting on who gets tenure, but I wouldn't claim this is universally true.


Working in two research lab at the same time – unethical?

So my question is, is it unehtical for me to do this?

Unethical - no. Smart? Probably also no.

Firstly, as Corvus correctly states, it seems very unlikely that you can perform well in both roles and do your undergrad studies in parallel (and I am not even talking about going outside and doing people stuff occasionally, which you should also not forget about).

Secondly, you should not forget that professors are human. Even though you are not doing anything "wrong" by any stretch of imagination, it is not difficult to imagine scenarios where either of the professors (or both!) don't take it well, and I am assuming you want letters from these guys down the road. The professor that you work for, for instance, may assume that you find his research very unfulfilling if you feel you need to invest your spare free time into a completely unrelated area instead of hanging out with friends etc. (S)he may assume you are really doing it only for the money / letter. The other professor may be disappointed at some point when an important deadline should be met that you can't commit more time to her/his project, because of your other duties.

Finally:

  Professor A doesn’t know about this.

That's never great, and you should change this ASAP. Even if the professor basically does not care about the issue at hand, (s)he may get mad simply because you didn't tell (I certainly would). And I think you are aware that the chance of you keeping this a secret forever are slim to non-existent?


PhD programs: select a very specific one in order to narrow down my area of interest? or a more general one and specialise as a postdoc?

I'm not entirely sure what you mean by spending 1-2 years studying for a scholarship, but you must formally stay in academia. Your MS was your 1-2 years of prep for a Ph.D.

My suggestions would be as follows:

1) Apply to your ideal top-tier universities (Cal-tech, Yale, etc...). Spend a considerable amount of time on your application. Especially your statement of purpose since you do indeed have a clear goal to go there. Do well on your GRE. If not you will get filtered out before they really evaluate the rest of your application. I know they changed it since I took it but when I did it was a completely beatable test (at least the quantitative section). Practice. Practice. Practice.

2) Apply to the universities/labs that actively or recently collaborated with the labs you ultimately want to work with. Probably more than half the post docs in our lab came from collaborators (or competitors) labs.

3) Apply to your "fall-back" universities. You'll want to at least stay active in the field.

4) Do you best to attend conferences that your top-tiers will be at. Make contacts, friends, collaborations, etc...with members of the group you want to be with. As a Ph.D. student we ended up evaluating many of the Post-docs that applied to our lab. Know that what you mention to these members in passing will often come up during your evaluation. Be aware and make this an advantage.

Realize that you are probably a poor judge of your own talent (good or bad). Don't let the reason you didn't make it be that you didn't try.


Poster Presentations: Is it acceptable to present an update to a currently ongoing project as a poster at a conference?

Along with the commenter, I agree that it will depend on the field and the conference.

However, in all likelihood there is a way to make it work, if you are just super interested in doing the trip. Consider to position the presentation clearly in the title and to carefully construct your abstract.  You want to clearly show the connection to the earlier work, but that things have changed also.  Use your judgment on how to do that.  "Progress" is likely too weak, but "Breakthrough" too gushy. In other words sell the talk (without being too blatant but still...don't hide your light under a bushel.)

Probably, there are also some pitfalls to avoid.  Although I think the downside risk is not so huge.  But try to avoid losing a follow-on publication if that is something you care about.

Of course, you need to understand the conference if they decide not to have you.  Even if you got a breakthrough or unexpected results, they have a reasonable argument that the audience has at least seen the scope of the research problem and initial approach already.  Depending on their own supply/demand for participants will impact if they want to have you again.

Personally I would opt more to go somewhere new and get some new people to see your work (from your own interests, not out of altruism).  It is also nice to use travel to see new cities. (I'm sure some will scold me for having boondoggle as even a small fractional component of academic travel, but researchers are not Biblical cows with bound mouths...getting an occasional fun trip to go along with hard work in the lab is not unreasonable.  Life is short.)


Approaches to finding potential collaborators and co-authors

Here are a few key observations I've made about the process of starting collaborations:

Most people one would like to work with are already quite busy, and have many random people come to them looking for collaboration.  If you want to be taken seriously, you need to have a specific and detailed idea of a way that their work can make a difference to your goals or your work can make a difference to their goals.  Once you start discussing, you might end up somewhere totally different, but clear and specific thinking is key to getting things started: I suggest Heilmeier's Catechism as a useful framework for your thinking.
Most collaborations thus start with a discussion with between PIs, but are only fully realized if a graduate student or postdoc becomes involved to do a lot of the work.  Early career researchers may play the role of both PI and postdoc themselves.  Be careful, however, to keep acting as a collaborator rather than turning yourself into a free postdoc.
Almost no interactions turn into collaborations.  A good rule of thumb is that for every 10 people you meet, 1 will become a potential collaboration; for every 10 potential collaborations, with 1 there will be meaningful follow-through on the possibility, for every 10 with meaningful follow-through, 1 will actually turn into a significant collaboration.  Don't get discouraged, but also don't waste time pursuing people who indicate they aren't interested beyond the point you are at.


Does it make sense to accept an early career identity in academic publishing?

In addition to awarding the Young Author Prize, the jury decided to request the Population editorial board to review the other finalists’ articles for possible publication. The other candidates in the first selection will be sent referee evaluations and juror comments to assist them in future submissions.

This makes it seem like the “finalists” were papers good enough for publication. It would be interesting to know how many of the finalists actually ended up getting published. Although 1/31 is low, 6/31 is much less stringent and I think that might be the number you should be looking at.

Acceptance rates wildly vary by field, but it’s not implausible to me that only 6 of the 31 submissions warranted publication. Submissions by recent grads tend to not be as good, so the acceptance rate amongst recent PhDs should be lower than the average acceptance rate overall.

There’s also nothing that I see that says you can’t submit it both ways. All in all, I don’t find this particularly unreasonable. I’m not sure what added benefit there is, unless you win/are a finalist and can put it on your CV, but it doesn’t seem particularly amiss to me.

Tracks for young researchers often have more support than other tracks. For example, your link mentions that every submitted paper gets peer-review feedback, which isn’t going to be the case for a general submission. I’ve been to conferences with similar set-ups, where all submissions in the “young professional” bin get more attention and more feedback than general submissions. The value of feedback like that is hard to overstate. I don’t feel like it degrades your work to call it done by a young professional. My first paper was presented at a conference for undergraduates, and my resume still has that line on it. It is a matter of fact that that work was done by an undergraduate. The purpose of these kinds of events is to provide better feedback and better access than you would get from the usual venue, and I haven’t seen any analyses that say that they’re ineffective. My personal experience with them has been entirely positive.


Do I have any chance to acquire funding for a PhD after admission?

They cannot fund you directly, so you need to bring money from elsewhere. Your best bet is to ask them, as they would be aware of the possible agencies that provide grants in your field. They should also be able to help you put together a stronger application.

In any case, your position is uncertain, so don't overcommit to this place, and keep applying elsewhere.


How much does it hurt admissions if I don't take an essential class until after I apply to schools?

I cannot speak directly to antenna engineering, but more generally, having research experience, strong letters of recommendation, a high GPA and a good SOP will almost certainly strengthen your application much more than having simply taken a specific (yet relevant) course. This is true for both masters and PhD programs.

Take a look at this write up of the admissions process decision making for the Computer Science PhD program at Carnegie Mellon University (a very prestigious and difficult to get into institution for Computer Science). Notice that the author doesn't say something like, "The student has taken operating systems. That is an absolute must!" and it should make sense why -- because it's a poor metric of your potential to succeed in a graduate program. If that was the metric they went by then a huge proportion of computer science undergraduates who applied would be accepted. Of course, this is not the case.

On the other hand, having done research and been published is a strong signal of your capacity to succeed in a program. It shows that you have talents and creativity beyond your courses, and that your professors respect you enough to work with you. In addition, having strong letters of recommendation matters significantly more than having taken a single course. If a colleague of theirs speaks highly of your skills and potential, they will likely weight that heavily, given that they know what it takes for a student to succeed in a graduate program as well.

Now, that does not imply that you shouldn't take relevant courses to your discipline (and that failing to take important courses may have an impact on your application). However, when considering the whole spectrum of the admissions process, I believe that not taking a single course will play a much smaller role in comparison to the other factors of your application.


Is it possible to publish a research paper as an independent undergraduate author?

Your question contains three questions. Is it possible? yes. Do you have a reasonable chance? Probably less than any other researcher because you lack the training but not zero. What mistakes to avoid? Well, that is what research education partly is about.

Writing a paper involves many aspects, providing the proper background, explaining the research, putting the research in perspective and reaching proper conclusions. There are many mistakes that can be made: you do not show you know the field, you do not describe the methods/theory/experiments well enough, your discussion does not hold and your conclusions are not well founded. All of this can come from poor understanding or from not writing well. So as long as you can tick the boxes from the subject specific to the methodological including writing skills then you would stand as reasonable a chance as any. In the end there is likely only one way to find out, try.

You state that you work independently and that is all fine. But, in science we all benefit from having others read and comment on our work to improve it so your chances of success can increase dramatically if your writing can be read and commented on by peers (with at least a PhD would be recommended) to weed out problems and any lack of clarity.


Co-authorship for a revised but relatively new article?

In this particular case, I would not change the authorship for the revised version (unless there are better reasons than what you have communicated).

You must not forget to keep your personal relations oiled. If you re-submit this article as a single-author paper, i.e. remove your supervisor, your relation to them would certainly not be helped. In the future, it may be important/useful to have that relation intact and well working for ongoing/future collaborations.

Moreover, by having them as co-author they are somewhat in your debt (which cannot be a bad thing) and may return the favor by adding you to one of their papers, even if you contributed as little as they did to yours.


In ABET accreditation criteria, what is the meaning of "one year of X"?

ABET formally defines a "year" as

  The lesser of 32 semester-hours (or equivalent) or one-fourth of the credits required for graduation [1].

The wiggle room in the definition is almost certainly because of the wide variety of credit systems used by various schools. "One and a third years" would then equate either to 42 semester hours, or four full trimesters or quarters of study for those on alternate study schedules.

[1] http://www.abet.org/eac-criteria-2014-2015/


Nervousness in the face of uncertainty is normal. Ask any astronaut sitting on the launch pad. What you experience is pretty common. Overconfidence can also be a hinderance.

You seem to have good study habits ("weeks in advance"). But note that cramming the night before an exam is counterproductive for nearly everyone. If you are tired, so is your mind. And it will be focused only on what you studied last, rather than having a more general and nuanced sense.

One "trick" is to do something active in the last couple of hours before a big exam. Anything to get your blood flowing and let your mind rest. Even deep breathing as a calming exercise has benefits.

I also have a bit of a mantra that I use at the start of an important activity, such as an exam. "Some things are beyond my control. I can only do my best."


If your advisor has contacts at any of the universities you'd like to work at, I would ask him or her to reach out for you. If you are looking to work with a specific faculty member, that is probably the trickiest route, as faculty members often use the summer to travel themselves, and it is rarely worth the hassle to hire an unknown student for the summer, anyway.

If you don't have a networking contact through your advisor or other faculty members at your school, my next suggestion would be to start networking at a conference, or through a professional organization that you are affiliated with (e.g., IEEE, AMS, etc.). Start getting the word out that you are looking to spend a summer at a U.S. school, and see if anyone has suggestions.

If you are looking for a paid internship, you may be at a disadvantage as an international student, and you are probably more likely to find something if you can fund yourself. If that isn't an option, you might also consider looking at internships in industry, as they tend to have more money for summer interns.


Should I bring a copy of an article I wrote in a science journal to my interview?

Yes you should.

I expect that a common question in any interview would be to ask the candidate about any piece of work of which the candidate feels particularly proud or pleased. Being able to refer to your publication -- and have a copy of it with you -- would be a positive thing.

Regarding your opinion of the work -- you might be your own worst critic. Clearly the journal editor felt it was acceptable for publication. In a positive spin, you could outline in your interview where you feel the work could have been improved, showing a capacity for reflective practice.


People change programs, this happens, and your advisor may or may not be understanding and supportive depending on the circumstances of your case.

Don’t misrepresent yourself in your CV! If you were a graduate student, say that, and mention that you switched programs in your statement of purpose (saying you did so due to personal circumstances is fine). If you say you were a research assistant and mention nothing about the PhD it’ll look like you have something to hide.

Good luck!


I feel like I got screwed over by my PI? No name on publication

I'll follow up on my comment, as none of the answers go in this direction, and I don't think you're getting the greatest advice.

  While I have no way of knowing whether this applies to you or not,
  making figures and such might not reach the intellectual contribution
  necessary to be counted as an author. This is why Acknowledgement
  sections exist. Before deciding on how to respond, think about what
  your scientific contribution was.

You may or may not have made a contribution that merits inclusion as an author.  Some labs/PI's are very generous about this, and some are not, but if your work was purely "technical", my own inclination would be to offer Acknowledgement and not authorship.

Generating figures:  scientific illustrators do this every day as a living (less so these days, but they're still around) and don't get authorship.  Photographers too.

Writing code:  this is a little less clear, and probably depends on direct contribution to algorithms.  If you are, for example, writing code that takes the mean and standard deviation and spits them out in a readable format, that's technical.  If you HAD TO UNDERSTAND THE SCIENCE in the paper to write the code, that would push me toward authorship.  If I could hire a contractor who knew nothing of the research to do it, I'd lean toward acknowledgement.

There's a disconnect here between the your perception of the contribution you're making and your PI's perception.  Just because he feels that your scientific contribution was "minimal", that does not mean he doesn't believe your work is valuable.

You might sit down with him and ask if there's any way you can make deeper contributions to his body of work, or if there's a small project you can really make your own.  Another option would be to use the experience you've gained there to apply for summer research opportunities (depending on what year you're in).

Of course, there are curmudgeons who just won't believe that an undergrad can make author-level contributions regardless of the contribution made, and that's unacceptable.  As I said before, from your description I have no way of telling whether you're dealing with someone in this category, or whether your contributions were of a basic technical level that arguably don't merit authorship.

I can say that many moons ago, as an undergrad, I was doing single-unit neural recordings in spinal cords (running electrodes up and down, listening for neural activity), and building electronic lab apparatus that helped with the experiments, and doing histology.  Some of the rasters I generated were used directly in publications.  I didn't consider that authorship level work then, and I still don't, as any technician could have done it, but it was certainly a valuable experience that helped launch my career.  Now, almost 30 years later, I'm still in touch with the PI of the lab (I was working for his postdoc), and he's been a wonderful advocate of mine throughout my career.

Your PI's recommendation, at this point, should be treated as a valuable commodity, and if you negotiate this disconnect with maturity, that letter will be even better.  Also, the experience you gain now will give you something real to talk about during interviews, which is also incredibly valuable.

Directly relevent: What are the minimum contributions required for co-authorship

http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html


To what extent do visit weekends impact graduate school applicant's final decisions?

I visited 5 schools as well, and did not choose my "dream school" because of visits. I had actually started doing research with a professor there (and it was published during my first year of graduate school), but during the visit I realized that the department was not what I was looking for. One big thing that got me is that, on paper, they (and every program) seemed "interdisciplinary", but when you talk to them you realize that the "math biologists" don't talk to biologists. Add that the students seemed to not be interesting and I started thinking that, although it's a top school in the field (math), I wouldn't graduate as the person I would want to be.

The other program started with biologists and mathematicians together in the same courses, then you split off after the first year. Everyone was really interesting and I kept in touch with them after the visit. I met with a bunch of professors one-to-one and found about 6 I would like to have as an adviser and already had projects I wanted to start. Lastly, they showed the funding statistics and showed the available computing supplies. I got the impression that this school would really help me become who I want to be, and so I chose this school.

Then again, some people choose simply by the ranking.


How do I approach a postdoc interview when my background is not same as the professor's?

My background is in computational mechanics, so I have some background to answer your question. It seems to me that you and the professor would make a good research team because your research interests and experience are complementary. Do not assume that the professor wants you to work on weak forms and model formulation. S/he might want to go in a more applied direction as @astronot said. Instead of assuming that the professor wants to produce more papers like s/he has done in the past, ask in the interview what you'd be expected to do.
Second, it might also be useful for you to learn weak forms, just like it might be useful for someone with a mathematical background to learn applied stuff using commercial packages.


Is it normal to be suspicious of a really interesting finding but in an obscure journal and/or by authors from unknown universities

I am concerned by your choice of words:

"Obscure": one person's obscure may be another person's core community.
"Low IF": IF is very dependent on both community and "trendiness."  A lot of very good work is published in low IF venues because they are the appropriate place to publish the result.
"Unknown ... and unexpected": again, not unusual at all for something interesting to come out of an unexpected place.

All of these words, to me, point to lazy "popularity-contest" thinking in evaluating the context of a work.  Instead, I think that you should use more scientifically meaningful heuristics, such as:

Does the investigator have a history of solid work, into which this result fits?
Does the venue have a clear, well-defined focus and community, and does it have reputable management?
Is the work well-suited for the venue?

If a work doesn't pass these filters, then I think you should be highly suspicious and not bother digging more deeply.  If it does, however, then you should be just as skeptical as you should be for work coming out of a high-prestige laboratory in a leading institution---and no more.


How to put a position you could not attend due to visa problems in CV?

I would not do it.  Only list things you actually did, not stuff you turned down.


In fields that alphabetize authors, which author to contact

Purely alphabetical author-list conventions and no designated contact author tends to show up in theoretical fields that usually have fairly short author lists.

As such, if you're going to contact the authors and don't know which to contact, why not put them all in the "To" line of your email?


Is undergraduate research typically funded? Should it be?

All undergraduate research positions should be funded. Most currently aren't.
The children of families who can afford to have their kids not work aren't smarter than the children of families who can't. Spending $60 billion a year on government supported research in the US and nickel and dimeing the next generation of scientists so 75% of them have to give up science is a real stupid way to invest in the future.
As for mechanisms, the NSF and NIH already have them and they work. I write NIH student supplements every year.


I would advise to first talk to this professor, and ask what you should do differently to get a good grade in his class. Write down his advise, and mail it to him, just to have a written overview of what you discussed. When you understood him correctly, he does not need to respond. When you misunderstood, he might respond to that.

I would refrain from discussing with him whether it was justified that you failed his class or received a poor mark for the assignment. Such discussions will be very unlikely to deliver any result that is positive for you.
Rather focus on what he thinks you need to do now. If you work with that, you are much more likely to get a better grade.

Maybe, you are right, and he did evaluate you unfairly. Maybe not. You can put a lot of effort and energy in trying to proof that you are right, but this will alienate the professor only more.

Life is not always fair. Sometimes it is smarter to focus on how to improve a situation rather than on what is fair.


Is it worth to switch from Bibsonomy to Mendeley?

Yes, Mendeley does offer export - BibTex, RIS, and EndNote XML.

The search is pretty decent, though I often find I use Acrobat search instead - its word-stemming seems better.

Batch replacement is very weak - the only way to do it is to go into the database yourself and tweak it. Very unsatisfactory. There is some batch update, in that you can select several papers, and add the same metadata to all in one go: but that's not the same as a batch search & replace. The one batch search & replace it does do very well is that when  you get two versions of an author's name, you can drag one name onto the other, and all the papers will get updated accordingly.

I've also found the technical support to be very slow, and often unsatisfactory.

The auto-grab of references from the web is patchy, and you may find you're often correcting it. Often, its guesses seem utterly bonkers, like it's just grabbed a few general words from the title, and gone off to find the closest match for those, in some subject that's completely alien to me.

The interface is klutzy, though I've yet to find a reference manager that had an interface I did like.

Earlier versions of Mendeley did occasionally corrupt the metadata, doing things like swapping round the lead and second author - unbelievably frustrating. This may have stopped now - I don't use Mendeley so much any more, because of this and other problems.

Mendeley does have its evangelists, and it seems to have been very slick at cultivating its fanbase - more resources seem to have been spent there than on the software. The feedback forum has now become pretty much unusable - there are plenty of important things in there that have been "planned" or awaiting assessment for 2 or 3 years.


How do I find a supervisor for PhD studies?

The difference between "spamming", which you should not do, and a completely acceptable contact is how targeted your emails are. Make sure you know what you want and what the professor you are contacting does their research in, and that these two things align. Explain in your first email why you want to work with that specific person, what your background is, maybe also include your university transcripts. You do not need to know the professor personally before contacting them.


There is some inconsistency in how different sources list Ramanujan's Notebooks and the two people deserving credit for it:

The Library of Congress catalog entry lists Ramanujan a bit ambiguously under "Personal name", but describes the work as "edited by" Berndt.
The British Library catalog entry lists Ramanujan under "Author" and Bruce Berndt under "Contributor" with the notation "Ed." (again implying that Berndt's role is that of editor).
Google Books lists Bruce Berndt as "Editor" and has the convoluted string "Srinivasa Ramanujan Aiyangar Bruce C. Berndt, Bruce C. Berndt, Ramanujan" under "Author".

It sounds like these three sources pretty much agree that Ramanujan is an author and Berndt is an editor. I don't know if there's an authoritative answer to the question of whether Bruce Berndt is also a co-author. I can only assume that either one of the famous national libraries I linked to above would be regarded as authoritative enough that no one will fault you for relying on their listings.

From a more philosophical point of view, whether Bruce Berndt is considered an editor or author is immaterial. His compilation and editing of Ramanujan's original notebooks was a monumental achievement, and that is what really matters.


How can I justify my skills against the required person specification?

"Strong communication skills" is included on virtually every faculty job posting because it is an important facet of faculty life.  A professor who can't or won't communicate effectively and respectfully can't work well with others - and academia is not a solitary profession. No department chair wants to run around cleaning up after a faculty member who has sent rude emails, alienated students or done anything else that will trigger a call from HR or the Dean's Office. No search committee wants to hire someone who will become a headache - they are looking for a new colleague. It would be a mistake to assume a well-written cover letter or research agenda is sufficient to demonstrate strong communication skills.

When applying for any job, it's important to highlight your skills and experiences in terms closely aligned to those in the posting.  Think about the types of communication a good faculty colleague and instructor would need: working collaboratively on committees and departmental programs, sharing lab space and other physical/equipment resources, teaching or supervising a wide range of students, engaging with other departments on campus, etc.  Give some thought to your communication style (written, oral, instructional, professional, etc.) and highlight skills that would make you a desirable colleague. Have you served in any leadership roles or on any committees, written or taught as part of a group, mentored students, helped solve a sticky situation, have good teaching evaluations that you can cite (especially those pertaining to your communication with students), etc? Your examples needn't be extensive or even strictly academic (maybe you were an RA or sold insurance as an undergrad or you've worked on a community or advocacy project?) but you've got to demonstrate that you understand the importance of communication in faculty success. It is - even in the sciences!


Asking questions in class: how can I "exit" a Q&A when I haven't really understood?

The situation is complicated so there is no simple answer. Over time you and your instructor(s) will have to work out a modus vivendi.

From my point of view as a teacher, I want you to try to continue to ask. I find more students hesitant than persistent - and it's the persistent ones who force me to be clear.

At the beginning of each semester and often again later I tell the class that any question that occurs to you has probably occurred to many of your classmates who are too shy to ask, so you will be doing yourself and them a favor by speaking up.

Students often start questions with "this is a dumb question" or "I have a short question". Often neither is true, so those are not good opening lines.

When a student seems to be in the loop you describe in your question and I sense that I am not quite helping him or her or the whole class I may say that continuing to struggle with it right now on class time isn't useful. I might cut the discussion short with "Please see me after class and we'll work this out" or "Can you come to my office hours?"

So final advice: keep asking while answers are useful, be prepared to continue the discussion one on one if necessary. Hope your instructor cooperates.


How do I refer to my PhD studies in my CV; under education or experience?

I put it in both places. Under Education I list my time as a graduate student, and under Experience (as "Appointments"), I list my time as a Graduate Research Assistant. I've seen this on lots of CVs in the US. Both are true, and both convey the right meaning.


Withdrawing an article out for review when another journal posts a call for papers for a special issue that is right on topic?

I would suggest the following steps:

Ask journal #1 if the review process has started.
If it has not yet started, ask if it can be kept on hold for a few days.
Meanwhile send a pre-submission inquiry to journal #2.
If journal #2 seems positive about your paper, send a request to withdraw the paper from journal #1.
Be honest about your reason for withdrawal, and add a word of appreciation for the editor's cooperation and understanding.
Submit to journal #2 once the withdrawal is confirmed.

If the review process has started, it would be advisable to let things be and not withdraw from journal #1. If your paper is rejected from journal #2, you could consider submitting it to another journal rather than going back to journal #1.


Contact info for a professor's letter of recommendation

Yes, it is okay for a professor to have alternative contact information on their letter of recommendation. If you are a student worried about this, you need not worry further.


The complication of not inviting my ex-supervisor to a podcast dedicated to our sub-field?

Using your position as an organizer to not invite the people you don't like to your thing is the only real reason anyone in academia ever organizes anything. They might retaliate but it doesn't really sound like your relationship is worth anything anyway. Just make sure not to actually say what you're doing, if anyone asks you about it just make up a generic excuse about scheduling.


Does publishing greatly affect my chances of getting accepted and funded (TA/RA) in a PhD program?

It is not clear what you mean by publish. In the simplest form, with predatory publishers a check and some gibberish, and the gibberish might be optional, you can get published. Even respected publishers do not always peer review (e.g., ArXiv only moderates) meaning the quality does not need to be particularly high. To get published in a respected peer-reviewed journal, or conference proceedings, requires you, or the team you are working with, to produce novel and exciting research, write a clear description of the results, format the results to meet the journal's specifications, and address comments by reviewers.

Having been involved in the production of novel and exciting research is very helpful for admission to a PhD program. The ability to write up results is also important, but this can come across in your application and doesn't require a publication. Formatting to a journal's specification and dealing with reviewers is not something that admission committees really care about.

In general, publishing is the end product of the research process. Admission committees don't generally care if you make it to the end of the process.


Should I choose a "Pass" grade instead of a letter grade due to the study disruption during the Covid-19?

You can choose “Pass” if you want but everyone will understand you made this choice to preserve your average, so your file will still look bad admission to a PhD program.
With “Pass” you may technically qualify to apply but I doubt admission into a PhD is simply a matter of meeting the technical requirements. Regardless of what you choose, you need to do better next term, so you can establish that this past term was just a one-off due to COVID.
On a related matter: are you sure you can still choose between “Pass” or a grade?  For most students the window to make that choice closed with or near the end of exams (at the latest).


How can I write a book about paper writing which contains real examples without violating copyright?

The best solution would be to get permission from each copyright holder for each paper/snippet you use. This is often seen in books ie a list of figures and a statement of permission from each author X and Y and Z.

Using the material may be ok at the moment because it is for an educational purpose, but to put that into a book is probably going to be more a business/profit purpose which is different for copyright...

But I get the impression that you don’t want to do this as you mention “I have hundreds....”

You will need to check this properly with a copyright lawyer / legal team...


What are predictors of the success of PhD students?

The major quantifiable predictor of success in research is... success in research. People who have done research successfully in the past are more likely than not to continue to do so.

For students that have not done research in the past, the best predictor I have seen for success (whatever that may be) is expressed in a quote from The Unwritten Rules of PhD Research, by Marian Petre & Gordon Rugg:

  A willingness to learn for themselves and good judgement about when to stop and ask for feedback.*

It's not exactly quantifiable, but you can get a sense for it in an interview.
(Of course, this quality can be learned, so a lack of it doesn't necessarily predict an inability to succeed at research.)

* I took this quote completely out of context; the authors there are actually discussing the role of the PhD advisor, and they mention this quality in reference to a student "who can be pretty much left to get on with it, with supervisory meetings being something that both parties enjoy, and where each party learns from the other."


Where does the funding in business school PhD programs typically come from?

I don't know the answer for sure, but here's a few things you can try that will probably uncover the answer:

First off, go to the school's website and look at the pages for current or prospective PhD students. Usually this will explain what financial support is offered, and possibly where it comes from -- e.g. departmental fellowship (coming from the department's budget), or research assistantship (coming from faculty research budgets).

Look up the current PhD students. Scan through their websites and CVs for any fellowships. Then look at their papers. See if their papers acknowledge funding sources. All of my papers from my PhD student days have a footnote thanking support from a National Science Foundation (NSF) grant and this is indeed what paid for my studies.
You can also look up some of the faculty that have PhD students. Do their websites/CVs acknowledge any funding?

Lastly, business schools tend to get a lot of money from MBA students. Harvard's MBA tuition is $73,440 per year and their current enrollment is 1,859 students.  Ignoring financial aid, that's a revenue of $136,524,960 per year. They can definitely afford to support a few PhD students! I suspect that this is the main funding source.


Should I go for a PhD in Oxford University?

If you will think of time spent on the PhD as time wasted, don't do it.

However, in considering the pros and cons, do remember that PhD students who are having problems are much more visible than the ones who are enjoying the experience.

Supervision should be a benefit, not a downside. I remember some very interesting conversations with my academic advisor.

People working excessive hours, other than for short periods during emergencies, are less productive than those who are getting enough sleep, exercise, and social life.

If you experience isolation, you are doing it wrong. A PhD is a time to network with other researchers in your chosen field, including but not limited to fellow graduate students.

Writing your thesis may be the one time in your life in which you can write about your research area without limiting yourself to a few pages. Why would "thesis work" be a negative?


Is US experience usually required for TT jobs?

This is a bizarre requirement that I have never seen and sounds unwise to me, except maybe for a position requiring specific U.S.-centric expertise, e.g. a search for a law school faculty member specializing in U.S. constitutional law (even then, requiring a U.S. PhD/postdoc sounds to me like the wrong way to ensure that the candidate possesses the relevant expertise). And no, I do not see why it should matter that this is an Assistant Professor position.

Based on my experience with bizarre/illogical rules at organizations, I'm guessing that what happened is that the department that is requiring this at one time had a really bad experience hiring someone without a U.S. background, and after that someone there decided to make sure that that particular mistake would not be repeated, no matter how many good opportunities that would mean missing out on.

Note that while I think this is a silly requirement, at many U.S. universities a tenure-track candidate who has no U.S. teaching experience could reasonably be considered by some people to be less competitive than another candidate who possesses such experience, all other things being equal. But this judgment call does not require a special rule, since being well qualified to teach to the standards of the university is already a requirement of the job.


Should I tell my referees that my application got rejected ? (I intend to re-apply)

I think the answer may depend on the exact relationship you have with your referees. I would think that if they were willing to write you a reference letter in the first place, they are invested in you and your academic success enough to warrant an update on your graduate admissions status. I think if you just emailed them for a new letter, they may wonder why you're requesting more letters relatively late in the application cycle, or they may ask about the status of your past applications. In either case, it is likely that you will need to disclose your rejection, so perhaps disclosing it first is a better strategy.

Plus, this may be a good opportunity to solicit feedback from them on your past application so you can incorporate any feedback given into your April application.


What specific techniques can help someone facing mental health problems (depression, anxiety, ADHD) have a productive academic career?

First, please know that you are not alone and that it is possible to pursue a graduate education even with mental health issues. Several studies have actually indicated very high rates (as much as 40-60%) of anxiety and depression among graduate students (Arnold, 2014; Bernstein, 2015; Wyatt & Oswalt, 2013). So, there are students who have mental health issues who are still pursuing a higher degree. That said, just because it is common doesn't mean it is accepted. Stigma is common in academia, as it is in the rest of society (Pescosolido, 2013), and students may fear being stigmatized if they discuss or reveal their condition. Also, mental health issues, like any physical illness, bring additional challenges that must be managed. Fortunately, there are several things you can do to identify the self-management approaches that may help you succeed.

(As personal context, I have a neurological condition and have experienced periods of depression. I am successfully engaged in a doctoral program).

Take care of yourself

You rightly noted that some of your cognitive difficulties may be due to your mental health symptoms. Depression, anxiety, and ADHD have all been shown to compromise executive function, such as attention, concentration, memory, and problem solving (Biederman et al., 2006; Castaneda, Tuulio-Henriksson, Marttunen, Suvisaari, & Lönnqvist, 2008). As you continue with treatment, you may find that some of these difficulties begin to resolve. Whether you pursue graduate school or work,  prioritizing your own health and wellness is key (Myers, 2012). Some graduate programs are notorious for suggesting students engage in “self-care” but have such grueling schedules that this is difficult. Guard your well-being ruthlessly. If your physical and mental well-being suffer, so will your performance in other areas of life. Specific suggestions:

Be open with your mental health providers about your academic and
career intentions. Discuss treatment options in the context of being
able to effectively function in a graduate school environment. If you
find certain medications are causing side effects that impact your
academic functioning, bring it up and address it. Determine whether
there is a risk of developing a tolerance to your medications so that
they would become ineffective. If that’s the case, work to identify
two different medication regimens, so when you develop a tolerance to
one in the middle of the school year, you can seamlessly switch to
the other. I have found many professionals are sympathetic to
students who express interest in higher education and was able to
effectively partner with my providers.
Identify a routine that contributes to your well-being and stick to
it. For example, if you know that an irregular sleep schedule
contributes to your anxiety, make your sleep schedule a priority. If
you know your depression worsens when you don’t get enough light, and
realize you’ll be working in a dark, interior office, ask your
provider about light-box options.
Consider tracking your schedule (sleep/waking times, eating times and
amounts, etc) and symptoms on an ongoing basis, or in periods when
your symptoms seem to worsen. This can help pinpoint instances where
your routine has become disrupted.

Operationalize your academic challenges, then identify possible solutions

First write down a detailed, specific list of the ways in which you are struggling academically. I posted several follow-up comments to your initial question, because it wasn't clear to me how your studies were being impacted by your symptoms. Determine if there are specific activities or tasks that seem to have become harder in recent months. Once you have list of specific examples, it will be easier to identify specific solutions. Some examples include:

Problem: Low energy/motivation. Possible Solution: Create a concrete schedule, identifying when you will complete brief, manageable assignments. Unlike a to-do list that is open ended, this involves scheduling writing your methods section for your biology paper at 6pm on Tuesday. Rather than dread completing a task at some point, you’ll know exactly when you need to knock that out.
Problem:  Poor concentration makes it hard to focus on long assignments. Possible Solution: Break tasks into smaller components (e.g., breaking a paper into individual sections), and take breaks in between. Remove other distractions (cell phone, email, TV) from the area where you are working. If you can’t resist temptation, go to the library and leave your phone at home.
Problem:  Poor attention makes it hard to take notes during lecture. Possible Solution: Audio-record lectures so you can listen to them later at your own speed. Join a study group where you can compare your notes and understanding with other students.
Problem: Difficulties with memory impact school work. Possible Solution: Identify new ways to study, such as taking more extensive notes, re-writing your notes (this is more effective than re-reading them), or using mnemonic devices.

Your therapist should be able to help you think through many of these issues. Additionally, your school may have resources for adapting to learning difficulties.

Identify external supports

In addition to the internal coping skills you are developing personally and academically, it is important to identify external supports. Social support is crucial to successfully managing ongoing mental and physical health conditions (Gallant, 2003; Kolbe, 2002). You’ve mentioned some feelings of embarrassment and worry about how you will be perceived due to your diagnosis. Disclosure of a mental health diagnosis is a delicate subject, primarily because there is still a great deal of stigma towards mental illness. Your decision to disclose will likely depend on whether you trust that the person you are speaking with will be accepting and that the disclosure will not result in negative consequences. In some cases, you might decide if feels safer not to disclose; this is your choice.

Possible sources of social support include:

Family and friends
Your therapist and/or medication prescriber
Professors, colleagues, classmates – You may find you are comfortable
discussing issues with trusted classmates, but not with your
supervisors. Also, keep in mind that schools and employers cannot
legally ask about mental health conditions in interviews and you are
not required to mention it. However, once you are hired, you can
request certain accommodations (see next point).
ADA officer – If you live in the United States, mental health
conditions are protected under the Americans with Disabilities Act,
meaning that employers and schools must make “reasonable
accommodations” to allow you to function within that environment
(Leibert, 2003). Examples of accommodations include longer testing
periods or moving through the program at a slower pace. Most schools
have an ADA officer or office that oversees students who want to
receive accommodations. Even if you choose not to disclose your
condition to your program, you can use the school’s ADA officer as a
source of support (Willyard, 2012).
Some academics and graduate students have been open about their own
mental health conditions and the impact it has had on their careers
(Keely, 2013; Kelsky, 2013a and 2013b; Shine, 2013). These blogs can
provide additional examples of managing mental health conditions in
academia.

There are two brief caveats. First, if you choose to disclose you might need to educate people on your conditions. They may not initially understand how it impacts you. You can choose how detailed you want to be; sometimes a general explanation is sufficient. Second, when illnesses are “invisible,” and the symptoms are not immediately apparent to those around us, even people who know you have a certain condition can “forget” about the impact it has on your life on a daily basis. You may need to remind them from time to time, and you may also need to remind yourself! This leads to my last point…

Remember to give yourself credit for managing both academic and personal challenges.

Managing a long-term health condition requires a constant amount of mental and physical energy (e.g., ensuring you get enough sleep, remembering to take medication each day, coping with ongoing side effects). Keep this in mind when you are tempted to compare your own performance, achievements, and routines to other students. Other students may not be facing the same difficulties, and may approach their academic endeavors differently. I’m not suggesting your illness will be an excuse to perform less well than others; rather, remember that in some ways you might be starting at a disadvantage, which makes your accomplishments all the more hard-earned.

References

Arnold, Carrie. (2014, February 4). Paying graduate school's mental
toll. [Web log post]. Retrieved from: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_02_04/caredit.a1400031
Bernstein, R. (2015, May 13). Depression afflicts almost half of STEM
students at UC Berkeley. [Web log post]. Retrieved from: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_05_13/caredit.a1500125
Biederman, J., Petty, C., Fried, R., Fontanella, J., Doyle, A. E.,
Seidman, L. J., & Faraone, S. V. (2006). Impact of psychometrically
defined deficits of executive functioning in adults with attention
deficit hyperactivity disorder.The American Journal of Psychiatry,
163(10), 1730-1738.
Castaneda, A. E., Tuulio-Henriksson, A., Marttunen, M., Suvisaari,
J., & Lönnqvist, J. (2008). A review on cognitive impairments in
depressive and anxiety disorders with a focus on young adults.
Journal of Affective Disorders, 106(1), 1-27.
Gallant, M. P. (2003). The influence of social support on chronic
illness self-management: A review and directions for research. Health
Education & Behavior, 30(2), 170–195.
Keely. (2013, February 11). How to keep moving forward, even when
your brain hates you. [Web log post}. Retrieved from:
http://www.littledose.keelium.com/2013/02/11/how-to-keep-moving-forward-even-when-your-brain-hates-you/
Kelseky, Karen. (2013a, February 13). Academia and Mental Illness: A
Preliminary List of Resources. [Web log post]. Retrieved from:
http://theprofessorisin.com/2013/02/13/academia-and-mental-illness-a-list-of-resources/
Kelseky, Karen. (2013b, March 13). Managing Mental Illness in
Graduate School: Some Recommendations (A Guest Post). [Web log post].
Retrieved from: http://theprofessorisin.com/2013/03/13/3546/
Kolbe, J. (2002). The influence of socioeconomic and psychological
factors on patient adherence to self-management strategies. Disease
Management & Health Outcomes, 10(9), 551–570.
Leibert, D. T. (2003). The mentally ill and access to higher
education: a review of trends, implications, and future possibilities
for the americans with disabilities act and he rehabilitation act.
International Journal of Psychosocial Rehabilitation, 7.
Myers, S. B., Sweeney, A. C., Popick, V., Wesley, K., Bordfeld, A., &
Fingerhut, R. (2012). Self-care practices and perceived stress levels
among psychology graduate students. Training and Education in
Professional Psychology, 6(1), 55.
Pescosolido, Bernice A. (2013).  "The public stigma of mental illness
What do we think; What do we know; What can we prove?." Journal of Health and Social Behavior 54(1), 1-21.
Shine, Jacqui. (2013, December 18). On Depression, and the Toll
Academia Exacts. [Web log post]. Retrieved from:
https://chroniclevitae.com/news/228-on-depression-and-the-toll-academia-exacts
Willyard, Cassandra. (2012). Need to heal thyself? gradPsych, January. Retrieved from: https://www.apa.org/gradpsych/2012/01/heal.aspx
Wyatt, T., & Oswalt, S. B. (2013). Comparing mental health issues
among undergraduate and graduate students. American Journal of Health
Education, 44(2), 96-107.


Is it acceptable to look up a student on the Internet to find out whether I have a conflict of interest?

First of all, let’s get something out of the way. You, and me, and everyone reading this, has on occasion googled the name of someone we know - a friend, colleague, student, professor or whatever - to see if we can find out more about them. Some of us do it more frequently than others, and some of us are fine doing it out of sheer curiosity while others feel a need to rationalize their behavior with arguments about trying to avoid conflicts of interest... but all of us do it. So, if it’s “stalking”, then everyone’s a stalker, and the word “stalking” ceases to have any meaning. Which would be a shame, since there are in fact genuine stalkers out there, and it’s sadly necessary to have a word to describe their behavior.

Now, getting to your specific question: you ask about ethics, but this simply isn’t an ethics issue. You can ethically google whomever you want whenever you want. It’s what you do with the information you obtain once you have it that may or may not be ethical. It may also be inadvisable to google your students, or generally to develop the habit of googling lots of people, for reasons unrelated to ethics. Personally I try to keep my people-googling to a minimum so that I don’t walk around feeling that I’m a nosy person who gets into other people’s business that doesn’t concern me. (I also worry that I might find something I would be better off not knowing, and then I’ll have to either pretend that I don’t know it, or admit to the person that I know it because I googled them - pretty awkward either way...). In any case, I don’t think it’s unethical, and if you feel like you have some good reason to do it, I think it’s perfectly fine.


How to remind a professor about my previous mail that was sent two months ago?

Simple! Forward the same email to the professor, and let him/her know if he/she has any update on the position. Then the professor can catch up with the last email you sent by scrolling down to this forwarded email.


Academic Statement of Purpose vs NSF Personal Statement

There will be many common features, but the NSF has many highly stylized requirements, including "broader impact" and such, which would seem stilted or hypocritical outside that venue. NSF has a page limit, rigid formatting requirements, many other formal requirements, none of which matter in a statement of purpose. You have room to be more sincere, more genuine, explain more fully in your grad school application's statement of purpose. Also, unlike the NSF, where there is some compulsion to pretend that you already know what you're doing and will start research immediately, grad school applications (e.g., in mathematics) can easily and reasonably acknowledge that it might be premature to be thinking about PhD-level research prior to grad school.

(I don't necessarily hold a grudge against NSF over some of this, because they have to "make the sale" to Congress, in terms Congress-people can understand and find compelling, in order to get the money...)


Are Governement Open File Reports "published" online later published as journal articles considered a duplicate publication?

Whether this is duplicate publication likely depends strongly on the nature of the report, the extract, and the journal's policy.  Let us set aside journal policy for the moment, and discuss the general principle from a scientific honesty perspective.

One of the key reasons to disapprove of duplicate publication is because it inflates the apparent value of a piece of work to the author (by adding to their CV) without significantly increasing the value to the scientific community (since the article is already out there).  So: what is the value that will be added by extracting this portion of the report?

With a thesis, my typical interpretation is that a chapter extract adds the benefits of peer review and condensation of a complex and often sprawling source material into a more accessible form with a clear and focused message.  Now let's apply this same analysis to a report: some technical reports have a strong internal community review process before publication, in which case the benefit of peer review is unclear; others are thrown together in a much more hasty and ad hoc fashion, in which case peer review has a much clearer value.  Likewise, if your material is already a neatly focused and separable subsection, then the value of an extract is less clear than if it is scattered throughout.

There may be other reasons that an extract publication would be significantly different as well: for example, regulations on the report process might have prohibited certain lines of discussion, or there may be new data that can be added.

The bottom line is this:

Consider the value added for the scientific community by creating an extract; if it is significant, then creating an extract is reasonable to do.
In interacting with editors, be completely clear and transparent about what you have done and why you think it's valuable, and while some editors may disagree and reject your paper, you will not face any accusations of improper behavior.


Peer review: Is this "citation tower" a bad practice?

I think this requires some nuance. You seem to suggest that citing the earliest usage is preferable, and it might be. But it might also be the case that each subsequent usage adds something to the context. That is to say that the citation appears in the chain for some particular use and the reader of the current paper might find it useful to explore that history. Each of those citations is surrounded by context that can be useful.
If you always cite only the earliest usage, then the reader has no hints about the overall usage context of that thing cited. And the current author might be inviting the exploration.
Of course, it might also be that the author(s) considers the lemma to be a minor point and has used the citation they found without chasing the chain back themself, not seeing any need for it in the current context.
Overdone, in mathematics, we just always cite Euclid.
So, I don't think citing a later, rather than an earlier paper is a bad practice necessarily, but could be in a particular instance.
You can always note the other citations in your review and point to the earliest one without making any specific recommendation.


What's a novel way to say "all errors are my own"?

Making the manuscript error-free is left as an exercise for the reader.


Asking for recommendation letter from manager for graduate school

It seems reasonable to me, especially since rec letters are typically on a hard deadline. Worst-case, line up another recommender in case the one you hope for doesn't come through.

Slightly tangential, but... I've noticed a few things about rec letters from people outside academe that can make them harder to take seriously:

Extremely brief -- like, five sentences or fewer brief. Cover-letter length is more desirable.
Vague and general, not giving a strong impression of the applicant's specific individual potential
Make mention only of very low-level skills and abilities (e.g. showing up to work on time -- nice to know, but not exactly helpful in an admissions decision)

You may want to coach your recommender a bit, carefully and politely, about things it would be useful for them to say. You don't have to ghostwrite (and probably shouldn't; that's on the razor edge of ethics), but you can ethically suggest anecdotes about your work, or projects you've done, that you think say something unique, positive, and discipline-relevant about you.


If the studies used in study X are relevant for the  discussion you are writing - and not just because the author of study X cited them, you should cite them individually.

However, as you are writing  a academic text, you should at least put some effort into contextualising methodology of other stories. The extend of this would of course depend on the overall relevance of study X to the main argument of your own paper.

Citing a work can mean two things:

a merely mechanical notice saying you have read a particular text and used some idea and/or wording from it
a complex statement on the orientation of your research, for example what research tradition, school or network you follow

So if you would like to quote your study X (as it is nicknamed in the question) simply for referencing a source on a statement, it would be enough to quote study X and not the underlying works.

However, if the underlying works of study X are important in the argumentation where you cite them in - for example in a discussion - it would be a good thing to show you have read and reflected on the literature the study X is based on.


When repeating a course, why are the grades averaged for GPA?

As others have said, different universities -- and even different programs within a university -- have different policies about when repeating a course is allowed and if so, how it counts towards the GPA.

Actually, it's even more complicated than this: the same student enrolled in the same program can have multiple GPA's! It is my understanding that at many if not most American universities, there is one GPA that is simply the average of the numerical scores (on a 4 point scale) over all courses one has taken.  With respect to this system, if you take a course once and get an A and then again and get a C, then it does not go into your GPA as a 3.0; it goes in as a 4.0 and a 2.0.  The average is the same, but the weight is twice as much, reflecting the fact that you completed two courses rather than just one.  However, GPA "in your major" may be counted with a different weighting system.

You seem to think that there's something unfair about averaging the grades.  To me, it sounds like a generous system: and in fact, I don't think that it is guaranteed that a student is allowed to repeat a course to improve their grade if the grade they got the first time around is considered "satisfactory".  This practice again depends on the university and the program.

You write:

  The student has exhibited an "A" level of "knowledge" so why penalize them.

Sorry, where is the penalty you speak of?  They got a C and they got an A, and both are being recorded.

  If the student attempted to learn on their own and did not attain "requisite" understanding prior to attending the course but ended doing very well in the course they would not be penalized.

Again, I don't see how anyone is being penalized.  A low grade is not a penalty.

  Or perhaps offer two measures of GPA, one as a summation of everything and one that only includes the students best performance for each course taken?

If you want to present this alternate calculation of your GPA to someone else, you can.  But you also have to record the official GPA.

Finally, I think that the practice of allowing a student to take a course multiple times and only record the best grade is a poor one, for several reasons:

i) It is fundamentally not transparent.  The standard unit of coursework in most American universities is the semester-long course.  You are registered for a certain number of courses each semester, and you get grades for each of them.  If grades get replaced by later grades, this kind of information is lost, and it may be that the student is recorded as taking nothing during that semester!  This leads to:

ii) Because high course grade are very desirable, this practice would encourage students who got good but not optimal grades to repeat the course until they got the highest possible grade.  If you think this through soberly for a while, you'll see it's just a bad idea.  The whole point of a grade like a B is that it's good enough to move on to the next course.  Students who repeat courses until they get A's could take much longer getting through the program.  It will create a culture where most students who are taking the course the first time are taking it "for practice only".  If courses were heavily populated with more advanced students who did well the first time around and are insisting on taking it again to get the highest possible grade, then that could seriously skew where the course is being pitched, which would encourage yet more students to repeat every course they take.  Finally:

(iii) We do not want students to be able to graduate with a perfect GPA if they spend seven years in college instead of four.  Moreover -- sorry to divulge the ugly truth -- we don't want a substantial percentage of college students to have the highest, or essentially the highest, possible GPA.  While the competitive nature of GPAs in the current university environment has many unpleasant aspects, the vast majority of American culture is fully bought into it...especially including the students.  If 50% of every class got a 4.0 GPA then most of the advantages of having such a high GPA would evaporate, and employers / graduate schools would hire you based on other metrics.  (Note that people often talk about grade inflation, but really grade inflation is only a problem to those who are not familiar with the current university system.  For everyone who is sufficiently informed, it doesn't matter whether the average grade in a course is a C or a B+.  Still, after taking about 40 courses, there will be a small tail of students who have gotten almost all A's.  So there is no problem here.)


Acceptance in PhD Program With Unfortunate Background

The pictures and the posts are rather different issues. Whether there are nude pictures of an applicant available on the internet is no business of an admissions committee, regardless of how they got there. This aspect is covered well in another question:
Can leaked nude pictures damage one's academic career?
For the racist comments however, the fact that you did not write them is essential. If you had written them, it would be very legitimate to hold it against you. If these show up on the first page of Google results for your name, you may want to include a statement with your applications that horrific comments with your name attached to them exist on the internet, and that you neither wrote them nor agreed with them.


Is there a citation network crawler [tool] for building a bibliography?

This can certainly get tedious, and searching in both directions (i.e., using the "cited by" entries) is certainly the way to go.  That said, if you start at your university library, especially a medical library, you will have access to tools that are tailor-made to do medical searches, like Medline.

If you're having issues, by all means, go talk to a librarian.  Their job is to help people like you get their jobs done.  They absolutely love to do it, and they're usually very good at it.

To put things in perspective, though, 15 years ago the only way to do what you're trying to do is to wade through hard copies of the Scientific Citation Index and photocopy the articles after finding them in the Medical library stacks. (i.e., -- we used to walk thirty miles to and from work, uphill both ways!)


Is using a survey classifications plagiarism?

If properly cited, I would not consider this plagiarism, but you should be very explicit in your citation that the categorization you use is specifically from paper X. I would be more concerned about reusing the categorization if you are going to essentially discuss the same works that the survey paper has already done; if so, you are probably better off citing that paper and only summarizing what is most applicable to your own paper rather than trying to recapitulate an already wonderful work.


If you simply want to work with them and don't require either a formal position or funding then you just need to talk to the PI of the research group and deal with visas and such.

But if you need funding, it is a separate issue that might be handled by the PI (via their grants) or by the university. You might be able to arrange your own grant, of course via some agency.

If you desire some official position, such as formal matriculation, then that can only be granted by the institution. That will generate an academic record for your stay. Later in your career, the position of Visiting Professor might be open to you, but from the institution.

But you need to talk to the PI in every case. Give them your qualifications and your interests. Treat it like you would any application. Convince them of your suitability and likelihood of success.


It is the difference between the role or job and the person who is doing that job.
The person has achieved the status and title of Professor. That person can take the position of the "Chair of Computer Science at the University of Somewhere".
Sometimes a particular Chair will have been endowed or funded at a University and then a Professor is recruited to take that Chair. That  person could have  moved from another Chair at some other University.
Some of  the Chair endowments are quite old, like this example from 1702 in Cambridge: https://www.ch.cam.ac.uk/alumni/new-name-our-oldest-chair


What factors do I consider before deciding to ask my summer research guide for a recommendation for grad school?

I am unable to decide if I should be asking this professor for a letter of recommendation

Of course you should be asking!

Specifically, you should be asking whether this professor is willing to write you a strong letter of recommendation. The word “strong” (or a similar synonym) is crucial here. You want to make it clear that a weak letter may do more harm than good, and you’d much rather receive honest negative feedback now, face to face, while you still have some time to improve, than to risk spoiling your application.

Stop trying to read the professor’s mind.  Stop trying to imagine all the impostor-syndrome-inspired weaknesses that the professor could write about. Every applicant has weaknesses.  Just ask.

  unsure of whether this is something that I'm good enough to do

Do not listen to the Impostor Syndrome. There is no such thing as being good enough; what matters is what you do.

And what you are doing is pursuing an internship that addresses the gaps you perceive in your own background. You see a gap in formal CS preparation (even though that preparation is rare among programmers, and even rarer among physics students), but you are addressing it by learning to program anyway. You see gaps in your mathematical background, but you are pursuing a mathematics internship that requires you to do a lot of independent study.  You are deliberately working outside your comfort zone to strengthen your background—of course you feel overwhelmed!

In short, you’re acting exactly like a researcher.

I agree with Buffy. From out here, it looks like you’ll be fine. Keep up the good work!