Fiancée has a position lined up, but none of the universities in the area are hiring. What else can I do to get an academic position in the area?

You (or rather, your fiancee) should talk to the department where she will be taking the tenure-track position.  Many universities try to support the employment of faculty members' spouses/partners, as part of their family friendly policies.  This support can take a number of forms.

The simplest form that the support can take is for the university to hire you in an academic position.  You don't mention whether your fiancee is also in mathematics, which may be relevant.  It's often easier to get the school to hire a partner in the same department.  The reason is that the hiring has to be done with the approval of the department that is going to be employing the spouse, and that may be easier to get if the department has already made a commitment to one member of the couple.  Sometimes (and ideally, I would say), the trailing spouse can be hired in another tenure-track positions.

Other times, the trailing spouse may be hired in a non-tenure track position, but one which can nonetheless be effectively permanent.  You say you do not want to work as a teaching-oriented lecturer.  Unfortunately, you are unlikely to get a permanent, non-tenure-track position in math as anything else; academic positions in math almost invariably involve teaching.  The situation can be somewhat different in the laboratory sciences, where people can be hired as research scientists with little or no teaching component to their duties.  At my institution, I know of a case where a professor was hired in the physics department, then his partner was hired as a research professor in biology.

The third possibility is that, even if they cannot offer you a suitable academic position, your fiancee's university may be able to help you locate some other kind of employment.  Some schools have official policies that offer this kind of support; but some do not.  However, even if there is no official policy supporting this, you may still find people (especially in your fiancee's department) willing to assist you.  The help could come through personal connections, or making some of the resources of the university's career office available to you.  After she finished graduate school, my own wife got some help from my institution finding job leads, which were extremely helpful.


How to express dissension as a grad TA while maintaining professionalism

I would strongly recommend against doing anything dramatic, such as resigning or publicly denouncing the course.  I feel bad about discouraging acting on your beliefs, but I think it could actually hurt your career.  There are two reasons for this:

First, the topic of how to teach low-level mathematics courses has become contentious and politicized in recent decades.  Unless this is actually your scholarly specialty, it's safest not to get too dramatically involved, particularly as a grad student.  The problem is that you can easily find people who will embrace you as a champion or martyr, whichever side you are on.  Even if you are sober and self-restrained (which would probably rule out a public letter), other people on your side will say provocative things and attract negative attention while supporting you.  Controversy is dangerous for academic careers, since it's generally easier to veto hiring someone than to generate an offer.  So if you acquire equal numbers of friends and enemies, your enemies can hurt you more than your friends can help you.  Plus, if you want a research career, being known for inflexible opinions about low-level teaching will distract attention away from your research accomplishments.  That distraction can be a problem even for people who agree with you.

Second, you risk coming across like a worrisomely disruptive colleague.  Most math departments contain at least one faculty member who regularly takes fervent stands on seemingly minor issues.  They feel they have logically analyzed these issues, and they can't in good conscience cooperate with anything other than what they see as the logical option, since that would be a betrayal of the basic principles underlying mathematics.  Coordinating with others or compromising play no role in the analysis, and it doesn't really matter how important the issue itself is (what matters is standing up for what's right).  These people drive everyone else nuts, since they make it impossible to get anything done without either giving in to them about their pet issues or spending hours debating.

I'm not saying you are necessarily disruptive in this way.  You have chosen an important topic to get upset over, and you might be completely right about it.  However, if a hiring committee hears that you resigned in disgust upon being asked to administer online quizzes, they will wonder what else you might make a fuss over.  This could put them off even if they agree with your concerns about teaching, and there's no way to reassure them that it's really just this one issue.

So what can you do while avoiding these dangers?  One approach is to let the faculty handle this fight.  If every faculty member disagrees with you, then your cause is hopeless in the short term and it's best just to calm down and finish your Ph.D. program without too much controversy.  If some of them do agree with you, then it's not likely that publicly joining them as a grad student will shift the balance of power in the department.  Instead, you can try to get your future TA assignments in courses they teach, while encouraging them behind the scenes in their attempts to change the department's approach.

To the extent you take direct action, I'd look for approaches that don't cause extra work for anyone else.  For example, if you resign, then someone will have to find a replacement for you (so they'll automatically be upset about it).  But you might be able to improve the course by strategic volunteering.  Could you prepare optional handouts meant to deepen the students' knowledge?  Could you offer a few additional review sessions before exams?  These sorts of things aren't going to effect the fundamental changes you seek, but they could at least make you feel better about having done something rather than nothing, and they may build some goodwill with the lecturer by showing that you really want to help the students.


What are the chances for a scholarship winner to be denied admission at Uni?

It very much depends on the admissions system. If the system is based (almost) strictly on grades (the way the German system largely is determined), then having a scholarship doesn't help with admissions. This is also the case if there are minimal tuition and registration fees associated with admission.

In the US, though, funding is a much more important issue in admissions. Students with their own funding source definitely have an advantage over other students of comparable quality, since they cost less money, and thereby can be admitted when other students can't. However, a student who has a scholarship but might not be a good fit for the department might not be admitted.


Should I do anything when I see several references that are not used in the text?

There's nothing inherently wrong with this.  It's sometimes done to mention sources that provided general background information, or that the author suggests for further reading, but which weren't needed to support any specific claim within the paper.  Some journals don't allow this, but it's a matter of style.

Even if the journal didn't want this, or if those references were included by mistake, it's a harmless error which just wastes a little bit of space.

If you have good reason to suspect that references were given in bad faith purely for padding, or to increase citation counts of other articles, then that would be misconduct - whether they were cited in text or not.  But otherwise I don't see that this represents anything improper, and there is nothing you should do about it.


Is Bsc from Netherlands in Computer Science eligible for M S from USA

That is probably dependent on the institution.  You may have to check with each college or university you apply.  Also, check with the department too, don't ask general admissions.


Do famous works of literature need citations?

When I published a paper on statistical analysis of various texts, which included really famous works, I gave full references. Why I think they are deserved:

what you consider a famous work may be in fact unknown to a reader and she may become genuinely interested in the work - in that case the more bibliographical data, the better (e.g. call me simple-minded, but I have never heard of Red Sorghum Clan);
you may be implicitly referring to a passage that was present in particular edition, but was not present in others;
where do you draw a line between a scientific work and a work of art that does not require a citation?
in your example you are not citing an original work (which, according to wikipedia is titled 红高粱家族), but a certain derivative work, a translation, done by a certain translator, who - inter alia - came with the English version of the title. I think one should then give precise pointers to this translation.

Also, check whether your manual of style says anything on the matter.


Am I allowed to show properly redacted exams to a colleague to determine if cheating occurred?

FERPA permits education records to be shared with school officials who have a "legitimate educational interest" in them. Examples of a "legitimate educational interest" include (via University of Northern Iowa):

  Performing appropriate tasks that are specified in his/her position description or by a contract agreement.
  Performing a task related to a student's education.
  Performing a task related to the discipline of a student.
  Providing services for the student or the student's family, such as health care, counseling, job placement, or financial aid.

Also, if the student is not personally identifiable from the anonymized exam paper, then the papers are not protected by FERPA at all. Via Wayne State University:

  With specific exceptions, FERPA defines “an educational record” quite broadly and it is not limited to “academic” records.  “Education records” include virtually all records maintained by an educational institution, in any format, that are “directly related” to one or more of its past or present students.  A record is “directly related” to a student if it is “personally identifiable” to the student. A record is “personally identifiable” to a student if it expressly identifies the student on its face by name, address, ID number, or other such common identifier.

  A record is also personally identifiable if it includes “other information that, alone or in combination, is linked or linkable to a specific student that would allow a reasonable person in the school community, who does not have personal knowledge of the relevant circumstances, to identify the student with reasonable certainty” – in other words, if it contains enough demographic or other information that it points to a single student.


If PhD programmes prepare the candidate for research, why do teaching positions require it?

In order to teach new ideas in any field, you have to (1) understand how research is conducted, and (2) be current on the state of research in the field. By allowing you to do original research, doctoral programs prepare you for both, even if you do not continue research activity.


Difference between experiential learning and hands-on learning

Experiential learning involves metacognative aspects of learning such as the concept of transfer which is the ability to take skills from one setting and use them in another. Often experiential learning includes hands on learning.

Hands on learning usually lacks the metacognitive characteristics of experiential learning. For example project for the sake of a project without a deeper application. Generally these two terms are used interchangeable when this should be avoided.


Is it unnecessary to write "Please refer to xx paper for detail" after talking about framework presented in this paper?

Since most people would understand that anyway, no, it isn't really necessary. It might be different if it were necessary for the reader to explore that detail before continuing with reading your work, of course. But in that case, you might want to make it more explicit.


Are PhD students allowed to extend their graduate studies to have a better chance at an academic job?

In the United States, there is a lot of opportunity for flexibility in scheduling graduation, assuming the faculty member has sufficient funding and motivation to keep the student around.

In most cases, however, the student would likely be served better not by delaying their graduation but instead by arranging for a transitional period as a postdoc with their same advisor.  In many cases, the cost of a postdoc is often not terribly different than a graduate student (higher salary is offset by lack of tuition), and there is typically little difficulty converting grant money from one to the other.

As a postdoc, however, there is no longer a question of graduation and thesis hanging over the former student's head, and they can be more free to focus instead on publication, networking, giving talks, and other things that will help to better position them for applying for academic positions.


What is the best way to deal with cranks?

Ignore the crank.

Unless you are in some location where you are required by law to respond to communications (I remember reading here about one country where it was indeed the case that it was required to answer emails as part of "open records" laws), you are under no obligation to waste your time on a crank's musings.

If it amuses you to respond, feel free to do so, but you waste your time at your own peril!


How much can one download from databases before it is too much?

According to this article, a student was arrested for downloading ~4
  million articles from an on-line database.

That was an extreme case. He had history of downloading and releasing large amount of information. In this JSTOR case, I don't think he had actually released the articles, although the indication was strong. He was charged with "unlawfully breaking in a protected computer," which I guess he probably downloaded the paper with unusual means, perhaps using codes or hacks. Overall, the whole case was very politically charged and I will not use that as a benchmark in your case.

  I want to review all existing articles in my interest area before
  writing my paper, so I need to download and skim through several
  thousand articles. I read the terms of service of my school's
  database, but it just says I should avoid trying to make a
  "collection".

When there are several thousands of articles that are pertinent to your research interest in ONE paper, I would suggest you to refine your research interest. And no, you don't need to review all existing articles, just pick the important seminal works, and then trace the major works along a very well define research interest. You can also use a few prominent modern works as seeds and use their reference list to snow ball your library.

  At what point does the downloading become enough that the databases
  start to complain? 1,000? 10,000? 100,000? 1,000,000? Do they send out
  warnings?

You should be able to download as much as you want as long as you follow the instructions and rules. For large download volume, I'd check with the librarian to clarify:

What the institutional limit is. There may be a download limit and if you'd get a warning letter it's likely from your school because your thousands of download could have cost them a lot more than usual. Some school libraries may ban accounts associated with a large download volume as well; it's better to give the librarian a heads up.
Your student account payment scheme. Some schools may have limit and beyond which the students may have to pay. I know that this is certainly possible for inter-library loan (which you may have to do if a few thousands paper is your goal.) A peer of mine got billed for more than US$500 because she ordered about a hundred papers through inter-library loan.


If you apply before the deadline, then I wouldn't consider it late.

Depending on the university and department, they might not review applications until after the deadline or they might review them as they come. So long as you make that deadline though, it should be fine! You may find this question helpful regarding the benefits of applying early.

I would certainly encourage you to apply now if you can. On a side note, I applied after my university's deadline and was still admitted but don't do that :)


Quickly pulling together thesis after unexpected failure of oral exam

If it helps, your failing is probably more representative of your committee criticizing your adviser rather than you alone. Let me guess -- you work for a assistant/junior Professor or a tenured professor who has fallen out of political favor within the department? My guess is they are "beating on you" as a proxy for your professor because that is how academia works.

My advice to getting out of this rut is to suss out who on your committee is your adviser's enemy and work more closely with them. To handle a similar situation I had in my PhD I attended "enemy" group meetings and presented updates on my work directly to "enemy's" group. I could learn any objections to my work from the "enemy" right away before presenting in the exam. Over time the deadline for retaking exam became more flexible. I ended up satisfying it a few months before defending my dissertation. Enemy turned to friend and helped me with providing materials and access to characterization tools. Enemy-turned-friend wrote stellar recc letters and helped organize job interview for me. I ended up drafting and publishing 5 manuscripts from the research, on 2 of the papers I offered "enemy/friend" coauthorship and he/she declined. After graduating enemy-turned-friend became department chair and took away my adviser's labspace and used my PhD apparatus for his/her own research.


Is it bad etiquette to contact a named reviewer?

If the reviewer has given you their name, then that is their choice. In my experience journals give the reviewers the option of anonymity. If they've chosen to reveal their name then I think there is no issue with you contacting them directly. Especially if you've discussed the work with them previously.

When you resubmit the paper, with the changes, perhaps you could then include this persons name in the list of people not suitable for reviewing the paper (Assuming that this journal asks you to submit names of suitable, and not suitable, reviewers).


Pseudocode, in a paper -- is it a figure or a table?

Pseudocode, in a paper, is figure or table?

Strictly speaking, both "Figure" and "Table" are wrong, given that code is neither. However, there is sort of a tradition of using "Figure" for program code (see for instance here or here for examples from the programming languages community in computer science, which unsurprisingly needs to deal with code often). Alternatively, especially short one- or two-line listings are often just inserted without label.

Your supervisor is hence "correct" in the sense that it is at least not uncommon to use "Figure", and nobody should fault you for it. Using "Table", on the other hand, would indeed look strange to me. There is no tradition for using "Table" in this context, and, well, it's certainly not a table.

An alternative that most styles at least seem to tolerate is to use "Listing". I see it rarely being used in other papers, but I have been using Listing for years without it ever being commented on.


What is work-life balance like in academia in Japan?

My personal experience is positive -- at least, in our institution, I don't really feel pressure from colleagues or management. However, I suspect it depends on a particular place. There are certain situations that I consider unavoidable, and thus I don't think people disrespect one's life-work balance, but unpleasant things happen.

For example, we might have grant deadlines or other paperwork in the middle of vacation, and of course, we are expected to get things done. Certain events like open campus, student competitons or entrance exams typically happen on weekends, and someone has to take care.

So, at least for me, most pressure comes from objective reality rather than someone's direct requests. When I have to work on a conference paper day and night to meet the deadline, that's for my own good, and I won't do myself a favor by missing it. The situation is more complicated in case of joint work when I can let down my colleagues, but perhaps Japan isn't special in such matters.

From the perspective of regulations, labor laws of course protect employees, and our administration actually asks us to take more vacation days to improve their stats, and they even offer additional vacations on top of what we have during the summer break. Your mileage may vary, but most professors around me don't push their students/postdocs too hard. I believe it might depend on the source of funding as well.


While it does not send you reminders of upcoming deadlines or anything, I find that this site provides a very nice overview of the deadlines of a number of CS conferences:

http://confsearch.ethz.ch

You can get all conferences from a certain field, for example:
http://confsearch.ethz.ch/confsearch/faces/pages/topic.jsp?topic=Theory&sortMode=1&graphicView=1
gives an overview of theory conferences (I do not see Operations Research mentioned, and I am not sure whether it falls in any of the other categories they have).

It looks like you can also customize the overview to include a specific set of conferences (see their help page for more info).

According to the website, they obtain their info from DBLP and from user input (you can indeed modify information about a conference manually, thereby I am not completely sure how reliable the information on this site is).


Prerequisite for research in discrete mathematics

This is a US centric answer. If you are applying to a mathematics doctoral program in the US and have a mathematics undergraduate degree then the specialty you want to pursue isn't especially important. First, a broad based undergraduate degree has what you need to get started in a US doctoral program. If your undergraduate degree is other than math, you have a more complicated situation, but admission is still possible if you have, in general, "enough" math.
But one reason that this is the case is that such programs start out heavy in coursework, so if you need more combinatorics, for example, you will be able to get it before starting research.
The prerequisites you need for research are probably at the discretion of the advisor you will (later) choose to guide you. They may have some specific suggestions.
The one thing you might need to consider, however, is whether the pure and applied math specialties are contained within a single department or split between departments. Some splitting is common, as having statistics (different example, I know) separate from math. If pure an applied are in a single department, then you don't need to make a selection before applying, and you may be able to delay that decision for a year or two while you take some courses and learn more about possible advisors.
In other countries the situation might be drastically different, of course, with more expected on entry but a shorter time-frame for getting the degree.


Going for PhD or MS in research right after under graduation?

In certain disciplines it's very common to enter a Ph.D/MS+thesis program straight out of an undergraduate degree. Computer science is one such discipline. Usually you spend the first year or two in the Ph.D program getting up to speed and doing research. For an MS+Thesis program, things are more compressed, but you also aren't expected to produce research of the same scope.

While it's always better to have some research experience as an undergraduate (and this helps your grad application) it's not a requirement for success at the graduate level.


Does it make sense to get a second M.Sc. while pursuing a PhD?

In Germany, as has already been pointed out, the Master's degree is a prerequisite for enrolling in PhD "studies." It should also be pointed out that in the German system, PhD students are Wissenschaftliche Mitarbeiter (research employees), so it is expected that they would devote all of their time to research activities. Enrolling in a second master's program would run contrary to those expectations, unless you are only a part-time employee (and receive a correspondingly reduced salary). That said, it is possible to sit in on additional classes as a listener. (And generally this is required if you are coming from a foreign country!)


A number of students requesting a number of reference letters. What to do?

Your director says "As many as you can" - in my philosophy these would be those where I think the letter would easily help and, as such, easily written.

Create a spreadsheet with comments, and evaluations, possibly link collections if that's easier than to search through mail.

Use automated template generation for the reference letter outline, possibly electronically added signature, and write short, crisp paragraphs on what impressed you about the student. One, at most two paragraphs are perfectly enough if you have something good to say. It's like feedback for an essay. "This student performed well because they ..., were able to ... and showed skilful handling of ... Whatever is relevant, give facts and a brief evaluation, this is perfectly fine.

Any awards, just mention them.

End on a standardized positive note. This is not a tenure reference. If you have to write many references, you cannot spend much time on refined formulations.

Group the references together for the same website/uni and fire them off.

For very strong students, usually it is possible (and pleasurable) to write more, as you will know more about what they have done. They can be treated in a more individualized fashion.

References for weak students, on the other hand, are very difficult to write, and so they will burn a lot more of your time if you want them to help at all; this will be like squeezing blood from a stone. I do not recommend doing that, unless you have some simple and strong thing to say about them and you wish to do so.
Although it's not up to you to decide whether they should proceed with a graduate education or not, if you yourself do not think they should continue, it is in your right to choose not to be part of the process in that case.


Are postdoc salaries in the USA adjusted for cost of living?

There is a wide variety in the range of post-doc salaries. In the biomedical sciences, the NIH's salary guidelines hold sway, as the NIH is the largest source of funding for such positions. So there's relatively little cost-of-living adjustments.

However, I think many institutes set their own scale according to "what the market will bear." Popular schools like MIT could pay somewhat less and still be competitive because of the "prestige factor."


Should a post-doc let his boss know before applying for a short term funding involving working in another location

Absolutely let them know before you apply. At my university, postdocs can't PI projects without a special exception from the university anyway, so you would need a support letter from your boss to apply in the first place. These kinds of rules probably don't apply to the kind of funding you are seeking since the money will go to you directly rather than being funneled through your current institution. However, if you are going to leave the group for a few months during your time there, your current boss needs to know this. Also, they should be glad to have you go and spend time with another group where you will undoubtedly get additional training and/or facilitate connections between your current group and the remote one. As such, your current boss might be able to help you write the funding application.


Can my adviser publish an under review work without my consent?

Can my advisers publish this work without my consent?

No. But why would you refuse it? Just to harm your supervisor? That seems petty. You have nothing to gain by sabotaging her and throwing away months or years of work for both of you.

If the problem is that you have no time to work on the paper anymore, just write that to her. She might be happy to finish the work herself.

  Can they remove my name from the paper given the fact that I will not work on this paper anymore?

No. Assuming your past contribution was substantial, you are rightfully an author.

It would be a major faux pas for her to try to get it published without your name. You'd have every right to complain and ask for retraction, and plenty of evidence from your dissertation (if what you write is correct). That sounds like major academic misconduct. Her reputation, and possibly also her job, would be at stake.

  How do I need to communicate this with area editor if at all?

What do you wish to communicate exactly? Are you afraid that she is going to remove you from the list of authors? That seems an unreasonable concern to me. (See above.)


Student found guilty of plagiarism is also academic at other university

This may be covered by privacy law in UK as it would be in US. You need to consult with a lawyer before you take any action that isn't already embodied in your policies, which I assume have already been vetted.

If you are permitted to inform the other university you should also consider whether you are liable to civil action if you do so. But your lawyer will have advice about that as well.


Is it good for the speaker to read notes during a presentation?

Twenty years ago it was not at all uncommon at international conferences in physics and electrical engineering to attend at "read" presentations, especially from old researchers from Asian countries who were not used to speak English.

How was it? Boring, utterly boring, and audiences drifted away. Please don't do or suggest it: if you feel uncomfortable speaking, rehearse, rehearse, rehearse.


Commercial product with the same functiality as my research project

You can totally reference non-free software in your work. The licence under which it is released has no impact on the technical and scientific merit of its algorithms and features. The only issue is that it is harder to know exactly what the system does if the code is not open, and that it will be harder (and probably more expensive) to reproduce any research based on it.

There are a lot of papers out there (often coming from private-sector reserachers rather than from academics, but still) which are exclusively focused on industrial products under proprietary licence. What is important is what is said about them, to which extent they are analysed, whether they are properly compared to other existing systems... Of course, it is easier to do that if you have inside knowledge of the product (i.e. you have participated to its design for instance), but it will remain difficult (not impossible) for the community to validate or refute your claims.

In a state of the art, if you know that a non-free system has a relevant feature, or solves a related problem, or contribute to the field, you just cannot ignore it, it would be a deep mistake, scientifically speaking (*). However, it might be useful to take precautions about the verifiability of the system's claim.

For what it's worth, the software development attached to my PhD thesis relied on a proprietary framework. It's not ideal in my opinion, but it doesn't invalidate the corresponding research, as long as the choice is duly motivated (for instance, no other framework provides feature X).

(*) "Listen to me: someone who doesn’t know the truth is just thick-headed. But someone who does know it and calls it a lie is a crook." (Berthold Brecht, Life of Galileo, scene 9 - you want to be a researcher? This play is a must read).


The question is very general so the answer is going to be as well.

A research question is a plan for working on some specific piece of research. Making the plan clear is an essential step. You should be able to give a specific answer to the three standard questions:

What is it? What is the object of the work and what is the context? Are there any similar questions already solved or studied in the literature?  How does your goal/question differ from existing works?
Why does it matter? What are the motivations for doing this work? What problem does it solve (or contribute to solve)? what use cases does it apply to?
How? Which method can be used? Why this method in particular? What are the potential limitations of this approach?

Having a clear answer to all these questions will allow you to have a discussion about the details with your supervisor: either they are convinced by your plan, or they can tell you exactly where is the problem in your plan.


I had performed mediocre in my core subjects during my PhD, is it justified for me to think about a future in academia?

There are a lot of reasons for struggling though coursework and you don't really give enough information to make any clear recommendation. But I can give perspective at least.

One problem you have is that you haven't much experience teaching, so it is hard to guess how you would do at it. But some people who struggle with a course can teach it well and others who breezed though it can't. The reason for that is that the "struggler" recognizes (perhaps) the hard parts and can help others past them, while the "breezer" just doesn't understand why others don't just find it as easy as s/he did. Some people do some things naturally and without effort and find it hard to focus on the parts that others don't get and provide the insight to get past the problems.

Many new teachers holding PhDs don't understand that the students in their classes are not like themselves. Only a tiny fraction of their students will have the same motivation and the same sort of motivation that they do.

A second, orthogonal, idea is that your learning doesn't end when your schooling does. You say you "aren't good" at some subjects. Well that isn't necessarily a permanent condition. Moreover, your standards may be so high that you find it difficult to measure up to them yourself. So your not good may be someone else's good enough.

Teaching, like research, is hard work. It depends on understanding the students as much as understanding the "material". Your students can learn if you give them meaningful work to spark their interest and build their skill.

So, while I can't provide an answer, I suggest that you don't give up easily and think deeply about the implications of your choices. Independent research is very difficult. Having the collaboration environment provided by a university (or industrial lab) is a great help.


A paper is published in a book, conference and its proceedings, should I cite it as book, conference or conference proceeding paper?

If you are writing a journal article, follow the journal's instructions.  If there are no instructions, imitate papers they have recently published.
If you are doing homework or writing a thesis, ask your professor.  Do not be surprised if they do not care.
So long as the paper is easy to find from the citation, any of these approaches is reasonable.


I think that it is a mistake and a waste to approach a tutorial like a lecture.

In my own experience both in leading tutorials (in a more STEM environment, but still one with some open-ended discussions) and in being a student in them (both STEM and liberal arts), the instructor needs to actively cultivate an culture of participation by the class.  Once such a culture is established, you can much better use the uniquely interactive format of a tutorial to really follow the students interests and needs in exploring the material.

Some tactics that can help in doing this:

Begin each tutorial by asking the students to set an agenda of things they would like to discuss.  Bring a few of your own that you can use to seed the list.
Along the same lines: be confident enough in your knowledge and the material to let the students see your process as you work through your thoughts on their harder questions. They will generally get more out of understanding how to engage with the material than out of the specific answer to a specific question.
Giving enough quiet space for students to feel comfortable to speak takes longer than you may think. You will often need to silence stretch long enough to be uncomfortable.
Avoid conversation being dominated by a couple of active students by occasionally saying things like, "I'd like to hear from somebody who hasn't spoken much today." This asks the active students to step back while avoiding the down-sides of calling on individuals to speak.
Set clear expectations about culture at the beginning of the class, and explicitly revisit your commitment to them from to time as necessary.


Is there any difference between PhD and D.Tech?

According to Wikipedia, the nature of a D.Tech depends on where it is issued, and who by.  In some cases, it is equivalent to a Ph.D., in other cases it is definitely lesser.  It is certainly not a commonly issued or recognized degree, but that does not mean it has less value if it is from a strong institution.


How to efficiently read mathematically and theoretically dense books in STEM fields?

I have never (as far as I can remember) read a technical book cover to cover from start to end.  Most of the time, I have a problem in mind that I want to solve, and I'm looking for tools to solve it; more often than not, if I'm trying to learn out of a book, I'm actually reading three or four books at once.  I dive into the middle of a book that seems most relevant; if I don't understand something, I'll back up, and if I don't understand that, I'll back up again, and if I get really stuck I'll put the first book down and pick up a more elementary book, and so on until I'm on firm ground again.  ("Getting really stuck" only happens after relying to work through/reconstruct details on my own, in addition to trying to understand them from the book's presentation.  I have taken months to read through one page, always feeling just close enough to understanding that I never felt "really stuck".)  Whenever possible I pop back up the reading stack with my target problem in mind, skipping entire chapters if they don't seem relevant (but backtracking if I discover later than I'm wrong), working forward again until I either find the tool that I'm looking for, conclude that I've been on a wild goose chase, or give up on the book.

Yes, I miss a lot this way.  Yes, I get a lot of weird ideas that I later have to kill off.  But I just don't have the patience to read large volumes of technical material that doesn't seem at least remotely relevant to some problem at hand, and prioritizing often leads me fairly quickly to tools that work.

Your mileage may vary.  Caveat lector.


How should one cite the entirety of a journal?

There are certainly interesting kinds of research where you would do this, such as bibliometrics, meta-analyses, history of science, intellectual history, or a subject bibliography.

The APA style blog opines that you would not need to make the actual citation for a meta-analysis: rather, you would simply mention the names of the journals (and the time periods you survey) in the text.

However, let's say you're looking at periodicals that are hard to locate today. Then a citation should help the readers find them. If they all came from the same database or archive, then perhaps it would make sense to cite that database or archive itself in the bibliography, with a mention or footnote about which journals were in which database or archive. Here's a page showing how to cite a collection of institutional records.

Or, if you're doing more of an intellectual history, you may be able to mark the beginning of each journal by citing the opening editor's note.

Then again, JSTOR allows people to download some journal information for research purposes. JSTOR's metadata fields for journals are journal-id (along with an identifier of who assigned this unique id), ISSN (possibly more than one if it changed over time), journal title (as of the time period you are discussing), and the publisher (as of the time period you are discussing).

Again, if you're doing a meta-analysis, the journals are part of the methodology but you probably don't need to fully cite them if they are current, modern journals.  If you're doing more of a history or a source bibliography, then you might just have a long "bibliographic note" appendix describing the journals, including where to access each and a history of changes to the names and publishers.

If all else fails, this is quite an ad-hoc citation, but you might try to find (or build) a reference type that uses the following:

Title: journal title

Publisher: publisher (might use organization field for this if there is no publisher field)

Organization: organization creating the journal (if available)

Address: city of publisher

Identifier number: ISSN (if available)

Year: Span of years

Archive: (database or archive info)

Location in archive: URL, shelf number, etc.

Note: How often is/was the periodical published; anything about disruptions to the run.

Update: If the otherwise best format requires an author/editor, you could use the name of the organization that created the journal, which is often promoted to "author" in the absence of a single author or editor. If that is not applicable, you might be able to use the name of chief journal editor(s).  You would want to make a note somewhere that you chose to record the information (editor, publisher, journal title, association, etc.) as of X date (journal founding, first issue in your time period, last issue in your time period, as of a given date across all the journals you're looking at).

Mendeley's Ultimate Citation Cheat Sheet might help you figure out desired formatting for your substituted-in components in the style you're using. It covers MLA8, APA, and Harvard, and if you're using a different style that might help you abstract the principles to that other style, if there is not sufficient documentation on that style's principles.


How flexible are number-of-pages submission guidelines for conferences?

None of the CS conferences I have ever submitted to had ever been lenient on page limits. There are often automatic checkers that will not allow you to upload a paper that exceeds the page limits. Conference guidelines are usually very clear and unambiguous, go and read them. Some conferences allow an appendix or a link to additional material that reviewers can read at their discretion.

Regarding splitting the papers - if you can do so in a clean way, and both parts make sense (tell a compelling narrative, have meaningful results) then sure. Otherwise, expect two rejections.


Guidlines for keeping adminstrative paperwork

Personally, I would recommend that you start taking notes at these meetings and toss all the handouts. Include the name & contact info of the person doing most of the talking in your notes so that you can contact them in the future if necessary. I use an electronic note-taking tool with user-defined tags to keep track of everything, as I've found it easier to search later on; experiment with different approaches to see what works best with you.

This approach works with most types of handouts, but for things like calendars and class rosters you'll still want to work with paper. Personally, I use something like this; I have two on my desk and I haven't needed more in a while, as I throw out folders when done with them. Even if you just stick them in a huge pile, though, it'll still be less huge than your previous pile, so at least you're better off.


Should a research proposal contain a discussion of my past experience and achievements?

If your next research steps are a continuation of your current line of research, then a quick summary of work you've already done on the topic is a great way to work it in naturally, provide context for where your research lies in the field's line of questioning, and explain why you think this research is worth pursuing (look how fruitful it was in the past! Self citation).
The etiquette is probably field dependent. Fancy grants and fellowships require specific tailoring, but for a normal postdoc in my field, even just submitting your research statement as a research proposal wouldn't be too rude or strange.


Are rejections usually quick for papers submitted to journals?

The answer depends on the journal, the paper, and the reviewer(s). You might hear relatively quickly if there is a trusted reviewer available quickly and he/she isn't too busy with other work and the paper is either especially good, or especially bad. Often the bad is easier to judge than the good, of course. The longest reviews are the intermediate papers, especially if different reviewers have different opinions about it. "We want to publish this. Do we have room in an upcoming issue? We have a lot of competing papers. I love it. I don't think it's quite ripe yet. Etc. Etc. Etc."

Note also that the reviews of intermediate papers (and even some judged to be quite good) may come with some advice for improvement that will, perhaps, lead to acceptance after additional review. This will depend on the journal, of course.

However, don't wait to hear the judgement of the reviewers. Continue work on the project, working to improve both the result and its presentation. Work to extend the result.


Is copying methods from a paper from the same group plagiarism?

Experimental and methodology sections are increasingly being recognized as "exceptions" from plagiarism, for reasons of practical necessity. For instance, I use the same basic technique to study different problems in engineering and material science. One of the sentences in my methodology section is:

  We use the SHAKE algorithm to constrain the bonds in water molecules [citation].

There are only so many ways to write this statement, and at the same time, I can't ignore this information, because it would imply a change in method. Is it plagiarism for me to reuse the same wording as in an earlier paper? If it is, I'm in big trouble. Similarly, if I were an experimental group, how many ways are there to say:

  We used chemical X from vendor Y as received.

For this reason—because often methodologies are very similar to previous methodologies within a research group–many journals now do not consider such so-called "self-plagiarism" of the methodology section to be a problem.


Should I apply for a master's or PhD if changing to a related field -- linguistics coming from B.A. in Spanish and Chinese?

(Disclosure - I am part of the admissions staff at a linguistics department in a UK university)

Talk to the department you are applying to first. Although they won't be able to give a definitive 'no - you won't get the PhD offer if you apply', most departments (at least in the UK) will be happy to talk, informally, about whether you fulfil the prerequisites.

There are some general points to remember though. A student enrolled on a PhD will be required to submit a substantial body of scientifically original work at the end of the course, and your ability to deliver this is what the admission committee will be trying to gauge. In your case, it is worth remembering that linguistics is the scientific study of language* - and actually has a very little to do with language skills themselves. Unfortunately, knowing Chinese and Spanish, and being able to teach English as a second language, do not provide evidence of your understanding of the science of linguistics (although they clearly show your enthusiasm with languages, which will be a plus). You have gone about correcting this in the right way, by doing MOOC and phonetics courses, but this may not be enough. The committee have to be sure you will be able to write up a good scientific thesis - if you are accepted, and are subsequently unable to write a good scientific thesis, (in the UK at least) they may stand to loose funding.

You don't say where in the world you are applying, but if it is in the UK, most prospective PhD's students have decided beforehand - at least vaguely - the broad sub-field they plan to do their PhD in, so they can approach a PhD supervisor at the department they intend to join. (So, for linguistics, subfields include semantics, first language acquisition, phonetics, prosody etc). This is why masters courses are so useful as a first step before a PhD - they allow the student to be sure of the subfield they want to work in, to work out if that department has the supervisor they want, and to familiarise themselves with the field so they can locate potential supervisors in other universities.

You say you aspire to be a professor one day - if so, perhaps a masters course would help you find that subfield of linguistics you really enjoy, and to find a supervisor that will inspire you to do great science.

Good luck!

*https://en.wikipedia.org/wiki/Linguistics

EDIT: Added after further information by the original poster

  I had actually considered asking but was worried about making a poor
  first impression. I don't want to start out appearing doubtful of my
  abilities to do graduate study.

If you are asking for information about the course, or clarification about entry requirements, this will not be seen as you doubting your ability. It will be seen as you having the maturity to find and clarify the information you need to make the right decision about which course is right for you.

  I plan to apply to UC Davis - who exactly should I ask, do you think,
  about their general admission standards for MA vs PhD?

The ‘graduate administrator’. For UC Davis’ graduate linguistics programs, the name and email address of their administrator can be found at the bottom of this page: http://linguistics.ucdavis.edu/graduate-program/admission (her title is ‘graduate co-coordinator’). If you email her, then she will answer any questions you have herself or forward it on your behalf to whoever is best placed to answer them.

I agree that (to me at least) the prerequisites to this course seem a little ambiguous, saying that, if you haven’t taken some of their prerequisite undergraduate courses, you can take them during the first year – which makes it seem like they are not prerequisites at all. But this is a perfectly sensible clarification to ask by email, something along the lines of:

I am considering applying to your department for a graduate course and I am trying to decide whether your masters or PhD course is more suitable for my circumstances.
I see that the prerequisites for the PhD on your website are courses equivalent to four undergraduate classes.
I have taken the online [fill in MOOC course here] linguistics course, which covered [X] hours of teaching and [X] hours of course work. Would this set of courses fulfil the prerequisites for your PhD program?

As I say, this is a very reasonable question, and the email itself will not negatively affect your chances of getting in. There are two further pieces of advice I would give based on the information you have given:

Each course they list as a prerequisite is 3 or 4 hours each. Some include course-work or discussions. I'm afraid that, if your MOOC course was not of a similar high standard, you should be prepared for the answer to be ‘no’.
You mention that you completed a TESOL certificate. While this is a great thing to put in your application to show your enthusiasm for the subject area of second language development, I suspect the admissions committee may not feel it demonstrates your ability as a scientist in this subfield. But again, ask the department first to make sure - they may feel differently.


Is it possible for someone with a BA in mathematics who is not currently a student to get an applied research job?

I'll explain my situation. Due to circumstances outside my control I was unable to apply for graduate school.

In the mean time, I am staying busy until I can apply this fall. Currently:

I am taking programming/CS at my community college.
I have been studying math, physics, and computer science on my own. I've been on here a decent amount, I do project euler, I have books, there's Coursera/MITOCW.
I live somewhat close to a very good university (UC Berkeley to be exact). I looked up the professors for ones that are doing research in fields I am interested in, and emailed them. I am current doing some reading with one of them which will probably turn into some research/writing a paper.
I looked at the classes I was interested in at the university. I emailed the professors asking if I could audit them. They all unequivocally said "yes", some even offered to grade my tests or said that homework was peer graded.
I have been tutoring a lot to make money (with a BA you could easily charge $30-40 an hour). If you really want to, you can get enough students to live very modestly while still pursuing your interests.
I know a friend who works doing data science. He might be able to get me an internship at his work.
The same friend might want to design some programs together.
Once I get a little better at programming, I was thinking about doing some freelance software/website/etc. development. I'm sure I could do projects here and there.

So do NOT feel hopeless. Honestly I feel like my passion for math and science has never been higher, and I feel very positive. There are TONS of things you can do. Please ask me if you want to talk more. :)


Accepted to PhD program but declined, but now want to return 3 years later

I did something similar (2 years).  I just went ahead and reapplied.  5 of the 6 schools that accepted me previously did so over again.

Didn't even think about not doing the applications.  What's the big deal.  You should know how.  Let them run their process.

I recommend to apply to several schools.  Always good advice but in this case to hedge your bets in case "A" doesn't like how they were cold shouldered earlier.

I would try to put a positive spin on things but not dwell on the previous decline (no mea culpa).  'Have had 3 productive years doing X, but now see more than ever that my skills would better fit in a Ph.D. level position.'  Hopefully they still want you.  Of course for any schools that you didn't decline earlier, you don't need to mention it as much.  Just say you worked a while and decided you belong in Ph.D.


About assistant professor job postings with no set deadline

One possibility to be aware of is that tenure track hires usually need to made after a national search. Yet some departments like to hire by going after "targets of opportunity". These are individuals already in faculty positions whom the department have identified as exceptionally talented and potentially willing to move. In order to facilitate this process, some departments keep an open search on the books for a protracted period of time.

The point is that some fraction of these rolling searches are probably not intending to hire from the pool of applications that come in unsolicited. That said, I also know of cases where the applications that come that way turn out be so strong that a department ends up hiring from that pool.


Can I ask for payment if my employer wants to use my dissertation?

I think your question is best rephrased as follows:

  If someone wants to use my dissertation, would it be ethical for me to ask for a payment?

Assuming you are asking about using the intellectual content of your dissertation, the answer is NO.  Whether or not that someone is your employer is irrelevant.

However, your actual presentation is protected by copyright, which for dissertations is normally completely held by the author.  So if someone wanted to use your specific words and/or figures beyond the limits of fair use, then you have the right to seek compensation.


How to politely reply to adviser for his mistake

I suggest a slightly longer response than Nicole's answer that allows for a somewhat graceful exit and has less potential for coming across as reproachful between the lines:

  I am not sure which part you are referring to; you did approve the abstract as such (see attached), but were you maybe referring to another piece of text?


Disclosing employment in acknowledgement of conference paper

In your particular case, your work got accepted at an IEEE conference. Congratulations.
IEEE has a relatively extensive website on author ethics. It doesn't seem to mention affiliations at all. Obviously, what you put into the paper should be correct, though.
But what is the role of putting the affiliation on the paper? After all, you speak for yourself, not your organization. It is (1) assigning credit, and (2) to make contacting you easier in case that is needed.
For none of these purposes, the asset management firm needs to be mentioned. It makes sense to declare potential conflicts of interest proactively, but as you wrote, there are none.
Many researchers do other work on the side, such as consulting, a small start-up, giving educational courses, etc. - I've not seen such a declaration of not having a conflict of interest in a (computer science) paper so far.
However, it probably makes sense to check if your main employer is fine with this (or even requires you to not mention them in the paper  - this could for instance be the case if they have no way of checking what you wrote is correct and hence don't want to risk their name being on the paper). Due to reason (2) for putting an affiliation on a paper, I believe it to be OK to put your asset management company as an affiliation on the paper if they insist.


NSF proposals: What exactly is wanted in the Intellectual Merit and Broader Impact sections?

I suggest the first port of call for an explanation is with the NSF itself. For Broader Impacts, I would start with this Dear Colleague letter on the Broader Impacts Review Criterion.

  The NSF Grant Proposal Guide uses a series of questions to illustrate
  the Broader Impacts criterion: “How well does the activity advance
  discovery and understanding while promoting teaching, training, and
  learning? How well does the proposed activity broaden the
  participation of underrepresented groups (e.g., gender, ethnicity,
  disability, geographic, etc.)? To what extent will it enhance the
  infrastructure for research and education, such as facilities,
  instrumentation, networks, and partnerships? Will the results be
  disseminated broadly to enhance scientific and technological
  understanding? What may be the benefits of the proposed activity to
  society? “

  These questions help to assess the potential of the proposed activity
  - beyond the research, per se - to benefit the Nation. Thus, the Broader Impacts criterion speaks directly to the mission of the
  National Science Foundation, “To promote the progress of science; to
  advance the national health, prosperity, and welfare; and to secure
  the national defense.” (NSF Act of 1950).

For even more recent descriptions, review Chapter II - Proposal Preparation Instructions of the NSF Proposal & Award Policies & Procedures Guide, Which includes these parts:

Intellectual Merit

  The Project Description must contain, as a separate section within the
  narrative, a section labeled "Intellectual Merit". The Project
  Description should provide a clear statement of the work to be
  undertaken and must include the objectives for the period of the
  proposed work and expected significance; the relationship of this work
  to the present state of knowledge in the field, as well as to work in
  progress by the PI under other support.

  The Project Description should outline the general plan of work,
  including the broad design of activities to be undertaken, and, where
  appropriate, provide a clear description of experimental methods and
  procedures. Proposers should address what they want to do, why they
  want to do it, how they plan to do it, how they will know if they
  succeed, and what benefits could accrue if the project is successful.
  The project activities may be based on previously established and/or
  innovative methods and approaches, but in either case must be well
  justified. These issues apply to both the technical aspects of the
  proposal and the way in which the project may make broader
  contributions.

Broader Impact

  The Project Description also must contain, as a separate section
  within the narrative, a section labeled "Broader Impacts". This
  section should provide a discussion of the broader impacts of the
  proposed activities. Broader impacts may be accomplished through the
  research itself, through the activities that are directly related to
  specific research projects, or through activities that are supported
  by, but are complementary to the project. NSF values the advancement
  of scientific knowledge and activities that contribute to the
  achievement of societally relevant outcomes. Such outcomes include,
  but are not limited to: full participation of women, persons with
  disabilities, and underrepresented minorities in science, technology,
  engineering, and mathematics (STEM); improved STEM education and
  educator development at any level; increased public scientific
  literacy and public engagement with science and technology; improved
  well-being of individuals in society; development of a diverse,
  globally competitive STEM workforce; increased partnerships between
  academia, industry, and others; improved national security; increased
  economic competitiveness of the U.S.; and enhanced infrastructure for
  research and education.

The Short Version

I think about it like this: intellectual merit is the "contribution" part of a potential publication or set of publications; broader impact is what administrators would like you to talk with the media team about so they can make a press release about how their people/funding are/is making the world a better place. In other words, the merit is the work itself and its findings, and the impact is what the effect would be on some defined portion of society if you succeeded in doing what you propose.

Both parts should be about what you are specifically proposing to do now (the thing the proposal will fund, and preferably with early results to support some claims), and should be deeply and believably connected to the research you are proposing. The farther out and more vaguely connected it is, the less compelling and believable it is likely to sound. "These findings could be built on to eventually obtain world peace in the next millennia" is not very compelling, for example.

Grandiose claims of widespread benefits must trade-off against believability and practicality. The more people you could help, in science and outside in general society, the better - but you should make the link very explicit and clear.

My source for the above is being involved with a few proposals in preparation, extensive reading of NSF program materials, preparing and succeeding with a fellowship proposal, and being involved with a few grant processes that were modeled off NSF criteria in the general area of technology/engineering/psychology. If you see any disagreement between my opinion and official NSF program materials, believe the NSF materials over me.


How to withdraw your paper from an open access journal where it has been accepted?

If it has been accepted but you have not yet signed any sort of agreement, then it's easy in theory: you just tell the editor that you have decided to withdraw the paper.  They might be unhappy, but you have a right to do this (both legally and according to academic norms).

If the paper has already been published, then there may not be anything you can do.  Retracting a published paper is serious business, done only in cases of serious error or unethical behavior.

If you have already agreed to some sort of license allowing publication and paid (or agreed to pay) but the paper has not yet been published, then you should move fast.  Legally the journal can go ahead and publish, and they may decide to do so, but your chances of convincing them before they publish the paper are higher than after they publish it.

There have been stories of unethical journals publishing papers that have been withdrawn and then demanding money.  If that happens, then it is serious misbehavior on the part of the journal (and proves you were wise to withdraw the paper).


Why does my Arxiv paper not show my affiliation?

By default, the Arxiv does not show affiliations of paper authors on its webpages. You apparently can add them by adding them in parentheses behind your name. See the help pages:

  If you wish to include author affiliations, put them in parentheses. Do not put a full mailing address. At most, include a city and country (no zip codes, postal codes, or street addresses). If you have several authors from the same institution, you can use a footnote style for the affiliations. Here is an example (be sure to do it in the form presented here, including all parentheses, and using numbers and not letters):

  Authors: Author One (1), Author Two (1 and 2), Author Three (2)
          ((1) Institution One, (2) Institution Two)

However, this feature is rarely used in my experience.

However, on the actual preprint (i.e., the PDF, PS, or whatever), you can show affiliations as you like (well, they should be correct). These are not automatically added by the Arxiv; you have to do this yourself. The content and layout of the actual preprint is controlled by you (except for a watermark from the Arxiv).


PhD admissions - (undergraduate) credit/no-credit influence on acceptance

I wanted to expand on the point made by @StrongBad in the comments.  Even if the courses in question are not offered through the Linguistics department, any grade in a course that is closely related to the proposed graduate program will be weighted much more heavily than a random course taken for general-education or general-interest purposes.

For example, when I was on a graduate admissions committee in physics (during my grad student days), we did look at the student's performance in mathematics classes.  These courses didn't carry as much weight as their performance in physics classes, but a C- in multi-variable calculus or linear algebra would be troubling.  Seeing a "pass" indication in such a class would make me wonder what happened there, and would make me concerned that the student didn't really get everything out of the class that they would need for graduate studies.  Even if these classes weren't required for the student's major (an applicant who had majored in chemistry, say), it would still give me pause.  In effect, it's better than nothing, but not much better than that.

If I'm reading your post correctly, you're proposing to take Computer Science classes pass/fail and then apply to a program in computational linguistics.  I'm not a computational linguist, but this seems like a bad idea to me.  On the other hand, you might be able to get away with taking a French class pass/fail, since the skills you would be learning in that class are not as directly related to computational linguistics.  (At least, they wouldn't be if your classes are anything like my college French classes were.)  And if the classes are completely unrelated (a class in History or Economics, say), then it's probably fine to take those pass/fail.

On a related note: if you do decide to take these courses pass/fail, you should be absolutely sure that you can still complete the proposed minor.  Many institutions (for example, mine) do not allow you to count pass/fail courses towards an academic major or minor.  Check with the department in question about this, if you haven't already.


What is the proper way to cite the usage of an API?

I don't think you'll find any documented correct way to do this. Personally, I would write a sentence saying that I did it, a sentence describing what an API is, and a link to the version-specific API documentation website (i.e., https://developers.google.com/youtube/v3/ for the API Version 3 instead of https://developers.google.com/youtube/ the general Youtube API help website).

If you're including code in the submission, consider adding the API code in an appendix.


Is it appropriate to email some new information to my recommendation-letter writers on Thanksgiving if the deadline is a few days later?

Asking is always possible.
Expecting any response or action ... well, that, as they say, is another story.


How do applicants for an NSF fellowship come up with a research plan for the research statement part of the applications

Having reviewed GRFP applications,  and gone through the NSF orientation sessions, I'd say it depends very much on the level of the applicant, but generally, literature reviews are not anywhere near as important as you thought they were.

This process only vaguely resembles a research grant review, primarily because there is ZERO effort to match reviewers' expertise to those of the applicants.  Broadly, electrical engineers will review applications of electrical engineers, and biologists will review applications from biologists, but that's as fine-grained as the process will guarantee.  This means that you can't display fundamental gaps in knowledge that any practitioner in your broad field should know, but in all likelihood, nobody is going to go check your sources, or know much about the very special second messenger system that impacts a new subtype of cation channel that 2 people in the world study.

As to where the research plan comes from, that's going to vary incredibly by the level of the applicant.  A student about to start a program, who hasn't even set foot on their campus yet, is very different from a student that's been placed in a PI's lab for a year, and both can get funded!  For the young student, reviewers are looking for your ability to put together a cogent hypothesis-driven study and communicate it well (and not many reviewers would believe this is the study you will actually do your graduate work in) along with a somewhat viable path to get yourself established with the type of resources you would need to actually do similar research, and somewhat more than that for an experienced student.  My recollection (though I could be wrong) is that there is some earmarking of awards to the four levels  of application status, and that young applicants will get a competitive amount of awards, even though the experienced students clearly have more polished packages.

Reviewers are trained to assess you in two areas; "Intellectual Merit" and "Broader Impact".  Both are rolled together to make a holistic assessment of your application package.  Reviewers are looking for evidence that 1) you've got the intellectual goods to thrive in science, 2) you've made opportunities for yourself and have taken advantage of them, and 2) that you see areas where you can bring your skills to the larger community.  I can't say that you'll be successful if you can demonstrate success in these areas, but I can say that you won't if you can't.  Using your literature would be a part of this, but I'd say that if you don't make any mistakes in your use of the literature, you won't be hurting your application.

As to whether you should apply this year or wait until next year, that's a tough call.  The risk with the "make believe" type of applications, where you aren't even affiliated with a lab yet, is that one reviewer might not buy that the path you've outlined is viable, and considers this to important to recommend funding (I try hard not to do this, myself, though naivete can certainly be a strike against intellectual merit). This will kill your application.  I don't believe you are excluded from applying a second time, though, so the risk of application this round seems minimal.  You should verify eligibility for a second submission on your own, though (i.e., don't take my word for it).


The wording here makes me think that the 6500 word count includes figures, tables, and references, as "to include" seems like a synonym for "including". However, it is always, always good to ask for clarification, especially when the wording, as in this case, leaves room for interpretation. I would email or otherwise contact the journal editor and ask for clarification. Contact information for the journal you linked in the comments can I believe be found here.


Should I put two loosely related results into one paper?

Just reading and trying to understand your question made my head spin, most likely due to use of generalization (X, Y, A1, A2), but not only that. Therefore, IMHO, the safest approach to solving this dilemma is to separate results into two papers. The rationale for this approach is the following.

Each paper would have a clear and, thus, easily understandable scope, goals, methodology, results and their interpretation. That would significantly improve readability and overall quality of each paper and chances to form a positive impression.
Since the problems A1 and A2 are "loosely related", shoving them into a single research study simply doesn't make sense from an architectural / logistical / layout perspective. It would be very difficult to present two sub-studies in a synergistic manner ("tell a story", as you put it).
Based on the above-mentioned points, I don't see how combining the studies would make the resulting "study" of higher quality, thus, warranting a publication in a more major conference. Quite the opposite most likely would be true (due to coherence and, thus, readability issues).
Your advisor's recommendation in regard to improving your work is quite strange, to say the least. It is based on the assumption that combining two studies of different scope/topic with weaknesses would make the resulting "study" less weak. If anything, it would make it even weaker, since weakness is one of multitude of characteristics, exhibiting additive properties.


Does a master's research project (not a thesis) count as a "publication" for PhD applications?

If it's printed in your institution's library it is fair to say that it was published by your university. You may want to explicitly list it as a technical report in your bibliography to clarify the type of publication that it is (your audience will want to know if your publications are peer reviewed or not).

Under the list you have here it would be an "Other" that is "Published".


Ask clarifications to a professor of another university

Yes, you can certainly ask.  But here are some suggestions to increase your chances of getting a useful answer.

Before contacting the author, make a diligent effort to resolve the question for yourself.  Check other books or resources that you think might have the answer.  If there is someone else at your institution who is an expert in this area, consider asking them.  If there is an active StackExchange site for your field, consider asking there!
Put some effort into writing a question that clearly and concisely expresses what you are asking, and that can be easily understood and answered with a minimum of effort.  If the author can't understand what you are asking, or it is extremely long or complicated, she might not be willing to invest a lot of time trying to figure it out.  If you are unsure whether it is clear enough, or whether the English is understandable, consider asking someone (such as your advisor) to proofread it.  (You might read through Raymond and Moen's essay "How To Ask Questions The Smart Way".)
If you are asking about something that you think may be an error in the author's work, it is safer to express it as "I don't understand this" instead of "I think you are wrong".  It will be less embarrassing if they turn out to have been right.
Write in a way that makes it clear that you aren't asking a homework question or anything like that.
In general, your chances of getting a useful response are better if you are asking about a more specialized work that has relatively few readers.  If it's a lower-level, introductory, or extremely popular text, consider looking for help elsewhere.
Be patient.  Professors are usually very busy, and responding to questions about their books is usually among their lowest priorities.  I would give them at least 3-4 weeks; if no response by then, you could send one followup email.  If you don't get a response to that, then it's likely they are too busy to respond or not interested: stop emailing them, and look elsewhere for help.


Should I use self-made animations in my scholarly presentations?

Nate and cbeleites have handled well the finer points of the advisability of making the animations. I would encourage you to go ahead with them, but there are a large number of detail-dependent considerations that need to be made. I want to weigh in on the intellectual-property aspect of your question.

  Would it be unrealistic to be paid for some of my [animation] work during graduate school?

In a word, yes. You are already being paid to produce research and its corresponding dissemination materials. Asking your group to pay extra for a specific class of dissemination material will strike people as odd and probably as very selfish. I think it is unlikely that anyone will agree to this and you risk alienating your group and the rest of the community.

In addition to this, I do not think you should attempt to limit the spread of your animations. Instead, get ahead of the market, and engineer a situation where (i) people will want to share and use your animations, and (ii) people using your animations will bring credit to you and your group. More specifically:

Make sure all your animations identify you as the author, and your university and research group. Make this visible enough that viewers will see it and have enough time to register it, but discreet enough that users of your animations will not be tempted to remove it or skip over it.
Keep your animations publicly available in a visible and discoverable place online. This can be a YouTube channel, GitHub repository, university webpage, something else, or some combination of the above. Make it easy for people to find the animations from you, instead of getting nth-hand copies from someone in their lab.

This online space can then grow to include, say, your research papers, potentially turning some of your animations traffic into interested readers of your publications. This gives you as direct a benefit to your career from your animations as you can really hope for.
Provide clear licensing details for your animations, which could be CC-BY or CC-BY-ND. Make this clear but concise and easy to follow. It is up to you to gauge your audience, but I would claim that people are much more likely to use your content in ways that you would like if you (1) actively give them permission to use it, and (2) clearly state the ways you would and would not like your content to be used. If you provide your animations under CC-BY and state as the attribution requirement that people provide a link to your repository, you are creating a contract of sorts between you and those users, which adds a barrier on their side of the channel (they need to actively breach the contract to misuse the content).

Moreover, if you do this early then you can get ahead of the game and set clear rules for how you want your own research group to treat the animations. Make it easy for people, and particularly for your own group, to know how to credit you, and they are very likely to do it.

Academia is a weird place, and there are many ways to be compensated for work which are not monetary. (Think, for example, of journal editors and paper referees, who perform their jobs on a voluntary basis, in the understanding that they are service activities that actively contribute to their standing in the community, and therefore indirectly to the visibility of their research, their avenues for further collaborations, and ultimately them keeping their day jobs.) You should not expect direct financial compensation from your animations, but there is no reason why you can't market on them and use them to further your career. You just need to be somewhat more clever about it.

In this sense, the situation admits a clear analogy to the (sad) state of the music publishing industry over the past twenty years or so. People are going to pass around your animations, whether you want it or not, in much the same way that people are going to share music illegally if it is the cleanest way to obtain it. The music industry we have spends all its resources trying to clamp down on this, with little effect beyond alienating people; don't be like them. Instead, be like the music industry we wish we had: actively trying to harness the new technologies and media to generate new, fresh, legal ways to get the content, that actually make you want to use them. This is what I mean by beating the market.


What should I prepare for a postdoc interview?

Most likely they will ask you to quickly summarise the paper and then discuss strengths and weaknesses.

Usually is more important to get the idea of the paper and present your opinion on it than details.

But nobody can really predict what they will ask. It might also be worth checking if the paper comes from a competing lab or a collaborating lab (EDIT: or the lab itself!).

The most important thing (apart from the paper) is to show that you will be on fire for the proposed research (just to like it is not enough).


Are there any "non-research" jobs in Asian HiEd available to foreigners?

In China, there are some lecturer positions in universities that do not require to do research. The salary is lower than that of an assistant professor (that does research) and also the teaching load is higher. For example, at some university, lecturers are required to teach over 350-400 hours a year. The salary as well as living expenses can vary quite a lot depending on the city and university. There is a great need for English teachers but other topics can be possible. For the work permit, as I remember it requires a bachelor degree and 2 years experience, and as a Canadian, you are in the list of countries considered as native speaker eligible for teaching English.  Other possibilities for teaching English is to teach in a training center for professionals rather than teaching for kids.  For English teaching jobs, there are several agents looking for teachers that you may contact or you may talk with universities directly.  By the way, I think you also need to check the requirements for entering the country. During the pandemic, some countries have stricter rules for giving work permits (e.g China). It may not be the best moment to look for a job.


Can the GRE Sub in Psychology compensate for my low GPA?

Almost certainly not. Although I'm not in psychology, I'm in the social sciences and we generally do not consider the GRE subject exams to have much probative value in regards to the ability to do doctoral work in a field.

Remember that the admission committee is not trying to evaluate whether or not you score well in standardized tests, but rather whether you are capable of rigorous coursework followed by independent research. Our best way of ascertaining that is from your letters of reference and your statement of purpose (and to a lesser extent, your undergraduate grades).


Find information about research grant calls from around the world

Here are several options:

Research Raven. This site focuses on calls for papers and conferences, some of which include funding. Most of the listings relate to medical and healthcare related opportunities.
ScanGrants. This is a sister site to Research Raven, and is "designed to facilitate the search for funding sources to enhance individual and community health....
Funding sources most frequently listed here include those of private foundations, corporations, businesses, and not-for profit organizations. Finding and listing less traditional funding opportunities is also a priority. Federal and state funding sources are typically not included on ScanGrants™ because they are readily available on other sites." Their listing are somewhat US-centric, though.
European Research Council. I am not very familiar with ERC.  The website states "ERC grants are open to researchers of any nationality in the world, any scientific field, any age. ". It seems well worth checking out.
The Wenner-Gran Foundation suppports collaborative research with a focus on anthropology. You have not specified your field, but depending on your circumstance this may be worth looking at.
Conference Alerts will provide you with a free alert system for conferences in your field, for any or all countries. Although this is not a grant-finding/listing service, the individual conferences may have funding available to you.
Finally, this Google search may bring some useful results.


Typically reference letters should come from faculty, as you implied.  If you were supervised by a graduate student, ask the graduate student's faculty advisor to write the letter.  Very likely the faculty member will ask the graduate student for assistance in writing the letter.  This will get you the legitimacy and the content you need.  It can be awkward because faculty need to create the impression they wrote the letter themselves, but you can finesse it.  When I was a PhD student supervising undergraduates I just told them that I would ghostwrite the professor's letter.


Are papers on Research Gate publicly available?

In my experience, the papers are often not online, but RG let's you "request" a paper, meaning the website sends a canned email to the author, which they may or may not respond to. This is regardless of whether or not the user has an account. RG infamously listed authors with their publications who never registered, and these would thus receive all sorts of spam. I'm not sure if that is still the case.


What care do reviewers take when writing a review for a published paper in mathematics?

MathSciNet reviews are not the kind of reviews an editor would get for a submitted paper. Rather, what is posted on MathSciNet is more of a summary of the article and someone putting it into the context of the broader field -- something that would help a reader understand not only what the paper provides, but why it is relevant. As such, the authors of these reviewers don't have to go through all proofs with care -- they don't even have to understand the proofs as long as they understand the theorems.

On the other hand, reviewers of math papers often go to great lengths to ascertain that the proofs in the paper in question are in fact correct. That typically requires a great deal of care, detailed insight, and work.


Till what point do you do exercises while studying?

Learning is a life long activity. Graduating with a PhD is not a license to stop learning, it's a license to (eventually) get paid to do research and learn more :)


What are the Do's and Don'ts of Computer Science PhD viva?

Some obvious points that come to mind. In my view there is nothing special about a Computer Science Phd Viva that would differentiate it from another subject. There are minor differences between countries in the conduct of a viva so some of the answers are may be UK specific and some general to all Phd defence. For example, in some places the viva is in public and anyone can ask questions. In the UK it is usually held in private and often the research supervisor does not attend and you have a different internal examiner and also an independent chair who sometimes comes from another subject. The external examiner would usually be a national or international subject expert, but there is a degree of variability of panel makeup and regulations.
Yes; you can show off, as if your Phd is very good that would perhaps make you one of the countries or subjects experts in the topic of your Phd. It may be something you can be proud about. However, attempting to show off when the external examiner (another subject expert) thinks you are wrong may be a mistake. You have to read the social cues to ascertain which it is!
Certainly there be be some very in depth discussions. They want to know what you know.
Some do's and don'ts:
Do

Come prepared, Bring notepaper, pens. Take notes when appropriate. Bring a rough copy of the thesis you can write all over if they suggest a change, or use to show them where in the thesis is the answer to their question.
Sleep beforehand. Be rested and alert so you can clearly understand what you are being asked.
Remember the independent chair will be on your side. Their role is to ensure fair play. If you want to take a break, ask for one. Ask for refreshments if you need them.
Try to attend in person. Even if a remote viva is offered, like with Skype or Facetime this is never as satisfactory as talking across a table. If the viva goes badly you will regret saving a few pounds on that airfare.

Don't

Get into a philosophical fight with the external examiner, or imply the external is an ignorant nincompoop for not understanding your research. It will not go down well, as the external is the representatives of the subject experts. They are expected to know what they are talking about. They outrank you on every scale.
Expect your supervisor to come running to your aid, speak for you, or tell you the answers to hard questions. They are usually not invited anyway. If you got this far with your supervisors hand-holding you will now find yourself alone and on thin ice. This is you test that you make the grade alone.
Assume that critical questions mean that they don't like your work or think it not worthy. They just might be testing how fully you understand the implications of your work. Handling critical questions well is a sign of a good candidate.
Don't take it too personally, which is often very hard. Being critical of your writing does not mean that you or your conclusions are in some way lacking. It is their job to examine in detail and they are only doing their job.

Some general point, which I hope are somehow helpful. Best of luck.
(I answer as an experienced examiner and independent chair).


Wrong email id on letter of recommendation

Never ever manipulate a letter written by a third person.

Explain the discrepancy, yes. You have to hope they accept the explanation.

However, if you manipulate, you are committing fraud, breach of trust, and you will be blacklisted where this is possible. You may also lose your recommender for the future if he gets to hear about that (e.g. if they manage to check with him). In some countries (such as Germany), manipulating official documents is explicitly a crime and can be punished with years in prison.


How can I distinguish harsh treatment from my advisor from "tough love" and direct feedback?

He's probably giving direct feedback. If your adviser really hated you, he wouldn't spend the time in improving you.


Could your adviser make you commit to work on your paper before signing your graduation form?

I am not a lawyer, but this type of promise strikes me as a good example of a contract that is very likely to be ruled unconscionable, and hence legally unenforceable, if a court of law were ever to consider the matter.

In a more academic context (since academia sometimes obeys unwritten rules that don’t always coincide with the written law), your adviser’s requirement strikes me as unethical and highly problematic. Your adviser’s job is to approve your dissertation if, and only if, they judge that the work that you have done to date meets the requirements for a PhD. A PhD is not indentured servitude and your adviser cannot exert control over your life into the indefinite future, or indeed into any future that extends beyond the moment they sign that piece of paper. I see it as highly improper for your adviser to attempt to impose such a requirement. If I were a colleague of your adviser who heard about their behavior, I would lose a lot of the respect I hold for them, assuming I had such respect to begin with. And if I were a university official hearing a demand from your advisor to revoke your PhD over a breached promise of this type, I would laugh them out of the room. Of course, I cannot guarantee that other academics would have the same reaction.

I can’t advise you how to proceed, but some options that I can think of are:

Make the promise and be true to your word.
Make the promise without planning to satisfy the requirement. The rationale here is that a promise obtained under coercion is ethically void and you are not bound to satisfy it. (Again, that is the notion of unconscionability I was referring to earlier, but in an ethics rather than legal context.)
Do not make the promise. Explain to your adviser that the demand is inappropriate and hope that they will be convinced, or possibly negotiate to get the adviser to relax the unreasonable condition so as to allow for uncertainties about future events.
Complain to relevant authorities at your department and/or university.

Some people might think less of you for choosing option 2. Personally I think each of the choices I outlined above is reasonable and moral, although option 2 is certainly distasteful and I would try to avoid it if I could.

Good luck!


Is making non-culture-related exam questions culture-specific ever a good idea?

Assuming that the class is not on American culture, you are essentially asking if it is ever a good idea to evaluate students on the basis of knowledge that was not taught in class and that they could not have any reasonable expectation of needing to know.

(Example: I wouldn't expect to need to know how american football scoring works when I went to sit an electronic engineering exam. At minimum, for a question that uses the setting of a score counting machine, someone who's watched football games in the past would need much less time to understand the prerequisites, and likely notice discrepancies in the machine's behaviour more easily. For fields like sociology, a cultural context might be unavoidable. In that case, the class should also contain this cultural context, so students can know what to expect.)

If your goal is to evaluate how well students have learned the class materials, then no. It is never a good idea.

If your goal is to measure how well-integrated they are into american culture, maybe? I'm not sure what kind of exam that would be, though.


Is it ok to ask professor to read my published article?

I think it is fine to send the article, but not even necessary to ask him/her to read it. It is enough just to make it available, with a note about where it is published. It will be read or not, whether you ask or not. It is also good whether it is closely related to the professors area of research or not.

But making it available easily is a good thing to do and should enhance the application. It shows something about your ability, even if the sub-field is different and even if it isn't read.


If enrolled in Ms-PhD, do I have flexibility not to progress beyond MS?

(Copied from my comments)

Firstly:

In some cases the terminal MS program costs you more because you are expected to only do coursework, whereas in the MS-PhD program you are expected to service the department as a research or teaching assistant.
I would expect that if a school offers both options they would frown upon your entering the PhD track with the intention of quitting after the MS
Most importantly, this is something that you can and should ask the administrators at the schools you are looking at. There's a good chance that the policy is different school to school.

To answer your second question, it depends on what you mean by consequences:

If you meant only financial ones: I've known many cases (not in CS) where students quit after the masters, and in none of those cases were they asked to pay the school back. Mostly because of point (1) above. In fact, some departments offering the MS-PhD program seem to take it as a given that some students will drop out. But depends on what you want to do, there could be non-financial consequences: People who've invested time in you may be reluctant to write you recommendation letters etc.


Is it unethical to ask for homework help on StackExchange?

This might depend on your university's policy on cheating and plagiarism.

For our university (though the precise details may vary from course to course), you are allowed to use StackExchange to help you to understand concepts, but you are not supposed to use it to help you solve assignment questions.

We tell the students that if there is any risk that they may have read an answer or some code or whatever that might have influenced their answer, then they need to cite it. With a proper citation, they cannot be accused of plagiarism. We may, however, ask the student to answer extra questions in such a case, in order to demonstrate their knowledge.


What is my institution when submitting to journal

Ask the editor which they prefer, but (IME) the most common approach is to give your old institution (the one at the time of submission) and add a footnote saying "Now at...". An alternative would be to give two affiliations. Omitting your old affiliation entirely would seem strange.

(Bear in mind this may well vary substantially between disciplines, as with almost everything else! Again, if in doubt, ask the editor. It's their journal, after all...)


Having trouble getting recommendation letter for masters

You are not required to provide a recommendation from people who are professors. What is needed is people who can comment on your ability to do research. While it is helpful to have recommendation letters from people who work as researchers (whether in industry, academia, or other non-university organizations), if they are not available, you have to work with the resources you have at hand.

What can such people comment on? Well, your ability to solve problems independently and creatively, as well as any capabilities or skills in teamwork and leadership would also be helpful. Other "soft" skills relevant to research—good oral and written communication skills, and so on—would also be helpful. Of course, just mentioning that you have the above abilities is insufficient; the letter writers should provide helpful examples to support their claim (just like in research!).

One thing to also note here is that having letters from your undergraduate professors is not entirely helpful if they only knew you in a classroom context. Three recommendation letters from such people would probably not be as helpful as someone who knows you in a more work-related environment.