Why are research papers written in language that's difficult for undergraduate students?

In short, because it is difficult to express something concisely, and precisely in language that any undergraduate can understand.

Conciseness is required not just because without it every report would be inconveniently long to write and to read, but because it would be harder to understand.
It would be harder to understand because the jargon neatly encapsulates a bundle of concepts (e.g. its definition and related properties) into a single concept.
And we can only be thinking about so many concepts at a time.

Consider the statement about the Stone–Weierstrass theorem:

A mathematician might say:

  Polynomial functions are dense in C[a,b] ⊂ (ℝ→ℝ)

To expand out the math, so that one does not have to know the notations on gets:

  Polynomial functions are dense in the space of continuous real-valued functions defined on a closed interval.

But still perhaps the word dense is beyond the understanding of an undergrad.

So let's expand it to not use that:

  For every continuous real-valued function defined an interval; then for any positive real constant one might care to define, a polynomial can be found such that for every point on that interval the absolute difference between the value of that polynomial and the value of the real function at the point is smaller than the constant.

So that is how much most space it took and how many more ideas one has to keep track of for that fairly simple use of jargon.
When thinking about such a problem rarely is the mathematician thinking about what is going on with the distance of points in a hypothetical polynomial.
They are just thinking "it is dense".

Now imagine expanding all the terms in the generalized version of the above:

  Stone–Weierstrass Theorem (real numbers). Suppose X is a compact Hausdorff space and A is a subalgebra of C(X, R) which contains a non-zero constant function. Then A is dense in C(X, R) if and only if it separates points.

(This last is a direct quote from the Wikipedia page on the Stone–Weierstrass theorem, the preceding quotes are not, though are to some extent paraphrases.)

Then to go the other point on preciseness,
There is a really high chance someone is going to comment on this answer saying that actually my statement is not quite correct, that I've not fully captured the definitions in my explanation

While, yes, every paper could repeat some introductory information,
then that would inconvenience any reader who is looking to find the core idea,
since it would be drowned in a sea of background material.

And you might say that "this answer is hard to understand, in the expanded form, you did a poor job at making it understandable to an undergraduate.",
and I'ld say "Fair enough; I'm not great at making things easily understandable."

And that statement holds for most other researchers too.
Not what most are good at -- it is why there are specialists in scientific communication.


While applying for PhD in mathematics, am I better off dropping a course I'm performing poorly in?

(I am the graduate coordinator of the math department at UGA.)

Point set topology is a good course to take for an undergraduate hoping to go to graduate school in mathematics, but it is not a required one for admission to any program that I know of.

If you are asking whether it looks better to have a transcript containing point set topology with a poor grade vs. a transcript not containing point set topology at all, I would say: if it doesn't appear at all, it looks much better.  Point set topology is an introduction to the abstraction / generality of graduate level mathematics, perhaps more so than any other undergraduate course because nowadays we don't really have separate undergraduate versus graduate offerings in the subject: the point set topology that you learn as an undergraduate is in many cases the point set topology that you take with you through your graduate career.  So doing well in that course looks like a good predictor of success in graduate level coursework.  Thus by doing badly in it, you're showing a clear data point which is not in your favor.

I should say though that dropping the course is not helping out your education or graduate preparedness at all: at best, it's papering over the problem.  Are you sure you can't redouble your efforts and actually do well in this important course?  Or the flip side of the same question: are you sure that you can truly drop it with no stigma whatsoever?  E.g., will it show up on your transcript as a withdrawn course?  Will faculty who write your letters know that you really struggled in this important course and responded by dropping it?  (If I were writing a letter for such a student and had this knowledge, I would probably feel honorbound to mention it.)  These are things to think carefully about and discuss with faculty advisors.


References in supplemental material - include in main reference section?

It's common practice, however, these might differ between journals.
Likely, when you include them in the main references, they will be flagged as not being mentioned in the manuscript and removed. Unless otherwise instructed in the author guidelines of your journal of choice, simply add them to the supplementary material and see what happens.


Is it unethical to use not your real name when asking for questionnaire survey?

This is going to depend on your IRB/ethics review. Not revealing your name is probably ok. Hiding your affiliation is going to be harder since the IRB will want to guarantee the participants can contact someone if there is a problem. That said, if it is relevant to the research, the IRB can probably work with you to figure out something that works.


PhD thesis defense - is there a separate defense session with one's graduate committee?

That varies from place to place, even in the US. Your advisor will give you the best advice. But yes, a private session with your committee is pretty common. They want to assure themselves that you are "seasoned" and have both the required depth and breadth to be awarded the degree.

Again, your advisor will tell you what to expect, but it is possible to get questions that are unrelated to your thesis, or even to your specific subfield. In mathematics, members of a committee often have different specialties and may want to know what you can say about their own field as they may have only a sketchy knowledge of yours and of your thesis.

Don't, in general, expect it to be just a presentation. The public part needs to be a bit less technical in tone, since many of those present are looking for an overview. That isn't enough, of course. You need to say what you did and the key ideas that got you there.


Paper based on Master Thesis - Disclaimer necessary?

Yes, this is necessary.

Self Plagiarism may seem like a strange thing to be worried about, but there are many reasons to avoid it the way you would any other plagiarism:

Some journals use double blind reviewing, so reviewers can't distinguish between self-plagiarism and plagiarism.
You may have received funding for your thesis, which is probably acknowledged in your thesis, but not necessarily in the paper version.
People reading your paper may want to read the full Master's thesis, since theses generally contain more detail and are less space-constrained than papers.


What to do when PhD is becoming hell due to non-cooperation from supervisor?

My 2 cents :

Graduate as soon as possible, The fact that this is with high or low grades is not relevant here
Apply for a postdoc position in a place where PhDs are not graded (France for instance)
Publish the (very good) stuff that you intentionally kept hidden until your graduation

After step 3 your record will be clean, and all this "hell stuff" will be far from you. To obtain a position in academy, the only thing that matters is the quality of your research (that can be seen in the papers) and of your teaching (for that you requires references), nobody will care about what happen during your PhD.


How to deal with inactive students in a testing session?

It seems to me that students are permitted to spend exam time "as inactively as they choose," and that barring some truly exceptional edge cases it is neither fair to them nor the best use of your own time to try to deal with inactive students during the exam itself.

I'm sorry the behavior is stressful for you, but I don't have a good understanding of why.  Not working or writing on the exam is not an effective cheating technique; falling asleep or staring out the window less so.  If you see students with wandering eyes in a way that actually makes you concerned: okay, tell them not to do that when you catch them doing it.  But that's a problem of unwanted activity, not inactivity.  Moreover, you write

  Frequently the paper I get back is mostly blank after an hour of inactivity like this.

I find it kind of strange that you think that a student (whom you know is registered for your class; no funny business there) who turns in a mostly blank exam is somehow cheating.  Cheating means trying to succeed through illegal means; if they are pathologically avoiding trying to succeed, I somehow doubt that cheating is the explanation.

You write

  It puts me on edge because it's so inexplicable,

Okay, I get you there: it certainly must be distressing as an instructor to witness students walking into an exam -- i.e., a situation which is a pressure-packed performance opportunity to most students -- and respond to the high pressure situation by basically doing nothing.  I agree that there's something going wrong here.  However, I don't think that you should fix the problem by proctoring the exam differently: rather, during the exam you should take note of which students are behaving in this way, and then make a point of talking to them about it after the exam (presumably after it's been graded rather than immediately at the end of the exam).  In my experience, if a student is otherwise even moderately engaged with the course (coming to class, turning in homework) then they are very likely to be responsive to such questions on the part of the instructor.  Maybe once in a blue moon you get a student who really doesn't want to work much on their exams and really doesn't want to talk to you about it.  OK: you tried, they didn't, they'll fail.  But they have the right to play it that way, it seems to me.

Let me end by commenting on another answer which suggests running future courses with a policy that says students' exams can be taken away from them if they are not working on them.  While clearly well-intentioned, I think that's a bad idea.  You simply do not have access to students' interior processes and you shouldn't pretend to do so: maybe a student who is staring out the window for half an hour is nevertheless working on the one problem that they don't know how to do and is going to write out solutions to all the problems in the last ten minutes.  (I mean, probably not, but maybe.)  It's just not defensible enough to respond to inactivity on an exam by taking the exam away from the student (and especially, with a policy to return it later on if they show suitable penitence).  A student who has an exam taken away can go to the department chair or the dean saying "My exam got taken away from me just because I was thinking rather than writing."  If I were the chair or the dean...c'mon: the student has a very strong case.


How long should a cover letter be when asked to include statements of teaching philosophy and research interests?

For readability, it is certainly preferable to append.

If you feel your cover letter is a little skimpy, I suppose you might put something autobiographical in the cover letter, that was perhaps a little to personal for the actual statement.  For example, "my teaching philosophy was largely developed during my year as a VISTA volunteer teaching in ...."  (That's just an example -- your situation could be completely different.)

The cover letter is a good place to tie the threads together of the various portions of your application, to show yourself as a whole person, to project your personable qualities, and to get the reader interested in learning more about you.

I think you're right to keep it to one page.


Can a professor post a grade online and then change it?

In the US, universities generally have a policy that describes under what conditions a professor can change a grade that has been officially posted to the student's record.

For example, in my university, the official policy is that an instructor may change a final grade that has been officially posted to the student information system if there was an error (e.g. in the calculation of the grade) or if the instructor overlooked some work that the student submitted1. The web interface asks me to supply the reason when I submit the grade change request:

When I submit a grade change request after grades have been posted, it goes through another layer of approval (department head) but barring exceptional circumstances, these changes are routinely approved.

"Intermediate" or "unofficial" grades (e.g. grades that are posted in Blackboard but not in the official student information system, midterm grades, grades on assignments that aren't the final course grade, etc.) typically are not subject to those rules, and can be changed more easily.

1 Although students persist in asking me to change their grades for all kinds of other reasons.


How to cope with feelings of powerlessness on a PhD?

Although I agree it may be worth considering whether you're suffering from depression as Alexandros suggested in his comment, and it's something you should bear in mind. However, I think that's either a symptom or a related-but-not-the-main-problem-here-problem. This seems to be, at the core, a case of professional burnout. Possible triggered by depression, possibly causing you to feel depressed, and certainly something you should bear in mind if you feel it is affecting your life: but for the rest of this answer I'll focus on the direct issue, while suggesting you consider seeing a counselor.

You've likely been in education or academia for the last 20 years or so by now, possibly including 3-6 at your current institution, and perhaps you need a change. If you were in the working world, you'd probably be starting to look for other opportunities if you felt like this: moving on to pastures new, the next challenge, something which interests you. This is pretty common at this stage of a career, most people move on from their first job within 2-4 years of graduation (as an undergrad). If you see your PhD as employment following your degree (albeit one that confers another degree) you can draw the parallel (lol, maths joke)

Unfortunately with a PhD, you're "locked in" for a fixed period. You have a vested interest in time and, likely, money, along with a concern that if you back out of it before it's completed, it will look bad on your resume.

It's certainly a slightly tricky problem to negotiate, but let's look at your options

Continue with the PhD, battle through, get it done and then look at what you really want to do. This has the advantage that you'll complete the task, which looks good on your Resume, but may be too much if you're still fairly early in your PhD
Back out gracefully. Accept that you've made a mistake in your career path, apologise to your supervisor that you've only realised this now and then move on with your life in the direction you'd like to go. Your supervisor will likely be disappointed, yes, but I hugely doubt he will think any less of you. People change their mind, people realize that they're on the wrong career path all the time, and people involved in education tend to understand that. His disappointment will not be that you've upset him, but because he almost certainly believes you will be an asset to the discipline/department.
Try to change the current situation - talk to your tutor and explain your issues and concern. See if there's any "wriggle room" for changing the approach and the way you interact. State it tactfully, in a "Would it be possible to try xyz, which I think will help me because abc and def" way, rather than a "You do abc, and it annoys me". This may help you to actually enjoy the PhD for a while.

My personal opinion is that you're better off backing out unless you're in the last 18 months of the PhD (in which case you've already invested a lot of time/effort and it's probably worth powering through). If you intend to move away from Academia, you probably don't really need a PhD anyway, and I think it's better to cut your losses and go find something you really want to do.

I'd also recommending this answer which covers some of what I've just said, but also some things I haven't.


Pros and cons of teaching assistantship as a masters student intending to go on to industry job

I can't really comment on the financial side, that all depends on your own financial situation. The main advantage of TAing, besides the money, is that if you want to teach in the future in any capacity then getting some experience teaching is vital. If you don't plan to teach in the future, then the work experience is probably negligible. There are probably some "soft" benefits that could be useful in industry, such as learning to effectively condense and explain material in your field, but I doubt they would be very helpful in terms of getting hired.

In terms of balancing work, that also mostly depends on the courses and your own productivity. I will say that at many PhD programs, 3 courses + a 15-20 hour TAship is a pretty standard workload for the first couple years (assuming you don't do significant research your first year or so), so it's probably doable.


Professor expects me to attend a conference. I can't afford to go,even with 50% funding

I am really hesitant to discuss my financial shortcomings with Prof.
  M, or else he assumes that I can afford the travel.

I think you need to get past this. You do not have financial shortcomings, you just don't have money. Working on a PhD without family financial support, with existing student debt, and with limited school support is not easy. I respect you for doing it. Take pride in making the hard choices that involves.

With that attitude, explain to Prof. M that you cannot afford any travel expense, and will only be able to go to the conference if your expenses are fully covered. Check any funding sources he suggested, and ask advisors at your current university if they know of any sources.

From comments: Also check with the conference organizers. They may have scholarships or be able to discount the conference fee, and find free or inexpensive accommodations. You may need to work several angles to align the total cost with the available funding.

If you can't get the full funding you need, tell Prof. M. that you regret you cannot attend the conference. At the worst, you will have to withdraw the paper. However, there are alternatives the conference may permit.

Remote video presentation
If anyone from your current university is attending, ask them to present the paper
Prof M. may be able to get a current student or a collaborator who is attending the conference to present it.


What's a realistic workload per blackboard hour for teachers during the semester?

In my opinion this is hugely course-dependent, and standards vary a lot between universities and disciplines.

If your task in the class is really almost only lecturing (e.g., you have assistants that run any class projects etc., and who answer most of the "standard" student questions), and you already have everything prepared, your actual effort for the course may be close to the "blackboard time" - but even in such cases, you probably want to count in at least half an hour before each class to refresh your memory on what material you plan to cover in a specific unit.

If you have any other tasks at all in the course, "blackboard time" quickly becomes a very bad proxy for your actual effort. In my experience, course planning, answering student questions, office hours, organizing and/or holding supervision sessions, giving feedback on in-class exercises, dealing with exceptions, preparing and grading exams, or dealing with teaching infrastructure can take a large, and highly variable, amount of time. These factors are also virtually independent of how often you actually speak in front of the class. Not all classes have all of those activities, but most classes have at least a few of the above elements.

In the course I recently wrapped up, I would estimate that a maximum of 1/5 of my actual work was done "in class", while 4/5 was preparing, grading/giving feedback, and organizing. However, in other classes I have spent close to 70% or 80% of my course work time "in class". It really depends on the course, your role in it, and how effective you personally are. Unless you have good reasons to believe this will not be the case I would assume that your workload outside of class will at least be as high as in-class (i.e., assume that if you are teaching one full day a week you will spend at least another day dealing with the various paraphernalia of teaching, even if you have everything set up and prepared - if this is not the case, I personally calculate that I will spend at the minimum one full day to prepare a two-hour session from scratch).


I got a very bad review from one reviewer, but the paper was not rejected

Since

the editor did not reject my paper and asked me to provide a revision

you can revise the paper and resubmit with a fair chance that it will be accepted. Respond to all the comments in the favorable review, either by changing something or explaining in your cover letter why you didn't.
Try to put the  tone of the unfavorable review aside so that you can decide whether addressing  any of the comments there will in fact improve your paper.
You could write the editor in advance to ask if this is a reasonable strategy. You don't have to withdraw just because one reviewer was unprofessionally nasty.


How to navigate convincing professor to submit a letter of recommendation without falsehood

I would say that this would be a different situation if the recommendation was for a potential employer, rather than for graduate school admissions. If this were for a potential employer and you might be expected to do Y, this would be a bigger issue, in my opinion.

Although the letter does not represent your abilities 100%, calling it a lie suggests that your professor knowingly stated falsehoods about your abilities on the letter, rather than it be an oversight as you describe. Sometimes these things happen. His writing a recommendation for you is outside of his other academic duties, so you are asking him to volunteer more work on top of what he has already volunteered to do.

In my many years on graduate school admission committees, we have only contacted references of candidates in cases where there is a questionable part of the application that suggests that the candidate is not prepared for the program or would be a potential problem. If everything else in your application looks fine, this may go unnoticed. Plus, the graduate admissions may find it strange that your reference submitted a revised letter. In my opinion, I would just wait to see if this comes up. Then, you can simply state, "Yes, my professor said in my letter that I did Y under his supervision, but I really was more involved with X and can only speak about X." This is very different than if YOU stated in your application that you could do Y. Your reference making a mistake would be more forgivable than if you knowingly made the same statement (if all else is fine with your application). If your professor didn't give you a copy of the letter, you would have never known that this is an issue.


Is it normal in Europe for graduate courses to be all in the evening?

Europe is not a country, but a continent. There is a lot of variability inside Europe. So no, it is not a European thing.

All Bachelor's, Master's and PhD courses I teach (in Germany) are between 10:00 ad 16:45. About 15 years ago I taught a course (in the Netherlands) in the evening for a part-time Bachelor's program aimed at people who work besides their study. For obvious reasons those programs tend to organize their courses such that they happen in the evening. However such programs tend to be the exception rather than the rule in my field (sociology) and the countries I am familiar with (Germany & the Netherlands).


Switching PhD programs after earning M.S

professors are people and understand that life happens. I do not think I would enjoy working with a colleague who would have a vendetta against a student for wanting to leave the program in order to move with their soon-to-be spouse. Be open with your supervisor and ask for their advise.

Also, if you want to go into industry/government, do not underestimate the importance of a phd. The ability to apply for grants or oversee a lab is valuable.


What can I do when some people stole my master thesis work and published it as their own work?

I have this one paper that has already gotten copied and submitted to some spam journals 5+ times. It literally happens multiple times per year (it has a catchy title that seems to appeal to a certain class of plagiarizers). I also usually learn about this through a Google Scholar alert.

The first two times it happened, I tried exactly the steps recommended by other answers. I contacted the authors (no reply ever), raised a stink with the journals (no reply ever), and contacted IEEE (the copyright holder of my original paper). IEEE indeed did react that they will look into it after quite some time, but nothing ever came out of it.

My lesson learned was that these things are basically impossible to fight. The authors or journals could not care less about ethical integrity, and for IEEE the measurable damage of one of their papers being "reprinted" in a different title and with slightly different words in an obscure scam journal that nobody ever reads is not large enough so that they would make an effort hunting down who is legally behind these shopfront journals.

The good news is that it is also completely irrelevant to you. I can assure you that your scientific contribution will not in any way be lessened by this paper existing, nobody will read the other paper (because nobody reads these "journals", period). For future promotions etc., the existence of this paper will not be in any way an issue for you. Science as a whole suffers (to a degree that we could argue about), but the fact that it happened to be your paper that they copied (as opposed to a paper by me, or somebody else) makes no difference at all.


Studying for the exam or for learning? Is there time later?

In my experience (which has been both as a student and a professor), the best way to do well in theoretical physics graduate school is to get a really good understanding of the material.  That will give you the best path forward.  If you try to memorize a bunch of recipes for solving all different kinds of exam problems, you are missing the forest for the trees.  Moreover, once you are done with courses and exams, you will need to put what you have learned to use in a research context.  In doing research, it's how well you really understand the underlying physics that is going to matter the most.

To solve particular problems in E&M or quantum mechanics, you may learn a lot of mathematical techniques, which can seem unrelated or disconnected at first.  However, many of them are really variations on the same underlying methodology.  For example, the solution of the Schroedinger equation using energy eigenstates is really a form of separation of variables, like that used in E&M.  Similarly, separation of variables in spherical coordinates is really the same as a multipole expansion.  The best way to see these connections is to work examples problems, and most good textbooks at the graduate level have problems that are specifically designed to illustrate the deeper connections between the different techniques you have learned.

So my advice to you (and to the students I teach) is to go for deeper understanding of the physics and why certain strategies work in certain situations.  If you master that, you will also learn how to apply various techniques as a necessary corollary.


Working on multiple research projects as an undergraduate with different professors

If he is just concerned that you will not have enough time to do both, it's up to you to prove that you can handle it.

But a general feature of academia is the presence of a lot of difficult and fragile personalities. It's not impossible that Prof. A took your choice personally, especially if there is any behind-the-scenes tensions between Prof. A and Prof. B. It's worth thinking about these things, but not too much. If Prof. A is going to be professional about it, there should be no further repercussions in your relationship with him.

To elaborate in response to your more specific questions...

  Was I wrong in not going to Prof A for advisement about this new opportunity, considering all he has done for me?

No.

I can't say whether or not you communicated with Prof. A in the most optimal way. Maybe things would have gone more smoothly if you said something sooner. But on the other hand, maybe you didn't need to tell Prof. A anything at all. There is no set rule or etiquette, it just depends on what your relationship with him is like.

  Or was I correct that I have the right to go and find other
  opportunities if I wish?

Yes.

You have every right to pursue whatever opportunity you think will be best for your education and professional development. Do your best to maintain good relations with the people you work with, but don't let that stop you from doing what you feel you need to do.


When I compare my results to others in the literature should this go in results or discussion?

The results section is for your results. The discussion section is for discussing them - and this includes the significance in light of other results.

Keep the former purely for statements, the facts of the matter. The latter is where you move into interpretation (and expanding on very brief comments which are necessary for reading results reported).


How to read 2 academic papers a day without confusion?

I do of course not know what your current work strategy looks like so I can only provide what I think are generally helpful tools.

Note-taking should be a priority, not only to avoid confusion but also to help you get an overview. set a target to summarize the paper in a about a page and try to capture the following:

What is the major question covered by the paper?
Why is it important?
What was done (experiments observations data)?
What are the major conclusions of the paper?
Did you find any new information of particular interest to you?

You may come up with similar or different key questions depending on th epurpose of your reading. The point is to make such short summaries of the papers.

Once you have the summaries you could consider organizing them in some fashion. There is no exclusive model to use and in fact the organization may depend on the purpose of your reading. You may find that after reading a number of papers a possible way to organize them can become clear. The main  purpose of this step is to bundle papers that have specific points in common.

You should also sort your papers (printouts or files) with your notes. There are many ways of doing this rom the analogue to data bases. Try to use a free reference data base system to get everything organized.


Journal editor made bad edits to my (accepted) paper - how do I respond?

I finally received proofs of the article, and was (more than a bit) upset at the edits.

How to respond?  Do not respond while upset.  Wait until you can respond in a calm way.

This is a perfectly normal occurrence.  Remember the journal relies on getting your work for free in order to get subscription fees to pay its expenses.  They need you more than you need them.  Do not hesitate to ask for anything that will help your publication improve.


Does taking a long time to graduate impact my Ms/PhD admission?

As a rule of thumb, the time you took wont matter, but the failing grade will.

However, if your goal is to get into a masters course in Brazil, many of them won't look at your undergraduate marks (I've served on graduate committees on two top brazilian math departments).

In these cases, you can be admitted by doing well on an admitting summer course, or on an admission exam (many of them nowadays use the Extramuros examination, or a local exam).

Even for institutions that will judge your undergraduate marks, it's not uncommon that a student with a failing mark get accepted. Usually they would indicate in their statement why they failed and how they did well on this course on the next time. The fact that you had to work is enough justification, if that's a localized problem and you have strong marks otherwise.

After doing well in your masters, your undergraduate marks will have a negligible impact on your PhD admission.


I just received a shameful F on 1st Year Writing. How negatively will grad school look at this grade

It depends on the school you apply to, but it's usually not a big deal to have one failure in first year.  I am making the assumption that by "first year" you mean literally first year - as in this is your first year in university and last year you were in high school.

I can speak with confidence only from a Canadian perspective, so please see what others say from around the world.  The vast majority of schools in Canada require you to maintain a certain average in your final two years of study in your undergraduate program, and the first two years are not considered.   I have at least two colleagues who failed more than one course in their undergrad first and second year and were still admitted.  See here as an example of what these admissions requirements are.

Doing a cursory glance at some international schools, the "last two years" thing doesn't appear to be universal but the admissions requirements are.  For example, TU Delft in the Netherlands requires a minimum 75% overall GPA and "scores in key subjects to be good", which I presume is dependent on the program see here.  No mention on failing grades and no inadmissibility is mentioned due to a failure.

Since it depends so much on where you apply, I can't say with 100% confidence that you will not have any troubles with your F.  However, I can certainly assure you that you are not the first person who failed something in first year and still got in to grad school.

A more serious question you need to solve for yourself, probably with help from your academic advisors if they exist where you are, is how to recognize and prevent this from happening again.  Failing a course basically means that there is a pattern of behaviour throughout a school term that led you to that state.  Unless your writing course had a single, 100% final, it's unlikely that you were surprised by the failure.  Recognizing the patterns early will help to prevent this again.


What are the differences between teaching in the quarter and semester system?

There is another variable at play, actually. Some places 2:2 will mean two courses each semester where the courses meet 3 times (hours) per week, where 2:2:2 means two courses each "quarter", but where the course meet 4 or even 5 hours per week for fewer weeks. The students also, typically, then take fewer, but more intense, courses in a term.

But that means that you may be able to handle about the same amount of material in a course under each system as you meet for more hours and the students are (hopefully) more engaged in your course.

Another possible variable, is the quality of the students (and faculty). Dartmouth has traditionally been on the quarter system, and the students are very (very) good. And in CS, at least, they work very (very) hard. You may have a challenge keeping up with them. This is likely true for other similar institutions as well.

I'll note for completeness that some institutions, including Dartmouth, use the quarter system so that they can run four terms of equal length per year (hence "quarter" system). Faculty normally get to choose three of those four terms, but may not, in general, be permitted to avoid summer quarter always. Students likewise, my be required to have schedules that include some summer quarters and some "time away" quarters (for travel in Europe, duh). This makes better use of other facilities and funds.

Under such a system, it is also (theoretically) possible, if not encouraged, to have a year's "sabbatical" "every" four years if you teach for six consecutive quarters, then take off for a year and then teach six consecutive quarters. Twelve quarters over four years is a full load, if you are required to teach (on average) three per year. This requires the dean's ok, of course, which is granted only occasionally and for good reason.


Use of words like "herein" in research articles

Here's a factual and quantifiable answer to your question :)

As you can see in the Google NGram, the word "herein" has been the popular way to convey this idea historically but has since 1920 lost popularity. "in this study" and "in this paper" together outweigh "herein" almost double up at this point.

(end:facts, begin: speculation)
Take the following with a pinch of salt; but if you consider why this is the case, I'd say "herein" is the old way of saying the exact same thing as the other two. Sometimes people associate older phrasing with being finer, more eloquent and indeed sometimes even more intellectual, in a Twain-esque way. Please note that I am not accusing your colleague of thinking in this way, but sometimes people tend to choose the fancier/older word because it "sounds better".

I have to say I really don't buy the argument of "herein" being shorter; you save 2 words or 6 characters (incl. whitespace). I would presume that you don't refer to the article more than 4-5 times throughout the course of the paper, so your saving is approximately 10 words, or 30 characters, which is not that much. I am willing to accept that excuse for an abstract maybe but certainly not for a research article where you typically have 5000 words or more to describe your work.


Is it appropriate to ask for an opinion about a preprint from researchers I don't personally know before submission?

In my field (mathematics) it is somewhat common to send out preprints like this, especially for junior researchers like yourself.
In my experience, the most common way is to send a copy of the paper as an attachment, briefly introduce yourself and the paper, and say something like "I would welcome any comments if you have any. Thank you very much."
In particular I would not recommend asking questions, at least not in an initial email. I would especially avoid questions such as "would you find this of interest", which can be very awkward to answer. As you said, you want to avoid looking like you're asking them to serve as a reviewer or supervisor.
That said, in my opinion, sending a paper and indicating that you'd welcome feedback is a perfectly fine thing to do. I've got some interesting feedback this way as a grad student, and more recently I've responded to similar emails coming from students.
Good luck!


How to write horizontally across the blackboard while keeping handwriting as horizontal as possible?

Writing works different on different heights, so train writing at different heights. For me it is easiest to write horizontally if the baseline is about the height of my  mouth. Writing at the height of my stomach or my chest is almost impossible and I need much more care and it takes much longer. If you have to write at that heights, you could also squat down, but be aware that the things you write down there may be too low for some people in the audience.
If you can move the blackboard up and down, move the blackboard such that the line you write is on your favorite height.
Do not stand still and stretch your arm more and more, but move your whole body along as you write.
Related to the previous point: Use short lines. Two halves at a ten meter blackboard still make five meter long lines. Depending on the size of your writing, this may still be too long.
Try to get good chalk. I prefer chalk that slides over the board more easily. (The people over at mathoverflow have something to say about this, see here and here).
Try to adjust your font such that it helps you to stay on the line. Writing cursive for text (not equations) may work, but I think cursive needs more care on the blackboard.
If you practice, try to find a blackboard that has lines, a grid or crosses that help you stay in line.


Should I send email expressing my gratitude to professors who provided me with letters of recommendation?

I think a short, cordial email informing the letter writers of your admittance and thanking them for their help and contribution to such an outcome is absolutely appropriate.


How to address in the thesis that the abstract is translated by someone

A small piece of translation like this should be clearly credited, but is not large enough that I think that it should be considered a significant piece of independent work.

As such, I think that a statement in the thesis acknowledgements would be sufficient.


Submit an extended version, of a paper presented as short one in a conference, to a journal?

If the paper is considered a 'paper' in your field and you are submitting to a journal which requires submission to be new and unpublished, then this is not appropriate. (I am assuming that the two papers are indeed as connected as implied (a short paper, and an extended paper using the same work, discussion, conclusions and adding perhaps more detail but otherwise the same work).

The one scenario that I can imagine in my field (physics) that this might be appropriate is if the conference 'paper' is not a paper, just an extended abstract  that is done for the program booklet.  If it isn't even something I am going to put down on my CV as a publication, then I don't consider it a 'paper'.

As a referee, when I know a similar paper has been published previously by a group in a conference proceedings or if I check up on their webpage and see that a very similar paper has appeared earlier, it sets up a red flag, particularly if the group did not reference it (hid its presence). It implies to me that the authors are hiding something for a reason.

If the 'new' paper is similar to the un-referenced conference proceeding, but has nothing new in it, then I conclude that the authors deliberately hid the conference paper. My journals require that a paper be 'new' and 'original' and previously unpublished. Writing a paper with different words but the same data, conclusions, main points and discussions with more detail is not new and I would both reject it and point out to the authors and editor the problem. I feel sorry for the authors if they had transparently referenced the prior work (I do also check their work they reference), but not at all sorry for them if they hid it.

If the submitted work has additional data, or a focus on a different aspect of the problem  or other features that make it 'new', then I will referee it on its merits and in the review mention the previous work ad suggest they add it to the references. But depending on the relevance of the prior un-referenced paper, it can make me wonder whether they deliberately chose to hide it thinking it would hinder the publication of their new paper. That makes me in future remember the group as potentially suspect.


What are pros and cons of submitting a PhD thesis to ProQuest?

I don't see any advantage to posting your thesis to ProQuest, but I don't see any real disadvantage either.

Since your thesis is already on ArXiv, it's already permanently (and freely!) available. So I don't see any advantage to also making your thesis available through a more painful interface that requires your intended audience to give other people money. Presumably the results in your thesis will also be (or have already been) published in other indexed publication venues, so even having your thesis indexed by ACM isn't a clear advantage.

You can list your thesis in your dissertation even if you don't submit it to ProQuest. In fact, you must list your thesis in your CV, even if you don't submit it to ProQuest.

(JeffE's answer.)


Your advisor is not the only person to go to, to get answers to the questions that research papers are raising for you. Talk to other researchers, in your department, or online with peers at other universities.

But it does sound like you are getting insufficient advisory support. Do you really just have the one advisor? Time to build up your supervisory team.

Talk to your advisor about what's expected of you, and what's expected of them. It sounds like you've got a mismatch between your need and their resource, and it's important to get that fixed as soon as possible.

You'll also find a lot of good, relevant advice on these questions: skimming a paper and running a reading group.


How should I convince my parents about a career in mathematics?

Your parents are thoroughly incorrect when they say that there is no career opportunities in mathematics.

Further to Dave Clarke's answer, many (applied) mathematicians find work in the City (as in the financial services sector of London) running risk analyses, for instance.

If however, you are looking at finding work as a research academic in mathematics, then jobs are there, but sought after. Teaching mathematics at university level provides wider prospects, however.

To answer your question about money, the amount you have to pay largely rests on the tuition fees that you can afford. This will depend on which university you choose to attend.

There is also the middle ground of studying mathematics with a view to putting that study to work in medicine. Consider that statistics (yes, probably not the subject you are interested in), was essentially developed as a response to a medical situation (plague in London). There is also a vast amount of work requiring pure and applied mathematics in medicine (nuclear medicine, MRI, NMR, for example).


Math reviews, how to interpret "the summary as review" cases?

When I review for MR I often use a paraphrase of the author's summary when it is a good description of what is in the paper. I don't mean that to say "not worth reading" or "I didn't read it". I would probably not use the MR option that merely reproduces the abstract, precisely because it might suggest a negative opinion of the work.
That said, I tend to review short papers that are OK but not earthshaking. A review of an important paper should do more than repeat or rephrase the author's summary.


Manuscript acknowledgement for students who helped with lab maintenance

Personally, I would be generous with the acknowledgments.
Adding somebody there costs nothing and generates goodwill.
But, check with your advisor.
Part of your advisors job is to mentor you on being a scientists, including cultural norms such as writing acknowledgments.
Perhaps they have their own standards.


Collaborator omitting my name from their CV

Some of what your colleague did is unethical, some of it is not.

For listing grant funding, I haven’t seen a whole lot of official standards for how they should be presented. Listing one’s own role (PI, co-I, etc.) should be sufficient. One need not list all the principals for the grant (unless specifically asked).

However, when it comes to papers, leaving off who’s a coauthor on a paper is definitely unethical. It’s also unethical, in my view, to list a paper that you couldn’t produce if asked. So anything that’s just in the planning stage should not be listed.


What a PhD student should do when their supervisor orders them to have a name on their paper just because of grant purposes?

Have you written a grant proposal? My SO at the time was a prof and geochem research scientist. She has generated millions in grants for her collaborators, students and herself to push their research forward. The latest grant I saw her work took many months gathering data and papers, hashing out schedules and compensation for collaborators, students and contractors. She had to prospectively estimate everything from travel costs for the people gathering samples, to costs for reactor and instrument time.

Would her time have been spent better doing science or assisting her students? Absolutely, but grant writing can be difficult as it requires intimate knowledge of the discipline and particular work being done on the project. This is a difficult role to fill that is usually done by researchers themselves, if they want to stay in the "biz".

If she wasn't already one of the lead authors on this research, I would say she undoubtedly deserved to be named on the project. Just because you are writing a paper does not mean the paper is your final product. The paper is a description of your final product, the process of creating the product, and credits those who assisted.

The person that procured your grant absolutely assisted in your research, consider how your project would have gone without it.


How does "Living review" style of publishing work

The Living Reviews that I know

solicit articles from authors, rather than accept submissions
ask the authors to revisit and revise the articles to keep them up to date.
are online review articles only.

Other than that, they are "standard" journals and peer reviewed.

The revision history of articles can be seen explicitly on each article, as this example shows.

Whilst many reviews are written, few are revised to keep them up to date, and even fewer are revised more than once. From what I've heard the process is: editor hassles author to bring article up to date, author replies that not much has changed or that they don't have enough time right now, wait a year and repeat.


proper grading fairness when certain questions dropped on exam

This is a common complaint.  Anytime a professor relaxes a requirement, the students who achieved it are unhappy (turn in time for a paper, whatever).

As far as those questions, it is not clear if professor decided they were wrong, ambiguous or just too hard.  In any case, what he did had the impact of removing them from any relative ranking (which is why the screams from those who got it right).

I wouldn't get outraged over it.  Sometimes there is no perfect answer. (Consider also the possible damage from leaving the questions in if they were flawed in some way.)  Just get over it, work hard, keep doing well.


What are the common signs that a graduate interview has been a success or a flop

We try to be meticulously fair during our interviews. We tend to ask similar questions and try to retain a similar demeanor across all of them.

You should know that we don't usually make up our minds during the interview itself. It's not like a job interview. The answers you give will form just one component of our entire impression of you.

And up until the final committee meeting when all of the finalists are put up on the board and ranked against each other, it's very hard to say with specificity who got in and who got rejected.

p.s. While I try to send my interviewees a quick note by e-mail thanking them for their time, I would be aghast to think that if I forgot to do so that someone would read devastation and gloom into that oversight. Sometimes a missed e-mail is just a missed e-mail.


Stuck with an advisor who is unprofessional

Run away! The most important thing to success in your graduate education is your desire to succeed and your advisors desire for you to succeed. I've had friends and family with advisors who were immoral or emotionally unstable, and they are much happier now that they switched institutions/advisers or left the field entirely.


Pursuing a Master's remotely while working in industry?

I think what you're forgetting is that a master's involves a lot of coursework, not just research.

Your idea is only likely to work if the courses are designed to be taken remotely.  Take into account that even when you are attending the classes in person, you had some trouble.  It wouldn't be fair to put you in suboptimal conditions and suddenly expect a strong academic performance.  One might be able to get by in an undergraduate program with C's, but that wouldn't fly in a graduate program.

You're considering a binary choice right now, work full time or work full time and pursue a master's at the same time.  There is a third option -- get started in industry now, and go back to school later on at some point.

By the way, there is no rule that you must be enrolled in a degree program, or even that you get academic credit for doing research.  If you are interested in a research project for its own sake, you can always work on it for the satisfaction itself.

However, it might be wise to wait to get started with such a project until after you see how much time and energy you really have to spare.  In other words, allow yourself to get in the swing of the new job before committing.  Perhaps you could leave things open with the professor you have in mind working with.


Why do others have these highly specialised research topics and I don't?

Professors usually love to find PhD students in search of topics, since they tend to have ideas that they hope someone will work on.  Even students who come with a defined idea often find advisors nudging them in a different direction than what they really wanted to do.

Talk to some professors that you think would be good people to work with as your PhD advisor, and see what thoughts they have on this.


Why do some universities charge an application fee?

A system where everyone applies everywhere is not in the interest of any of the participants. Handling the applications requires significant effort on both sides and the applications are less meaningful. In particular, plenty of people will receive multiple offers inevitably turning all but one down. That requires waiting lists etc. In the end, some positions will even go unfilled.

In countries with a centrally-run system (for undergrad places: eg UK or Germany), this can be avoided on the central level. If there is no such system, then application fees are a means for the universities to encourage the applicants to send out only a small number of good applications.

That this disproportionally affects students from poorer backgrounds is an unfortunate side effect while the extra income is fortunate for the university.


Is it okay to include a historical summary of your research area in a MSc thesis?

I did something similar with my own MS thesis because the history of my particular field was not well known and somewhat interesting (the algorithms were independently discovered 4 times in different fields starting 1927 until it finally caught on). More importantly, it helped explain what I was doing. If it fits in with your narrative and your advisor is okay with it, then go ahead.


Is it a requirement that at least one of the authors of a paper holds a PhD?

If a journal wanted to impose such a rule they would most likely state it plainly. But I think that is very unlikely. It isn't the qualifications of the authors of a paper that make it important, but what the paper actually has to offer. Of course, editors like to know that the authors know what they are writing about, but that is the job of the reviewers to determine and normally reviewers will spend more time with the paper than with the credentials of its authors.

In fact, a paper by an independent researcher without an academic credential might be especially "interesting" if the arguments and conclusions are sound. It might even introduce new ideas into a field. When Einstein did his early work he wasn't well respected by the established intelligentsia of the day. That only came later.

And on the other side, a paper by a brilliant and credentialed researcher that seems to spout nonsense can cause quite a stir.

But, I suspect that in this case, there is some flaw in the paper that the editor noticed independent of its authors. Maybe it was just a poor fit for the journal, or even for the editor's current needs.

One further thought. A restriction on who can publish in a journal, such as requiring a doctorate, would, over time, have a pernicious effect, lowering the quality of the journal. It is the restriction itself, actually any sort of restriction, that leads to some high quality papers not being submitted at all and other, lower quality, ones filling any gaps. The effect would be small, but additive over time.


How to write proper nouns such as company names whose spelling is nonstandard in reports?

I challenge your contention that these things are spelled incorrectly.  When you write 'Toys "R" Us' you are correctly spelling a proper noun.  Names are signifiers, and the entity who controls the name controls how it is correctly spelled.  I would not have told my high school friend whose last name was "Tomson" that his name was spelled wrong just because for most people it was spelled "Thompson."  Likewise, 'Toys "R" Us' has chosen a particular spelling for its title, and that's the correct name.

So now comes the question of how to communicate such titles, and here, I see four basic cases:

Just use it as written, and count on people to understand: not great with Toys"R"Us since quotes are semantically loaded, but fine for a well-understood "misspelling" like Google.
Often, there are commonly used variants that are simpler.  If you say Toys R Us, people will know what you are talking about even without the quotes, so its OK.  Same with the artist formerly known as Prince. If you say Toys Are Us, however, you've gone a step too far and "corrected" the name into something incorrect.
Put it in quotes, like I did in the first paragraph: 'Toys"R"Us' (here I made the unusual choice of single quotes because of the presence of double quotes in the name).
If you think it is still strange enough that you think people will think you misspelled it, you can add [sic] afterwards, as in "Tomson [sic]"

I don't like italics, as a solution, personally, since I generally see italics used for emphasis or for definition, and neither is the case here.


Why do top universities prefer candidates with work experience for their MBA programmes?

It is always better to do an MBA when you have some practical knowledge of how an organization works. If a fresh graduate joins an MBA course, she might understand the theoretical aspects, but might not be able to relate the knowledge to real life situations. A person who has worked for sometime will definitely be able to understand the workings of an organization better and will be able to connect theoretical concepts to the way an actual organization functions. Possibly, that is the reason why most top B-schools prefer candidates with work experience.


Department member writing reference letter for job applicant for a position in that dept

I see no ethical or practical problem as long as you are not otherwise involved in the hiring decision. For your own future, I'd also advise agains any lobbying on the applicant's behalf other than the letter itself. If the applicant is rejected you don't want it to reflect back on you.

Just be honest, and otherwise keep your distance, just as if you were located in another institution.

Likewise, giving an honest appraisal of another (or again, another) applicant should be no problem as long as you have some idea of the individual capabilities of each.

And if you are later asked by your colleagues to rank the various people  you have recommended, avoid it, mentioning that it would be improper and is the job of the committee.

If I were a member of the hiring committee, I'd have to consider refusing to provide a recommendation, though there might be other solutions, such as recusal.


Is it advisable to use non-scientific method to teach science courses?

"What if..." Is the bread and butter of science and mathematics. Making outrageous guesses and then checking them is part of the toolkit for professional thinkers.

In your examples, you say that the author takes the stance that one event only potentially explains another, which seems fine from a scientific point of view.

As others have said, when you popularize you often intentionally leave out some subtlety. This is really a function of your intended audience. I leave out some subtlety when I teach intro calculus.

As to whether or not the author you reference does this badly or irresponsibly, I can't form an opinion without reading what they wrote.


What is actually confidential in communications in state universities?

As Nate notes, it is challenging to answer a question about fifty different state laws. By a happy coincidence, though, I sort of did it in 2005 :-)

At that point - it may well have changed in the last twelve years -

Every state had some kind of local freedom-of-information law, and in general they all appeared to affect public universities.
In some states, private universities may be covered to the extent that they are spending public money.
Academic institutions operated by federal government departments (eg the National Defense University) are subject to the federal Act. Public universities in DC (all one of them) are covered by local law; it varies in the overseas territories. And finally, there is a lot of ambiguity around what FOI legislation, if any, applies to the tribal colleges and universities.

Exceptions
Delaware had a strange law that appeared to exempt the universities in general, but the Boards of Trustees, and financial records, were explicitly covered.
Kansas had at least one specific exemption for a specific part of a university (I am sure other states had similar provisions buried somewhere I missed).
Several states had legislation that only gave rights of access to state residents (though this was constitutionally dubious and one had been successfully challenged).
Explicit topic exceptions were often provided in the law, and most frequently tended to mention recruiting for university presidents, library records, examination processes.

That answers the basic question of "can I use FOI for a university": yes, if they're public, with some caveats. This is generally consistent with international practice.

For the more specific questions, the only possible answer is "...it depends massively on local legislation, caselaw, and practice". I would strongly recommend you look at the relevant state's legislation. If the law is well-established and well-used, the university may even have some handy guidance on this.

My gut feeling, generally speaking, and no more than a rough guess, is that:

  Can I file FOIA request to see all the emails that a professor receives including all of their unpublished research progress and interactions with their students and postdocs?

Many jurisdictions would balk at "give me all of person X's emails" (as opposed to "give me all discussions about Y". It may well be seen as unreasonably complex to provide, if there is any kind of review stage - the costs for having someone read through all the email to check there's nothing that shouldn't be disclosed ramp up fast, and this can sometimes be a get-out clause. ("We would do what you ask, but we'd have to hire someone for three months, so...")

For ongoing research, there is sometimes an explicit exception, or indeed an implicit one, in the law. (For example, some legislation takes the position that if something is going to be published and that process is underway, it's fine not to release it until publication happens - which would implicitly cover most academic research.)

On the interactions with students & postdocs... "interactions" is an odd word. Routine emails between a couple of public employees (which is another way of describing a professor and a postdoc) wouldn't be automatically problematic. But it's almost certain that something in the full range of "interactions" would be considered confidential. For students, I would assume the assumption of confidentiality would be drawn wider than for postdocs - but, again, local law will be your guide here.

  Can a postdoc request to see the recommendation letters received or sent by their advisors about them?

Maybe. It is a borderline issue and one likely to be handled differently in different jurisdictions. It is complicated by the fact that one party is involved in the request, and there may be other more appropriate ways of handling this than FOI. There may also be explicit or implied promises of confidentiality for referees that are enough to ensure they are treated as fully confidential.

Note that "received or sent" may be significant - in the UK, for example, which has fairly robust personal-information and FOI legislation that is probably stronger than that in most US states, you can get copies of recommendation letters received by the public body, but not sent by them.

So on the whole... it varies. At least you know the law probably applies to some degree!


Leaving academia for financial reasons - how to communicate the reason of departure in a professional manner?

Express that you have enjoyed working in your department. (Even if this is not entirely true.)
Explain that you are only leaving because of an opportunity "too exciting to turn down." Don't volunteer exactly why it is exciting; if asked, talk about what you'll be doing, not what you'll be paid.
If there's a way you can help the department while you're in industry -- serving on a committee, helping with accreditation, accepting an intern, things like that -- it would be kind of you (though it is not obligatory) to volunteer unasked.
Keep your resignation letter short and cordial.

These tactics should suffice to keep your departure as amicable as it can be, assuming you're doing the normal things to minimize disruption (e.g. not leaving mid-term).


Would graduate school be worth it for Computer Science?

The answer will always be it depends.  You've done a pretty good job of listing out the negatives of the MS degree, principally another year not earning a salary, and not paying down student debt.

The biggest question you ask is

  would a masters help or should I directly apply to a PhD program?

The answer is likely yes.  You will get to work 1 on 1 with professors, and will have a better idea who you'd like to work with in the PhD program.  You can also use your time in the masters program to find funding for your PhD internally, further increasing the chances of your PhD application being accepted.  Finally, if you find you do not enjoy getting your masters degree, you should certainly not get a PhD.

Here are some other positives of having a masters degree.

1) Some private companies and almost all government/public jobs will give you a salary bump just for having it.

2) You can choose to specialize in an area you are interested in, which may lead to a job in that sub-field.

3) If you find yourself in a tough job market, it may give you and edge in the hiring process.


How to prevent physical/psychological health side effects of workaholism in academia and research?

I put my health first by committing to healthy activities that involve other people, so I will have to stick to them.

For example, I

Have a standing weekly running appointment with a faculty member at my school. I won't cancel this appointment because she will be disappointed.
Have a standing non-academic volunteer commitment one afternoon each week (giving back to my community is essential for my mental health). I won't cancel this because there's a classroom full of 12-year-old girls waiting for me to come help them with their homework.
Spend 25 hours each week, from Friday night to Saturday night, completely disconnected from the Internet and anything work related. (I do this as a religious observance, but it's definitely good for my physical health, too!)
Hold meetings with students and faculty in other buildings in their offices, not mine, so that I am forced to occasionally go outside during daylight hours (if only to walk from one building to the next).

All of these things are non-negotiable to me. That is, no matter what how busy I am or what deadlines are coming up, I will not compromise on any of these things. They're essential to my health and well-being, I arranged them so that other people are depending on me, and so I prioritize them.


Writing thesis with corrected data after being published

Talk to your advisor.
write the thesis with the most up-to-date data. Analyse the data as a progression if necessary ie including the historical data if applicable - see 1...
contact the journal / editor (may or may not be the same editor you used when publishing originally and decide whether a follow-up paper or an erratum should be the way forward.


Is wanting to quit part of the "PhD experience?"

If at any time you feel

You are not understanding what supervisor is saying.
You are not on the right path.
Your colleagues are performing better than you.
Only you don't understand a thing and lagging behind in deadlines.
Your supervisor is not happy with your work.
Your advisor is rude to you but you saw him laughing with another student.
Your work seems easy but others' work is very impressive.
You just want to quit.
You can't quit because of social pressure.
You just wanna go with flow.

Any other symptoms like above mean you are doing PhD and almost every student get such mood swings any time.  I almost gone through all but when I talked with my colleagues they were thinking exactly like me, some even saying my work is very nice and their work is easy etc... So don't worry just work and read.


Can I teach the same course I developed at one university at another university as well?

I would say it is generally allowed and that exceptions would be rare. But a policy forbidding it would need to be spelled out.
At one level, universities are in competition with others, but this isn't normally at the level of instruction. At a more important level, universities are cooperative and encourage their faculty to also be cooperative.
I've never heard of a university claiming that any given course was unique to it and therefore proprietary. I once taught in a unique program, but that was just because no one else took it up. We certainly didn't claim ownership over it.
Another issue, however, is that universities may frown on faculty teaching at two places simultaneously, no matter the course.


Where to put related works in a PhD thesis (Computer Science)

Personally, I think what you are proposing makes better sense in your case than having a traditional separate literature review chapter. Moreover, arranging the theoretical background in close proximity to the relevant methods would probably make it easier to revise the thesis for journal article publication after you've defended the thesis. However, if you choose to do that, I recommend that your "Background" chapter have a subsection dedicated to discussing the broad literature that spans the general theme of your thesis without specifically focusing on any one theme.

That said, ultimately, you need to talk to your advisor and see what they are comfortable with. If your advisor prefers the traditional dedicated chapter, then you should go with that. Your advisor needs to be comfortable with your thesis structure, too, since that would enable them to be will be your advocate with other people, such as your committee members or outside evaluators, who might not be used to your non-traditional approach.


A senior colleague that belittles my contributions, expertise and won't acknowledge a published error that I identified

When we went to publish a paper ... my boss made the suggestion that we equally share first-authorship, Emily was so upset that she wasn't the sole first author that she literally screamed in my PI's office about it and then didn't come into lab for 3 days after.

If possible, it is always a good idea to negotiate contributions and authorship of a paper prior to conducting the relevant research and drafting of the paper.  This kind of dispute can best be avoided by having all the researchers sit down prior to the research project and agree on the roles of each of the researchers, and how the authorship will be allocated (i.e., who is a co-author vs an acknowledgement, order of authors, etc.).  In some cases the actual contributions may end up differing from the initial plan, and so a renegotiation of the authorship could occur, but in many cases you can avoid disputes by having a clear set of expectations at the start of the project.  Once a dispute arises, there is going to have to be some negotiation and decision made about the dispute, but in the future it would be best to avoid these problems by agreeing on authorship details in advance.

  ... I'm currently working on several papers that build on those published findings.  In working on these new projects, I've discovered an important error that Emily made in the published paper that we are co-first author on.  She denies that there is a mistake...  The mistake needs to be corrected in order for me to continue with publishing my recent projects (but fortunately does not change the main takeaway of the paper).  Emily plans on telling our PI that I’m just a trainee and that I don't know what I'm talking about and that she did not make a mistake (again, I can definitively prove that she did with the email chain).  She also has some clout with our PI because she's been there much longer than I have and is more experienced.

Firstly, you should do everything possible to see if you, Emily, and your PI, can reach an agreement on whether or not there is an error in the published paper.  I would suggest making a meeting with your PI where all of you can look over the details of the claimed error, check your working and discuss the matter, and see if you can come to agreement about whether or not there is actually an error.  If you can get your co-authors to agree with your view, then you could all submit an erratum to the previous paper correcting the error.  If your co-authors can convince you that there is no error, the matter is also resolved.

It sounds like this might not be possible, and so if you try all this and exhaust all possibility of agreement, then here is what I would suggest.  You are the author of your new papers, so it is up to you what to write in them.  It is perfectly acceptable for you to claim in your new papers that you have identified an error in the previous published paper.  For full disclosure to your reader, you should make your claim in the paper, but also note that the claim of the error is disputed by your co-author.  (You can give relevant details in a footnote, but keep it succinct and professional.  Do not bog the reader down with excessive detail or a big shit-fight.)  Re-run the previous analysis without the error, note the new results, and proceed with your new papers on that basis.  Emily will be just as entitled to submit new papers claiming that she is correct and there is no error.  (Both sets of papers would be vetted by referees, but it might be difficult for them to tell who is right, so you might find that some referees will be reluctant to recommend publication.)

If you are unable to come to an agreement on the alleged error with your co-authors, ultimately that is going to mean that you end up claiming one thing and she ends up claiming another.  If these are your papers, and you have tried and failed to reach agreement on the matter, I see no reason why this issue would require any further intervention of your PI, so her greater "clout" with the PI should not make any difference.  You are entitled to submit research to journals making claims you believe in good-faith to be true.  (If you want to, it would also be legitimate for your to submit an erratum for the previous paper to the original journal, notifying your co-authors, and noting clearly in your erratum that your claim of an error is disputed by your co-authors.  I suspect that the journal might not accept this, but you could submit it if you wanted to.)

  Unfortunately, I lost my cool a little bit and some of my responses to her were harsh and less-than-professional. ...  we both made some statements that were unprofessional.

That is a problem, and you are both going to need to cool it.  (And it is probably worth apologising for any comments that were unprofessional.)  Keep your focus on the work, and the correctness or incorrectness of the methods and results.  If you cannot engage with Emily without making unprofessional comments, you should disengage communication with her.


How to cite a paper when I don't know where was published?

Sometimes the route that seems most tedious can end up being the most efficient. I would try looking at some of those 60+ references. Any work that's been cited so many times will have to have the source listed in the bibliography sections of those references.


How long should I wait before accepting a PhD admission offer in the US?

You should ask both institutions.

Some institutions will fast-track deciding on if they’ll accept you if you tell them you have an outstanding offer. By contacting the outstanding offers, you can probably find out sooner.

Additionally, you should contact the department that made you an offer and tell them that you’re interested and honored by their offer, but have some outstanding applications and ask when they want you to get back to them by.

EDIT: I completely missed that the title says “in the US.” As the other excellent answers have stated, you very likely have until April 15th or later to make a decision. A large number of universities (see the 2014 list here) have agreed to give all students at least that long to decide to respond.

It is worth noting that the April 15th Resolution applies to offers of payment and funding, not acceptance. However, since in the US virtually all engineering PhDs are funded, it de facto applies to admissions as well. If you were applying for an unfounded masters program, it wouldn’t apply.

Some schools give longer than April 15th to decide, while others will pressure you to accept on the 15th or soon after. So for now, I would advise you to wait. If in early April you still haven’t heard back from a school you really want to go to, I would advise you to contact them as I said at the beginning.


Differences Between Academic Research Positions in US and Canada?

I am predominately based in Canada as a post-doc, but do have partnerships with few universities in the US and have gone down there for extended periods of time for research purposes.

I mean, they are not vastly different, but it depends on school and the position itself. Some universities are more prestigious than others- but depends on your field. There are many US scholars here - particularly at universities such as UofT hire heavily from the US. In terms of impact - its so different from university to department, but looking online and checking out Maclean's university rankings could help - but again, so department and field specific - and of course there is some great work happening across both countries.

In terms of funding, again department specific where some are very well funded and others not so much. The major grant competitions are CIHR for any health type related work and SSHRC which are both granted by the federal government across a number of priority areas and disciplines (however, many researchers still rely on large US funding such as NIH). Provinces also have their own grant competitions as well. If you've applied for an NIH, you'll be familiar with the federal grant structure but it is tedious and the platform is archaic. Funding competition is tight, but if can align with their priority calls you could have a good chance, and try to be a Co-Investigator on as many applications as possible. However, at any institution they would be very familiar with this process, and as a post doc or early career researcher there is access to lots of resources such as government run and university run seminars to assist in the application, you'll have an advisor or mentor, and others who can help you navigate the red tape the first time.

In terms of living - Canada is great (again depends where you end up!). Some things to consider is access to free healthcare if you work or study here, which could be a big difference from the US. Rent in major cities is comparable, still expensive, but I gage slightly cheaper (Vancouver or Toronto versus, for example, Santa Monica). The culture is very similar to the US, so I think it would be a very easy transition for a US scholar.


How to frame/explain that I built datasets used on several publications, but I'm not on the papers

I would cite this as work experience in your CV, without citing the publications themselves. You could mention a number of papers/projects contributed to, or mention more specifically what the projects were.

You can also see the advice on this somewhat related question: Should I explicitly remind people to include my name in the acknowledgement?

There, someone is asking about how to make sure they get properly acknowledged, but several answers and comments point out that acknowledgements aren't really cited as acknowledged papers. I'm not sure whether you are mentioned in acknowledgements in the papers you refer to, but whether you are or not the advice there would agree with mine.

Adding from @Buffy's comment, if you think this work is particularly important to your job (for example, if you are applying to a position where you will be working with datasets outside of your field and want to emphasize the breadth of your understanding) it may be appropriate to get a letter of recommendation from your collaborators.


Finish previous work during current position

As an academic working with a couple of post-docs, my rule is you can do what you want with your time as long as you do what is required for the project that employs you.
It is also the case that I know (and indeed expect) that post-docs will have work of their own that they'll want to finish up or extend.

I would not be happy with option 1, but option 2 would be good for me. Weekends are your own. If you spend them writing more papers, I will not object. But please do have some rest and relaxation time.

As a post-doc, you are starting to build your own career, so writing independent papers, and thereby forging your own way,  is a good thing. But there are a lot of benefits to be had from integrating yourself in your new working environment, and working too much on your own stuff means that you will miss that opportunity (and possibly make a bad impression).


How/when will I know if my conference paper will be selected for a special issue?

If you haven't received an invitation a month after the conference, it's safe to assume that your paper won't be invited to the special issue.

Special-issue papers for theoretical computer science conferences are normally selected by the program committee chair (or a small subcommittee), based on nominations and discussion from the program committee.  The two natural times to solicit those nominations are (1) at the end of the review cycle, months before the conference, when all the papers and reviews are fresh in the PC members' minds, and (2) immediately after the conference, when all the talks are fresh in everyone's minds, and the PC chair's work is otherwise finished.

Once the PC chair selects the papers, there's not much else to do.  Under normal circumstances, the guest editors (usually the PC chair, but sometimes other members of the PC) email invitations to the selected authors shortly after the conference.  Occasionally the invitations go out even before the conference, but that's rare.

That said, sometimes additional papers are invited later, especially if some invited authors decline, and some PC chairs are just less organized than others.
If you have good reason to believe that the PC thought your paper was especially strong (for example, unanimously strongly positive reviews, or PC members telling you at the conference how much they liked your paper), it can't hurt to send a polite note to the PC chair or a close colleague on the PC asking whether the special issue papers have been selected.  (Asking whether your paper will be invited is a bit presumptuous.  Just don't.)


Academic affiliation on papers written while between jobs

I suggest using the postdoc affiliation (precisely for the reason you mention and also because you will probably still be there while the paper will be reviewed) and thanking for support the university where you did your Ph.D. in the acknowledgments.


How to work with a student who has a tendency to overcomplicate things?

He has been reading a book that is related to the paper only in title.

This along with him not making progress might be a sign that he is missing pre-requisites. Maybe the paper requires mathematical tools he is not familiar, or has several words which are new to him.

Usually, I'd go with some assisted reading/reviewing. This is very harsh, so be careful and prepared before attempting.

Set up a meeting with plenty of time, explain that you'll be studying the paper and he should try to read and understand by himself first. Mark some time you know he should be calm (i.e. don't do it last hour of Friday or right after a difficult test, also make sure the student isn't hungry). Schedule at least two hours, but preferably have more allocated time on your schedule, and try to know that he'll be free after the scheduled time as well. Ask him to bring a laptop or have a computer in front of him at the meeting place.

Then, the strategy is to tell him to read the paper and interrupt him at least once per sentence asking for clarifications (what does this word mean? Can you rephrase this? Why is the author making this exception?). He should know that your are trying to measure gaps in his knowledge and habits, so tell him to be honest if he does not know anything and that it doesn't matter if that's the case (might be a particular poor strategy when dealing with people from a cultural background who have issues admitting they don't know something). The tense scenario will naturally keep him focused (though you should try to put him at ease).

When he doesn't know anything (I don't know this word!) you can either explain to him (and check if he understood) or say something like "and how would you look it up?" (that is why I've suggested leaving the computer close by). Very often, you'll notice he has poor googling skills, so you'll present him with some useful websites (Linguee comes to mind when dealing with translation issues, it is simple to use when you know it exists, but a student might not find it out by himself). Maybe you'll need to introduce him some book on the matter, and go through its index (some students may have only learned an important topic over classroom notes that he/she threw away, he might be unable to name a single book he could check some equation if needed be).

Additionally, this will reveal gaps in the student background, maybe there is a complete theory that is relevant to the paper but the student knows very little about (something like: "yes, you need to know trigonometry before learning calculus" or "Yes, you need to study electrodynamics before studying quantum mechanics"). Many elective courses try way too hard to remove pre-requisites for students, and then student simply don't know about things that should be the pre-requisite in any sane place. The process of asking for clarifications over each sentence usually reveals this kind of gaps.

Often, people read complex texts ignoring parts they don't really understand. Maybe because they expect that part to be clearer as the reading progresses, perhaps they think they'll get it with more context, or they just hope that weird word lies in a sentence that isn't actually important. This is a poor reading habit that almost everyone has at some degree. However, struggling students might take it to a whole new level of reading without understanding. Part of the idea is to identify when this is happening and forcing the student not to ignore too much of the text.

After a while doing so, you should:

Have taught the student how to use some tools that you are used to, be he never heard about.
Have provided him with good basic references if he needs them.
Have identified topics you expected him/her to have mastered, but he/she actually knows little about.
Improved his/her reading habits a bit.

Explain to him that this is not to be done often, as it is too much time consuming and stressing for both of you. Also, the whole point is to fill basic gaps, once they're filled, this tool should no longer be used. Over time, he should get better at identifying these gaps by himself, and asking for assistance as needed.

Another note on how to handle the student:

  I have two other students who are working on similar topics and they get it.

Unless they have very similar backgrounds (i.e. same bachelor degree at same university) to the struggling student, the comparison is more likely to be unfair than otherwise. Even if just in your mind, avoid comparing colleagues directly, and specially never compare colleagues in front of them (or speaking to either).


Online Computer Science Masters as PhD Prep

These are professional masters programs.

My department (Illinois) does not consider even our own online MCS program to be preparation for a PhD, because there is no requirement—and therefore in practice almost no opportunity—for research experience.

Moreover, it is unlikely that any instructor of an online course can provide useful recommendation letters for their students for PhD programs, because useful letters generally require direct, personal, one-on-one interaction.  Sure, they can write a letter describing your class performance, but such letters are nearly useless; we can already see your grades on your transcript.


Is a paper more likely to be accepted if one of the authors is an associate editor for the journal?

In principle, no.

In actuality? It likely does, under a couple of different mechanisms:

An editor might be slightly more likely to give your paper the "benefit of the doubt" if its a borderline case between Revise/Reject, etc. This may also be true if your co-authors are "known" names, regardless of their editorial position.
An AE at a journal likely has extensive experience writing for, and reviewing, papers in that journal. As such, they probably have a good sense what kind of papers they're looking for, the tone they should be written in, etc.

So the answer, in a practical sense, is likely "Yes, but not by a huge amount." And possibly not after controlling for recognition and experience.


Your fundamental mistake is to assume that our civilization is run with goals.

It is simply not the case that we have a well-coordinated world of that type.  Instead, the allocation of money and political power are tightly intertwined, and the resources that are devoted to science are determined by the interplay of political struggles and economic markets.  Those produce very different outcomes in different places and times, from the fairly high investment in science in places like 1950s and 1960s America to the dismally low investment in science in, say, the mid-Ottoman empire or contemporary Somalia.

Arguments such as the one that you put forth must contend against many other arguments, including people's need for food, shelter and security, their desire for power over others and to advance other causes (wise or foolish), etc.  Right now, scientists are not rich, and if you wish to change that fact, you should not look to science to bring about such a change.


Grades are too high for the department - what should I do?

One really wants to say that the vice-chair is an idiot, but I will refrain. The policy is idiotic in any case. I've taught at places in which nearly every student excels on every measure I could devise. Why would I want to pit one student against another for the purpose of an artificial "average"? They weren't average.

If you have the twenty best people (students or employees for example) in the world and you measure them in any single way, then half of them will be below average. Just how fine can you make the graduations so that someone can be "called" worse than someone else.

On the other hand, if the average, as measured over several runnings of the class, is around 85 and if there are clear differences in behavior and outcome, then "rewarding" everyone equally is also idiotic.

You set a standard. People met it. The standard was not that you must do "better" than someone else. If you change it now you have an ethical failing.

I hope you have enough standing in the university and in the profession that you can stand up to such unfair and unethical suggestions. If your group of students was exceptional there is no reason not to mark them as exceptional.

If you want to lower the average in future, with a different group of students, make the course more demanding.

But if you change the grading structure after they have finished their work then you are doing evil, not teaching.


How to offer a reviewer to be co-author?

Seconding other comments and answers: surely no one would be offended if you tried to make such an offer...

However, as already noted, if your offer is made prior to final acceptance, it might be misinterpreted, as your trying to clinch acceptance.

And that possibility surely has to be systematically excluded, so a foresightful editor and/or journal would surely not want to set such a precedent. A journal would not want authors to (be able to) solicit reviewers as co-authors, since this would create a conflict-of-interest situation, and cast doubt on the general validity and impartiality of their refereeing process!

That is, while it would be weird and awkward to publicly state such a policy, I would anticipate that the journal/editor would object as a matter of principle, to putting the reviewer on as a co-author.

Sensible reviewers would also understand this situation, for similar reasons, and in advance would expect no reward beyond "job well done". Even the anonymity of the referee should be maintained, as a matter of principle. Thus, we do often find effusive thanks to "the anonymous referee"...


Submitted to a non Scopus-indexed journal, later found that University only accept Scopus journals. How can I submit to another journal?

If your paper is submitted but not accepted or published, it is still time to withdraw your submission. This is generally done by writing to the editor. I would recommend to do this as soon as possible to avoid wasting editors and reviewers time.

Now if the entire process is already over and you only have the APC to pay, it might be more difficult to withdraw but you can still try.

Once the paper is published you only option is retraction but I would not go that route just to please your institution's wishes.


Transcripts required for application, but my school doesn't really have any

The request for transcripts makes sense for students from PhD programs in the US, since the PhD program typically includes a substantial amount of course work. In your case, all that you can provide is documentation that you completed the PhD.  I've seen many applications like this.  That should be sufficient to get your application to the search committee although the committee may be uncomfortable with your lack of graduate level courses.

For positions in which teaching is important, and the candidate will be expected to teach a variety of courses, it is reasonable for the search committee to look for evidence that a candidate has a broad enough background to teach a variety of courses as well as a willingness to do so.

You might be surprised by the breadth that is necessary.  For example, although my PhD dissertation was in optimization, I've taught lower division courses in calculus, discrete mathematics for computer science, linear algebra, and differential equations, plus upper division and graduate level courses in linear and nonlinear programming, combinatorial optimization, numerical analysis, numerical linear algebra, mathematical modeling, vector calculus, probability and statistics, stochastic processes, time series analysis, and discrete event simulation.  I acquired much of the background for this by taking courses in my PhD program and preparing for and taking preliminary exams in several areas of mathematics.

In my experience interviewing candidates for faculty positions, I've often been disappointed by candidates with non-US PhD's who were too narrow in their background and teaching interests.

Although you don't have a transcript of courses from your PhD, it would be in your interest to provide a transcript of courses that you took in your undergraduate and master's studies to provide some indication of your breadth.   You should also make a point in your teaching statement of explaining what you would like to teach, what you could teach even if it isn't your favorite area, and what you wouldn't feel properly prepared to teach.   This is also a question that is likely to come up during interviews.