Getting a scientific article published with no qualifications to any scientific journal?

There are two different types of "no qualifications":

A person may be "unqualified" because they don't have the usual pieces of paper
A person may be "unqualified" because they are not familiar with the standards and practices of the field.

Don't worry about the first one.  Worry about the second one.  For example, one of the other comments raised the issue of getting human subject experiments approved.  Likewise, there are lots of subtle challenges in experimental design that have to be dealt with in order to  getting a valid psychological result.  But high school students and undergraduates do real scientific work all the time.  Consider, for example, the iGEM genetic engineering competition: students from around the world, both high school and undergraduate, get right out to the bleeding edge of science, and some of their work goes on to be published.  Or consider the Hackerspace/DIY movement, which is bubbling over with innovation and certainly knows no age barriers.

Now, what most of those folks have, and what it sounds like you don't currently, is mentors who know the ropes.   A good mentor might or might not be "qualified" in the sense of pieces of paper, but should have a good sense of the scientific method, and at least some ideas of who else to get involved if you start thinking you've got a unique result and want to figure out how to get from awesome science on the internet to a formal publication.

Don't worry about the uniqueness or publication part of it too much.  First, find some good peers and a mentor if you can, and just start doing some science.  Then see if you actually enjoy the thrill of the knowledge chase enough to overcome the frustrations of experiments that don't work and people who point out the problems in the ideas you have come to love.  If you fall in love, not just with the idea of science, but with the process, then as time goes by you can sort out which of the many science-related career paths ends up being a good one for you to pursue.

Maybe you'll end up published before you turn 20, and maybe you won't.  If that makes a big difference to you, then you're in it for the wrong reasons.


How do I respond to papers that present the authors' views and opinions as scientific fact?

If you believe there are significant problems with an existing manuscript, then you should present these issues to the journal in which the "offending" articles appear. The format this response should take depends upon the nature of the problem.

If the issue is in fact "forging experimental results," then the paper deserves to be retracted. However, this is a difficult allegation to prove, and you would need to have strong justification (not evidence, per se) backing up your allegations.
However, if the issue is misinterpretations of results or previous literature, this does not quite rise to the level of "academic dishonesty" as forging results. It is not necessarily correct to have the paper retracted. Instead, you should consider writing a "comment" or "letter to the editor" or even a longer paper in response to the problems in the earlier work.

Note, however, that if the paper has appeared in a reputable journal, it has gone through some sort of peer review process. As a consequence of this, it will be necessary to present a more "airtight" argument than if the paper merely appears in a repository such as arXiv. In the latter case, however, then there's probably not much you can do beyond the aforementioned "response article," as the paper has not been published, and thus retraction depends on the author "self-retracting" the work.


Is it possible for an undergraduate to get involved in an independent research project unrelated to his/her concentration?

TL;DR: This is possible, but there are costs and you need to decide whether this is worth your while in the long run.

At the undergraduate level, there is some benefit to you learning about research methods. I find that undergraduate students get a better sense of the breadth and messiness of research methods when actually engaged in a research project. In my view, this experience can take place in a number of fields, although I would prefer that this not be the case. The reason is because the experience of research is much more than the method. Beginning students can pick up research habits that are at odds with the way research is conducted in their own field.

Let me give you an example. A medical student wanted to do a systematic review on health promoting hospital design on patient outcomes. She was interested in a particular approach involving an architectural perspective, so she partnered with the academics from the School of Architecture. Now, systematic reviews are performed quite differently in architecture than in medicine. The systematic review was completed and it was a confusing read because the approach was strange. She submitted it to a medical conference with no luck, but it did get accepted in an architecture conference. Good on her. Still, given that her main academic field is medicine, she has admitted to me that she had found it difficult to unlearn some of the habits she picked up in the research project and wished that she had learned within the field.

In another example, I often have quite a number of research tasks requiring completion and regularly issue invitations to undergraduate students to work with me. These tasks involve clinical contexts -- osteomyelitis, carpal tunnel syndrome, obstructive sleep apnoea -- that may not be relevant to student assistants from the Department of Civil Engineering or the Department of English Literature. I don't reject student volunteers because of their degree, but inform them that the techniques that they will learn may be less relevant to their degrees.

Good luck to you.


What is the purpose of career objective in an Ph.D. admission form?

There is no single answer for this question and must be determined on a case by case basis. I will rule out the career objective section of your CV since it's a matter of personal preference. Assuming you're asking about a section in an official application form, there are number of ways to address. In most cases, the career objective will indicate how your future research and/or potential research project relates to your long term career goals. It becomes significant when the application is for a funded PhD and/or the research project is related to industry. Most universities are interested in the publication of research in top journals, so you can address this issue by demonstrating the potential of your proposed research. In this way, you also implicitly address the question of becoming a future academic. Finally, if you are coming from industry to academia, then you can mention your transition from organizations to academia. The last point is somewhat trivial unless the proposed research is in industry as well.


Is it good practice/advisable to sum up passages from a reference into a few sentences in my own paper?

I know people who restate whole proofs of mathematical theorems, either because the proof itself is interesting, or simply because the original presentation of the proof is poor in their opinion.

It is completely fine to summarize works of other people in your work, you just have to make it completely clear that it is not your work. But you can quote even whole paragraphs IMHO, without much problem (surely in math/natural science, I'm not sure how's it in philosophy and such).


How to reply to unprofessional negative review from a journal?

It sounds as if the editor asked for a revise-and resubmit. In that case, your best move is to simply respond to Reviewer 2 as professionally as you can.

For outright false claims ("The data of the manuscript are NOT available"), reply something like "The data for the manuscript are available. We have revised p. X line Y to make this more clear."  Don't be sarcastic or exasperated or angry, simply make the statement.

For sentences that don't make sense, try to find a nugget of sense in there and address that. It's generally safe (and often a good idea anyway) to response with something like "We have clarified the manuscript on this point" (and of course, try to clarify).  If you simply can't understand the point no matter how you try, say something like "We are unclear on this reviewer's suggestion here. If the editor feels this is an important point, please clarify this and we will attempt to address this."  (This is a last choice option and shouldn't be used more than once.) The message you are trying to give here is that you are trying to be cooperative, and again, the overall aim is to be professional even if a reviewer was not.

What if the editor rejected the manuscript on the basis of this bad review? (It doesn't sound like this happened, but it's worth discussing.)  You have two choices: Accepting the decision and sending the manuscript elsewhere, or contacting the editor and asking for a re-consideration.

The first choice -- sending elsewhere -- is almost always the right one. It's rarely worth arguing with editors. Keep in mind that the editor has probably already recognized that the review is unprofessional and has taken that into account in their decision, so your argument is unlikely to change their mind.

But sometimes there are reasons to focus on the original journal -- the article might be a poor fit anywhere else, for example (perhaps a focused review written for a specific special issue). In that case, contacting the editor and politely and professionally explaining why the review is so bad is a possibility.

Will the editor agree? Maybe, maybe not. If they say the rejection stands, thank them and move on.

I've done this once, with a very unprofessional review, and the editor agreed with me that I could ignore Reviewer 2. I didn't completely ignore it, responding as best I could to the understandable points, and made an extra effort to be very cooperative with Reviewer 1. The paper was accepted after review. So it can work, but I would only do it under very specific conditions.

Edit to add one more point for the general case, not necessarily this particular situation: Before you talk to the editor, be very, very sure that the review in question really is that bad. It has to be utterly unprofessional, without a shred of redeeming value. We're not talking about someone who missed the point in a couple of comments, or who prefers a different model, or who has bad grammar.  We're talking about a reviewer who doesn't believe in germ theory. They didn't even read past the title. They're critiquing a completely different paper. It's written in crayon.

And don't decide this immediately, because every review looks like it was written by an idiot when you first read it. Set it aside until you calm down and look at it again after a few days; you may be surprised how much more sense it makes when you aren't filled with adrenaline. Show it to someone not involved, to be sure you're judging it properly.


Not best practice.  You would be better off having that in a section of the Discussion (at the end of the Discussion) with at least a paragraph of explication.  You can use an identifying subheader ("future developments", "economic implications", etc. within Discussion).

Then in the Conclusion, I would stick to more of the traditional method which is to restate the main results. At that point, you summarize all your findings.  And then give a single sentence about the implications.

I think this is better than opening a segue within the Conclusion.


How familiar should you be with a topic before assigning it as a thesis to an undergraduate?

Here is one rule of thumb: You should be sufficiently confident with the topic to be able to guide your student to success.

This means in particular that you should know the topic in which the student is supposed to work in well enough such that:

You are certain that the workload is manageable in the time outlined by the examination regulations.
You know that there is enough low hanging fruit in the topic such that it is clear that even a mediocre student should be able to write a thesis that is good enough for the standards of your field and school.
There are some types of results that a student may obtain during the thesis work that would suffice for the student to write a great thesis, possibly leading to a subsequent publication (given interest by the student).
You think that you can advise the student with the problems that you expect to occur in the scope of the project.
You have sufficient time to actually advise the student and in particular have the time to read into the details of the subject in case the student needs some guidance on them.

Depending on the field, it is debatable whether it is OK to hand out topics of which the advisor has comparably little knowledge, given that all requirements from the list above are fulfilled.
Also, the list above focuses on the minimum requirements. Again, it is debatable whether satisfying all points on the list is enough already (unless I forgot something important).

As far as coming up with new thesis topics is concerned: probably everyone has their own approach for this. One way is to collect the ideas that you have in your own research into idea lists, and after some time filtering them by the criteria above.


Submitting a paper that contains the researcher name to a conference that employs double blind reviewing

It is hard to see how it would be obvious to a reviewer that the researcher whose name is used is also an author. In this case there should be no issue about reviewing.

But, you could also inform the conference chair and ask for advice there.

In some similar cases it might be possible to obfuscate the name for review purposes, but your description indicates that isn't possible here. But, you might need to change a few phrases if they make the relationship explicit. And note, also, that the final version is normally a bit different from the reviewed version. Reviewers themselves often suggest changes.


Is it a bad sign, if reviews are completed very early?

Required reviews completed means required reviews completed! Nothing more and nothing less.

There are particular seasonal patterns for the journals, to be flooded with a lot of manuscripts at some times (lets say this time ~ May-June), while Sept-Oct are less hectic months. Likewise, referees, who are generally faculty members at universities, are less likely to review fast in the middle of the semester, and more likely in the period when they are free and not away for visits or conferences. It is possible that you sent your manuscript at an opportune moment. Another possibility is that the editor of the journal may himself have chosen to be a reviewer. Another possibility is, you used a method which was pretty bread and butter for the reviewer, so he didn't have to waste time trying to understand what you did.

I can sense your surprise over the time period of just 10 days, but no need to panic here. (especially until the editor reaches out to you.) Nothing more can be said till then, reviewing over in 10 days may mean instant rejection, but it may also mean an acceptance if the reviewer was very well familiar and saw no issues. Nothing can be conclusively said until the referee reaches out to you.

Hope that helps :)


Second Masters (Art therapy and then educational psychology)

It is certainly ok to get any degree for which you are qualified. I don't know why you might question that. Whether there is a better path to your life/career goals no one can say. To me, who knows little of either field, they would seem to complement each other for some kinds of professionals, actually. But you can also get a doctorate in clinical psychology, I know. You might look at that.

But what it takes is to apply to some programs and get accepted. Write a good Statement of Purpose for any proposed degree, explaining why you want the second degree, no matter what it is.

I suspect you can have a career in either field as a private practitioner, though you may need a license from some government to do so.


Publication sponsorship for research conducted elsewhere

At least in the cases I'm familiar with (math departments at US research universities), funding for travel is more likely to come from an individual department than from a university-wide source, so this would be a matter of department policy.  That's a little less true for publication costs, because some universities have started funds to pay for gold open access, but everyone is setting it up a little differently so I don't think one can announce a general rule.

At the department level, this really varies.  One department I used to be at provided a certain amount of travel funding to each student, to be used however they wanted (as long as it was for academic purposes, of course).  I think that's a little unusual, and many departments don't make a decision until the student applies for funds.

If you are in a field in which these costs are an important part of publication (not pure mathematics, for example), then this is probably the wrong question.  In such fields, the funding usually comes from the advisor's grants, rather than the university.


Is it appropriate to ask a student I tutored how their exam went?

I expected her to inform me how the exam went

I'm not sure why you expected this. While it's certainly not unusual to follow up with a tutor (or thank them), it's not a requirement.

  Is it appropriate to ask her how the exam went?

I see no reason why not.


What is the "chain search" method for literature search?

This sounds like formal name for a way that I frequently end up exploring the literature.

Somebody points me at a relevant paper or I search and find something myself, e.g., "Xu et al., Journal of Obscurology, 2012."
I find the paper interesting and valuable, and notice that its conclusions depend on a couple of other papers, "Friedman et al., Obscurolytica, 2007", "Xu & Gupta, Journal of Obscurology, 2010," and go get those papers to look at.
I also notice that the paper cites as related work the competing approaches "White et al., Soc. Obscure, 2003" and "Garcia et al., Obscurrant, 2011", and go get those papers too.
Then I wonder if the paper has been cited in development of other significant works, and skimming through its citations, I find that "Gupta & Xu, Obscurolytica, 2015" and "Prokoff et al, Applications of Obscurology, 2016" look particularly interesting and go get those papers too.

I keep on repeating this process, chaining through relationships in the literature, until I feel like I've gotten a sufficient sense of the community of work linked to this particular paper.

As noted, however, this will only trace out relationships within a connected community of literature, and as you cannot reasonably search more than a few links per article on average, there is a chance to missing highly important connections. Still, it's a good starting point for non-systematic search of the literature and will generally pick up the main threads of argument within a particular community.


If you don't apply, you won't get the job.  So, apply!

Yes, it's possible to find a job in industry and many Ph.D. graduates in mathematics do this every year.  There are lots of things that you could have been doing earlier in your graduate career to help you prepare for a career outside of academia, but there are also many things that you can do starting right now to help you develop a non-academic career.

One very recent resource that you might find helpful is the book:

Rachel Levy, Richard Laugesen and Fadil Santosa, Big Jobs Guide: Business, Industry, and Government Careers for Mathematical Scientists, Statisticians, and Operations Researchers.  SIAM, 2018.


Is it a good idea to express my gratitude to a co-author with a gift card?

Others may differ in opinion, but I personally think that gift cards are a poor choice for expressing personal gratitude.  The problem is that gift cards are effectively cash with spending restrictions.  Your colleague has invested time and energy in helping you, and giving cash would essentially be saying how much per hour you feel their time is worth.

Instead, I would recommend offering something like taking them out for a fancy lunch, which invests your time and gives the two of you a chance to do some informal bonding and building of your professional relationship.  Unless, of course you don't actually want to spend time alone with this colleague (many possible good reasons for that), in which case I would still recommend looking for some way to express gratitude that shows an investment of time and caring beyond just money.


Going to Industry and Keeping Publishing

I am a good example of how it is quite possible to keep up a strong publication record in industry, as long as your job supports it. I submit my Google Scholar profile for evidence: I moved from postdoc to industry in 2008, and though I have contemplated (and been offered) opportunities to move back to academia, to date I have actively chosen to continue in my current position.

Likewise, no healthy scientific community will hold a prejudice against authors from industry, any more than they hold prejudice against authors from less well known universities.  Unhealthy communities do sometimes have cliques that make it difficult for anybody outside of a clique to publish.

In certain cases, you can even have an advantage in research when you come from industry, as it is often useful for academics to have "industry partners" who often have a broader perspective are capable of doing things that they are not.

You do, however, need to have a job that supports publication.  For that, I recommend looking into research consulting companies, rather than normal "product" companies, where you will typically have little time to publish.  If publication can be part of your job, you can keep up publication; if it is a "second job," it will be far harder.


Can I use data and images found online in my project report, under the fair use clause in copyright law?

The following is NOT legal advice. I am NOT an attorney. You should ALWAYS consult a competent attorney about any legal matters, including this matter.

Generally, raw data is not covered by copyright law in the US. I don't know exactly what the data you're using looks like, but if it's something akin to baseball statistics (a bunch of numbers), those can't be copyrighted (though their presentation can be). If it's just raw data, you don't even need the fair use exemption as there is no copyright protection.

As for images, those are almost certainly covered by copyright law.

Fair use is a four-prong test that is measured by a court. A good way to get a sense of whether or not your situation falls under the fair use exemption is to consult a competent attorney who can compare your situation to past rulings. Keep in mind, though, that an attorney can make an educated prediction, but cannot guarantee an outcome. The four factors considered, to give you an idea, are:

  the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes;
  the nature of the copyrighted work;
  the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and
  the effect of the use upon the potential market for or value of the copyrighted work.

While all four prongs may be considered, you do not have to meet a specific requirement for all four. It's up to the court which of the criteria matter, or don't matter, in your situation and how much.

Keep in mind also, from a pragmatic standpoint, that copyright law would only be enforced if the publisher of the data decided to file a law suit. If that's unlikely, all this discussion is moot.

Finally, you can always just send in an email and ask. Given the nature of your work, they might just want a citation. And if they give your permission, you have nothing to worry about.

Update

@Jacob added some more details about the situation.

What struck me as interesting in the added details was the statement This document is provided on the basis of strict confidentiality. If the data is truly in need of protection, like if it is a trade secret, it might be smart to exercise some extra caution here. Having posted the data on the open Internet, the company probably could not do much to keep you from using it. However, if it's truely valuable, they may fight to protect it which could create a huge headache, to say the least.

I think I outlined why you might be able to use the data with and without fair use above. I want to add however, that does not mean you should use it without permission. Even if the data is not protected by copyright, it would be best to ask permission if for no reason other than basic courtesy.

Being turned down does not change the law. If something was not protected by copyright before you ask, it will not be protected after you ask. If something falls under fair use before you ask, it will still remain under fair use after you ask. You really have very little to lose by asking. I can tell though that you are hesitant to ask so I will suggest you do so without revealing too much information about yourself and your work. Instead of diving in with a long, detailed explanation of your research, put your toe in the water with some basic details and see how they react.

For all you know, they might be interested in your work. Since it seems like your area of expertise, this might even lead to something more like a job interview. There is a lot of potential upside.

I don't want to say too much more about whether or not the specific data is covered by copyright because this is not a place to get legal advice and I am not someone to give it. But in general, if you put the raw coefficient numbers in the prose of your work, you are probably safe regardless of fair use. If you want to copy any photos, graphics, or detailed descriptions of the numbers, you'll have to do so under fair use and/or with permission.


Do academics get paid for examining thesis?

No, examiners are not always paid.

This also holds for external examiners. I have been asked to examine several theses in the last years, some internal, some external, and have never been paid. However, if the examination involves travelling, then I usually got reimbursed.

(This is an answer for Germany and Austria.)


Postdoc at a research hospital for a physicist (non radiation)

I'll answer the second two questions.

  Is there anyone who successfully did the physics-medicine transition?

Yes, medical physicists exist.  Some are specially trained in that field, others made the transition.  A few years back they were in high demand.

  And is it possible to go back to more basic science after a
  biochem-med postdoc?

Possible, yes.  Probably few people want to because it's likely to lead to a pay cut, as last I heard there was high demand for medical physicists.


How do I request that previously taken classes be counted toward my current program?

Now I'm being told that I have 4 because I have to retake A&P 1 and 2 with cadavers.

While I find blanket condemnations of the passive voice to be misguided, this is a case where such an objection is well-founded. Who told you you have to retake them?

There are two main options. One is to go the professor in charge of the course. Go to office hours, and tell them about the courses you previously took. If you took the courses. Ask them what sort of discretion they have as far as granting course credit. For instance, Sometimes a professor can grant credit based on a course challenge exam. If they don't have discretion, ask them who does.

The other option is to talk with the chair of the department. Seeing them in person would probably be be best, but if they don't have office hours or other opportunities to see them, you can email them. As far as how to "respectfully" ask: really, the main thing is just to present it as inquiry rather than a request, and definitely try to avoid giving the impression that you feel entitled to an affirmative response. Showing a willingness for a compromise, such as taking the final exam for the course in lieu of taking the whole course, rather than expecting to have the requirement completely waived, also helps.


How would you give your students a tournament as assessment?

Eager et al. describe how they use flipped classrooms to teach a mathematical biology course. As part of their course, they use "competitions" to motivate students. They discuss some of your concerns in a method paper:

  One of the difficulties in teaching a class via the flipped classroom is how to properly assess and examine student learning [3]. Because the class is very modeling focused, and modeling is a time-consuming process, traditional exams are very difficult to administer in a course like MTH 265. The authors’ solution to this problem is to do away with traditional
  exams in favor of both individual quizzes and group mathematical modeling competitions.
  The individual quizzes involve the students choosing two small modeling questions from a
  group of three questions and solving them with help from their class notes, homeworks,
  past computer programs and video lectures. These quizzes are given over a 55-minute time
  period. The questions in these quizzes are structured in such a way so that, after the student
  chooses which two problems to work on, he or she can solve both questions in a combined
  40 minutes—meaning that some (but not all) of the modeling process is given to them. These
  exams provide the students with an incentive to learn the material on their own (which is
  nontrivial in a flipped course with a large group component), as well as the motivation
  to become proficient in using some of the elementary skills a mathematical or quantitative
  biologists would need to possess (e.g. diagram building, script writing/amending, elementary
  algebra and calculus, scientific writing).

  The mathematical modeling competitions stemmed from the successful 24-hour Wisconsin
  Mathematical Modeling Challenge at UW-L, as well as the success of similar activities in
  other mathematical biology courses [8]. These competitions complement the individual, inclass
  quizzes by providing students with more open-ended modeling problems and a longer
  timespan to produce their solutions. These modeling problems can ofen be introduced with
  only a few paragraphs of text—with few or no equations. The students, in groups, then
  have 24 hours to come up with an appropriate model for this system, as well as answer
  the biological question posed. The group of students with the best solution is rewarded
  with perfect homework scores until the next modeling competition. The class has either
  an individual quiz or a modeling competition at the end of every other week for a total of three individual quizzes and three modeling competitions during the semester worth roughly
  30 percent of each student’s final grade.

Full citation (in case link breaks):  Eric Alan Eager, James Peirce & Patrick Barlow (2014) Math Bio or Biomath? Flipping the mathematical biology classroom, Letters in Biomathematics, 1:2, 139-155, DOI:
10.1080/23737867.2014.11414476

As a disclosure, I have collaborated with Eager and gave guest lectures in his Bio Math course about my own research.


To share or not to share (your student evals)?

Where I worked in Germany, faculty were required to share the statistical results of the survey with their classes, and allow for time for feedback. So I see no issues in sharing results when no student-specific data would be given away. (Note that the surveys thus effectively represented "midterm" evaluations.)

As far as comments, that's a bit trickier. I'd err on the side of leaving out anything that talks about the student instead of about the class.

  I think that X

would be fine, but

  Because I transferred and hadn't studied Y at my old university, this class was very hard

would not, since it might give away some information as to who said it. You could present a redacted version:

  Because I . . . hadn't studied Y[,] this class was very hard

if you want to remove anything identifying individuals.


How do I / Should I, console a former classmate and stressed out PHD/MD applicant?

If you decide to reach out again, I would try to reconnect over a different topic first. It sounds like it has been a while since the results were announced, and bringing up their past disappointment over and over again will probably not help them get over it. If all of your interactions are focused on this one topic they might start to wonder if you are either secretly judging them about it, or if you are just pumping them for advice on what mistakes to avoid in your own applications.

If subsequently they bring up the topic on their own, you can express sympathy at that point. But I would follow their lead in whether they want to dwell on it or not.


Leave postdoc in the middle of contract to start work with another professor while being in one postdoctoral research

You should be as up front about the situation as you can --- with both parties. Prof. A needs to know that you are interested in a one-year deal but cannot currently commit to anything longer. Prof. B should know that you are interested but have another opportunity and will need to know about the funding. Worst case situation, you join Prof. B's team 12 months down the road. By that time he should know about the funding.

As to #1, you answered this yourself. Once you commit yourself for one year, you should stick it out. Of course it is always possible to get out of any contract, but at what cost? Seems that it would not be worth your while to antagonize Prof. A. What is not clear to me is who makes the decision to extend. If Prof. A does not want to let you go after 1 year, are you stuck?

As to #2 and 3, forget about it. Once you go to China, you will be there for 12 months, and you will work on Prof. A's project. Everything else is unrealistic.


Do newly hired professors have to take a drug test before they start?

Is this a serious question? I would refuse to work anywhere where my employer would require me to do such a test. It is simply none of their business.

I am actually not aware of any (European) university that would require anyone to take a drug test. In fact, it would be illegal in many countries to do this (or at least, there are very strict rules about the circumstances in which it would be legal).


Does research experience in a different but related field help in PhD application? (Pure Math->TCS)

I'm not an expert, but, from what I know, your experience is quite valuable.  Even if you had computer science research experience, there's a good chance that what you would actually end up doing in a PhD program is far from the domain of your undergraduate research.

If you're still worried, note that theoretical computer science is all mathematics.  I was an applied mathematics and statistics major and am currently taking a graduate course in approximation algorithms--it's literally a graduate course in theoretical side of applied mathematics.  Other theory courses in automata, computation, machine learning, etc are also all math courses, but in the computer science domain.  I actually think that your math/research background, if anything, is a huge plus.

What PhD programs are really interested in is whether or not you have done research in any discipline (preferably math/engineering for CS) and if you enjoyed it and showed an aptitude for it.  You're ahead of the game, don't worry.  On that note, if you know that you want to do TCS research, you could start now.


Why does the Discipline of the Bachelor Degree matter for most Non-US Architecture Master Programs but not for US Architecture Master Programs?

In the US, a bachelor's is almost always half or more liberal arts - that is, a bunch of different subjects outside the major. It is run in such a way that basically little more than literacy and slightly more than arithmetic are assumed to have been developed in previous education.

For example, a student often has 4-5 classes each semester for 4 years. Of those, only 1-2 are usually in the major each semester, though some majors start with 0-1 classes in early semesters to "get the general education classes out of the way", then later semesters are more focused. This is one of the reasons double majors are not so rare here - if you can count some of the other majors requirements as "general education" (you often can), and take electives in the second major, you can end up managing to do both majors without taking much longer to earn the degree.

At the master's level, the extent to which a closely related bachelor is preferred varies, but is rarely required regardless of subject - only at very picky departments is it a big deal.

Is 1 year of focused master's education a replacement for having a same-subject master's degree? It isn't a perfect replacement, but mostly yes. It will tend to be more demanding and hard on the student as they have to play catch-up, so this is not as attainable for all students - but it is well within the realm of human possibility, especially when motivated by the fact that all the coursework is much more likely to be strictly necessary to support future courses. There is a lot of optional "not that hard to figure out on your own if you actually cared and had a use for it" stuff in higher education, after all.

I personally know some CS and art/design people who've done MS in architecture in the US and they seemed to do fine. I'm sure it is harder the less applicable your previous education is, but it is not at all an alien thing here to switch subjects like this.


As a PhD student, should I give a talk at a conference outside my supervisor's field?

As @eykanal stated, the answer is simply to talk to your supervisor.

To specifically answer your questions:

1- Yes, it is more than OK to go to the conference. Being invited to an international conference is a great achievement that you should be proud of.

2- I don't see how it could be unethical to your supervisor.

I'm not sure from your question if your advisor has already refused the funds. I would suggest to not overthink this. Budget are generally tight. If your supervisor is a normal human being (most are), he's probably proud of your achievement. If for some reasons he doesn't approve, but does not clearly forbid you to go...well that's a strange situation but you can't guess his mind, can't you? If your relation is good, discussing is the only way to know.

Just remember that the goal of the PhD is to create an independent researcher out of you. Not a duplicate of your supervisor.


What methods can be used in online exams to genuinely test the students' knowledge and capabilities?

First, a two hour time limit might be difficult to enforce or to guarantee, especially if it uses a real-time clock. At some level of scale you may start to find that some students didn't get the exam paper or were unable to return it by the deadline. So, I'd start by rethinking if a time limit of less than a day is really essential to your exam.

Second, you can pre-vet any questions you ask by doing searching yourself online for possible answers and responses. Reject questions that have too much online presence, or be prepared for getting that back as answers. Presumably the test isn't about effective online searches.

Third, give up the idea of asking students for facts. That is obvious, I'd think, as facts are cheap. But even facts requiring computation, such as in mathematics or statistics can be generated with tools such as MatLab or Mathematica.

The best sort of questions, I think, are those that require either or both of interpretation and insight. Questions about the why of things rather than the what and how are much better. However, these are the hardest to create, the hardest to answer, and are likely to have the widest variation in quality from students. To grade them might require quite a lot of interpretation: does this student show any insight at all into the subject? Pass-fail grading can be considered. Repeat attempts can be considered.

As an alternative to an exam, you can consider individual portfolio development by students. Students write or otherwise create some artifacts according to some criteria. Plagiarism concerns come in to play here, of course.

I'll note that honor codes can help to a certain extent, though provide no guarantees. And honor codes created in the moment are probably less effective than those of long standing.


The IEEE does not generally have any strict guidelines on how to format code for papers in their journals or conferences, so you have some freedom of choice in how you do so.  The general guideline is simply to use a monospace font and formatting choices that are not blatantly incompatible with the rest of the paper.

Now, if you are writing for IEEE, you should probably be using LaTeX.  This means that there are a number of excellent packages, such as these, that will format your code in a nice and professional manner that is generally quite familiar to IEEE reviewers and editors.  If you pick one and use that, you should not expect any problems.


Is it offensive to ask my PhD advisor for permission to record our research/technical discussions?

You need to ask first, and you need to ask without the recording device in your hand.

But sure, why not ask?  If I were asked, I would find it a little strange at first, and then I would think about the fact that this shows a real commitment and diligence to keeping track of what is said during our meetings.  One of the biggest issues with student/advisor meetings is that it feels like they should happen very informally, but information is often being provided in a way which the student cannot easily or perfectly understand or even take in.  So there is often a lot of repetition over a period of weeks, months or years.  (Not just between students and advisors, come to think of it.)  With that in mind I would be inclined to say yes.

I also strongly disagree with another answer which suggests that an advisor might drop a student for making such a request.  This seems to contribute to a sentiment that students should be afraid to discuss things with their advisors, which I see so much of on this site and think is very unfortunate.  It would be incredibly unreasonable behavior to drop a student for making this request or really any request which has anything to do with the student's academic or professional life.

Added: My response is not meant to apply to interactions with other people aside from the OP and the advisor.


What to do when PhD advisor wants student to work on two disjoint projects?

The most important line in your post seems to be one that you didn't give much weight to: "my stipend comes from [the collaborative project]". From my experience, this is a common situation, where the money for your stipend comes from a project you're not interested in pursuing.

Unfortunately, the only real alternative for you is to write your own grant proposal, which is a significant investment of time for both you and your advisor, and carries the not-so-minor risk that the grant won't be funded, which leaves you exactly where you started, with the added problem that there hasn't been much progress on the existing grant.

The second alternative is to leave the advisor and try to find someone else, but I would recommend against that for two reasons. Firstly, it's hard to find someone else with funding on a project you like. Secondly, the problem you're having now—the funded project is less interesting than the unfunded project—is one you'll likely face again in the future. Your advisor's approach of pursuing both projects is (again, from my experience) a typical way of dealing with this, and it will likely benefit you to have experience with this approach during your PhD years.

I recognize that it means extra work for you, and I don't really have much advice on that front. Try not to think of it as extra work, but rather as extra publications in different research areas. That helps minimize the sting.


Can I add a poster session to my CV if I wasn't there but had my name on it?

This might depend on the field. In computer science, for example, conferences are more than just "get togethers" and serious research is often first presented there and might be published only in proceedings. In such a case it would be good for a young researcher, especially a student, to list poster presentations on a CV.

As you say, it isn't just the "presentation" that is important. It is the work that went into the research behind it. If there is no other publication of that research at present, list it, but be clear.

I've learned some interesting things walking through poster sessions and talking to students about their research. It was the research that was important, not whose face I was looking at.


Using IEEE Citation style, how should I Cite a Figure, that was based on one in a text?

The most common way folks in my neck of the woods handle this would be to say "... A DNN initialized using the DBN (adapted from [1])."


Advisor asking me to do review work after my PhD is finished

I think this dilemma can be best understood by separating it into two sub-questions:

To what extent should you be doing reviews after graduation?
Assuming you are doing reviews, does it matter whether they are sub-review requests coming from your former advisor?

For the first question, there are already good answers on this site about number of reviews and about whether reviewing is mandatory.  Both essentially say that reviewing is good community service but never required, and it's better to not review than to give a poor quality or resentful review. Considering this, if this paper came as a direct review request to you from a journal / conference rather than a sub-review request from your former advisor, would you be willing to review it?  If the answer is no (which I think it might be given what you wrote in your question), then the fact that it came from your former advisor is beside the point; you can politely decline just like you would if you had been asked directly.

Now, if you would be willing to review if asked directly, but not when asked as a sub-reviewer by your former advisor, you need to ask yourself why this is, and frame your response accordingly.  For example:

If you are concerned about getting credit for your service and the review request is from a journal, then you can tell your former advisor you're wanting to build relationships with journals and ask them to have the journal transfer the review request (conferences may be unwilling to transfer, depending on how they manage their program committee).
If you're feeling resentful because you want to "leave the nest" and the way that you were asked makes you feel your advisor is still treating you like a student, then you might respond by saying you are very busy in your current position (no doubt true) and suggesting that your former advisor send this to one of their current students instead of you.

Other reasons may have other responses, but these are the main ones that I could think of, and I think may cover the most likely possibilities.


Position and prominence of 'Acknowledgements' in a publication

I generally make acknowledgements their own \section and place it at the end of the paper's body, before the references or any appendices.

But I really don't think it matters.  The referee is not going to care, and it won't affect the acceptance or rejection of the paper.  If the journal has a preference, you will hear about it from the copy editor when the time comes to correct the proofs.

You might as well check the Instructions for Authors to see if it addresses this, but otherwise, just pick something reasonable and don't worry about it.


Adding Presentation and data in Google Scholar

Google Scholar usually (not always) just crawl the contents which are organized like a research article. If it's just a presentation (e.g. powerpoint, LaTeX beamer, poster, etc.) you could upload it in F1000Research or Figshare which could give you a DOI and will be fully citable. But it does not guarantee that it will be indexed by Google Scholar. Also I like Figshare cause you could share your data with presentation/paper/pre-print under Common Creative license (it's not the only license available in the Figshare).


How to find a list of most influential or cited papers in a given branch of math?

If you are after highly cited work, MathSciNet has such a functionality under the tab  Citations:

You can search highly cited work e.g. by subject or by year but note that citations come in slowly into MathSciNet, so data from a year ago may not say too much yet.


Is it appropriate to include a List/Summary of Theorems in a paper?

If the lemmas and theorems are unrelated (unlikely) then a list might be fine. But if the purpose of the paper is to prove the main theorem(s) then giving that purpose and naming just those in the introduction is probably more standard and easier for a reader to get a sense of purpose.
So, my guess is that your second suggestion works better. If there is one main theorem then focus, primarily, on that. But if one or two of the others has some independent use then you could expand a bit.
Mathematicians are used to following a train of proof through a fairly long argument, but knowing the goal ahead of time can be helpful.


This is ok (happens all the time, because usually you do not have severaly years for a big project), as long as you make sure the your citation is done right. Just don't claim you did the other experiments and you will be fine. (I know this should be clear. I just mentioned it, because I know of a case where that apparently wasn't clear enough...)


Using a viral CV/ cover letter LaTeX template for undergraduate research internships

I'm sure that the recipient won't really be concerned with which template you use for your CV or cover letter. Most probably they are not familiar with what templates are available. What  they will be concerned about  is the contents, and do you offer what experience and qualifications they are looking for.
The documents just have to look respectable, that is all. You are overthinking this.


Can students bargain over admission date?

delay my possible admission for a year

In theory, yes, you can delay the admission for up to a year but you need to know the rules.

As mentioned in the comments, this is called deferring. Each university/institute has certain rules regarding the deferment. At some places, you may not be able to defer the offer so long. While others, which allow the deferments for up to a term or two, it might be easier to delay for one semester/term (4 to 6 months) by providing a reasonable excuse. However, this can be extended for one more term (3 to 6 months) but in special cases and may require the agreement of the prospective supervisor, HoD etc.

  Which points do I have to consider prior to send an e-mail to uni X when dealing with such an issue?

Try to know their rules through the website or by email.

See what is the maximum period (P) they can allow you? 4+3=7 or 6+6=12 or ...

Does (P) satisfy you?

If yes, then what would be the special conditions for the extension?

Would you be able to manage to deal with those special conditions?


At the various levels of a post-graduate career, how much freedom of research will I have?

First, you can always research anything you want on your own time and your own money.

Thus, I assume that your question boils down to what range of research topics will I be able to get paid for?  That depends heavily on:

Your level of ability.  If you are sufficiently outstanding you can get awards that will fund you to research whatever you want at almost any career stage.  For instance, grad students who have, say, a government fellowship (in the US these are things like NSF, or DOE CSGF) are often given a lot more leeway to pursue their own research agenda.  But such fellowships are rare and highly competitive.  What's more, almost any professor will be willing to take such a student.  At the other end of the pool, if you are a relatively weak student it may be difficult to even find an advisor, and when you do they will probably require you to follow their research plan.  Similarly, a young professor who gets a CAREER award can more easily follow their interests.
Your communication skills.  If you can give persuasive presentations and write excellent grant proposals, you will be able to obtain more funding for the projects that interest you and therefore be free to work on them.  You may also be able to buy yourself out of teaching responsibilities and so spend more time on research.  Of course, this is intertwined with #1 above.
The nature of the research itself.  In experimental or observational areas, you need to buy equipment.  If you want to study gravitational waves (observationally), you will need a lot of money -- or collaborators with a lot of money -- to get started.

Finally, let's talk about career stage.  The three factors above are operative at every career stage.  There are brilliant grad students who can work on just what they want because of their talent, and there are tenured professors who can hardly do research at all because they are required to spend nearly all their time teaching (this may also be a choice -- research is not the top priority for everyone).  That said, on average your freedom to direct your own research increases at each successive stage.  The "restrictions" at each stage are well illustrated by the comic linked in the comments above.


How do I differentiate between addressing two professors with the same last name?

There are few things you can do.

Call each by their full name like 'Professor Ann Smith' or 'Professor Bill Smith'.
Ask whether you can call them by 'Professor first-name' like 'Professor Ann' or 'Professor Bill'.
Continue to use 'Professor last-name'. They'll either decide who will answer or ask you to clarify which person you wanted.
And the easiest, as pointed out by Buffy, ask the professors if there's an alternate, unique name you can use so you can differentiate between them.


Leaving a Graduate Program in a Polite and Professional Manner

This goes the same for those leaving jobs for similar reasons- the more you can explain how there are personal reasons for your transfer and do not emphasize that there are deficits with your current program, a professional academic will understand even if he or she is disappointed.

Remember that not all academics and administrators are always professional and that despite your best efforts he or she might not be understanding. However, being professional and cordial is the best you can do to take the high road.


What to do when there are no courses available to help with my research? How will it affect me?

Part, or most, of a PhD is about self-learning, so you have to step up and work on those subjects you need.
A PhD is usually to push the boundaries of knowledge in topics / areas etc so learning methods or techniques relevant to moving your research forward is what you have to do - simply said your supervisor is correct.


Lectures in Germany are normally given by professors, who by law need to have a PhD (and sometimes a Habilitation). There may be some wiggle room for adjuncts, but normally Wissenschaftliche Mitarbeiter—the research staff working under the professor—assist with teaching discussion or recitation sections as well as grading, but generally do not give lectures except in the case of absences by the professor.

Part of this is because the funding for academic groups is based on the number of exams graded by a given chair. So faculty will be reluctant to give away lectures, and thus lose out on the “credit” associated with the teaching.

There might be a room for an exception if there is a vacancy due to retirement or poaching. Otherwise, it’s probably hard to get a university lecture with just a master’s degree.


Is it appropriate to reject a manuscript based on language (minor) issues after first review?

It is hard to see how ethics enters in to it. Had you paid them something and they rejected it, keeping your money, then it is a different matter. But a submission is just an offer and it can be rejected for any reason. It may not represent the best policy in general, but it isn't unethical.
And, perhaps there are other issues as well and they all piled up to indicate a reject. That is impossible to judge without more information that only you and the editor might possess. It might be as simple as not wanting to do a third round.


Why are some good math journals not indexed by Thomson Reuters?

The selection process used by Thomson Reuters for choosing journals is described, in detail, on this page: http://wokinfo.com/essays/journal-selection-process/
The basic standards (see the link for more information) are:

TIMELINESS
Timeliness of publication is a basic criterion in the evaluation process. It is of primary and fundamental importance. A journal must be publishing according to its stated frequency to be considered for inclusion in Web of Science. The ability to publish on time implies a healthy backlog of manuscripts essential for ongoing viability. It is not acceptable for a journal to appear chronically late, weeks or months after its cover date. To measure timeliness we need to see three consecutive current issues, one after another, as soon as they are published.
INTERNATIONAL EDITORIAL CONVENTIONS
Thomson Reuters also determines if the journal follows international editorial conventions, which are intended to optimize retrievability of source articles. These conventions include informative journal titles, fully descriptive article titles and author abstracts, complete bibliographic information for all cited references, and full address information for every author.
FULL TEXT ENGLISH
English is the universal language of science. For this reason Thomson Reuters focuses on journals that publish full text in English, or at very least, bibliographic information in English. There are many journals covered in Web of Science that publish articles with bibliographic information in English and full text in another language. However, going forward, it is clear that the journals most important to the international research community will publish full text in English. This is especially true in the natural sciences. There are notable exceptions to this rule in the Arts & Humanities and in Social Sciences topics. This is discussed further below. Nonetheless, full text English is highly desirable, especially if the journal intends to serve an international community of researchers. In addition, all journals must have cited references in the Roman alphabet.
PEER REVIEW
Application of the peer-review process is another indication of journal standards and signifies overall quality of the research presented and the completeness of cited references.6 Inclusion of Funding Acknowledgements is also strongly recommended. Not only do they help create a greater context for the journal, these acknowledgements also function as a confirmation of the importance of the research presented.

Once again, for a more detailed description visit http://wokinfo.com/essays/journal-selection-process/
Edit:
In response to Benoit Klockner's comment, I thought I would also quote the 'Citation Analysis' that is used by Thomson Reuters.

CITATION ANALYSIS
The Thomson Reuters Journal Selection Process is unique in that Thomson Reuters editors have a wealth of citation data available to them. Because Web of Science is a true citation index, all cited references from every item in every journal covered in Web of Science are indexed whether or not the cited work is also covered as a source publication. Through these data it is possible to measure the citation impact of journals under evaluation.
The importance of interpreting and understanding these data correctly cannot be emphasized too strongly. Using quantitative citation data to measure impact is meaningful only in the context of journals in the same general discipline. For example, smaller fields like Agricultural Engineering do not generate as many articles or citations as larger fields like Biotechnology or Genetics. In some areas, particularly in the Arts & Humanities, it may take a relatively long time for an article to attract a meaningful number of citations. But in other areas, such as the life sciences, it is not unusual for citations to accrue rapidly and peak after two or three years.7 These facts must be taken into consideration if citation data are to be used correctly.
Citation analysis takes place on at least two levels. Thomson Reuters looks for citations to the journal itself, as expressed by impact factor and/ or total citations received. For new journals that do not yet have a citation history at the publication level, analysts examine the citation record of the contributing authors and editorial board members. This allows them to see if the journal is able to attract contributions from scholars whose prior work has been useful to the research community.
Likewise, established journals that are not covered are often re-evaluated. These journals can experience new growth in citation impact resulting from changes such as translation into English, change in editorial focus, change in publisher, publishing medium, etc.
As noted above, because Thomson Reuters captures all cited references from each of the over 12,000 journals covered, citation information is available on journals not covered as well as those that are covered.
Self-citation rates are also taken into consideration. The self-cited rate relates a journal's self-citations to the number of times it is cited by all journals, including itself. For example, journal X was cited 15,000 times by all journals, including the 2,000 times it cited itself. Its self-cited rate is 2/15 or 13%.
It is entirely normal for authors to reference the prior work that is most relevant to their current results, regardless of the source journal in which the work was published. However, there are journals in which the observed rate of self-citation is a dominant influence in the total level of citation. For these journals, self-citation has the potential to distort the true role of the title in the context of the literature of its subject.8
Among all journals listed in the 2010 JCR Science Edition, for example, 85% have self-citation rates of less than 15%. This shows that self-citation is quite normal for most journals. Significant deviation from this normal rate, however, prompts an examination by Thomson Reuters to determine if excessive self-citations are being used to artificially inflate the impact factor. If we determine that self-citations are being used improperly, the journal's impact factor will be suppressed for at least two years and the journal may be considered for deselection from Web of Science.


How should I approach a situation where my head of department doesn't want me there?

You shouldn't worry so much about political issues in the department. What is important to you right now is to focus hard on the research and publish in significant journals with your supervisor or collaborators. Hence, in this way you can justify that are a serious student in the department, and you can established connections for you career after graduation the PhD program.


Suggestions to turn an "accepted, pending revisions" into an "accepted"

When they say that, they send you a list of suggested revisions (or several lists, one from each reviewer).  Just follow those suggestions.  When you send it back, explain which suggestions you followed, and which you did not (and why not).


Choosing an undergraduate research advisor

Talking to some other students who went through this before me, I have heard that one should take a class with the professor before asking them to be one's research advisor (I thought this was BS and tried reaching out to profs, but got stonewalled - this seems to be systemic in my uni/dept).

Well, take it from a professor's point of view. They received an email from a student they don't know, who's only vaguely interested in their work. If you don't even know what subfield you're interested in, it's hard to write a convincing email explaining why you're interested in their work.
Mentoring an undergraduate is a time investment, not a time saver. So professors like to see motivated students who understand the problems they work on in their lab, which is part of the answer to your question below.

Why is it better to find a new prof rather than using a well-known prof?

Some people might say that older professors are busy as heck, and a newer professor might have more time to invest in a promising undergrad. Unfortunately, with COVID, finding a professor with time for an undergrad will be harder.
However, this isn't universal, and you should talk to previous students before assuming a professor is a good or bad mentor.
In summary, identify a few top professors, take their classes (as was suggested), and do well. That's at least a foot in the door to open the conversation.


There indeed is plenty of web sites where you can shelf articles, preprints, etc. (Mendeley, Zotero, CiteULike, and so on; a fairly comprehensive list is available on Wikipedia) but if you also would like to have the possibility of adding reviews like in GoodReads, the things are somewhat different.

One site that I know of that allows you to do this, in addition to merely bookmarking the items, is ResearchGate with its Open Review feature, but you can only bookmark and review items that already are in their database (you can add the articles that you (co-)authored but I doubt that reviewing them is your intention). Perhaps there are some other sites with a similar functionality: e.g. according to Wikipedia CiteULike has it too; on Mendeley you can share articles' annotations within private groups.

Also, there is a number of sites allowing you to bookmark and review arXiv preprints (e.g. SciRate) but not the other kinds of items like the books.


Is it advisable to contact a professor if I fear failing a graduate-level course?

When I read the headline, my immediate impulse was to say "yes, of course" - assuming, that the course is still running and you need advice on how to proceed and come to a good result.

After reading the full question, my answer is a clear "no". I'm located in Germany, but I assume the following thoughts are applicable to the US too:

If you explain your situation to the professor right now, it will feel like you want to influence his objective grading attitude. I would never accept such an attempt and I would in fact be angry because just because you told me, I will be influenced. I won't rate you better, but I might even be stricter in cases where I'm unsure whether I should give a point more or less, just to avoid beeing unfair towards the other students.
If the professor would react on your situation, it might even be illegal, it would be definitely unethical. In the worst case, he could be fired. #Everyone has to be treated equally.
Most (all?) universities have defined rules on how to treat sickness, bad personal circumstances, etc. You should check your local regulations and get advice from either other faculty members, students organizations or the responsible university staff. In many cases, there are options to re-do an exam.
You should check the regulations mentioned before, but I would not take any measures before the results are out. After they are published, you could ask the professor on advice on how to proceed and explain your situation afterwards. Maybe there are some options like a second attempt or otherwise.


What is the average teaching load for a math postdoc position in the US?

The general answer isn't really a number. I expect that in most cases a teaching load is similar to that of a regular faculty member, though that isn't necessarily the case.

The semester, trimester, quarter system defines how many regular terms there are per year, with trimester and quarter often being synonymous. It is the number of terms that most students attend in a given year. Two semesters make a year on the semester system, etc.

A post doc is more likely at a research institution than a liberal arts college and the teaching load differs. In some R1 universities the teaching load is one course per term. At Dartmouth (quarter system, "Dartmouth System"), the load was four courses per year, or one per "quarter", though you didn't need to spread them out over the four quarters. I don't know if the system has changed and my knowledge is very old. The summer term was just like any other and students were expected to do something academic, but perhaps academic related travel.

At some State universities, the load is two courses per term, so four in a year on the semester or six (shorter courses) per year on a trimester system. Again, it might not be necessary to spread them out evenly and it might be possible to "buy" yourself out of a course or two using grant funds. The load might be lighter than that at some places, but not likely heavier at an R1.

At most R1 sorts of places if you have more than one course to teach in a term it is more likely to be two sections of the same course than two different courses, but not guaranteed. At some places the tenured faculty (and probably post docs) teach in their specialty in advanced course, but, again, not necessarily.

At a liberal arts college the load might be four or even five courses per term. But there are few post docs at such places.

A post doc might possibly not have teaching duties at all if the are paid out of grant monies. It would be uncommon, I think, to have a higher load than the regular faculty. In some situations you might actually have to beg to get teaching duties at all.


Scheduled graduate admission interview never occured

I would send another follow up email 1-2 weeks after the first one you sent. Inquire politely, and offer to reschedule the interview. However, do it in such a way that they're allowed to save face. Meaning, phrase things in way that don't inadvertently point a finger at them. It might sound silly to placate egos, but...welcome to academia. :-/

If nothing comes from it, I would write this program off. As Astronat said, this is pretty poor behavior, and I would add that it might be indicative of what's to come if you were to be part of that department.


Who is the copyright holder of a PhD thesis published in ProQuest?

The original author is probably the copyright holder.

Two other options: it is possible that it is the university/research institute (see, eg, this MIT policy for an example) but this is relatively unusual; alternatively, if it was done with industrial sponsorship, the company might own copyright. If either were the case, though, I'd expect to see some kind of indication on the thesis itself. Absent a clear hint (eg an existing university policy, a commercial-looking funder) that someone else would hold copyright, I'd work on the assumption it's the author.

You can try and trace them - this is not quite as impossible as it sounds, as the university alumni office may well have contact with them and be able to pass on a letter. If you have tried and failed, you might still have the option of using them without permission and an apologetic footnote...


For senior personnel (like the principal investigators) the NSF limit salary to 2 months salary for each person per year, which is held across all NSF-funded grants (so if you are listed on 100 NSF grants you still can only get 2 months per year for yourself in total).

As to the budget questions - yes, you'll need a budget, plenty of supporting detail and reasoning, and yes there are lots of rules about everything from computer equipment to salary for clerical workers. Most common questions can be answered by reviewing the NSF Proposal & Award Policies & Procedures Guide. There is no single rule of thumb on how much to ask for, as the range of awards varies quite widely (and for the NSF is usually stated in Dear Colleague letters or public grant invitations on specific topics), but in general if you don't have a really good idea of how much things might cost to go into the budget for what to ask for, the panel will probably quickly notice you haven't thought things out in enough detail and reject it easily in an early round. You can be reasonably assured that someone - and probably many people - will look at each line item in a submitted budget, so they will need to be sensible, clearly defined, and obviously necessary or highly desirable for ensuring the success of the project. If the budget given does indeed seem arbitrary to someone who has looked at hundreds of grant requests in the last month (or week), that will not bode well for the likelihood of success.

If you are affiliated with an institution that applies for NSF funding in general, there is probably a dedicated staff member (or a whole department) dedicated to supporting grant requests, so you should also definitely reach out to them to get information on what sort of support is available - which is much easier than trying to figure out everything on your own. They may have templates, workshops, guides, internal reviews, etc. - or at least, some institutions have all that. Check to see before doing it all the hard way.


Is it okay to refuse a laptop from a new university if you already have your own personal laptop?

It surely matters where you are.

In the U.S., at many universities, "privileged information" of various sorts is supposedly not ever to be kept on "personal", as opposed to "institution-owned and maintained" machines. Or, as in some comments, as soon as you do have work-related data on your personal machine, that machine becomes liable to Freedom-of-Information warrants, and you yourself can get into various sorts of trouble for insufficiently guaranteeing security.

A similar issue exists (depending on jurisdiction, etc) with regard to email accounts. My (U.S. R1) university account is subject to search without too much probable cause. Some of my colleagues hesitate to have any substantive-sensitive discussion by email because the University's policy is that we are not to delete any such email, but preserve it indefinitely. That kind of thing. (No, it's not clear how this would be enforced, nor what the impact of "pleading ignorance/technical-incompetence" would result in. Maybe it's just CYA policy on the part of the institution.)


Quoting instrument prices in a scientific paper

One reason why usually no definitive prices are publicly communicated is that the manufacturers compete against each other when bidding on a tender, where e.g. one lab might ask for quotes from several possible sellers. It would be a disadvantage for a vendor, if their competitors would have knowledge about the specific prices.

Apart from possibly releasing undisclosed information about the prices, another difficulty that I can see with publishing those numbers is that the prices might differ significantly depending on who is asking for the quote and the intended use. Industry customers might have to pay different prices than public institutions, non-profit organizations or individual persons. The instruments might further be discounted depending on how many one would purchase. Also, prices might change on rather short time scales and not be valid anymore after as short as a couple of months.

Therefore, you should take into consideration that any price information available to you might not even be accurate or generally applicable to the audience of your paper.


What is the best way to respond to students adding teachers to facebook?

Do as with any other person you don't want to have on Facebook: ignore the request or cast a silent no (pro tip: if you configure Facebook in pirate language, it becomes "begone, ye scurvy dog!").

Most people will get the idea: you don't want them there, and will not think further. If someone insists beyond reason, use Facebook's tools to report harassment (chances are you are not the first nor the last one). For anything in between (a message saying "would you like to be friends with me?"), a polite answer saying you don't feel it is appropriate should work.

If you are asked in real life about it you have two options:

Be direct and say "I prefer not to disclose it" or "that is personal".
If you want a more diplomatic indirect way, claim you don't use it much and change topic.


Patent agent work from the research career perspective

I am wondering about whether helping those people to formulate their ideas in a clear and defensible manner can be counted as an informal co-authorship of some kind.

My impression (based on my own experience as well as what I've heard from others) is that patent attorneys or agents typically make no contribution at all to helping their clients formulate ideas in a clear and intellectually defensible manner.  Instead, the contribution is entirely on the legal side: formulating things in a way that is likely to pass the review by the patent examiner and any subsequent legal challenges, while at the same time claiming as much intellectual property as possible.  This is a very valuable contribution, but not the sort of value that most of academia rewards (it's simply orthogonal to the intellectual contributions).  It's possible that a law school or business school might specifically hire someone because of this experience, but for most departments experience as a patent agent would not count as anything remotely like research.

You could try to make a special argument for your case (maybe your activities would differ from those of the average patent agent), but you would face a lot of skepticism.

  In other words, is there some ethical authorship credit that would be attached — again, informally — to patent agents' research portfolio and enable them to further return back to mainstream academia at some point?

This is no such convention, and you would have to be very careful if you made any suggestions in this direction (since it could easily come across as trying to take unfair credit for other people's work).

I don't have any statistics, but I believe returning to academia after spending time as a patent agent is rare.  I've known several people with Ph.D.s who became patent agents, and I've known of others, but I've never heard of anyone returning to academia afterwards.  (I wouldn't be surprised if it has happened, though.)

  Considering the above-mentioned point and, perhaps, other aspects, how difficult would be for a Ph.D. graduate without significant research portfolio (at the moment) to return to academia (as postdoc, then faculty) after having worked as a patent agent for some time?

It depends on what sort of academia.  Let's assume you wouldn't be teaching law or business, so those aspects of your experience would not be relevant.  You could still make a case that your time as a patent agent gave you an unusually broad perspective on how your field is applied, and this could be attractive to departments.  However, under ordinary circumstances it could not make up for a lack of recent research publications.  If you keep publishing or apply to jobs without a strong research component, then you may be OK, but if you stop publishing, then it will be difficult to return to a research university, even as a postdoc.


Master's thesis, should I inform my supervisor about the mistake?

Everybody makes mistakes. What separates good researchers from poor ones, is how well we own up to them. I don't know the details of your work, but it is very possible that what you think is a devastating mistake, is an oversight which should simply be improved upon if the work is later submitted as a journal article. Note that it is very rare that a Masters thesis becomes a journal article unaltered.
You should get in touch with your supervisor and tell them that you have discovered this paper, which you think might be warning that your method is questionable under these specific circumstances. Then let your supervisor form their own opinion.


Could publishing a book on a subject prior to a PhD reflect negatively on me later if it has errors?

Anything you write places you at risk of being wrong somehow. Certainly a book of this kind is asking for a wider audience that then might be aware of those mistakes. Alexandros points out in a comment that you certainly need to do your due diligence now to assure that what you write is as correct as it can be. No one is going to blame you if you suggest a response to a certain legal framework which is overhauled in three years but if you describe a chemical solution that could never react in the way you claim that one is on you. So how certain you can be that your work will remain correct/useful is somewhat field dependent.

The big question is about this hurting your ability to start and pursue a PhD after writing such a book. I don't think it would. Except in the rather extreme case of your book becoming well enough known and wrong/controversial enough to annoy members of a PhD admissions committee. For the most part I would suggest that already being an active member of a practical field (read: has published work discussing the field) would be a very helpful piece of an application for a PhD program.


At many (but by no means all) universities in the US and Canada, professional librarians (usually with a terminal Master's of Library Science degree or perhaps a PhD in some academic discipline) are treated as members of the faculty, including eligibility for tenure, participation in shared governance, etc.

In many other universities, librarians are staff members and not considered part of the faculty.  In a few places, there is a mixture with some librarians on the tenure track and other librarians who might have an MLS degree who are strictly staff members.  Most libraries also have lots of support staff and student employees who aren't professional librarians.

In places where librarians are considered faculty, they are usually expected to be involved in some kind of scholarly (research) activity and in teaching students.  For example, a librarian who specializes in archival collections might produce a catalog of a special archive and publish it.  Librarians often teach courses in how to use the library to do research and might be involved in teaching courses in library science to future librarians.


Do I need research experience to be admitted to a highly ranked mathematical physics master's?

Having research experience will certainly help your application to an elite program.  However, it is definitely not a necessity.  Moreover, the graduate faculty at top institutions are used to fielding applications from all over the globe; they should be reasonably familiar with what kind of preparation students from Germany will typically have.

However, if you are serious about pursuing graduate studies, only applying to a small number of top programs is not usually a good approach.  The top programs frequently need to reject a significant number of totally qualified applicants, simply because their space is limited.  I would suggest that you apply more broadly if you want to ensure that you can get into a top program.


The situation you described is quite problematic and (having heard only one side of the story) seems to involve misconduct by your advisor - as well as lack of perspective and/or complacency on your part as you've been faced with her behavior.

But let's start with what you explicitly asked and move on to more general suggestions/advice.

  I want to know how much authority does a PhD adviser have over your thesis.

Ethically, little. Your advisor should only verify that what you intend to submit is academically acceptable as a Ph.D. thesis: Sufficient contributions, adequate novelty, work which you did either yourself or as the primary involved researcher, no plagiarism, errors etc.

Technically, however, in some universities you require your advisor's explicit authorization to submit your thesis. You need to check whether this is the case in yours.

Even if that requirement is in place, however, it's not as much as a hurdle as many people worry it might be. if you have a PhD thesis written up, that you've gotten a bit of review on to correct any glaring problems, and that you've typeset and maybe even printed a copy you can wave at people - it would be quite problematic for an advisor to say "no, you can't submit" without a valid reason. If you contact your department/faculty's Professor in charge of graduate studies and wave your thesis at him, saying "My advisor won't let me submit", and with this being after 7 years - significant pressure is going to be put on her.

  Can she ask me to remove important sections of my analysis that has been with her for over an year?

You're putting emphasis on an invalid point. Nothing has "been with her", it's  in the draft of your thesis. It can theoretically be her opinion that you should remove something. In the case you describe, obviously this seems unjustified. The main issue is the justification.

Also, you are not at all required to oblige her and you can put whatever you like in your thesis (under the conditions I mentioned above).

  I am asking this because of a strong suspicion that she might want to scoop my work once I leave school.  In that case the only proof of authorship of my work is the thesis document.

Then publish that part of your work somehow before she has a chance to plagiarize it. As publication does not preclude work from being part of your thesis, it won't hurt you in that respect. Also, if proper, peer-reviewed publication of this part of your work time-consuming/difficult/prolonged/won't work out for some reason, go for a pre-publication - on a website like ArXiv, or on your personal website - as some sort of a technical report. That should be enough for her not to be able to plagiarize your work.

  If I have to press forward with my work, how should I diplomatically go about it?

Make sure that your friends and colleagues know about the situation you're in, sans your suspicions of your advisor. Specifically, make sure whomever of them who can understand your research knows exactly what you've done yourself (so as to be able to back up future claims of plagiarism). That last bit may also be pertinent to other senior academic staff members, so perhaps find the opportunity to bring it up, e.g. when sniffing potential future collaboration. Maybe schedule some colloquium talk about it.

Also, contact whoever is in charge of graduate studies in your department, and tell them you are having trouble with your advisor - without making accusations for now. Talk about your efforts to finish up and that it doesn't seem like your advisor is helping you get there; perhaps also talk about things that happened over the past several years before the thesis business came up. Be sure to mention at some point that part of your work that you're worried might be plagiarized - of course not this worry of yours, just try and make sure it's clear that you've had results doing whatever it is you did.

No less importantly: Talk to your graduate researcher's union. When I was vice-chairperson of our (half-recognized) union, a PhD candidate came to me with a similar situation: I promised him what your union should promise you, which is that if actual foul play begins on her part (like publishing your work under her name), we would go have a talk with her on your behalf. And if she refused to rectify things, there would be a massive scandal; her name and picture would be up on posters all over campus branding her a plagiarizer; we'd get the local media to report on it; we would file disciplinary charges (not that management would entertain them, but who cares); we organize protests in her classes - whatever it takes.

... but all this depends on actually having a functioning union. If you don't, try the same with whatever graduate student organization you do have, although then it's less likely you'd get the kind of backing you need.

As for your interaction with her, I don't think you've given us enough details for me to be able to make suggestions about that.

Finally, I think you've mishandled the situation so far. You see, your Ph.D. is your own project. Your advisor merely advises; you carry out research, you write it up, you publish, you submit. A Ph.D. is an exercise in being an (sort of) independent researcher. And feedback is something you can, and should, get from other people - in your department, your university, and elsewhere. You should go to conferences, especially if you're in the US where they're close, even when you haven't published there sometimes. You should have tried, at least, to form relationships with people in your field that are not mediated by your advisor. If you had done that, her lack of attention (or even abuse) would not have had that much of an effect.

Now, true, if we're talking about an experimental lab setting, then the head of the lab is more dominant in determining whether your research life sucks or not; and I know it's easier to give this advice than to act on it (and I'm struggling with the same challenge myself even now, as a post-doc) - but it sounds like you've been mostly depending on her support and feedback. I'm sorry you're having to change that under such unfortunate circumstances.


Transfer Over of EPSRC Funding When Changing Universities

From the tags I assume that you are a PhD student funded from EPSRC.

Unlike First Grants, Standard Grants, and Fellowships, PhD stipendships can not be transferred. The reason is that the EPSRC does not fund a PhD student directly. Instead, EPSRC funds Centers for Doctoral Training, and successful candidates get their funding from these centers. PhD students have financial "contracts" with CDT's, not EPSRC. Every CDT has a separate budget. For this reason, if you want to move universities, you can not take your stipend with you.


How is the Scimago journal ranking (Q1-Q4) defined?

Q1 to Q4 refer to  journal ranking quartiles within a subdiscipline using the SJR citation index.

Thus, a first quartile journal (i.e., Q1) has an SJR in the top 25% of journals for at least one of its classified subdisciplines.

What is SJR?
The SJR is an index of weighted citations per article over a period of three years ( https://www.scimagojr.com/aboutus.php ). As far as citation based indicators of prestige go it is quite good.
Citations and documents applied in this formula are based on the Scopus database.

  SCImago Journal Rank is a measure of scientific influence of scholarly journals that accounts for both the number of citations received by a journal and the importance or prestige of the journals where such citations come from. (Wikipedia)

How is ranking done? As noted, rankings are done at the subcategory/subdiscipline level. So  for example, journals are not ranked at the level of "psychology" or "chemistry". Rather they are ranked at the level of "analytical chemistry" or "clinical psychology".

Note also that journals are often categorised in multiple subdisciplines, and the quartile can, and often does, vary based on the subdisscipline.
The badge shown on scimago seems to take the most favourable ranking. So, for example, if the journal is ranked in the top quartile for at least one, it will have a badge as a Q1 journal.

Critical commentary:
In general, I think subdiscipline ranking based on SJR is superior to impact factors. It overcomes several biases in impact factor:

It uses a 3 year document window (impact factor uses 2): This is a better window across a broader range of disciplines.
It weights citations by prestige which can reduce the capacity for gaming and aligns within common sense that not all citations are created equally. I believe this also incorporates the idea that each publication only has so much prestige to give, so a citation from a paper with 100 references is worth less than a citation with 20 references.
It uses a more inclusive database of articles (i.e., Scopus) compared to Impact Factor which uses Web of Science.
Even after controlling for many of the above factors, differences in citation practices exist between disciplines, so within sub-discipline rankings are often fairer. Furthermore, often researchers and evaluators are trying to make decisions like where to send their best work or how to evaluate the quality of work of a researcher who operates in a particular subdiscipline. In this case, SJR within subdiscipline can be particularly useful.


What are the long-term advantages of a US PhD compared to Europe/Oceania?

I think the key question is: What do you want to do after the PhD?

There are some points that you may consider to choose a programme if you want to stay in the academia. The advantages or disadvantages of the length of these programmes depend on your training/background.

Your background. If you are familiar with the topic you are planning to work on, then you can probably start checking the relevant literature immediatly, in this case a 3 years program may be what you need. But if the topic is unfamiliar to you, then you would probably have to attend lectures and to read textbooks, in this case a 5 years program may be better.
Your CV. A work in the academia usually involves teaching and research. If you have teaching experience, then you can focus on developing your CV in terms of research. In this case I would go for a 3 years programme and get involved full-time on research. If you do not have teaching experience, then you might want to consider a 5 years PhD where you have the opportunity to teach and develop your CV in both lines.
The topic. Some research projects by their nature itself require different amounts of time to develop. For instance if you are going to work on modelling a specific data set vs. having to obtain the samples directly in the Amazon.

Regarding the mobility, I think after the PhD what really matters is your CV. Either if you graduate from Oxford or the University of Tuvalu.


Is it common to feel CS lectures useless as a CS major student?

I'm a computer science student as well, and I find lectures to be useful for getting a general understanding / "overall feel" of a concept. The prof often poses some question that makes you spend some time thinking about the problem at hand. I also feel that lectures are a good way to introduce a new topic to students, because learning some completely new topic from a textbook can be difficult.

However, in order to learn specific syntax and understand the deeper details, I don't find lectures to be that useful (since you need time to slowly learn complicated material). Rather, notes and code samples that my profs post online are much more useful, as I can methodically read them over and then practice writing code myself.

You should remember that a degree isn't all about just learning how to do something... rather, it also involves getting a higher understanding of a topic. To this end, attending lectures and trying to learn from the prof's experience can be rewarding. Besides, a degree from a more established institution will probably give better job prospects than a degree from an online university.


Does undergraduate school matter for PhD admissions (international student)?

I am sure some people will disagree with me, but this is what I can say as a person actually reading application documents and hosting international students (including PhDs).

First, your school name does matter, but to a lesser degree that one might expect. A "well-ranked school" on national level might be virtually unknown to people in another country. As a rule, top national schools plus top schools from international ranking lists ring the bell, but the rest is "large unknown", so it is very possible that school A in your list is not that familiar for the program's committee members as you may believe.

Second, we have to look at school names due to absense of better criteria. Consider this: tons of people send their applications to MSc/PhD programs. They all have reasonably high GPAs, they possibly had work experience, etc. What's the difference? OK, school name is one such factor that can make an application stand out.

However, there is a much better way. If you aim at PhD level, you must make your personal part of the application stand out. In practice it means that you should publish  scientific papers, and the higher the rank of the respective journals/conferences, the better. Think how to strengthen your profile as a scientist, and you will greatly increase chances of admission anywhere in the world. Also don't think in terms of "sending students" to a program. It is your personal endeavor, and school's power in pushing you as a candidate for another university PhD program is usually limited.

(Of course, here I have to note that it is probable that a better school can be more effective in supporting your research activities, but this is another issue).


Generally speaking, when are the deadlines applying for PHD's in Europe?

Unlike in the US, there are no "application seasons" in Europe. PhD positions are announced throughout the year, and every vacancy has its own deadline.


Can my recommendation letters be repeated?

Yes, they can.  Sometimes letter writers make minor changes to the letters, for example to add information specific to a given program, but this sort of fine tuning is optional (and almost nobody makes major changes).  The default is to send the same letter.


At least in the US, a Ph.D committee will have 4-5 members, and there are rules about the composition of the committee (there might need to be at least one person from an external institution, and at least one person from a different department, or variations thereof).

The committee's formal job is to assess the Ph.D student's dissertation proposal, determine that the work being proposed is sufficient for a dissertation, and then evaluate the final dissertation defense and decide whether to grant the student a Ph.D or not.

Informally, a Ph.D committee provides a set of resources/expertise for the student to tap into for advice, research directions and even contacts for future work (yes, there's life after a Ph.D :)). There's prior discussion on how to choose your committee.