How common is it for a professor to require students to work for him?

To quote JeffE: Run, don't walk.

Remember that first and foremost, you are a student. The purpose of being a student is to receive an education - if you wanted to work full-time at a company, you would not be paying for graduate school.

  ...halfway through our first year, our professor told us to come work for him at his company during our free time...He gave us a little bit of pay but it was irregular and we never knew how much we would get.

Working for a company part-time as a graduate student isn't unheard of; not being properly compensated for your time, however, is likely illegal. That doesn't necessarily mean getting a salary, but it does mean getting more than just "experience".

  After a while, he said we should come work for him at his company everyday unless we had class. My classmates and I didn't want to go anymore, because the work was only vaguely research-related and completely unrelated to our desired thesis topics....There was no contract or anything.

A bunch of red flags here. First, if the work you are doing is not interesting to you, find a new advisor. Easier said than done perhaps, but the advisor-advisee relationship is one of the most important of graduate school - indeed, it's a significant part of what separates graduate studies from undergraduate studies.

Next, being asked to work for a company without any form of contract is indentured servitude at best...and quite possibly much, much worse. Think of it this way: would you ever work for a company like this if you weren't in graduate school right now? (Hint: the answer should be a resounding NO.)

  One classmate said he wanted to stay on campus to focus on his research, and our professor belittled his research ideas...

Again, advisor-advisee relationship. These are not traits of a good advisor.

  When another classmate tried to leave, our professor gave him a very difficult software problem and said that if this student could solve it, then he could leave the company. The assignment was in an area that this student has no prior experience in, so he was unable to solve it and was too afraid to try to leave again.

Yes, in graduate school you are asked to tackle tough problems. And yes, often you have little experience or background in that area. But the whole point of graduate studies is to grow your knowledge of a particular field that you find interesting - and your advisor is supposed to help you do that. This does not sound like helping.

So, to answer your questions:

  What kind of position is this? Would this be considered an internship, research assistance, or just research?

I'm going to go with "abuse". Get out as quickly as possible.

  In the global academic world, do professors have the authority to require their students to work for them? Should my classmates have the option to do something else?

No they do not (at least not in that capacity), and yes they should (unless graduate school in Asia works differently, the most you can be held accountable for is tuition and fees - beyond that, what you all do is entirely up to you). But the individual you are working with right now is acting highly unethically and possibly (likely?) illegally, and you and your classmates have nothing to gain by continuing this relationship.


Getting notified when an article I cited in one of my papers gets retracted

Perhaps you could set up a Google Alert or set up a similar event handler at http://www.changedetection.com/.

I have tried both of these services.  Once in a while they both catch the same thing, but for the most part they complement each other.


If a publication is either published or accepted at a journal, list it under your "normal" publications - if you want, you can choose the caption "Peer-reviewed publications".  If it is not published yet, write "accepted at $JOURNAL", or similar.
If the paper is still under review, or otherwise not published at a peer-reviewed journal, but available as a preprint, list it under "Preprints".


"You are paid to answer my questions!" - how to handle silly questions?

I got angry, but. . how should I handle similar situations?

Got angry? No good!

You're not necessarily paid to answer his question but you are paid to help advance knowledge and learning.

Unfortunately, the tone of your answer doesn't let us know exactly how "silly" the question was (was it silly because it was personal question that had no bearing on the course? Was it silly because it was not relevant to the course material but possibly relevant to the overall subject? Was it silly because you had already covered the material in class? Was it silly because he was asking at the end of the lab session?) so unfortunately the exact way in which to respond might vary, but you might try:

If it's a matter of time and you can't answer it because you have to clear the room, tell him, "Give me a few minutes to pack up my things to get out of the classroom." Clear the room, entertain question.
If it's a matter of you having another appointment, then get him to submit the question over email or in writing or before next class.
If it's silly because it's not related to the lecture, I usually do my best to entertain these kinds of questions because it sometimes means the student is interested in other topics around the material. If my class is on object-oriented design and programming in Java, but the student asks me about "how can you use design in procedural programming languages like C?" I'd probably give some ideas on how it could apply to that situation.
If it's a personal question that you don't want to answer, you can say, "I don't feel comfortable answering that", "It's none of your business", "I can't talk about this", or similar.
If it's a stupid question because it's sooooo obvious or because you covered it before, then, sorry, it's not a silly question but is something the student needs explanations for. Get him to visit you over office hours for extra help.
If it's a matter of the student talking on and wasting time with questions, then you can ask the student politely to keep questions for after the class. If the student is trolling you with questions and is otherwise being a nuisance this option usually works as well.

Yes, it is rude for him to declare "You are paid to answer my questions!" but it's also rude to say that "Your question is silly". You are the teacher, the role model, the example, so you should be more patient with them than they are with you. Besides, if you tell them  you'll answer it later, you can simply say, "Just wait - I haven't answered your question yet."


Should I resend the emails if professor do not reply to my email?

Do not send too many emails-- this will undoubtedly annoy a professor who is possibly on vacation somewhere when they return to see 10+ emails from the same undergraduate(?).

As to your second point, that is absolutely a no. Why are you even asking professors with whom you are not close enough that they do not even think that your major is related?

I feel like you may have more major problems, but I would not send more than a couple of emails at this time. If anything, the fall semester will begin soon and you can approach any professors in person to ask for a letter.


How to introduce myself briefly in a get together for new faculty members?

Partly, you'll want to copy what others are doing.  If everyone else only talks for 15 or 20 seconds, then almost anything that you say in a 3-minute monologue will be poorly received.  Information that you'll likely want to mention includes: name, department, research interests, possibly where you've just moved from, and maybe a bit about you personally (I enjoy triathlons; married with two kids; active in a barbershop quartet; etc.)  One point about your research interests: keep it very nontechnical.  Rather than give many details, say something like I write computer programs to help blind people use computers, or I study 18th century literature, particularly the works of SoandSo.  Most likely, this activity will be pretty informal.  If you're still a little nervous about it, you might ask another junior faculty member in your department.


What is the benefit of writing lecture notes for an introductory course vs using a textbook?

As someone who's tried to do both, there are some very valid reasons to prepare "formal" lecture notes.

The primary reason why you'd want to create your own notes is that for many courses, a single good text is not available, and as a result, the instructor has to cobble together material from a number of different sources to produce a coherent set of lecture notes—or recommend that students work with multiple source texts. (Given the out-of-control nature of textbook prices, the latter alternative is unlikely to work out well.)

If you have a single-text class, it may not be necessary to provide students an additional set of notes, provided your lectures stick to the main text material. However, if you bring in alternative or additional topics into your lectures, you may want to include notes for those topics, and refer students to the textbook for places where you follow the "standard" outline.


Why would a professor agree to write recommendation letter, then mention in it that he doesn't know student very well?

In many cases professors agree to write letters for students we do not know well because we are the best option, according to the student, for them. Some students do not have good enough relationships with enough professors to get all the letters of reference they need. They may approach a professor and say, "I know we do not know each other very well and I only took a class with you/worked in your lab for two weeks/etc, but I need someone else to write a letter and I think you are in the best option I have". At which point, the professor may agree. If the student is not as up front, hopefully, the professor was clear and said something like "I don't know you very well, but I can write you a letter and talk about X." Again, some students will agree.

While it is not desirable to have references from people who do not know you well, including in a reference that you do not know the person well is not inherently bad. In fact, it probably is better to be up front about the relationship because it explains why the letter is so narrowly focused.


Research topic already covered, change direction or what?

You can cite the previous paper. You should consider whether your work contributes to the literature in addition to the previous paper. If you proceed, you can explicitly explain how your paper provides a novel contribution during your introduction.

Some possible places you could extend the previous work might be:

Making changes to the methodology
Updating the paper for more recent results
Extending the previous results
Further validating the previous results
Examining the question historically

You may also want to consider contacting the author of the previous paper; he may be willing to work with you.

In short, you might want to revise your research question and paper slightly, but you can continue with your research if you give credit to previous paper and can convince journals that your paper is important.


Demand code and/or data as a condition of peer review?

I would suggest first spending a little bit of time reflecting to yourself on why you want to see sharing of code and data, and which code and data you would want to be shared.  Is it more ideological in nature ("information wants to be free"), or at its root is it a belief more about scientific ethics and efficacy?

I am almost certain that you do not actually want all data and code to be shared.  For example, you probably do not want identifying information about subjects to be shared.  Likewise, you probably do not care too much about little bits of utility code that don't have anything much to do with the science.  Where do you draw your boundaries and why?

The reason I would suggest doing that, is that you will then be in a good position, as a reviewer, to persuasively argue for the inclusion of code and/or data for objective reasons that the editor and author are more likely to agree with, even if their personal preferences are different.  I don't think you'll have much effect by refusing to review (unless you can get a lot of colleagues to exert pressure along with you), but I think you may make much more difference by refusing to accept poorly justified conclusions in the absence of result and method information to support them.


Am I graduate student or underpaid employee?

The downside of academia that you are describing definitely exists.  Have been hearing this for generations now (don't get me started on the pyramid, tournament style rewards, job prospects, etc.).
All that said, it is irrelevant to you.  Do NOT cut your nose off to spite yourself.  You are too close now.  Just buckle down and finish and get the degree.  It is helpful. And you will kick yourself if you miss it.
Be a little selfish about taking care of yourself on papers, etc.  Focus, focus, focus.  Pick your spots,  but I would avoid volunteering always and also occasionally push back on collateral duties.  And push, push, push for papers.  They really are the score card...don't let anyone kid you the opposite.


Can publishing on arXiv create copyright issues?

Nature especially states how pre-prints should be handled:

  Preprints

  Nature Research journals support posting of primary research manuscripts on community preprint servers such as arXiv and bioRxiv.  Preprint posting is not considered prior publication and will not jeopardize consideration at Nature Research journals.  [...] Authors posting preprints are asked to respect our policy on communications with the media (http://www.nature.com/authors/policies/embargo.html).

  [...]

  The original submitted version of the manuscript (the version that has not undergone peer review) may be posted at any time.  Authors should disclose details of preprint posting, including DOI, upon submission of the manuscript to a Nature Research journal.

Taken from Nature's webside about Publishing licences and compliance with open access mandates.

TL;DR You can post your pre-print on arXiv prior to its submission to Nature.

Important: These condition may not only vary by publisher but by journal/conference.


What favour is suitable in return for running a costly software?

There are probably two important parameters for this question: (1) how close are you to the other party?, and (2) how long will it take the other party?

If you are good friends with the other party, and it will only take a few minutes - probably no favor is needed, as long as you don't need this service all the time.
If you are good friends with the other party, and it will take hours or days to do - in this case I would consider whether it is possible to set up the project in a way that co-authorship for the other party is legitimate. Yes, just running predefined scripts or doing some analyses that you have clearly laid out may not be enough to warrant co-authorship, but typically it's not a given that this is the only thing they do. Just get in touch with them early on in the project, and collaborate.
If you don't know the other party well or at all - in this case, it seems unlikely that you will be able to convince them to run your software just as a favor, even if it does not objectively take much time. Your best bet is to get to know them better, and see if you can start a collaboration that will include, as part of the collaborative work, that they run the costly software for you.

(of course, all of this assumes that the other party actually already has the software and using it for your purposes will not incur significant additional costs)


Using teaching materials I found on the internet for my own teaching

Note: I am not a lawyer, and this is not legal advice.  Seek a lawyer's opinion if you need a definitive answer.

Merely finding something on the internet doesn't prove you have the right to use it.

It might be provided free for certain uses, but with restrictions.
It could even be completely illegal (such as stolen content).
Quite commonly, material will be posted without a clear statement of how you can legally use it.  And under most copyright laws, it is presumed that you do not have the right to copy and redistribute material unless that is explicitly granted.

Check the license, if there is one. Some material might be provided with an explicit copyright license, such as one of the Creative Commons licenses.  If so, you can simply check if reusing the material for academic use is allowed.

If there is no official license, but the website has an informal statement allowing the material to be reused, that's a gray area.  Technically, this probably isn't sufficient to grant you a legal basis to use the material.  However, I would probably be happy to proceed on this basis for a low-risk activity like handing out material to students.

If there is no license, seek permission.  Contact the author and get permission in writing.

In either case, clearly attribute the material.  If the author of the material isn't clear, add a statement.  A copyright license, such as Creative Commons licenses mentioned above, may also have specific requirements for attribution, which you should follow.


More formal way to write "canned algorithm"

I would recommend naming the algorithm and then saying what library or software you obtained the implementation from. That way, the reader has enough information to adequately understand what you have done and compare it. As for an adjective: "frequently used" is sufficient, I think.


Is punctuation necessary for displayed formulas in academia writing?

In mathematics there is a near universal consensus that displayed mathematics should not be treated differently from inline mathematics with regards to punctuation. By this I mean that the vast majority of papers on the arXiv follow this convention, most journals will add punctuation according to this principle if it's not already there, and so on.

Thus whenever you're unsure whether or not to include punctuation at the end of a displayed equation, try to replace \[ ... \] with $ ... $ - whatever punctuation mark looks natural when it's inlined should be included also at the end of the displayed equation.

I don't think that texts without punctuation after displayed equations are necessarily ambiguous, but then again, a text without punctuation after inlined equations would probably not be ambiguous either. The main purpose of punctuation is after all not to reduce ambiguity but to increase readability and "flow" of the text.


Course Requirements for Mathematics and Applied Mathematics Phd admission

I would also like to know if its possible what kind of undergraduate
  requirements does an Applied Maths program usually look into? Would I
  be correct in assuming that they won't be looking in to algebra that
  much?

Not having had an undergraduate course in abstract algebra wouldn't be much of problem for admission to the graduate program at my institution (which focuses on applied and industrial mathematics.)  Background in analysis, differential equations, modeling, probability, and numerical analysis is much more important.  Significant background (such as a minor) in some area of science or engineering is also helpful.


How to answer the question "Why do you deserve a scholarship?" when applying for a scholarship?

Committee must be convinced that the money will be well used. It would look best if you told you would invest the money to become better at the field of your studies (buy literature, go to conferences, pay for some courses or certifications, publishing your articles in journals). However, trying to look perfect could backfire. In my country it would be reasonable if you wrote that part of the scholarship would be spent on something not related to education. But that depends on the country, culture, traditions, committee members etc.

You must also convince the committee that you will do good in studies. That is why you should mention your study results and achievements.

You must convince the committee that you like the field of your studies, you are passionate and will keep working hard. If your studies have helped you at your work, mention that. Also mention your short and long term goals - educational and professional.

You can also mention your strongest characteristics and give arguments. (example: leadership abilities, you lead a student team in project x which was successful. )

The motivation letter as a whole is the answer to the question "Why do you deserve a scholarship?”

edit #1: I changed the part about spending scholarship money on something not education related, because of the comment by Trylks.


Mathematics application cover letter, one page or two

My (limited) understanding is that longer cover letters are more common in the humanities and social sciences.

I've been on multiple hiring committees for tenure-track assistant professors at a mid-tier research institution. We didn't expect two-page cover letters, and for the most part cover letters were quite brief and pro forma. I don't remember seeing two full pages even once, and I don't remember any of the candidates we interviewed saying anything noteworthy on their cover letters. This was expected and fine with everyone on the committee.

There are some situations that might call for a longer cover letter (or at least for you to pay extra attention to this). In particular, I would recommend this when applying to liberal arts teaching-oriented positions. From what I have overheard, my understanding is that, on average, teaching-oriented math departments care about "fit" more than research-oriented departments do. (And moreover, when research-oriented departments do care a lot about fit, they don't seem to expect candidates to anticipate what the department is looking for.)

You might also write a longer cover letter if you can genuinely make the case that you are a good fit for a particular department. Don't BS, but offer good reasons if you have them.

A longer cover letter might be a good idea if your application is in any way unusual. If you are finishing up a postdoc, it is understood that you will be applying to a huge number of jobs, and a brief cover letter is usually fine. If you already have a tenure-track position and are applying elsewhere, or would prefer to work at a teaching-focused institution despite having a research-heavy CV, etc., then you might consider explaining yourself more fully.

Good luck on your job search!


Is it acceptable to use working hours to read general interest books?

It's socially acceptable to do (almost) whatever you want during academic "free time". Ultimately what matters are the results you produce, and as long as you're able to do that most people will not care if you're reading general interest books, drinking coffee, or answering questions on StackExchange.

Of course, if you have assigned duties (e.g. teaching duties) then using that time to read books is not going to be permissible.


Filing a patent which my research advisor will found a company on it

Disclaimer: I'm not a layer so the answer is not an advice but a collection of thoughts based on my experience. And each particular situation can have many facets which one with limited knowledge may not foresee. Also intellectual property law varies from country to country, so additional details would help answering.
I start from last question:

No, your supervisor can not exclude you from the patent as you are a coinventor. If she or he files the patent without you, you can claim against it in front of the patent office. Make sure you have some proofs of your authorship. If you had exchanged emails with your supervisor on this topic, it can be also useful. Note that in patent right public disclosure of invention leads to loss of patentability. In simple words if you tell someone (non-inventors) about invention and they can prove it, the patent application can be rejected.

The first one is the more difficult question. Here it strongly depend on your relations with your employer and country laws on intellectual property. In some countries having a contract with your employer would mean that intellectual property (IP) generated within this contract belongs to the employer. Depending on country you may keep parts IP of it or get only a bonus from employer. In situation you describe, it is difficult to give you an answer without knowing details of your contract and IP laws of the country. In any case typically the patent can be licensed to whoever wants to use (the startup company in your case) it by IP owner (inventors or/and your employer).

Hope it helps to proceed with more detailed search.


Academic changing universities: How to negotiate start date to minimise problems with leaving previous university with little notice?

Also look at Possible to leave a contract academic position shortly after signing new contract? [closed]

But the decision appears not yours to make from my reading of the wording of the question.

If the current institution says no to a one semester contract, then the answer is given, as it would be kind of ridiculous to keep putting off the new position (assuming one wants to accept it) for however many years the old place keeps renewing the year-to-year contract.

But lets imagine that the OP is in a position where he/she is negotiating with both sides to stay one semester. The former department has requested that they 'need' the OP just a little bit longer. Accommodate the request or not?

There is no ethical obligation to stay (how would people ever change positions otherwise?). A junior faculty in a field where everyone knows everyone and a collaborative team player reputation is highly prized, might find it a smooth move to attempt to negotiate to stay one last semester at the desperate request of the former department. (If the new place says no, well then, figuring that out as soon as possible is more important to the old department than anything else).

But, even so, I get a sense from the question that the OP feels guilty for leaving, (which is normal).  I also suspect that is it pretty easy to mistake anxiety-over-getting-out-of-project  with being indispensable. ("It won't be done the way I would have done it" is not the same as being indispensible)


Project design and scope: "interesting" vs "incremental" science

You have different but overlapping responsibilities to all three; you can't say that one "overrides" the others.

You have the responsibility to do "good science." By "good," I do not mean "high-impact" or "prize-winning" or anything like that; I mean "ethical": you carry out your experiments or calculations without trying to achieve a desired outcome to support a preconceived model or explanation.

You owe your advisor and yourself the same level of professional conduct: do the science properly, and let the results be what they are. You also have the responsibility to respect and properly use the resources your advisor provides: money, facilities, and time.

Finally, you have a responsibility to yourself: do work that you feel satisfies you, and that keeps you motivated. Don't do research in an area just because that's what's "hot" right now; fads come and go, but good research survives that. Second-rate research likely won't survive.


When the letter of recommendation will be asked for by the hiring committee?

Nobody outside the committee knows. Maybe you are not under consideration. Maybe they ask for letters at a later point of the evaluation process. Maybe they never actually ask for letters.

I understand that applying for jobs is a high-pressure situation, but trying to infer information from noisy signal like that is, generally speaking, not useful. There are just too many variables that you (and we) have no way of knowing.


Why is research at highly productive research institutions better than those at not-so-highly productive research institutions?

Your question is a bit circular. The "best" universities are at the top of the list because it's a list of the "best" universities -- however that is defined. :)

What makes a "top" university is largely a rich-get-richer feedback loop: The "best" universities attract the "best" researchers, which makes them the "best" universities. The "best" researchers get the most funding, which helps them do the "best" research. The "best" universities get the most money, which helps them spend more on research.

That explains why older universities tend to have higher rankings. They have had a long time to gradually build up that feedback loop. However, external factors have a big impact -- availability of funding and university management is important, as is the desirability of the location/country. Countries like the UK and US have a lot of good universities because they are attractive places to live and their government provides adequate research funding and, importantly, this has consistently been the case for decades or centuries.

One important point you are missing from your list: Some professors are teaching six courses per year -- they have no time for research. Other professors are only teaching one course per year -- they have plenty of time for research.


Is it conventional to acknowledge someone who read a draft of paper but didn't suggest any improvements?

Acknowledgements are mostly yours to do with as you please---in my experience in computer science, at least, there are few hard and fast rules.

For my own part, I typically keep my acknowledgements relatively spare, reserving them for people who made significant and meaningful contributions, but who did not rise to the level of authorship.  As such, I tend to not acknowledge anonymous reviewers, people who gave feedback that didn't result in large changes in the manuscript, etc.  You should feel free to be more liberal in your acknowledgements if you choose, however---the only real limitation is if either a) your manuscript may have length limitations or b) you do something that can be taken as silly (which can be OK for a thesis but generally not so much in a peer-reviewed manuscript).

It is pretty much always the case, however, that acknowledgements say what a person is being acknowledged for.  If you say that, then people will know how to calibrate the contribution.  If you have a hard time figuring out what to write, that may be a sign that the person didn't do enough to be acknowledged.


Should your PhD students call you by your first name?

Yes, a PhD is essentially an apprenticeship in academic research, so they should be treated as a colleague in potential (it seems normal practice for an RA to refer to their supervisor by their first name).  Also I think it is a bad idea for researchers to be overly formal and deferential towards their supervisors; if you ware working at the cutting edge of your subject, not all of your ideas will be good ones, and the PhD student should feel comfortable pointing out where they feel this is the case.  This sort of self-skepticism (being comfortable with the idea of being wrong occasionally) is a key component of being a good scientist, and it seems to me to be difficult to communicate this by example if the student is constantly reminded of their place in the hierarchy by making them call me "Dr Marsupial".


Revising timely submitted paper after hard deadline

For most conferences, there is an informal grey area in the submission deadline.  The conference typically states that nothing will be accepted after hour X on date Y in timezone Z, but often the system doesn't actually shut down submission at that time, but a little while later.  This may be for any number of reasons, frequently including:

Giving a grace period for technical problems or slow uploads
Supporting extensions that have been requested by and granted to particular authors
Just plain not seeing any reason to bother with precision

From my experience, the most important driver for all of this sloppiness about time is that the point of the submission deadline is not so much to stop submissions as to enable a fair and well-organized peer review process to start in a timely manner.  Thus, as long as the submissions are shut down fairly promptly after the deadline and review assignments can be sent out on schedule, nobody really cares all that much about timestamps: there's nothing magic about 11:59pm in American Samoa.  Likewise for a camera-ready / revision deadline: the point is not to stop submissions but to allow publication to begin.

As such, I see no issue with what you have done.  The formal deadline is the point after which you have no grounds to complain if you can't change anything any more.  If you happen to notice a further correction to make and the system is still accepting them, well, that makes things better for everybody, and it's likely the organizers won't even bother noticing, let alone be unhappy that you did so if they do notice.

Now, it's possible that you might run into a program chair who is unusually dedicated to precision and does not share this opinion, but I have never yet encountered such a person in my professional life.


What do I do if I really only figured out what I want to research just after applying

I saw this sort of thinking/discussion all the time. Something like, I'm a second year Ph.D. student but I want to start another one, because X is big and I'm excited about it. This is a bad way of thinking about a Ph.D. program.

Here is the thing:

One of the main pitfall of PhD students is that they can't get their mind into one problem.

Here is another fact:

During Ph.D. you learn how to think and read/write as a researcher, regardless what you are working on.

Advice: I say choose one among all the offers you get. Drop all, unless you have a pretty good damn reason for it (e.g., got a job at NASA).

Answering 'what I want to do for research' always changes! Thats the nature of research. You can not keep up with all trends during Ph.D. First, you need to think, read, and write as a researcher; and you learn them during a Ph.D. Then, you can follow the trends as a postdoc or an academic.


how do I add an article to google scholar

In general, Google is somewhat closed-fisted when it comes to peeking behind the curtain of their indexer.  However, they do provide some advice to people hoping to get their articles indexed by Google Scholar here.

That said, unless you have control over the hosting of that particular book chapter, there isn't much you can do to attempt getting this chapter indexed by Google Scholar.


Does timing of PhD application submission matter?

I doubt that it matters in a formal sense at very many institutions unless the school used "rolling admissions". However, it is possible that if you apply early and there is some flaw or lack in your application that someone, even a clerk, will catch it and give you a chance to correct it.

Sometimes a department head will try to shepherd early applications since it is his/her responsibility to make sure that there are enough applications to build a new cohort. That is separate from formal acceptance, however.

It is also possible that an especially "juicy" application will be passed to a professor who might be looking for a certain kind of background. But again, that is separate from acceptance.

In rolling admissions, students are accepted or not as the applications come in. The deadline may mean only that the process stops at that date.


Should I share my extensive notes summarizing literature in my field?

Pros:

Contributing to an open and collaborative scientific process

If you've put a lot of work into something, it is great if that work can benefit others as well. If you can save another researcher a bit of time, or even better provide them with some inspiration, that is great for science in general.

Raising your profile as a researcher

It's almost always a good thing for people to know your name and be aware of what area you are working on. If people read your notes and find them useful, this will give them a positive impression of you and could make them more likely to collaborate with you in the future.

Provide motivation to continue updating your notes

Pretty sure it's an established psychological effect: if you share your goals with others it provides incentive to meet those goals.

Ego boost

As you said yourself, it would feel good!

Cons:

Possible negative impression to authors you are critical of

You mentioned that a lot of your notes are critical of the papers you read. I would say this is normal - we tend to focus on weaknesses when we pick apart a paper. But to the author, this might create a negative impression if they feel that you are unfairly harsh, or that you get hung up on details and don't "get" the main point of the article. On the other hand, researchers tend to be fairly thick-skinned and will be used to dealing with criticism.

Unlikely to be formally cited

Given that your notes don't contain much in the way of original material, they are unlikely to get cited. People are more likely just to cite the original papers that you refer to.

Overall, you can probably tell that my personal opinion would be to go ahead and post them - it sounds like a very positive step. But it might be worth spending a bit of time checking through your more critical points and perhaps moderating them slightly, or balancing them against something positive.


Shall I quit academia or continue doing research without too much luck?

You write "My life already suffered from my research career." This is worrying.
Think about this: what do you need the most for a satisfying life? Is it being close to home? Having a fulfilling relationsship? Having a garden? Living in China? Living near the sea? Being a researcher? Find out what it is for you and focus at first on that. Then find out what else you can do while realising your first priority.

Don't get too hung up on Academia. Being a researcher is not a higher calling from some God, at the end of the day it's just a job. There are many good and satisfying jobs out there. Find out what else the world has to offer.


Do industry-sponsored papers contain more incorrect results than papers that aren't industry-sponsored?

I think your hypothesis is implausible that industry-sponsored research is more incorrect or less reproducible than non-industry-sponsored. Or can you give some reasons for this assumption?

On the contrary looking at many of the meta-surveys (partly conducted by industry, because non-industry-sponsored research maybe is less reproducible to their experience) that investigated the reproducibility of academic research in the recent years, rather the opposite is maybe the case and known within industry.

Additionally, I don't see how it makes a difference if money financing a PhD student comes from industry or not? Wouldn't the rationale rather be, if money is spent by industry, then rather PhD scientists/Professors are hired for a project than cheap and still learning PhD students pressured by publish or perish? And to my knowledge more of the spotted scientific misconduct has been caused by untenured researchers. Again, publish or perish

And when industry research can't reproduce 70–90% of academic laboratory findings, then a better question is probably if most of the research projects are funded by industry or not and what kind of researchers are on average hired for industry-sponsored projects (PhD students, PhD's, tenured)

What maybe sounds plausible, that researchers carrying out industry-sponsored projects tend even more to make up results or buzzy headlines ("new battery technology allows charging up within 10% of normal time" which I read every month or so), is rather implausible to me, because important and valuable results in industry-sponsored research projects are often rather published as a patent than a paper.

More importantly, there is a clear correlation that research in branches being strongly entangled with industry (engineering, physics,...) is much better reproducible than weakly linked branches (social sciences, psychology, biomedical,...). Most of the meta-surveys are in such fields.

To take up your case of drug development, such only become legalized after 10 years of clinical trial, so I think the incentive for some PhD student is not significantly higher and often the PhD students have no clue if the money financing them comes from industry or public. And professors being biased by the funding source mostly don't conduct and evaluate the experiments and would have to alter the results (which also happened, but rarely)

Summa summarum I think there is no such study (my googling didn't find one but many meta-survey on reproducibility partly published by industry companies), as your hypothesis looks very implausible to me. There is probably a good virtual database with so much meta-surveys and the necesssity to name funding sources in a paper, still to me the important question would be, which kind of researcher (students, tenured,...) are typically hired for non-/industry sponsored projects? Because, the conclusion from the published meta-surveys in social sciences, psychology, biomedicine and the low reproducibility to be drawn is not that researchers in such fields tend to be more biased, tricking, cheating and therefore more incorrect results are published, but rather that industry is not much interested in such results and the level of scientific rigor is much lower than in hard sciences like quantitative physics or engineering, for which I didn't find a single meta-survey.


How to deal with a colleague who won't accept they're wrong

Use impersonal language
Hopefully this is obvious, but make sure that your language focuses on the ideas rather than the people. Rather than

I don't think you're grasping the subtleties of the situation

try

I think that there are some extra complications that need consideration in this case

Ask questions
Rather than taking a confrontational approach, try to adopt the role of the inquisitive student. Rather than

There is evidence in publications X and Y that directly contradicts what you are saying

try

What are your reasons for disagreeing with publications X and Y?

or

I'm having trouble understanding why the conclusions from publications X and Y do not apply here. Can you elaborate?

This will hopefully give your colleague a graceful way out without having to turn it into a matter of "you're wrong and I'm right". As a bonus, it also gives you a way out if it turns out you were wrong after all (however unlikely that is) or that you misunderstood your colleague's point. But as @R.M. and @CaptainEmacs have pointed out in the comments, take care not to overdo it, or you could come across as either clueless, or patronising.
Make someone else the scapegoat
Rather than voicing your concerns directly, put them in the mouth of a hypothetical reviewer. Rather than

I think there are these reasons for rejecting that argument

try

I think that a reviewer could object to that argument for [reasons]. I think we need to anticipate this using [different argument].


What is a reasonable number of grad schools to apply to for a PhD in computer science?

However many schools you find that have academics that you want to work with.

Research is like riding a bicycle.  You can obviously do it.  The application process for graduate school is mostly to vet applicants for those who can't ride the bicycle.  Therefore, the important next step for you is to find someone you will jive well with.  Applying to graduate schools should be more about that: find a professor that you'd be willing to enter into a serious personal relationship with.

With that being said, I have friends who applied to 9, 3 schools in 3 tiers: "dream schools", "realistic schools", and "satisfactory schools".

I applied to one.  I found a professor I really liked and started an email correspondence with him 3 months before I even applied.  When applications came around, there wasn't a question of where I would apply or whether I would get in.

Oh, and I'm a 4th year CS PhD candidate.


How does laboratory funding and money management work in grad school?

Bad things happen when a research group runs out of money. If it's a short-term cash flow problem (for instance, having to meet payroll in the aftermath of the US government shutdown of 2013), the university should be able to provide short-term funds to cover the gap. But this can come at a cost:

It may not be possible to order necessary supplies.
Travel may be restricted.
Normal operations (usage of expensive equipment, etc.) may have to be partially or totally curtailed.

However, if it's a long-term, structural problem—for instance, because the group has grown faster than grant funds to support the group—the consequences can be much more dire:

New students and postdocs can't be hired.
Support for undergraduate students (REU's, and similar programs) get cut.
Students may have to take on teaching assignments to receive their stipends.
Recently assigned students may be asked to switch into another research group.


How do I refer to a picture I added in my essay?

A good guide to MLA figures and tables may be found here.

In short, you simply say "Figure 1" for the first figure, "Figure 2" for the second, and so on.


Two PhD's in different UK universities, simultaneously, part-time: absurd idea?

Andrew mostly covered why this is administratively impossible, but I think it's also worth addressing the misunderstanding of what a Ph.D. is embedded in this question.  Pete Clark said it better than I can, but Ph.D.'s are not merit badges.  More is not better.  Getting a Ph.D. on one of these topics will not stop you from working on the other.  Working with one of these advisors officially will not stop you from staying in touch with the other, and potentially collaborating in the future.  You want to have ideas about other stuff to work on once you finish your dissertation.

I don't envy having to make the choice, and you will have to close one the doors part of the way to actually finish your degree.  But you don't have to slam it all the way shut, and you never know when ideas you know thought you had set to the side will come right back to you.


Citing low quality papers (solutions) in surveys?

Speaking from the perspective of a no-longer-quite-so-young mathematician, this is a serious question. I think one should acknowledge "prior art", even if one disagrees with many aspects of it. That is, to pretend that something doesn't exist when one is aware of it is dishonest. (I do not think that one's bibliography must only include things one has used... that can be subverted to argue, as I have heard a distinguished mathematician say, that one need not cite anyone else's work _if_one_is_careful_not_to_look_at_it_.)

Yes, there is the awkward issue of giving an opinion on "prior art" that one finds deficient. As @Shion comments to the question, one probably should hesitate before being too sure. The universal non-commital (therefore slightly dismissive, which is the right amount) comment is something like (at the end of introduction) "Compare [A], [B], [C]." Not saying that they're crap, or failures, or anything else. Just admitting one is aware of them, and pointedly not endorsing them... if that's one's intent.

That is, I think that published papers should not just be update-reports, but have sufficient scholarly context-setting to orient a genuinely interested reader not already completely expert, for example. I realize that the literal function of many "published papers" is merely "making a living", but it is not profoundly difficult to do somewhat better.


Is it good idea to put a slide about "National Teacher Appreciation Day" at the end of presentation slides at my masters defense?

I doubt that you showing or not showing the slide will make much of a difference one way or the other, but as a general rule, if I were one of the professors at your defense, I would not expect or want you to say or display anything that makes it seem like you are trying to ingratiate yourself with me in any way other than by performing well and conducting yourself professionally. I don't need to be thanked profusely, and don't need to be "appreciated" in any special way for doing my job.

Moreover, if you think about it, the reason something like National Teacher Appreciation Day was conceived is probably because in many countries being a schoolteacher is a very ungrateful, poorly appreciated job. For example in the U.S., teachers get paid very little, are commensurately not respected by much of society, and sometimes are outright hated by certain people for purely political reasons. All of this does not apply to university professors, who are generally treated quite well and held in pretty high regard by most people, and consequently aren't in great need for a "professor appreciation day".


How to find out whether a PhD dissertation is ready to submit?

You should talk about this with your advisor and your consultant professors. You can complete your report and show it to your advisers. They will read and tell you what lacks in your report. Also, you may talk to the members of your PhD committee orally before giving them your report. They may give you some guides or some of their expectations.

Talk to the previous PhD students and see what brought them to the point that their PhD was ready to be presented.

Another important thing is your PhD proposal in which you have clarified your goals of your dissertation. If you have completed your promises in the proposal (or you have strong reasons why could not reach some of your goals), then your work is completed.

Another thing may be regulations of your department. Some departments require their students to submit one or two journal or conference papers out of their PhD project. You can check your department's regulations on what are their expectations from a complete PhD project.


Is it possible to publish a paper when the research was done many years earlier?

Yes, IF the research is still relevant and novel.

When you publish a research paper you never write when was the research performed, you merely describe the research and explain why it is relevant. If the research is still a new/different method, then it doesn't matter when you did it. No one is going to ask. If the method was novel then, but now several people have published about it and you can not add anything to the current literature, then it is not worth publishing.

Just follow the same criteria that you would use if the research was done last night to consider if its worth of publication.


What to do when publishing a paper about mistakes in previous literature?

To begin with, I find it highly problematic that this journal has a policy of inviting authors to review any paper that criticizes their work. That seems to me to be highly inhibitory of criticism and likely to produce situations exactly like the one that you are facing.

I find it doubly problematic that this author has chosen to communicate with you outside of the review process in order to persuade you to change your writing. His communications can easily be interpreted as an unethical quid pro quo request: you drop your criticism of his paper, and he'll drop his criticism of yours.

What is not clear from what you have written, however, is just what the journal intends to do with the review that they have received. Surely the journal must understand the potential conflict of interest here.  So is the review mainly to allow an author to point out errors in the critique that those less familiar might overlook, or are they going to treat it just like one of the other reviews?

I would thus recommend taking the following approach:

Write to the editor and let them know that the author has approached you separately with what you are concerned may be an unethical proposal --- the editor needs to know about this and should be able to make their approach clear to you. Ask the editor how they would like to proceed.
In parallel, use all of the constructive parts of the criticism to improve your manuscript.
Consider slightly softening the language in your criticism in the manuscript. I do not know how you have written it, but it's often possible to use slightly less definitive language to make the same point, e.g., changing "Papers [1] and [2] should be re-analyzed to see if their results are affected." into "As it is possible that results might be affected, we would recommend considering re-analysis of papers [1] and [2]."  Same substance, but less confrontational and allowing you to write that you have adjusted the paper in response to the review.

Hopefully, the editor can provide you some clarity as to how to navigate the difficult situation that their journal has created for you, and judicious adjustment can allow you to pass peer review without compromising your ethics. If not, there are other good journals out there that will not have this unusual conflict-generating policy.


In what order should I list bibliography entries by the same author?

For a CV, it seems that a widely accepted rule of thumb is that the order of publications is inverse-chronological, i.e. one lists the latest papers first, and moves on with older ones:

Author, title1, ..., 2018
Author, title2, ..., 2016
Author, title3, ..., 2016
Author, title4, ..., 2015
...

In case of journal articles, I've never encountered option 1. (alphabetical). (In fact, I've never encountered this case at all) For the others:

(Historical) When the citation style is (Author, year) - then the citations in the list of references are sorted chronologically, and in the text it might happen (and is fine) that e.g. (Author, 2018) will be cited before (Author, 1990).
(Logical) When the citation style is [1,2] - then the list of references is sorted by the order of appearance in the manuscript, e.g. Author's 2018 can be [1], and Author's 1990 paper can be [79] (or vice versa).

Although, each journal has its own policy regarding the citation style and ordering of the references in the reference list. If the journal has a LaTeX template, then you let it do all the work for you. In case of issues/inconsistencies - the editorial office handles the final typesetting.


My mental health has been damaged. I don't want to quit my PhD but I don't know how to continue?

If your mental health is suffering, then the first thing you need is to seek professional counseling for that.

Once you feel you are in a space where you can make decisions clearly, you need to get out of your current situation in the least harmful manner possible—whatever you perceive that to be. If it means leaving with a master's, great. If you have to walk away, then you need to do that instead. No outcome is worth risking your long-term mental health.

Moreover, the fact that your advisor aired the dirty laundry in public is a serious violation of trust, and a clear sign that you can't really repair this relationship. You may be able to make something happen with the help of the human resources department or university ombudsman (or similar resources).


Asking professor to provide feedback on academic articles?

Reviewing a scientific article for publication is time consuming. By asking a prospective supervisor to review your scientific article, you were asking him to take hours out of his or her busy day. The journal you are submitting to will have reviewers who are volunteers and will review your article.


How important is it to submit papers early to a conference?

With a typical peer-reviewed conference, submission number has absolutely no effect on the way a paper is treated.  Lots of excellent well-established folks submit at the last minute, and paper assignment is generally not done until the deadline is passed.  Furthermore, paper assignment is often done with the assistance of a paper-handling system like EasyChair, which includes randomization and non-order-based heuristics.


Is it unethical to enroll in a low-ranked institution with the intention of switching to a better one if possible?

This is far from immoral or unethical. Theres nothing wrong with attending a program and transferring to another one that might be a better fit.  Making the transfer to another program would really be up to you, your work and the networking contacts you make while in your masters program.


How to display your own name in publications list when you are a middle-author on a publication with a large number of authors?

The bolding trick suggested by others is fine up to a point, but eventually it will get to be silly.

I'm coming from a nuclear and particle physics background and have papers with hundreds of coauthors. So I didn't take care that my name showed up. I just built my publication list using bibtex in the standard format for my discipline and assumed that readers who wanted to check that I was on those papers know how to use InSpire (the go-to publication database for these disciplines).

That means that my name appears on my publication list only a few times, but it is also there in big letters at the top of the page.


Leaving undergraduate schools attended off grad applications

Do the application instructions say to list (and/or supply transcripts from) all of the institutions you have attended previously? If they ask for all of it, that's what you have to give them.


Applying for posdtoc positions: is it okay to send out many applications?

You should remember that universities are also looking at the resumes of many candidates for a given position. If it is not rude on their part to consider many applications and rejecting most of them, why will it be rude for a candidate to apply to many positions and reject some of them?

This is a many-to-many matching market between applicants and positions. You are trying to optimize your chances, they are trying to optimize their interest. If you look at it from this game theoretic perspective, you will not feel any qualm of conscience.


Would an international student A in the US helping another international student B in Europe cheating be punished by US university?

You seem to assume that the academic honesty rules at a university will always stipulate that dishonesty only counts as being against the rules if it occurs at that university.  That is a dangerous supposition to make.  Many universities have academic misconduct policies that refer broadly to collusion, cheating, and other forms of misconduct, without stipulation that the misconduct must occur in relation to an assessment at that university.  In such cases, there would be a genuine argument over the proper scope of the policy, and whether it may apply to instances of misconduct in relation to assessments at another university.
Just to give you an example of this, here is the present Academic Misconduct Rule at my University.  Section 6 of the policy provides that "It is academic misconduct if a student: (a) in relation to an assessment: (i) cheats; ... (iii) improperly colludes with another person; or (iv) acts, or assists another person to act, dishonestly or unfairly in or in connection with an examination...".  While the policy certainly only applies to students enrolled at my University, you can see that it does not specify that the assessment in question must be an assessment at the University.  Likewise, Section 2 of the policy, which sets its scope, provides that "This instrument applies to all students of the University."  Again, observe that it does not specify that the instrument applies only with respect to acts undertaking in relation to assessments and other matters at the University.
If student A were a student at my University (subject to the linked rules), I think there is a reasonable chance that his actions here would be considered to be a breach of this policy.  The student would of course have an opportunity to argue over whether the policy applies to an assessment at another university, and they would probably argue that this should be implied, irrespective of the specified scope.  Perhaps they would convince the academic misconduct committee of this (such that their conduct is considered out-of-scope) or perhaps they would not.  I would think that most academic staff would be concerned about this behaviour, and would be reluctant to consider it out-of-scope.


How do I refer to my own work in an anonymous abstract?

Don't lose track of the purpose of an anonymous abstract. It is there to provide double blind reviewing so that reviewers aren't influenced by the reputation of the author. They aren't intended for final publication and an edited version is what will appear if anything does.
You could cite your own work as by "this author" listing it as unpublished or to appear or thesis, etc. That is sufficient for review. If the abstract is eventually published, it will be in a form in which you correct those references.


Elaboration on Above Comment

In economics and certain business school fields, a major part of junior academic hiring is the job market paper (JMP). The JMP is an original piece of research by the applicant that constitutes their best research to date. It is meant to serve as a signal of the candidate's potential for becoming a good researcher.

Bob Hall makes a number of nice points here, which I will condense and expand upon. Answers to the two questions posed by @Aleksandr Blekh after my comment are in bold below.

It should highlight the original contributions of the research.
Write "for a wide audience of highly trained economists" (replace "economists" with the appropriate noun).

Don't take this the wrong way, JMPs are a great place to showcase one's technical skills.
However, think very carefully about who might be on your committee.
Hall says to write for JPE or AER. More generally, think of the journal in your field that everybody at least skims through. Write as if you're submitting to them.

The JMP need not be published. (See also discussion in penultimate paragraph below.)

If you get a flyout you will probably be asked to present the paper at what is essentially a working paper seminar. Participants will not expect that it is complete. You can always substitute out a work in progress but it is far better to have one close-to-publishable paper than one publication and a half-baked paper (this is when all of the faculty who aren't on the committee will see you).
People are looking for good ideas, all of the finicky stuff that goes into a publication can be ironed out later (assuming your idea is sound!).

Hiring committees will probably only look at your JMP so that is what you should focus your efforts on.
Yes, do post your work to repositories where others in the profession will see it. This is probably a good way to gauge whether your paper is ready - are you willing to post it in a semi-official place like arXiv where you can't just take it down and post it back up willy-nilly?
For most people the JMP is their first publication. So, yes, do expect to publish the JMP in a traditional journal.

Some concluding notes about why economists bother with this JMP business in the first place (and a method to gauge how much this applies to your situation). Very few economists are coming out of grad school with publications. Ergo, hiring committees can't do the thing where they just scan down the list of previous publications and sum up the prestige (economists - of all people - would if they could). So instead candidates get one shot at wowing committees with their JMPs.

Therefore, if you can already signal to hiring committees that you're awesome (or not) in some other way (i.e. past publications), then the JMP may be something of a formality. This also motivates another reason for not using published work as a JMP: If you already published something in a good journal, the committee can easily incorporate that information into their deliberations. Using another paper gives them a second piece of information to go off of. I would also speculate that using a prior publication might be a negative signal in the sense that it suggests that the candidate is a one-hit wonder (of which there are many).

Best of luck! Let me know if anything needs to be clarified or amended.


Bad relationship with PhD supervisors, should I have them as my recommenders in job applications?

Not having the recommendation of the PhD supervisor is going to raise some flags, especially in academia. However, you can get recommendations from other senior people you collaborated with on research papers if you published any. Those people should be able to write decent recommendation letters for you. If you apply for non-academic jobs, you could also ask for a recommendation letter your boss from a previous job if you had one, or your diploma/masters thesis advisers.

Also, if you only have your supervisers to write you recommendation letters, you could still ask one of them who seems nicer. Even if they don't like you and think you're incapable, they would like it even less to have an alumnus flipping burgers. So, they might write you a reasonable recommendation for a non-academic job even though they might not be willing to give you a good letter for an academic one.


How to come to know that you have done some thing non-trivial in the research?

In a recent project I felt that I had somewhat trivial results, and that I needed to add more to it before writing the paper. The new steps turned out to be so non-trivial, and take so long time, that I decided to write up what I had in the meantime. By putting the work so far in the form of a proper paper - you know, with an introduction that attempts to convince others that the work is interesting and worthwhile - I ended up convincing myself that the results were non-trivial and made for a good paper already.

In hindsight I had worked on related stuff long enough that my results seemed less novel to me than they would to another person. So, my advice is to write it up, and trust your supervisor.


Is it common for a university to remain unresponsive to queries?

They complained that you've emailed multiple people; maybe that breaks some organisational hierarchy and given they are British, they might be too serious about the hierarchy thing.
You should probably send one more short email to exactly one specific, most relevant recipient, apologize for any mistake in correspondence on your part and politely share your query again while mentioning the urgency.


If I develop a product as part of a project at university, does the university have any ownership over it?

Usually, if you use the university's resources then the university has some claim to what is produced. If you produce it on your own time using your own resources, then it should belong to you. Some companies have rules in their contracts stating that anything you produce while you're employed by the company belongs to the company. Some universities lay claim to a percentage of your profits if you apply for a patent through the university's patenting office; you give up the headache of patenting, they take 30 or 50% of the profit.

In all cases, it depends on the country and your university's policies (hence the generic answer above). I would suggest you look for the IP/patenting office in your university and talk to them. You could also ask your professor. If you're really serious, then talk to a lawyer.


Someone reported cheating during a quiz, but I didn't catch it myself

You're the teaching assistant.  Inform the professor and let them handle the matter or offer you guidance.  That's their job.  In this case the evidence for cheating is tenuous at best, so I suspect nothing will be done against any of the students.  I've known more compelling cases of cheating to go reasonably unpunished, and one case of very blatant (and easily proved) cheating that was handled with just a stern admonishment and warning from the professor.  But you (and the professor) would rather the professor hear of the matter through you, than the possibly salacious gossip of the students.

So what what really needs to be addressed is:

Always keep your eye on the students during exams/quizzes.

As much as you want to believe that they're all perfectly moral and self-policing people (and quite probably most of them are), or that they can't possibly fit in cheating during "brief" windows, there will always be exceptions, and you owe it to the students who are such from giving such a clear opening to those who aren't (for whatever reasons).  You can't prevent all cheating all the time—it comes in a lot of forms, and some people are really good at it—, but this was easily preventable.

You may find yourself needing to apologize to the professor for this lapse, though I wouldn't get too worked up over that.  Most of us have made such a mistake at some point (although not all of us may be aware of it), and the minor value of the quiz helps take the edge off, such that a simple apology and recognition of the error is sufficient to make things right.


Conference Title - shall abbreviation and year be listed uniformly?

There is an important and unfortunate caveat for managing citations that I bring up because this refers to IEEE.  In IEEE, ACM, and many other computer science and electrical engineering venues, it is often the case that there are strict page limits and the citations are counted toward that limit.  This happens mostly with conferences, but sometimes even with journals.

Because of this, I often find it necessary to maintain both a "master" reference database and an ad hoc "abbreviated" copy of the database used for a particular paper.  In the master database, I keep the full everything in all its bibliographic detail to the best of my ability.  In the abbreviated copy, conference and journal names get shortened as necessary to purge the bibliography of widow and orphans
and extract those last few lines necessary to get the text to fit.  It's a nasty, undignified practice, and I consider it the lesser of two evils if it can preserve technical content without decreasing the ability of a reader to locate citations.

The ability to find the citation, though, is sacrosanct.  Authors, title, year (and volume and issue if available), must never be trifled with.  As such, the shortening targets that tend I use, in order, are:

"Proceedings of the..." can always go, as can the location of a conference.
"International Conference on" goes to "Int'l Conf. on" and then vanishes
Most EE/CS conference have acronyms: an exceedingly well-known conference can be entirely replaced by its acronym.

Thus, for example, "Proceedings of the 23rd International Joint Conference on Artificial Intelligence, Beijing, China" can ablate all the way down to "IJCAI", saving 1-2 lines in typical IEEE format bibliography.  It's an ugly business, and maybe I shouldn't admit to it out loud on the internet, but it's a useful practice that I still find ethical as long as the spirit of readily locatable citation is preserved.


Can someone who works in tech industry still publish research unrelated to their main job function?

The path to publication at a company strongly depends on whether the employment contract includes a "we own your dreams and family photographs" clause.  Some technology companies insert such a clause, essentially claiming rights over anything that their employees do that could possibly create intellectual property.

If you are faced with an employment contract of this sort, there is generally a possibility of specifically exempting certain activities as a sort of "pre-existing condition."  If you exempt your research area or if you have a more liberal employment contract, then you can generally do whatever scientific research and publication you like outside of work, as long as you do not claim endorsement of the company in any way (e.g., you may not be able to list them as your official affiliation in the publications: check with your supervisor or company legal).

Alternatively, tech companies with broader interests may be entirely fine with you working on projects unrelated to your responsibilities while acting as a company employee, as long as it does not interfere with your ordinary job duties.  This is often particularly true for companies that have a consulting or contracting business model, since for such companies "unrelated research" can often turn into "new line of business."  Likewise for companies whose product line serves the R&D community.  Companies that have a tight focus on a non-R&D-related product line, however, are less likely to be receptive to such "side-project" work.


How can I get recommendation letters for PhD application, while just starting a PhD program?

Seems to me that your best course of action would be to send short emails to your current letter writers. You can thank them again for their letters, but state that, unfortunately, for [personal/medical/visa/whatever] reasons, you'll likely have to leave. (Note that there is no need for all the details! If they're curious they can ask you to elaborate, but the first message from you can indeed be short.) Then ask if you can re-use the letters from the dossier service for the positions that allow for that, or if they'd be willing to send letters directly. If they wrote their letters hoping you'd do well they'd likely agree to both, or, ideally, even to update and adapt the letters for the new positions.

I think that tactic has a better chance of working than convincing new professors to use a dossier service they're not familiar with, and it avoids your letter writers from feeling you went behind their back. Indeed, things could go sour if one of the advisors you apply with were to contact your letter writers to check if everything's above board and cleared with them.


For interview questions about innovative or engaging teaching, is it OK to say I give lectures in the standard way?

When someone asks in an interview, no-matter what the topic, which cutting edge approaches interest you, they are subtly asking three entirely different questions (in order of severity):

Are you even exposed to any of them (which shows an interest in your subject in general)
If yes, do you have an opinion on any of them (which shows leadership, independent thinking)
Can you justify it with evidence (which shows critical thinking, experience etc)

Saying "no" is like answering "no" to all of the above.

Your answer is effectively saying "no I know nothing about that, nor do I care to know or have to justify myself".

Even if the end-message of your answer is that at the end of the day you prefer traditional teaching, your answer will be much better received if it first shows knowledge of all the cutting edge techniques in the field or even some experience in trying to adapt them to your own teaching, which show promise in general and which do not, your personal opinion on what works and what doesn't, why, how it fits your particular style or not and why, how you think students benefit or not, or tend to respond in each, and why you feel that traditional teaching trumps all of the above based on your experience, and critical judgement of the competitor methods.

Contrast that with "no I just teach". Doesn't sound so professional does it?


What is the difference between a Bachelor of Arts Honours and a regular Bachelor of Arts?

Speaking from my experience in Australia -- but I think it holds for most Commonwealth countries.

A Bachelor of Arts (or Science) is 3 year degree, purely by coursework.
Though potentially some coursework units may have large research components.
You can get into it based on results from high school or some other tertiary entrance exam.

The adding of Honour means the the addition of an extra year, after completion, where you do some coursework, but the focus is on research, you produce somehting which might be called a Honours thesis or similar. Depending on the university, students doing honours may count as post-graduate students, or not (or somewhere between).
It may make sense to think of the Honour year as being a separate qualification -- it is often possible (if unusual) to get into Honours at a different university to where you completed your bachelors.
To get into this Honours pseduo-course, you need to have done well on your units in your bachelors. At the completion your honours results are graded and you get back a result like "1st Class", "2nd Class Division A", "Second Class Division B"; There are more classes, but I've not heard anyone say they have them (presumably because it doesn't sound good to say I have 3rd Class Honours, and/or they don't stick around in academia.).

Honours 1st class is considered roughly equivalent to having done a Masters, as far as getting in to a PhD goes. Thus the Honours pseudocourse can be used as a "shortcut" by high achieving students to get into a PhD a year earlier than they would if they did a Masters -- at the cost of a fair bit of stress usually, because a lot of Honours projects are as hard as Masters projects, and they tend to have a lot of coursework at the same time.

Away from BA and BS, other undergrad degrees may have "built-in" honours.
Bachelors of Engineering tend to have them (Particularly if the B.E. would make you a accredited engineer, without having to go on and do Masters). In these cases Everyone does a research based Bachelors Thesis, but only those who have it graded above a certain cut off, and who meet overall coursework grade cutoffs get awarded a Honours classification, and get Honours on their certificate.


Can you give an example in a formal definition?

In the definition itself, no. It just should be that: A definition. You should add examples and/or motivations in the surrounding text, so your reader (a befuddled human being, not an automaton!) sees what is going on, and where you want to go.


Exploring something completely new, even silly.

What you are writing is pretty much exactly the reason why non-senior researchers in academia have advisors:

It is very hard to have a complete overview over a field, including which lines of thought have been explored, and where the open problems are. Many open problems are known to researchers in the field without this being obvious from the papers.
In order to perform meaningful research in a field that is not brand-new, the best way to get started is to focus on something small but interesting. Developing a completely new theory in Physics is, for example, probably not the right way to start. Coming up with research questions that are small enough so that they are unexplored yet interesting enough for meaningful research is not trivial and requires substantial experience.
To some extent, starting with research also means to refrain from too high expectations of what can be achieved. For example, as a computer scientist, you could reduce an aim to "build a 100% safe self-driving car" to "detecting a dog on a leash next to pedestrians that may jump onto the street from image data only". The latter is more achievable, yet fits into the big picture of building a self-driving car.

So my advise would be to get someone who is at the frontier of the field that you are interested in and who can give you guidance.


My revised paper was accepted surprisingly quickly; should I worry?

Unless you have some reason to believe your revised paper has some serious additional problems, I don't think you should worry.  It may not be best practices for referees and editors to operate this way (just looking to see whether the changes requested in the first report have been adequately completed).  Ideally, the referee should check over carefully that none of the changes have introduced new problems, but that isn't always done.

The referee and editor may have felt that the revisions were not really that big a deal.  You may have been overthinking things when you made the changes; they might have intended some considerably less sweeping editing.  Or the referee may have seriously underestimated how much additional work and explication would be required to fix the problems the referee pointed out.  The referee might even have told the editors that another round of refereeing would not actually be necessary; if you made the changes, then the paper would be ready for publication.  (For several of the journals I have refereed for, this is one of the options in the recommendation menu of the reviewing software; however, I also know, as an author, that this part of the review is not shared with the authors.)


Is this a realistic salary for China postdocs/ assistant professor?

Please take my answer considering my declared conflict of interests:
I am the author of the linked question "Persistent issues with salary pay as a postdoc in China: What can I do?". Here we are within just 5 days from departure and still the payment issue is a monumental struggle.
I shall update my situation in that question soon after I am gone.

Now, directly answering your question. I have been offered another postdoctoral fellowship at CAS/Beijing for (theoretical) 250k/year. My friends in that same lab (lower salary, Chinese PhDs) claim they never had issues with being paid, stating they get 9k every month sharp.
I have done some research around and in fact standard salary is within 120-180K per year, with the problem that typically some 35k off the total are withheld until the very end. They claim this is to ensure you'll complete your "duties".
However postdoctoral salary offers are on stead increase, and now there are several places offering >200k per year, up to 280k per year as the highest I've heard.
Mind you that the Chinese system works on a local logic of "meritocracy" which is solidly based on rankings. This means that highest salaries are offered to the youngest PhDs coming from top-rank universities from 1st world countries who published in top IF journals. These individuals will get offered >250k per year as postdocs with a wide margin for negotiating extra benefits.
This brings me to another point: in Chinese culture negotiation is never-ending. This means a signed contract is just a formality symbolising your engagement, and from that moment on rules and terms can and will be moved around depending on a complex game of mutual understanding. This is called "guanxi" in business in China and can be very hard for foreigners to understand & digest.
Finally, this brings up again the issue I face while here. What was written in the original offer and even on contract may be quite different from reality. Carefully read the discussion at zhihu.com/question/52131526/answer/232792998. This is a top university in China offering attractive contracts for postdocs and locals are complaining they finally get a fraction of the promised figure. I know how it feels.

Realistically, expect earning anywhere between 8-12k a month depending on your "qualifications" for local standards, while working 10h per day 6x a week and being asked for more. Expect some dirty game around your payment, possibly involving potentially illegal activity (e.g. being asked to generate fake invoices).

All points taken, it boils down to your personal reasons for taking a postdoc, and why are you considering this and that lab, and why in China. If you're the kind of righteous law-abiding animal-loving individual who enjoys straightforwardness and openness, a healthy work-life balance, and drinking some wine with a good cheese on occasion... probably coming to China might not be a good idea. If you're seeking a stable salary pay and a professional work environment towards erecting as a established professional, probably taking a postdoc may not be the shortest nor surest path.
I don't think you should focus your worries on salary, all the more in China where it may vary without warning.


How can a present software-engineer (with experience of 5 years at least) turn into a physics professor?

Your situation does not sound fundamentally different from any other university graduate.
Your work experience will possibly give you some technical and time management skills that others don't have, but you'll just have to put your skillset to good use like every other graduated student.
Note, that going to graduate school for the sole reason to become a professor is a bad idea. The odds are extremely slim. So if you're not enjoying the process/path you'll likely be disappointed. If you're loving doing research with very little income go for it!


Acknowledge the proofreader of the thesis

I acknowledged my two volunteer proofreaders, but probably would not acknowledge a paid lector unless he went above and beyond what the fee covered.

In the case of acknowledgments, I think a safe rule is if you're not sure, put it in.  After all, you could type, "Thanks to Jane Doe for proofreading," faster than asking this question.


Yes, get the letter from your employer. In general, people reading letters want to see assessments of your skills, work ethic, etc., and these can certainly be provided by someone not in academia. Certainly if all aspects of content were equal, it would probably be more useful to get a letter from an academic, since it would likely map more directly onto likely success in Ph.D. research, but a strong and meaningful letter from your employer beats a weak and generic letter from a professor.


In some countries (e.g. The Netherlands where I obtained my PhD degree) you are not considered a student but a paid employee (staff) with the university. To discern between these, people sometimes translate their status to English using term "PhD candidate". Btw, this has nothing to do with the length of the program or your progress.


Where would I report missing metadata in Crossref / Science?

From Crossref's FAQ:

  I’ve found a problem within your metadata - how do I get you to fix it?

  While we aren’t able to correct the metadata provided by our members, report any metadata issues to our support staff and we’ll contact the responsible member and ask them to make corrections.


Lack of mathematical training for a CS Ph.D

Lack of mathematical training is a gap, but not what I would consider a red flag, if you have strength enough in other areas.  The key is whether I, evaluating your application, would think: "This person can't handle math" vs. "This person did other things besides math."

It is definitely a good thing that you are increasing your training: a MOOC will likely not make a big difference on paper, but if it's making a real difference for you intellectually, that matters too. Furthermore, a good mental mathematical tool-kit will make your life easier in many ways (including detecting when you shouldn't believe something just because it has math).

As for the question of whether to start with a Masters: that really depends on where you are and where you are trying to go.  For example, in the US, many Ph.D. programs literally or effectively start with a Masters, so it might be redundant (though the MOOCs or any other prep work will allow you to do less remedial work as part of it).  In Europe, on the other hand, most Ph.D. programs assume you already have a Masters, so it's pretty mandatory to start there.  Another thing that you might consider is to apply to both, starting with the Ph.D. if you get in, and burnishing your credentials in a Masters first if you don't.


What happens if no one wants to advise me?

You have to have an advisor to continue in the program, and advising needs to be a mutually consensual relationship.  So if it really happens that absolutely nobody will advise you, then you'll need to leave the program (but you could probably transfer to another one).

But in practice, it should very rarely get to that point.  Your program should have a graduate chair or some similarly-titled faculty member who is in charge of the PhD program.  Talk to this person.  There are a couple of possibilities:

There are faculty who would be interested in working with you in principle, but they feel too busy.  The graduate chair can try to convince them, and exert pressure.  If the department is interested in having a good PhD program at all, they won't want to lose good students for no good reason; so eventually someone should be willing to take you on.  Maybe other workload bargaining will happen behind the scenes (e.g. Professor Smith says "I'll advise the student, but I want to be excused from serving on Committee A.")
There is something about your academic background or personal style that makes faculty reluctant to work with you.  This is less likely; if there were serious issues you probably wouldn't have made it this far in the program.  (In particular, you've passed quals, which is a very good sign.)  But if there is some issue like that, the graduate chair should be able to talk to you about it honestly; and then you can work on addressing it.
Least likely possibility: the program is totally dysfunctional, and faculty members don't really want to invest any effort in working with grad students, or are so completely overwhelmed with other duties that they cannot.  Hopefully this is not the case, but if after talking with enough people (including those at other institutions) you become sure that this is what is going on, then you should transfer to another program as soon as you can.


Where do other countries fall on the US-Europe continuum for PhDs?

In Canada it is standard to have a Master's before beginning a PhD. There are a small number of direct BSc/BA to PhD programmes but they remain the exception. Most universities will admit PhD students who do not have an advisor already lined up, but if you already have an advisor lined up you're more likely to get in.


I would suggest the following for an early-career scholar:

1) Figure out who from your current university is going to be there and identify any other attendees you already know. Let them know you will be attending and hope you run into them.

2) Make sure you go make yourself available right from the beginning. Spend very little time in your room. Arrive early, hang out in the lobby near the conference registration area or wherever the coffee is. Go to all the breakfasts, lunches, etc.

3) When you see someone you know, go up to them, say hi. Mention that this is one of your first conferences and you are really interested in meeting people. Ask if there is anyone that they would recommend you meet. Then ask them to introduce you. This especially works if you are at the opening reception or something like that.

4) Repeat! If a chat is going well, eventually ask the new contact if there are others at the conference who are interested in your topics that they think you should meet.

5) Also, of course, go to talks. After the talk, make an effort to talk to the speakers with follow-up questions, etc. You can also follow-up with speakers if you see them in the hall later, etc. If these chats go well, you can even ask those people to introduce you to others they think you should meet.

6) After the conference, follow up by email.

The result of this strategy should be that most of your introductions will be peer-to-peer "warm" introductions, not out-of-the-blue "cold" introductions. This should make people a bit more willing to chat with you and make you appear to be more of a junior colleague and less of a grad student.


Should citations on PowerPoint slides be shortened?

I would strongly recommend against putting the full citation at the bottom of the slide.  The problem is, when you are actually presenting, it will both a) make the slide look very busy as you note, and b) distract people away from the rest of the slide.  Another problem is that few people will actually be able to copy down the citation (unless you linger on the slide for a very long time).

Truncated references deal with all of these problems, generally giving just enough information for a quickly scribbled note that will give the reader the ability to track down the cited paper with a little bit of work.

In addition, however, if you will be making the slides available for others to read at their leisure, there are two other good places to put references:

A "bibliography" slide at the end, before or after where many put the funding/acknowledgements slide.
In the "notes" field associated with the slide on which the truncated reference appears.

This is especially good when dealing with funding agencies, who like to pull slides out of your deck for presentation to their own higher-ups.


Marie Curie fellowship - family allowance

Yes you are. Source: Been in the same situation.


Can my doctoral adviser take my dissertation and publish it without me?

I think there's a disconnect between what the assistant chair means when they say "take responsibility for finishing and publishing the papers" and what you're interpreting it to mean.

What I imagine they mean is that your advisor would have to do all the editing to get the results into a publishable format, tying up loose ends of experiments, submitting the paper to the journal, etc. -- coordinating the myriad things needed to get a body of work into a publishable form. I don't think she's talking about taking the paper, removing your name from the author list and submitting it behind your back. -- You'd likely be informed about the submission, even if it's merely at the level of your advisor emailing "here's the finished manuscript, any comments before we submit?".

You're absolutely correct that you, as author and a person who did the work, have a say in whether something gets published. And you're also correct in saying that it's unethical for your advisor to ignore you and publish without your consent (either with or without your name on the author list). However, it'd also be unethical for you to hold up publication of an article for non-scientific reasons [1]. As such, it's normally expected that any research work you do is probably going to get published, and if you don't do it yourself someone else is going to do the legwork to make it happen. (Giving you the appropriate credit [2].)

So it's all about how much "with[out] me" you're thinking about. Once the results are done, coauthors can have very, very little to do with the actual publishing of the paper. Other authors can do all the work of collating the results, analyzing them, writing, formatting, etc., and the coauthor can just look at the manuscript and say "Yup, looks okay to me!" and that counts as permission to publish.

[1] If you have scientific objections to the article as written, that's one thing - work with your advisor to address them. But if you think the article is scientifically sound but disagree with publication because you no longer care about it, or you want to hurt your advisor, etc., that's another.

[2] "Appropriate credit" drops off the less involvement you have in writing the paper. In certain circumstances, not actually writing the paper could knock you off of "first author" status. (For those fields which order authors by contribution amounts.)


Will flat earth society membership affect my graduate school application?

No, I do not think an admissions committee would check for this type of information.  Nor would they assume the poster with the same name is the applicant.


Starting an REU late because of quarter system?

I was an undergraduate at an institution on the quarter system and the three math REUs that I attended allowed me and others in the same position to start late. In my experience, math REUs are very accomodating with these sorts of things. I also saw other students leave slightly early or travel somewhere in the middle of the program for a week for various reasons. You should inform whoever is running the REU about your situation once you are accepted to check if starting late will be OK, however. There are also several REUs that start reasonably late, maybe the first or second week of June, so that a student on the quarter system should not have to miss more than a week.


How to cite a specific living document in a GitHub repository?

Please go ahead a create a DOI for the specific release yourself and use it to cite the work.

Also, you could fork your own copy of the wiki and keep it updated from time to time from the main branch.

Versioning DOI: You can also get a DOI automatically issued for every release of the 'Living Document' by Zenoda. Details are here.

Here is a guide: https://help.github.com/articles/referencing-and-citing-content/


Is it a good idea to write an inquiry email to professors when applying for a Masters program in Europe and Asia?

In Germany individual professors are not involved in the admission of Master students. So if you're hoping that it will positively influence your chances, there's no point.


Can I add an inscription on a bachelor thesis that I have been working on for almost a year?

If you want to dedicate your bachelor thesis to somebody, or acknowledge people: by all means, just do it!

It is your thesis, after all.


Prospective supervisor wants me to do irrelevant videos as a condition for supervision. Can I say yes when I mean no?

No, this is not okay.
If you lie your way into a position you are not suited for, you will almost certainly pay for it down the line.
That's a very general rule, and I think it applies here. If you say you are willing to do X while interviewing for a PhD position and, after getting the position, you refuse to do X, then you are going to have soured the relationship with your advisor. That is a very important relationship. If you say no in the interview and you don't get the position because of it, then it's probably for the best.


Can international students study via distance without applying for a visa?

Distance learning students who will not enter the United States are not required to get a U.S. visa. In fact, by federal law, online-only students are not eligible for a student visa.