How to approach a professor for research?

How should I contact a professor about joining his/her lab?

Email now. Express interest and see if they're willing to talk via Skype or would be willing to meet in person when you're both in the same city. You want to talk face to face. This is also a good spot to ask if they have any advice on what to read to get up to speed on their work if it's going to be a while until you can meet them.

  Do professors generally just look at resumes, or do they expect prior research experience?

No to both. Research experience is a plus, but you have to start somewhere.

  Should I indicate the topics I'm interested in?

You should be interested in the topics that the professor works on and should identify what those are in your initial email.

  I haven't decided about whether I'd like to do a PhD, so does my
  indecision make it harder for me to get a position at a lab for the
  1-2 years it'll take for my Masters program?

If you end up wanting to do a PhD you should go somewhere other that where you did your Masters and undergrad work. Any decent professor shouldn't expect you to stick around.

There are some professors who won't work with Masters students. There's nothing you can do about that. Others will want you to take their class first. Take it, ace it, and then remind them that you're still interested and now have other ideas from their interesting and wonderfully taught class.

Now for Ric's guide for getting into research

Go to your department's website and find the page listing all professors (hopefully with links to their websites).
Skim each professor's bio and see if their research areas interest you.
For every professor that sounds interesting, read through some of their current papers. Focus on more recent works. Read abstracts and intros. Use this to get a better idea of what they're working on.
For every professor you're still interested in, find a recent paper or two that you like and read it fully. In this step you want to try and figure out what they did, why they did it, and how their work fits into the current work in the field. This is the hard part, but the more effort you put in here, the better. Besides, you want to get into research, right? You need to learn to read papers =)
Send a short email to each professor. Something like:

  Professor Webb,

  My name is Francis Thurston and I am a first year Masters student interested in meta-physical topology. I was reading through your recent paper on non-Euclidean architecture ("His House at R'lyeh: Modern architecture of Greenland cults") and was wondering if you had considered Professor Atwood's claims on the subject ("Mountains of Madness: The innate wrongness of the city") in light of your recent work. I think that combining his claims with some of the results of your recent experiments would be interesting. Would it be possible for me to come by your office next week to discuss your work and any possible research opportunities?

  Thank you,

  Francis Thurston

When you meet with a professor. Ask questions that show you're interested in the subject and have put in some work. Extra points if you have ideas about directions their work might go in (e.g. areas to explore, experiments to run, &c.). Ask if they're taking students, if they would consider you, and what the workload would be like.


In a revision, is it essential to address editor comments, even if they misrepresent a reviewer comment?

Your best bet here is probably to contact the editor requesting clarification on what’s being requested before you put in a lot of work. Perhaps something along these lines:

  Dear $EDITOR, we welcome the reviewers’ feedback and would like to obtain clarification on the recommended changes. Reviewer 1 has suggested $THING1 but the summary proposes $THING2, which is different because of $REASONS and would be a broader change. Could you please clarify whether these broader changes are required, or if it will be sufficient for us to address $THING1?

Or, if you really don't want to do $THING2:

  Dear $EDITOR, we welcome the reviewers’ feedback and would like to obtain clarification on the recommended changes. Reviewer 1 has suggested $THING1 but the summary proposes $THING2, which is different because of $REASONS. It is not feasible for us to do $THING2 because of the amount of extra time this would involve. Would it be acceptable for us to submit a revision that addresses $THING1 without the broader changes implied by $THING2?


How to deal with overly helpful co-advisor?

Set a meeting with all three advisors, explain you'd like to focus entirely on the writing, and ask whether regular meetings can be replaced with less-regular meetings when you need support.


"Web of science" as search provider in chrome?

Could this Chrome extension be of use to you:

https://chrome.google.com/webstore/detail/web-of-science-quick-sear/nemobobcigeaigadamdpegpjkklkoeae?hl=en

Just click Add to Chrome and you should be jamming.


I am curious about applying my coursework from Masters program towards Doctoral in Economics in the US

There is no uniform policy in the US. You must check with each program you are interested in.

Graduate departments are generally give broad latitude in accepting coursework from other schools. Some may choose to give either credit or merely placement; some may offer both or neither. Some may require what they consider “core” courses to be retaken but allow electives to count. Other schools may have a limit on the number of transfer credits they will accept. There are simply too many variations, so direct questions to the graduate admissions officer or director of graduate studies (or the equivalent( is your best option.

As @Dawn has suggested in the comments below, it is indeed worth noting that one should likely not ignore the possibility of taking the core classes required to pass the department's qualification examinations, and most advisors will encourage you to do exactly that.


communication after job offer and acceptance

It's time to get the phone!

If you know some people working in your future institute, try to catch them by Skype. You can also look for some assistant or secretary telephone number in the institute. As long as you don't call by midnight, nobody will be annoyed by your call.

Yes, in Europe, things usually slow down in December / January, and mails accumulate or get trapped in spam filters. So, when in doubt, try and make a phone call.


Will one flawed grade outside of my major from my freshman year affect graduate school?

It is extremely unlikely that a graduate admissions committee/potential supervisor would look at your first year courses in any amount of detail. They are going to focus on the higher-level courses you take in later years, whether or not you do an honours degree/undergrad thesis, etc.

The only way I can see this affecting you is by lowering the overall average grade for your degree (measured in many places as a GPA). Many departments have a minimum GPA/grade requirement to be considered for admission to grad school. However, as long as you get consistently good grades for the rest of your degree, this little slip-up isn't going to matter much.


How to respond/reply to a reviewer who doesn't seem to "get" the paper

If the referees -- especially more than one -- are not "getting" the paper, then there are just a few possible reasons why this can happen.  In order of least like to most likely:

The reviewers are not expert enough
The author is submitting to the wrong journal
The author is not telling the story well enough

The first is rare, but not rare enough.  The third is very common.

The proper response to the first two, but for different reasons, is to resubmit elsewhere.  For the first, you'd be looking for a journal with a better referee pool.  For the second, you're looking for a more appropriate audience.

The proper response to the the third, bluntly, is for the author to write better.


Bombed an academic interview, should I do anything about it?

First of all, you should cool down before you take any action. Clearly, the interview was an emotionally intense event for you, so don't do anything in the spur of the moment (and "a few days later" may still qualify as "in the spur of the moment" in this context). Let a few more days pass, and see how you feel later.

Second, seek the guidance of a trusted person or mentor who is aware of the details. Maybe your advisor can feel out to what extent you have really bombed the interview quite as badly as you perceive it? Note that especially for interviews on grad student level, the committee will be positively used to people giving bad presentations and not being quite able to argue their case. Unless you have made a really monumental blunder, the committee has probably already forgotten about the details of your interview by the time the next coffee break rolled around.

Which brings me to the third point: no matter what you do, don't write an email reminding people that you did poorly or excusing yourself for not doing better. Don't try to argue your points, either. This won't make your interview better, but now people may also think of you as somewhat unprofessional. If you feel you need to write an email, keep it professional, thank them for the opportunity, and ask for feedback.

  Any alternative action that you would recommend? Or should I just let it go?

Letting it go is generally the right course of action in these situations. I have personally done my fair share of bad presentations, bad interviews, and (in retrospect) crappy paper submissions. Learn from them and improve for the future. You are a student. Mistakes are to be expected. Life will go on.


Found a mistake in my paper after submitting the final version. What should I do?

The first thing to do is to contact the editor and ask for advice. Follow it. The second thing to do is to check the conclusions of the paper to assure yourself they they are still ok. The third thing to do is to prepare an erratum note in case it needs to be sent.

But the editor may have a solution if you are fast enough.

But if the conclusions are compromised you may need to ask if the editor can pull the paper while you go back and rethink everything.


Any tips for preventing perfectionism when it comes to notetaking?

This question, combined with your previous one, makes me think that you are confusing two issues: transcribing information and understanding information. These are not the same thing.  In fact, if you focus more on transcribing information in detail, but you might actually learn less than if you had taken no notes at all.  See for example this article: https://www.scientificamerican.com/article/a-learning-secret-don-t-take-notes-with-a-laptop/
I think you need to break yourself of the habit of taking too many notes.  Here's what I suggest: read an entire chapter or lesson without taking a single note.  Don't write anything down at all, just focus on understanding the material.  Sit on your hands if you have to to prevent yourself from writing.  If you don't understand the material, read it again (or maybe look in a different book, find a relevant website etc,).  Once you think you have an understanding, try to summarize the entire chapter very concisely, for example just 10 bullet points.  if you can't do it that concisely, you probably didn't understand it.  Go back and read again.
After while, once you've broken yourself of the habit of taking too many notes, you can go back to taking a few short notes as you read.
Edit: To clarify based on Buffy's comment: I'm not suggesting this as a long term strategy.  Long term you need to find a balance with the right level of note taking.  I'm suggesting this as a short term (say a week or two) approach to get you out of the habit of excess note taking.


What is the importance of a very tangentially related minor in grad school applications?

Except in unusual circumstances, a minor per se will matter for very little indeed in applying to graduate school.  There may be value in the particular things that you have done related to this minor (e.g., the field project) or reference letters you might be able to get due to your work towards it, irrespective of whether you actually complete the minor or not.

I would not however recommend delaying your graduation and grad school applications just to be able to formally complete your minor.


Current adviser trying to switch me to a different adviser

Have a frank discussion with your advisor and stress that you really would prefer to stay with him/her.  Then, explore funding opportunities you can apply for together. Be proactive about the situation. The advisor will be excited about the potential for more external (or internal, if available) funding, and the process of writing the application may bring about new lines of research that you then share in common.  At the very least, this will buy you some time, since it sounds like the school will cover you anyway, at least for a while.  Even if the funding doesn't come through, your determination will be clear, and what you lay out in your application may be sufficient to convince your advisor to keep you on.  If he/she is ready to push you off to a different advisor, it may be that he/she does not have sufficient stake in your work.  If you can fix that, the rest may fall into line.


Applying to Ph.D, how to reach out to a professor with no exactly overlapping research topic with me?

My advice on making contact with rockstars is to have an intermediary introduce you to them. They are, by definition, very busy. (Concert dates, groupies, wild parties,...). It is natural for them to think of you as "a random student with a random research idea" if you contact them directly. They probably get a lot of messages, all of which turn out to be of little value.

If you can, find a professor in your field, such as your advisor, perhaps, and have them write on your behalf with just an introduction and a short recommendation that your research on "topic" is interesting. It is harder for even a rockstar to ignore a colleague than a "a random student with a random research idea".

And having a paper published gives the recommender a hook into explaining why the introduction is being made.

It is even better if your local professor/recommender is known to the rockstar. It is still better to tag along at a conference and get introduced in person (after the current pandemic dies down, of course).

But once you are introduced you have a chance to deepen the conversation over time.

But, in particular, don't flood the person with too much information initially. That makes it even easier to ignore you since it takes time and effort to evaluate what you send even to determine if there is anything of value in it. Many will be too busy to want to bother.

Personal note: It isn't exactly the same situation, but I was once able to get a good student accepted into the doctoral program at Georgia Tech by making a personal appeal to the dean, who was a friend of mine. The student wasn't a very good standard-test taker, so is GRE was a bit mediocre, but I saw his potential and expressed it to the dean. I was later told that my not-at-all-inflated recommendation was important in getting him accepted and he went on to finish and to get hired at a similarly prestigious place.


Unable to decide whether to submit the work to conference or journal. Possible mood switches before deadline and how to deal with it?

If your paper is ready to go and in good shape for a high-impact conference, I would recommend sticking with the conference.

The reasons that I would suggest doing so are:

In many subfields of Computer Science, a highly competitive conference publication is often effectively worth more than a journal publication.
The conference deadline is now. If it doesn't get into the conference, you can always choose to send it to a journal later.
If it's well received and/or you get interesting feedback from the reviewers or audience, you might end up changing your mind about whether to submit an extended version to a journal. You can't change your mind in the other direction.


Writing matters a lot, and a lot of the time probably most PhDs (and even postdocs) face a steep learning curve. This curve is particularly bad in a field where writing is your tool, such as Philosophy. Even when analysis takes the form of symbols, in mathematics and logic, it is essential to convey your ideas clearly. Clarity is particularly problematic for young researchers, because of our tendency to hide behind pretension. Pretension, confusion, clunkiness must be removed for your ideas to come through.

Overcoming these issues is not essential to get an inexperienced researcher to approve of your work, but any researcher worth their salt will know when what you say is bullshit, or when what you say might have value but is unclear. I say this as an experienced, but not necessarily a good, writer. My writing has often been criticised and quite rightly too. I wish I had learned to write better earlier, is my point and the advice I give.

Because writing is important, there is a second question. How to focus on improving it?

Read good writing.
Read a book on good writing, I recommend Joshua Schimel's Writing Science.
Once you have written, wait, and then go back and read it. And then edit it. You will read it from the perspective of another person and hence realise why writing is so important and partly what you need to do to improve.


Removing a grant number from a published paper

Depends on the policies of the venue at which you published the paper. Ask them.


How do I find the standing of a journal or conference for an academic CV?

Seems it isn't actually that important. I sent them an email to clarify and they replied:

  Don’t worry too much about the standing of the journal or conference, as long as you list any publications and conferences that you have.


How important is it for all recommendation letters to arrive on time?

It will take the search committee a while to complete the first round of review, and often they don't start immediately after the deadline.  So a delay of a few days is normally not a problem.

However, a month is really excessive.  If that's how long it takes, I think there's a very good chance that they will finish their first round of review before receiving the letter, which effectively means the letter won't be considered with your application.

And it's a serious concern that this letter is from your postdoc supervisor (if I correctly understand what you mean by "host").  It's generally very important to have a letter from your supervisor in your current position if at all possible, and the absence of such a letter may be interpreted as meaning that your work is so poor that your supervisor refuses to recommend you.  Typically, if there is some good reason why you don't have a letter (e.g. your supervisor is incapacitated, or has taken a dislike to you through no fault of your own) then the committee would expect it to be explained in your application and by your other writers.  So unfortunately, I think that such a long delay could in fact affect your job prospects.

Unless the professor has some really extraordinary circumstances, this delay on their part seems quite inexcusable.  Yes, grant applications are important, but writing letters is part of their job too.  It's hard to believe they really can't spare an hour or two, over the course of a month, for something with such a significant impact on another person's career.

So I do think it is worth pressing this person to submit the letter promptly.  You could, as Buffy suggests, offer to help them with the application or other work, to help free up their time.  I generally dislike the notion that you should have to "bribe" someone to write you a letter, but in this case it might be justified.  If you have another trusted mentor in this department, you could also talk to that person, who might have some ideas based on their knowledge of your host, or be willing to approach them on your behalf.

In the meantime, I would also suggest contacting the departments where you have applied (at least those in which you are the most interested), to let them know that a letter from your supervisor will be coming.  And if you really can't get your host to hurry up, you might ask one or more of your other writers to draft a supplemental letter to the committees, saying that your host is being slow for no good reason and that your work is fine as far as they know.

I don't think getting a letter from Recommender #5 will accomplish much.  This is not so much about the total number of letters, but about specifically having one from your supervisor.


Regarding applying to another university for PhD during the first year PhD program at a top research US university

Although more experienced heads may give alternative advice, my recommendation is to focus on what you want to research rather than the personal relationship reasons you have.

Remember what the SOP stands for: Statement of Purpose, why are you pursuing a PhD?

Professionalism aside, ad hominem attacks are not the subject of interest when you meet with potential advisers: you are the subject, what you are interested in, where you’d like to go, how you would approach a problem or issue.


Can I refuse a grant position I was offered and still hope to work there in future?

Professionally, they should understand, if explained to them in a polite and respectful way. After all it is your life, and they need to respect your decision. Yes, it is disappointing, but it should not burn bridges - good people are not easy to find and they should be happy to keep in touch; who knows what the future brings.

However, if they were so disappointed that they would be indeed offended by your decision, then it is likely that there are other problems lying in wait for you at that group, anyway.


PhD - Well known professor or well known school?

I can't see how either would be preferable to the other. What matters more to your career is what you do with the opportunities you have.

And note that disasters can happen even at the most prestigious levels.

Do good work. Make lots of professional contacts.


Answer to "Will you be able to provide proof of your identity and employment eligibility if you are hired"?

Unless you're already eligible to work in the US (e.g. as a permanent resident), you'll have to answer the second question with a "no."

The three aspects of US employment/immigration law that you need to know about are that

Newly hired employees are required to prove that they're eligible to work in the US by filling out an I-9 form and providing the required documentation.  Most universities  than use an online service called e-verify to verify the information on the I-9 form.  You'll typically be required to provide this documentation immediately upon being hired (not six months later when your first semester starts.)  You're being asked if you can fill out the I-9 form.
Practically all of the options for a visa that would enable you to work in the US require sponsorship by the employer.  This sponsorship requires the employer to declare that there were no qualified applicants that weren't already eligible to work in the US and obtain an authorization from the US Department of Labor.  The process takes weeks to months, and can cost thousands of dollars.  If you say that you're good to go, and the employer later finds out that they'd have to sponsor you for a visa, they may simply withdraw your job offer rather than sponsor you for a visa.
It's not legal to discriminate between various classes of people who do already have the right to work in the US (e.g. between permanent residents vs. citizens.)  The particular wording of that question is designed to protect against that kind of discirimination.

Going beyond the "yes/no" answer to this question, you could provide additional information that could be helpful.  For example, if you hold Canadian citizenship than its easy for you to be employed on a NAFTA visa, and you wouldn't need to be sponsored for an H-1B visa.  On the other hand, if you're currently on an expiring J-1 visa with a "return home" requirement, it could be difficult for them to sponsor you for an H-1B visa.


How to deal with journal requirements to share data when data comes from industry and industry partner would not permit sharing?

I am going to question the premise:

You ask: Any strategies to handle this situation effectively and convince editors about the non-availability of the datasets to other researchers?

I'm going to say: You can't and you shouldn't.

It isn't that the journal editors don't believe you when you say "This data is not able to be released for other researchers."
They don't really care why it isn't available,
but they do believe that without that data, it is not the kind of article they want to publish.

Some options which may be valid depending on circumanstances:

Find a journal that is Ok publishing without data. (For understandable reasons these might not be as good as the more stringent ones)
Create a new synthetic dataset, that has similar properties to your real data, and present your primary results on that. (And mention as a secondary point your results on the real data)
Work out what it would take to make the company happy to release the data:

Perhaps removing identifiers (E.g. for personal identifying data k-anonymity is a common technique)

See also the related question:
Can you publish studies based on confidential customer data that comes from private companies?


Are Mathematics graduate programs open to admitting a student out of high school with graduate work?

I know of one case in which someone went straight from high school into a graduate program, so it is theoretically possible if you can find a university that agrees.  However, it's almost unheard of, and it would be a bad idea for just about everyone (even setting aside the question of whether undergraduate education provides any benefits beyond preparation for graduate school).

What I assume is that you'd like to do important research and are looking for preparation that will help you accomplish this goal.  The minimal standards for a Ph.D. are actually pretty low, and you can squeak by without knowing much or doing impressive research, but this sort of dissertation will set you up for career failure.  Instead, you need to enter a strong Ph.D. program, ideally one of the top ones, and really excel.

It sounds like you've completed enough courses for a minimal undergraduate degree in mathematics, but probably not enough to be competitive at a top grad program.  The applicants at these programs have generally taken a more extensive and rigorous collection of undergraduate courses (e.g., abstract algebra, topology, complex analysis), and it's not uncommon to have taken more than two grad courses, sometimes many more and in a few cases starting in high school.  Plus it's common to have undergraduate research experience or other substantial independent work, such as a senior thesis.

Basically, imagine yourself in four years.  That's who you're going to be competing against for admission, the other extraordinary high school students who went to college and became even more knowledgeable and impressive.

If you could find a university that would admit you to graduate school now, you'd probably end up going to a second tier school, spending some time catching up on courses, and then writing a good thesis but not living up to your potential.  Your career would get off to an inauspicious start, you'd have trouble on the job market, and in the long term you'd likely end up with a less research-oriented job than you might have had otherwise.

Of course I could be wrong about this: you might have exceptional luck or be the next Terry Tao.  But diving into graduate school at a young age with minimal preparation is an incredibly risky strategy.

This is something that's really hard to discern from college catalogs.  They usually focus on the minimal requirements to complete each degree and move on to the next level, but that's not how people do things in practice.  Instead, the vast majority of future mathematicians spend at least three years on their undergraduate studies, and generally four (in the U.S.).  The operative question isn't how quickly you can complete the degree requirements, but rather how much you can achieve along the way.  Preparing well for grad school is far more demanding than completing an undergraduate degree.

So what I'd recommend is that you pick an undergraduate program in which you'll have really outstanding fellow students, so that you learn from and are pushed by them.  Being part of a cohort like this is probably the single biggest factor in success, and your goal should be to find amazing people to hang around with and discuss mathematics.  You should then take whatever undergraduate courses are needed to fix up your background (if any) and move on to graduate courses.  You should also look for research opportunities during the summer or perhaps the school year, but it's not worth obsessing over this.  No program will guarantee anything, but at the very least you'll surely have some success applying to summer REUs, and it's reasonable to hope for even more than that.  Perhaps you'll finish in three years, and perhaps you'll decide to stay for four, but either way you'll be far better prepared for graduate school than you are now.

It sounds like you're in a great position to do well, with a remarkably strong mathematics background.  However, I'm convinced that the right question is how to get as much as possible from your undergraduate studies, rather than how to skip by them as quickly as you can.


Is it ethical for schools to offer merit scholarships, when these are more difficult for students from some socioeconomic backgrounds to get?

Schools don't charge more to low performing students, they provide opportunities to attract and retain high performing students, through merit-based scholarships and grants. While it is probably true that low-SES individuals are less likely to qualify for such awards, it is not fair to surmise that schools are 'charging more' to low-SES individuals.  There are many 'rich' students paying the same tuition as their less-well-off peers.

The more pertinent question is whether there exist sufficient non-merit based scholarships for disadvantaged populations, and need-based financial aid, to give low-SES individuals opportunity (probably not).


I accidentally failed to disclose a school I briefly attended. Have now been admitted to grad school; how to proceed?

Your options seem to be: tell them, don't tell them and hope for the best, or withdraw.

If you tell them, the worst that can happen is they revoke your admission and invite you to reapply next year. If you withdraw, this will happen for sure. So, I wouldn't even consider withdrawing.

I usually suggest not over-analyzing things, but in this case, I wouldn't just let the sleeping dog lie. You don't want this hanging over your head for the rest of your career. So, I would just send a brief e-mail saying exactly what you did above (and just as concisely) and asking how to proceed. I expect they will say that they will update your record and do not anticipate any problems -- but you should prepare for the worst-case scenario just in case.


I think the most significant issue is whether anyone would know (or bother to find out) what "very positive" means in the context of some specific university's usage. Moreover, for academic purposes, very soon after your Ph.D. something like this becomes either trivial and distracting (because subsequent references to your dissertation and/or your publications in general will supersede anything this honor is likely to provide) or pretentious (if subsequent references to your dissertation and/or your publications in general are nonexistent or few). On the other hand, for non-academic purposes, it might be fine to do this.


Is it appropriate to ask for letters of recommendation from professor on maternity leave?

Yes

I think It would be different if say, you took one or two of her classes. But it sounds like she advised you a great deal, and thus she should have some investment in your educational success. Especially if you have talked about graduate school before. What is important is you give her notice as soon as possible so she can find some time to do it: Having a newborn is no easy job.

I would phrase it as follows:

  Dear X (unless you call her professor, then Professor X, but my
  advisors I call by their first name)

  How is your newborn?

  I realize you are very busy with your maternity leave, but I was
  hoping you might have some time to write me a strong letter of
  recommendation for graduate school. As you might know I am interested
  in ZQR, and your mentorship over my senior thesis has been essential
  to my education.

  Thank you for your time,

  user

I'd also like to add that while I was applying to PhD programs, the professor who eventually became my advisor was on maternity leave while I was asking her questions about the lab. In confidence, she enjoyed my emails because having newborns, while a joy most of the time, often lacks the intellectual rigor that most people are accustomed to in their day to day conversations.

My guess is she will be very happy to do this, and somewhat expects you to ask.


How to list a paper in your CV when having 1000 co-authors?

The quick answer might be to look up the CV of a CERN researcher...

From outside physics, when compiling institutional publication lists, I've occasionally dealt with a 100+ author entry (often a major report rather than a paper, but the same problem holds). As our motive for listing this is to note the local author(s), it's a similar situation to the CV.

In this case, I tend to do something like:

  Able, J., Anderson, M., Archer, C., [and 78 others, including Smith, Q.] (2015) A very tedious paper, J. Irrep. Res. 243(54)

or

  Able, J., Anderson, M., Archer, C., [et al, including Smith, Q.] (2015) A very tedious paper, J. Irrep. Res. 243(54)

where Q. Smith is the local author we care about. It's probably not a very theoretically sound citation style, but it seems to work!


I used external help for my masters thesis coding work

There are two independent issues here:

Did you take credit for someone else's work?  To avoid this, you need to explain the situation clearly and explicitly in your thesis, so that nobody will give you more credit than you deserve.  This has to be prominent enough to be noticed.  (If the code is a major part of your thesis, then it's not enough to mention the assistance just in a footnote on page 85.)
Did you do enough yourself to fulfill the requirements for your degree?  To ensure that this is the case, whoever grades your thesis (advisor, examiner, thesis committee) should be aware of the situation.

If you mentioned the assistance clearly in the thesis and your advisor was well aware of it, then you should be fine.

If you mentioned it clearly but your advisor was unaware, then you're probably OK, since it would be embarrassing for your advisor to admit that he/she didn't notice the clear statement in your thesis.  But you should have made sure your advisor knew.

If your advisor knew but you didn't mention it clearly in the thesis, then you should have written it differently.  You could be accused of academic dishonesty, but I think you are unlikely to get in trouble for it now, given that your advisor knew and hasn't objected.  However, if you publish the thesis results, you should be sure to mention it then.  (In my experience, people are more likely to get upset over credit issues for a publication than a master's thesis, so this is riskier.)

If your advisor didn't know and your thesis didn't mention it, then you are in a bad situation.  You probably won't be caught, because it's not so easy for anyone to find out, but if people do find out then you could easily be accused of academic dishonesty.  How serious this would be depends on the details of your case.


Are there tools to prevent students from cheating on a programming exam administered on computers?

At my university in the UK we have two kinds of assessment for programming courses. Pass/fail 'practicals' where students are given programming tasks, and are explicitly allowed to discuss them with each other and search online. When the student is ready to submit their solution a demonstrator will look it over and ask questions etc to make sure the student understands why they wrote the code they wrote. Students don't get a grade for this that counts towards their overall mark for the year, but they are required to 'pass' the practicals in order to pass the year.

Then there are written exams with no computer access. There are questions along the lines of 'write some code that will solve this problem', and also more conceptual 'why is this the case? When would you use that?' questions. For the 'write code' bits, the markers will deduct very few points for simple syntax errors and things like that. The question is not so much 'can the student write a program that will compile on the first try?' as 'can the student come up with a good algorithm which solves the problem and give a reasonable expression of it in code?'. Note that these courses (at my uni) are never for specific languages; they are courses like 'functional programming' or 'object oriented programming' or 'machine learning', which will each use a particular language, but we care more that the student understands the concepts than learns the intricacies of the course's language.

This also encourages students to learn ways of designing and writing provably correct programs: if they can reason about programs on a deeper level than intuition, then writing programs on paper is a better test of this than allowing them to experiment and test until the output 'looks right' for the inputs they've given it.

This seems like a good way to avoid cheating on grades that matter and encourage solid understanding of the important course material. That said, many students hate having to write code on paper without access to S.O. or a compiler!


When peer reviewers are public/open, are they less likely to be critical of a manuscript?

I have a similar history of reviewing papers at around eight years, though in the fields of engineering and robotics. Between the official reviews for journals or conferences (which are almost all single blind and in rare cases double blind) and informal reviews for colleagues, I would say I differ only in level of tactfulness.

The stakes in the official review process, however, are higher and I would not agree to review if my name was to be released.  I’ve rejected papers based on lack of contribution (to the extent where there were missing citations of seminal papers or even their own previous work to make the current paper look more significant) as well as lack of fundamental understanding of the involved system or experimental processes.  These types of issues are not things that can be easily fixed and the review becomes more of a statement of ‘start over’ with the associated large investment of time, money, and/or resources.

Peer review requires an already rather generous donation of time by those who participate. In an open peer review there is additionally a very real fear of retribution, which only the well-established can easily ignore.  My personal experience follows the results of the previously mentioned van Rooyen et al. – review quality in an open process stays approximately the same, but the number of willing reviewers decreases, potentially drastically.  The open review process certainly has some value, but I don’t consider it to be widely practically implementable with the current reviewer arrangement.


As said in the comments, the situation seems to be different for each of your papers. The font problem is understandable, but it's hard to see what you mean by "personal and even economic questions". However, if you didn't answer the questions, it's not surprising that your paper was not published in arXiv.

Concerning the essay, I quote from the FAQ, "arXiv accepts only submissions in the form of an article that would be refereeable by a conventional publication venue.", and in particular, " This excludes [...] papers that contain inflammatory or fictitious content, papers that use highly dramatic and mis-representative titles/abstracts/introductions". I'm in no position to scientifically judge the content of your essay, but at first glance, it seems quite provocative (assumptions that are not fundamental).

If you believe that your essay is "refereeable by a conventional publication venue", then the moderation appeal is there for this. Although the moderators do not have to motivate their decision as a reviewer would do, by bringing sufficient support that your paper meets the criteria required by arXiv (in particular by demonstrating that it doesn't fit in any of the categories listed under "inappropriate format", the fact that other essays have been published in the past is not really relevant, you would have to show the quality of your content on its own).

In general, arXiv moderators are human moderators, and it could be the case that the rejection of your paper was a mistake. However, keep in mind that publishing in arXiv is not a granted right, and that "arXiv reserves the right to reject or reclassify any submission".


Does a research paper automatically get published online publicly if accepted?

That depends on the journal. Some do put accepted articles onto their websites. In most cases, however, the article must first go through some kind of editorial process where the style of the manuscript is adjusted to the requirements of the journal -- for example, many manuscripts are submitted double-spaced, with figures at the end of the manuscript, and this will be converted to single-spaced, maybe double-column, with figures embedded in the text.

But then there are also journals that do not have websites where all articles are posted.

Finally, "publicly posted" can mean quite a lot of things. Some journals actually post a PDF of the article for everyone to read. This is often called "Open Access" these days. On the other hand, most journals are closed access: They will typically post the title, authors, and maybe the abstract of a paper publicly for everyone to see, but the body of the paper is only available for people who either pay for it, or who are with institutions that have (paid) subscriptions to the journal.


Whether a digital whiteboard is of use depends very much on what you want to use it for. It combines the advantages of a projector (being able to display a range of digital content) with those of a whiteboard (writing in real time).

In certain circumstances, there is more benefit than simply the sum of the two. I've been in video-conferenced lectures that used them - the actual screen is transmitted, and so is easier to see than a whiteboard captured with a camera. Sometimes it's useful to combine different backgrounds with real time writing, such as writing music on a stave. However, similar effects can be achieved with devices such as an ipad, which would be cheaper.

The downsides are: cost, training needed (and resistance), the start-up time required to get to an operational state, and the inevitable event that someone writes on the board with the wrong pen.

Also, I've found that the software being used on a digital whiteboard can have a major impact on its effectiveness. We got some at school, and a minor software 'upgrade' significantly reduced efficiency and increased frustration.


How to judge the quality of my own paper?

If your adviser is a coauthor, he has to agree with whether the paper is suitable for submission to a particular journal.

Otherwise, you could judge the quality of your paper by comparing it with published papers in the journal you intend to submit your paper to. However, I recommend asking for other people's opinion about the paper; this would be people you know, who have had some publication experience.

Is there an upcoming conference which you can submit your paper to? It is a good idea to submit the paper to a conference first.


Software to extract citations and abstracts for meta-analysis

Covidence is free for students. Other software includes DistillerSR. All of these will aid with citation management a step up from what can be done with EndNote, Mendeley, Zotero, etc.

Also, I hope you've searched databases beyond PubMed. Great tool, but alone not sufficient for an SR.


Why do lecturers give only couple of days to do exercises?

The instructor may not want the students to work far ahead in the class.

If the student does go on ahead and is doing exercises incorrectly (due to lack of knowledge of the subject), then it is may be harder for the student to learn the subject matter correctly due to the bad habits he or she has developed.


Is it a good idea to put detailed supplementary analyses to a publication on ArXiv or Zenodo?

If the journals you want to submit your work are not "ArXiv-compatible" you have few options:

1)Put the excluded material in the appendix of the arxiv submission.
2)Make a write-up, put it on your web-page, and cite it in the arxiv paper.
3)Create a technical report (with a time stamp) and cite it in your article.

I think the time-stamp feature is critical here.


I passed JPLT N5 exam with average score, should I be worried about MEXT examinations in Japaneese?

I think the evaluation varies a bit from country to country but in my case (from Tunisia in 2008 for doing Master degree), Japanese language ability was absolutely not required. We passed the English and Japanese test, but I left most of the Japanese test sheet blank, and my friend (who also got the scholarship) did not know any Japanese except for some words (konnichi wa, arigatou, ...).
The embassy then chose the topmost scorers from the English test and invited us to the interview at the Embassy. During the interview, there were many questions about our capacity to live in Japan and to adapt to life there (because many people get the scholarship but don't acclimatize well and drop off in 6 months or a year). Language ability was a bonus but not an absolute requirement because we spend the entire first year learning Japanese at the university you get.
This was also the case for many of my friends that I met in Japan: many of them had no japanese skills when they got the scholarship.
So unless things changed a lot in the last years, your japanese language ability should not have too much of a bearing on your application, and the fact that you got the N5 already is a boost!
Good luck for it!


Are extended periods of unpaid leave compatible with an academic career?

Frequent, extended periods of unpaid leave are easily compatible with certain types of academic careers, such as teaching as an adjunct on a course-by-course basis.  However, this involves low pay and no prestige or job security, so it's far from an ideal solution.

There will be a lot of obstacles to doing this with a tenure-track job.  Your collaborators will be unhappy when you put the collaboration on hold to go do something else.  You colleagues will be unhappy when you aren't available to teach courses or supervise students (thereby making the department work around what they consider to be your eccentricities).  Wanting to take substantial amounts of time off will be considered a bad sign, and everyone will worry about what you might do once you have tenure.  Your chances of getting tenure will go down.

Taking time off can also make you a less productive researcher, even normalized by the amount of time you spend on research.  The problem is that keeping up with the field takes a certain amount of time and effort.  If you work on research for only six months per year, you still need to keep up with twelve months of progress by others, so it's as if the rest of the world were moving twice as fast.

It's not impossible that you could find a flexible academic job.  You might end up with a specially negotiated soft-money position (funded by grants under whatever terms the funding agency will agree to), you might take a job at a less prestigious university than you could have (who are so eager to hire you that they are willing to make a deal), or you might happen to find an unusually accommodating department.  Unfortunately, this isn't something most people can reasonably expect to work out.  I don't know what the chances are, but I expect they are pretty low on average.  The academic job market is tough, and adding non-standard constraints makes it even tougher.  If you can't be happy without frequent, extended leaves, and you have good non-academic employment options that fit your needs, then that might be the way to go.

Another theoretical option is to take advantage of tenure: work hard, don't tell anyone your plans, and then quit doing any academic work over the summer once you get tenure.  You shouldn't do this.  Your colleagues will feel resentful, the administration will be upset, and you'll be manipulating the system in a way tenure is not intended to support (and thus weakening the case for having tenure at all).  If you're too extreme, you could run into trouble with a post-tenure review, depending on your university's policies.

[I'm assuming you intend to use the leaves for something entirely unrelated to your academic career.  If it's more closely related, such as applying your scholarly expertise to government service, then you may have better luck.  However, it doesn't sound like that's what you're talking about.]


Recommendation letter sent from non-institutional email

I use my gmail, but gmail has the capability to manage the sender addresses. You should authenticate your gmail to send from your institutional address. The recipient will then have the confirmation that you are indeed who you say you are, as gmail will have already done the authentication.

The authenticator in gmail  has the ability to either use the SMTP server of your institution to send (if your systems team permits it), where gmail is then acting as the mail client, or it can use the From headers to indicate your authenticated affiliation.

If you were doing it properly you could manage all your email through the gmail account and choose whichever outgoing account and sending method you choose. This is what I do, for the several academic institutional affiliations I possess.

So in summary: you can have it both ways. You can use gmail for official institutional correspondence and you can use the options provided in gmail to choose which of your attributions any particular email uses. It is appropriate to badge emails for official correspondence, such as letters of recommendation, with your institutional addresses. I would   suggest not using a personal email addresses for business purposes, but using the tools properly you can customise your environment in a professional manner.


I would tend to agree with your professor: a Ph.D. primarily certifies you as being capably of creative contribution to research, and secondarily as an expert in a narrow sub-discipline.  Combine that with the continually shifting landscape of the scientific frontier, are there is a great deal of flexibility in what a person with a Ph.D. may end up doing over time.

I have heard one of my close colleagues say that: "One way or another, in ten years time we can't be doing the same thing we are now.  Either we will have succeeded and need to move forward, or we will have failed and need to try something else."

In such changes, there is usually a significant degree of continuity that allows one to "pivot" from one area for another.  Like in your professor's example, there are a lot of ways in which dog anatomy and fluid dynamics are related, and it's natural that an expert in fluid dynamics might well be drawn to the parts of anatomy most relevant to their existing skill.

A nice real-world example of such a radical transition: Tom Knight made his name pioneering networks and computer architectures, then radically shifted into biology.  There is a nice interview with him about his history and how he made the transition, which involved lots of re-education but not bothering with the formality of another Ph.D.  He's also moved back and forth between industry and academia quite a bit.

That said, I could imagine some transition so extreme that it might require an entirely new apprenticeship, e.g., from astrophysics to medieval French history.  But that sort of change would be a rather extreme an unusual example.


Is an MS in computer science helpful in improving programming skills?

Although having done a bachelor in computer engineering without doing any coding at all is highly unusual, learning to code is mainly a self-taught art. Even if you had been fully taught many programming languages during your undergraduate years, they might quickly become obsolete. On a perfect world an undergraduate degree on computer engineering must have given you the necessary theoretical base on databases, programming concepts, data structures and algorithms. Then it takes many / endless hours of coding to learn how to successfully apply those concepts on real-world software applications. So, regardless of doing a MSc or not, you must still code on your own "free" time, either on your little self-projects, on learning / self teaching new programming languages or participating on open-source projects and communities like Stack Overflow (SO).

The fact that you avoided coding on your undergraduate years is a bad sign though. Successful programmers are usually partly (or fully) geeks who enjoy installing / testing a new linux distribution every few months, hack their laptops to automate tasks, participate on SO by coding and solving other people's problem just for fun. Are you sure that coding is what you want to do for the rest of your life? Programming is really a hard and stressful work (as you saw on your first real jobs) and is very hard to enjoy it, if you do not have any real passion for it.

On answering your core question, most MSc programs I know, are mainly focused on particular aspects of IT science, such as databases, networks, electronic commerce etc and not on teaching programming. If your core motivation is learning how to program, I would suggest to follow (and pay for) some industry certifications (e.g. Oracle for Java and Oracle DB) and their respective structured courses. There is even multiple free educational material for those certifications, so you might even not need to pay for it. Still, to really learn coding you must spend hundreds of hours of actually coding and you should not simply expect to learn programming by studying at yet another course or getting a new degree.


Should I still submit a manuscript to a journal if a member of the editorial board is advancing a competing theory that is incompatible with my work?

Many journals will allow you to suggest a handling editor, and pretty much every journal will allow you to specify reviewers that you believe should not review your paper due to conflict of interest.  This is an appropriate situation to invoke these options.

Depending on the particular forms the journal uses for submission, the right place to put an explanation of your concern may be either the submission forms or the cover letter.  You do not need to go into much detail, simply saying:

  "Editor X's student is working on a competing model, so I am concerned about bias."

If you are dealing with an honorable journal, that should be enough: this is an entirely normal and reasonable concern you should not have to back this up with published evidence (people understand that scientists talk, pre-publication), nor do you need to denigrate the character of Editor X in any way.  They have many editors for a reason, and many possible reviewers they can draw from as well, and every good scientist understands that it's usually better to be safe than sorry when it comes to dealing with conflict of interest concerns.


Should I accept authorship on large collaborations for which I have made little contribution?

What are the pros and cons of agreeing to be on such a paper?

Pros

Your contributions to the collaboration are formally acknowledged, both incentivizing you to continue working on it as well as putting the candle under your butt to get up to speed on anything you should be getting good at.
Leaders in the collaboration see you listed as a contributing member, allowing your candidacy for the next round of projects that need attention by working group members.  Generally, people reach out to include you going forward.
You will be put on mailings that automatically include all researchers on the paper, keeping you up to speed as developments happen in real time.
Your association with the project is beneficial to both your career (i.e., Look at this thing I worked on!) and the project itself (i.e., Look at this great contributor we have!).

Cons

None.  Literally none.

There is a related problem in academia called illegitimate co-authorship, or sometimes authorship inflation, but that is a problem to be tackled by policy.  If this problem bothers you, find ways to contribute to the policies and incentives that systematically reinforce this behavior.  Boycotting it personally will only serve to harm your career and be a drop in the bucket of the larger problem.


Style for first introduction sentence - citation required for lurid statement?

I think there is a non negligible chance that this will make a bad first impression on the readers.

Don't get me wrong: I love it when people depart from the dry and oft boring “academic style” of writing and try to invigorate their papers: more concise writing, less use of conditional, more direct statements, use of active voice, stating one's opinion when need be, etc. But this should be done with the goal of making your paper easier to read, and not hyping it. If you start with a broad claim that has little to do with your actual conclusions, you may alienate some readers (“hey, I read the paper because the first line said that a world without gluons would be beneficial in the long term, but then it's only a boring particle physics paper!”).

To give a specific example, when I read papers dealing with physical and chemical properties of water, oftentimes the authors think it wise to start their introduction with a broad statements like:

  Water is the most abundant molecule of the human body, and the second most common molecule in the Universe. Its presence or absence has dramatic consequences for human life and civilization: droughts cause famines and floods cause death and disease. Though it has a special relationship with our everyday lives, there is still much we need to learn about it.

and then end with:

  In conclusion, we reported the most accurate measurement yet of the bending vibration frequency of heavy water, with an uncertainty of 10–9.

It annoys me.


Okay, as you say, this is very broad, and possibly argumentative. So, I'll try to section off my answer for your various sub-questions, and talk not so much about how I do come up (and organize) research ideas, but how I see it done by everyone (including me).

Coming up with ideas

The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka!” but rather, “hmm... that's funny...” — Isaac Asimov

It's probably very akin to asking a large number of artists “how do you come up with inspiration?”, i.e. you can probably get one thousand different answers, and yet not useful answer at the same time. However, there are some elements that I think are common to all. You can't “trigger” new ideas to come into your mind, but you can put your mind into the right disposition to host these new ideas: recognize them and welcome them. Below is a list, certainly partial and limited, trying to detail my perspective in this matter:

Be challenged! Nothing sparks ideas more than being confronted with contradiction, healthy criticism, a spirited debate, maybe a bit of competition. Some people manage to do that by themselves, arguing against their ideas and improving them. I myself (and most of the colleagues and students I have seen) need an echo chamber, someone to discuss things with. If they're not exactly from your field, all the better, as they may have unusual/naïve/silly questions or expectations.
To give an example, some of the most “successful” ideas I have had came while answering questions, for example from a PhD student or colleague, and replying by “no, it doesn't work like that… in fact, it's probably always guaranteed to be false, because… see, it's linked to X… or maybe it's not? hum…”

Be curious! Ideas come from problems. Identifying worthy problems in your field of research, and dissecting larger issues into of specific problems of manageable scope, is at least as hard as coming up with new ideas. In the end my feeling is that, especially for a researcher, all ideas are the result of one’s curiosity.

Manage to get some free time for thinking (and not: teaching, supervising, tutoring, reviewing, writing, sleeping, …). Body and mind. Sure, an idea can pop into your head any time, but it's probably less likely to happen when you teach basic calculus all day that when you get some time to really think.

Know your field, know where a new development need to occur, what is currently missing. Read review papers, search for such ideas through people's articles or blog posts, discuss with senior colleagues who have a comprehensive view of the field, …
One of the ways you can come with ideas is by analyzing how different groups work in your fields, seeing what has been addressed and avoided, what big questions are still open, and how you can link between different works to build a coherent global picture… This is not always successful, but it usually generates some good ideas along the way!

Explore more or less closely related fields, and see if there is something from your background that you could apply to their problems, or ways you could build something together. Such ideas tend to be very strong, because you can oftentimes apply an entire branch of knowledge (ideas, methods, algorithms, etc.) to a very different problem. In that case, the added value comes from your different perspective, as you might try things that others would not think of.

Ways have been devised to come up with new ideas on a given topic, either alone or in group sessions. Brainstorming is probably the best know such method (and might be the most popular, in one form or another), but a really large number of creativity techniques have been developed. They can be applied both to enhance creativity or to boost problem solving efficiency.

Organizing ideas
A quote often attributed to Kant: “someone’s intelligence can be measured by the quantity of uncertainties that he can bear”. If that true, that has serious consequences for research. Accepting that your mind can only efficiently support a finite number of ongoing research ideas, you have to come up with ways to write them down, organize them, prioritize them, come back to them later, etc. Just as you cannot juggle with as many balls as you'd like, such “external” tools will help your brain focus on the ones that you assign high priority (or the ones to which it gives high priority; the brain works in funny ways).
Most people use very low-tech tools for that:

Notebooks, either sorted chronologically or thematically; in the later case, open a series of blanks pages for each new project/idea, and flip through the book whenever you want to check on them. I use a Moleskine (WP) for that purpose; having a nice, leather-bound notebook somehow helps me “value” it more and treat it with care (always have it with me, actually use it).

Post-it’s scattered through one’s (real or virtual) desktop. Downsides are obvious.

More people than I thought actually don't use any tools, and just keep all in their mind. Apparently it can be done, but I don't advise it.

But more complicated methodologies have been devised, that are supposed to help you with it:

Mind mapping, either on paper or software-based.
Using todo-list flat or two-dimensional todo-list software, or more complex task-tracking software (see, e.g. Trello).
The software side of this question is already covered (though possibly not extensively) here on this very Q&A site.

Finally, don't underestimate the possibilities opened by delegating: people in charge of a specific project or sub-project (PhD students or post-docs) can be tasked with maintaining a list of ideas by all contributors of the project, to come to later on.

Answers to your miscellaneous smaller questions:

What proportion of your ideas for past papers come from; (i) colleagues, (ii) intentionally browsing the literature for ideas, (iii) on the spot inspiration, (iv) conferences, (v) other?

Most ideas are hardly “traceable” to one source or another. A given idea might have formed in my head during a conference, seeing how people were failing to address a certain issue, then crystallized during a discussion with colleagues, but would never have occurred to me if not for a literature review I had performed a few months before.

I'll come back a bit later and continue working on this answer :)


Can I copy text from an article to complete my review article?

You can quote verbatim, iff

the passage quoted is reasonably short (about one sentence, but not a whole paragraph);
and you put the quoted passage in quotation marks and/or italic;
and you give the reference immediately before or afterwards.

For example:

  As John & Ali (2012) have phrased it "this is a verbatim quote from
  their publiation".

However, having said that, you should avoid excessive verbatim quotations. Quoting verbatim is frowned upon and reflects poorly on your ability to express yourself. As stated in point 1 above, quoting a whole paragraph or even more is inappropriate in any case, because it implies that your text lacks originality. The same holds for near-verbatim quotes.


Graduate student titles on funded research proposal

TL;DR: your name can be on the proposal as "other personnel" but not as "senior personnel".

From the NSF Grant Proposal Guide, Definitions of Categories of Personnel:

  A. SENIOR PERSONNEL

  (co) PRINCIPAL INVESTIGATOR/PROJECT DIRECTOR (PI/PD) means the individual(s) designated by the proposer, and approved by NSF, who will be responsible for the scientific or technical direction of the project. NSF does not infer any distinction in scientific stature among multiple PIs, whether referred to as PI or co-PI. If more than one, the first one listed will serve as the contact PI, with whom all communications between NSF program officials and the project relating to the scientific, technical, and budgetary aspects of the project should take place. The PI and any identified co-PIs, however, will be jointly responsible for submission of the requisite project reports. The term "Principal Investigator" generally is used in research projects, while the term "Project Director" generally is used in centers, large facilities, and other projects. For purposes of this Guide, PI/co-PI is interchangeable with PD/co-PD.
  Faculty Associate (faculty member) -- an individual other than the Principal Investigator(s) considered by the performing institution to be a member of its faculty or who holds an appointment as a faculty member at another institution, and who will participate in the project being supported.

  B. OTHER PERSONNEL

  Postdoctoral (Scholar, Fellow, or Other Postdoctoral Position) -- An individual who has received a doctoral degree (or equivalent) and is engaged in a temporary and defined period of mentored advanced training to enhance the professional skills and research independence needed to pursue his or her chosen career path. Postdoctoral scholars not identified under Senior Personnel above should be listed as Other Personnel.
  Other Professional -- a person who may or may not hold a doctoral degree or its equivalent, who is considered a professional and is not reported as a Principal Investigator, faculty associate, postdoctoral scholar or student. Examples of persons included in this category are doctoral associates not reported under B1, professional technicians, physicians, veterinarians, system experts, computer programmers and design engineers.
  Graduate Student (research assistant) -- a part-time or full-time student working on the project in a research capacity who holds at least a bachelor’s degree and is enrolled in a degree program leading to an advanced degree.
  Undergraduate Student -- a student who is enrolled in a degree program (part-time or full-time) leading to a bachelor’s or associate’s degree.
  & 6.   These categories include persons working on the project in a non-research capacity, such as secretaries, clerk-typists, draftsmen, animal caretakers, electricians and custodial personnel regardless of whether they hold a degree or are involved in degree work.


Chances of Acceptance after Institutional Action

The crucial question is whether your academic transcript will indicate the expulsion/suspension. If not, then I don't think it should matter to your graduate applications at all.

If the transcript does indicate this, then you are going to have to address the issue in your cover letter. You are going to have to say how sorry you are and how much you've learned your lesson. I, personally, wouldn't hold an undergrad mistake against you, as long as I saw that you weren't likely to do it again. Others might feel differently, however you can still try.


When applying to PhD programs in Computer Science, how much does subfield/specialty selection matter?

"Can I still conduct research" has some different interpretations which bear on your question. The short answer, at least in my experience, is no, you have not painted yourself into a corner. But let me elaborate:

There can be significant overlap between AI/ML research and Theory, so you may end up finding a thesis project which combines aspects of both to your satisfaction.
It's not at all uncommon for students to bounce around a little bit after they enter a program, and to have side projects in tangential areas. Even if you do your primary research in machine learning, you could participate and publish in other collaborations. I did this for a couple of different projects just to chase my own interests.
As @ben-bitdiddle alluded to in his comment, many programs (even most in my experience) are not so strict in locking down new Ph.D. students to a particular area/advisor. It can obviously present a problem if you're not aligned with one after your first couple of years, but at the beginning I think this can be very beneficial.
One important caveat is that if you're being funded by a faculty member on a research assistantship, you'll be expected to be doing research in that person's area and it likely won't be looked on kindly if you're spending a lot of time on other projects. This is something to discuss with the faculty in question, though, before you accept the RA if you have questions.

Many people end up doing something different for their dissertation than they indicated on their graduate application, so I wouldn't sweat this point too much if I were you.

Lastly, you mention that you've applied to several programs. I'd ask some questions surrounding this issue and consider those answers as I made my decision about which offer of admission to accept.


Transferring to another university due to discrimination/policies/healthcare availability?

I'm pretty sure that in most places a transfer would be based entirely on you academic qualifications and record. While individuals may be sympathetic to your problems, most systems are too bureaucratic to include such factors in decision making. If you have a good record and have a promising future you can probably move.

In an interview, however, you could raise some issues, especially better health care opportunities, but I'd be a bit cautious about claiming a discriminatory environment unless there is already public discussion of some incidents. It isn't that such things are unlikely to exist, but that they are hard to judge and probably wouldn't overcome academic deficiencies if there are any. Just be cautious.

But you might explore your current situation with a trusted faculty member or with an office dedicated to student support before you make firm decisions.


NSF sponsoring scientist already having postdocs under their supervision

I am not directly familiar with the NSF scheme, but for the NIH NRSA scheme choosing a PI with previous post docs is a huge benefit. In fact, from what I have heard from young colleagues, if the PI does not have current or previous post docs, the NIH likes to see a more experienced co-supervisor listed.


Do the fixed-term contracts in academia lead to a brain drain?

I can only provide anecdotal data, I was going to  do this as a comment, but it got too big.

I'm a postdoc (finished my phd in 2012), and I'm tired of it. In some cases (fapesp, brazil) postdocs don't have any rights or benefits (no vacations, for instance).

Worrying about how I'll provide for my family from next August, when my contract ends, compromises my performance... More than that, I don't have continuity, I can't think of anything medium term, because I have no idea where I'll be in one year.

I really like the projects I'm working on. But this whole thing has taken its toll on my and on my family. I'm seriously considering changing careers to get some kind of stability. I'd like to stay on research, but maybe research doesn't want to stay with me :)

update: I do not have kids, it is just me and my wife. We are postponing that exactly because I don't want to subject a kid to this. And its easier to move around when its only the two of us. If I'm honest, I don't know of any other non-religious profession that requires this kind of commitment. Maybe the military, but at least you got benefits, sometimes housing. And financial stability, if not geographical.


Do you include your thesis on a "publication list"?

I don't think there's a clear universal definition of what should go on a "publication list".  It's possible they only want peer-reviewed research publications, it's possible they want other works as well.

So the best approach, in my opinion, is to create a publication list with multiple sections.  Have one section for "traditional" peer-reviewed research publications, and one or more additional sections for other works of yours that have been made publicly available (hence "publications" according to some definitions) but not in typical peer-reviewed venues.  You might lump these all together under "other works", or if appropriate for your body of work, you could have sections like "dissertation", "posters", "preprints", "popular articles", "lecture notes", "technical reports", etc.

You can do the same on your CV.


Automatically, and freely, download PDFs for a set of references

The answer here uses proprietary/paid software. I propose a FOSS solution that works reliably for this task.

The cross-platform software JabRef has integrated fulltext fetchers to download the fulltext for any entry in the library. Import your bib file into Jabref and select a number of entries. Then, from the Quality pull-down menu, select Lookup Fulltext documents. However, you still have to manually confirm the download in a pop-up. But this is still just a bunch of clicking 'OK's at the same spatial location (for each pop-up that appears sequentially) with the mouse. Jabref does the heavy-lifting in the back to correctly download the PDF and link it appropriately by matching it to each relevant citation entry.

The latest master build of Jabref is recommended, since there were some recent fixes to the IEEE Fetcher. https://builds.jabref.org/master/ (if IEEE matters to the OP)


Can a US university force a foreign student to obtain health insurance from a specific provider?

According to the international student health insurance page at the Colorado School of Mines, which also requires international students to enroll in the school insurance plan, it is legal.

The legal rationale they offer is:

It's not considered discrimination to have different policies for U.S. citizen vs. international students, so long as the requirements are the same for all international students regardless of country of origin:

  "The University may impose such a requirement on all students who are not United States citizens. Such a requirement is not regarded as discrimination on the basis of national origin by the courts. See Espinoza vs. Farah, 6 FEP 931 (November 19, 1973). This is true so long as no distinction is made between citizens of different foreign countries” (Joseph Goldhammer, Resident Legal Counsel, Office of the Attorney General, Dept. of Law, State of Colorado, regarding Foreign Student Health Insurance).

Federal immigration law itself imposes certain health insurance or other requirements on foreign students:

  Most students come to U.S. institutions under an “F” visa. Federal immigration law requires that this subclass of non-immigrants provide proof of their financial ability to support themselves and the cost of their education. These requirements have not been found to violate the equal protection amendment to the constitution. (Anwo vs. Immigration and Naturalization Service., 607 F.2d 435 D.C. Cir 1979). Colorado School of Mines considers medical insurance an integral part of the students ability to support themselves. Federal immigration law also requires that exchange visitors and their accompanying spouse/dependent(s) coming to the United States on a "J" visa carry medical insurance. ( 22 CFR 515.14)

(Note that J-1 visa holders are required to have health insurance meeting certain minimum requirements, not just any health insurance.)
Courts have recognized that specifically mandating health insurance for foreign students is not discriminatory:

  Equal Protection Analysis/14th Amendment to the Constitution: The U.S. constitution requires that "no state shall... deny to any person within its jurisdiction the equal protection of the law." Is requiring health insurance of international students discriminatory? Does it violate those students' constitutional equal protection rights? Case law differentiates the legal rights of U.S. citizens and permanent residents from the legal rights of non-immigrant aliens, those persons who are in the United States for a short period of time and for a particular purpose. Courts have recognized that requiring health insurance protects the students' ability to exist in the community, realizing the high costs of health care in this country (Ahmed v. University of Toledo, 822 F.2d 26 6th Cir. 1987). Further, courts have acknowledged that requiring health insurance is consistent with, and supports the purposes of, federal immigration law. “International students do not have a constitutional right to attend American universities without complying with the institutions' reasonable regulations.” (Plyler v. Doe, 457 U.S. 202, 1982).


How to move your field away from a widely accepted practice that has a catastrophic error?

Two quotes immediately came to mind:

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. - Max Planck
I'm trying to free your mind, Neo. But I can only show you the door. You're the one that has to walk through it. - Morpheus from The Matrix

To elicit a change of the magnitude you indicate, four aspects must be communicated clearly and unequivocally:

The existence of the error (i.e., demonstrate that the prior approach is incorrect). Other academics in the field may not recognize that there is an issue.
The history of the error (i.e., why the prior approach was used and how it has persisted for 50 years). Given its age and prevalence, other academics may understandably presume that the prior approach has been validated before and may dismiss your claims on that basis.
The implications of the error (i.e., what negative impact the prior approach has). The effect of the prior approach may not be clear or other academics may perceive it as negligible relative to the effort necessary to adopt a new approach.
The change itself (i.e., the course of action to rectify the error - the new approach). Other academics may not know what should replace the prior approach.

You should first make sure that these have been satisfied in your previous publications. Assuming this has been achieved, there is really only so much you can do (see the quotes). You obviously can't force people to change their ways. In addition to being patient, you can (where appropriate):

Continue referencing it in future papers and conference presentations.
Highlight it in peer review.
If you teach, incorporate into your courses.
Write a review article of the error in your field (one way to address #2 above).
Communicate (1-4) in relatively plain language on your academic blog (assuming you have one).
Send your paper(s) to the authors of the undergraduate textbooks with a letter explaining (1-4) and why the change should be included in the next edition.
Write your own textbook.


I sent an email asking for letter of recommendation almost a week ago and have not received a response. Does it mean NO?

No, it doesn't mean "no". The most likely scenario is that your email is one of many waiting to be dealt with.

I would suggest politely and non-presumptively following up on the email. Reply to yourself to maintain the thread and include the date you need the letter by.


My friends wanted to kick out our lecturer

If the instructor has issues with teaching then hopefully this will be brought up to the department and they can work with him to improve his teaching.

As far as your question about what you should do, just continue through the course as you would any other. If at any time you feel like the instructor isn't providing you an adequate education, then try to have a meeting with him before politely bringing it up with the department.


How to demonstrate your ability to publish in high-impact venues? (Application form)

The ideal way to "demonstrate your ability" is by stating that you've successfully done it. So, an optimal answer to this question would be along the lines of:

I have published 12 papers in top-tier journals and conferences, including the Annals of Mathematics, Physical Review Letters, and the International Conference on Machine Learning. My h-index is 65 and 4 of my papers have been cited over 1000 times each. I am already pursuing many additional lines of research that will let me continue this rate of publication.

Now if your publication record is less impressive, you might not be able to give a strong answer like the above, but you'll still have to make the best case possible that you will be able to produce several top-tier publications if they hire you. This is different than the previous questions, which focused more generally on your skills, interests, and experience.


Applying to a PhD with a weak masters thesis

First, you may be judging your own work more harshly than is warranted. It may not be as weak as you think. It is fairly common for problem to appear easier after it is solved than before you began.

Second, no one is likely to read your master's thesis as part of a doctoral application. They will take note of it, and any grade you got, and the general field. At most a few people will read the abstract. They are too busy to read it, frankly.

Third, an application for doctoral study is normally judged on a wide range of criteria with different candidates scoring higher or lower on the various elements. But the overall picture is what is important. "Does this candidate have the necessary background?" "Does this candidate have a good chance of success now and hereafter?" And since most programs are competitive, "How does this candidate compare with others in the pool?".

But, if you are accepted then you still have two hurdles. The first is passing comprehensive qualifying exams. Some advanced coursework may still be needed to get you to that point. The other is writing an acceptable thesis under the direction of an advisor, along with whatever research enables that.

In the US a lot of doctoral students enter the program with no research experience at all. You already have an advantage there, no matter how your recent thesis turned out. And, even at the doctoral level, not every dissertation has the same impact. It represents early work, not the person's best career work.

Make sure your CV is solid with your background accomplishments. Don't negatively characterize your thesis. Make sure your SoP explains your goals, short and long term, along with how your background supports that.

And, though you name a specific school, don't cast a narrow net for a doctoral program. Give yourself more than one chance.


Is it acceptable to contact senior people suggested literature?

It is perfectly acceptable to ask for information. His lack of a response could be due to a couple of things. One (most likely) is that he is just busy and this has low priority for him. The other, of course, is that he feels you should be able to find the answers yourself based on the phrasing of the question you asked.

If it has been less than a couple of weeks, I think you can still expect an answer. You can always follow up, of course, but not too soon.

You might also be able to get an answer you need from anything published at the workshop. It might be good to start that in any case.

And, BTW, a post-doc is probably chuckling a bit to be considered a "senior" person. They feel pretty far down the pecking order, actually. But even full professors can be asked, and will often reply.


How to find the ISI-indexed papers for a specific institution?

The easiest way would be to do a Web of Science search using the 'Address' field, with the university name or institution name as query. This will most likely return lots of results, and you will maybe need to go through them manually to do some quality checking. You can also refine search results by 'Countries/Territories' to filter irrelevant results (e.g. similarly named institutions in different countries). You can also use the 'Address' field to search for individual department names while also including city and country for some good results.

You can ofcourse do similar searches in Scopus etc. as well, but if you are specifically after ISI-indexed papers you should use Web of Science (maybe even restricting yourself to only the Web of Science Core Collection database).


What does being acknowledged in a medical journal imply?

From the Lancet:

  Acknowledgments — written consent of cited individual

From CMJA:

  Authors should specify, in the acknowledgements section, contributions to the paper that should be recognized but do not justify authorship, for example critical review of the study proposal or assistance with statistical analysis. The Canadian Medical Association Journal (CMAJ) requires that these people give their written permission for their names to appear in print.

From Infection Control and Hospital Epidemiology:

  Thank you notes. Persons should not be thanked in the Acknowledgments
  section without their knowledge and consent. Authors will be asked
  during the submission process to confirm they obtained permission from
  all persons thanked by name in the Acknowledgments section.

I suspect some of this is from the very defined notion of what constitutes authorship in medical journals, and the likelihood that someone who had some impact on the reported study would not make the authorship list. For example, the same ICJME that has developed the most widely used authorship standards also has this to say about non-author contributors:

  Because acknowledgment may imply endorsement by acknowledged
  individuals of a study’s data and conclusions, editors are advised to
  require that the corresponding author obtain written permission to be
  acknowledged from all acknowledged individuals.

Basically, the assumption is that, by being acknowledged, there is the possibility that you could be seen as endorsing the findings of the study, and that erring on the side of caution, you should have to obtain permission before acknowledging someone.

This is even true for not medically-specific journals. Consider, for example, this entry from PLoS One:

  Authors are responsible for ensuring that anyone named in the Acknowledgments agrees to be named.


How to know whether a journal is indexed by Thomson Reuters or Scopus?

Scopus journal list:

https://www.scopus.com/sources.uri

Thomson Reuters Master Journal List:

http://ip-science.thomsonreuters.com/mjl/


Discovered that my BA topic has been discussed thoroughly ...after i finished half of it. What to do?

Like @PatriciaShanahan said in her comment, you have the following possiblities:

Check it up if the previous work is the same as the one that you are actually doing. At this point, it would be advisable that you present to your supervisor with your current work and some past articles that resemble what you are actually doing. He could help you to see if its the same or not.
If indeed your work has been published before, then you can make a literature review about it; adding your own experimentation and so on. That could become your thesis for your BA degree.
If  your proposal is new or at least an extension of what has been done before, then you can continue it, but aiming maybe to a future publication.

In all the cases you can, and should, continue with your current work. Remember that what your professors or teachers look after your BA thesis is that you manage to amalgamate what you have learned on your undergraduate period, but not necessarily to present some novel contribution as it happens on the PhD studies.
Good luck!


Is it proper etiquette to keep religious content on official course page?

In general, probably not, but there are cases where it might be reasonable. Religion is an immensely powerful force in human society, so inevitably it will impinge on science and sometimes it's appropriate to talk about that.

For example, the science of evolution has been under attack since its inception by those who believe in a literal reading of the Old Testament and other such texts. In a course on evolution it might be quite appropriate to present a quote from the Book of Genesis in order to discuss that opposition to evolution. What would not be appropriate there is to present it uncritically, casting young-earth creationism as some sort of equally-valid alternative to evolution.

Robert Oppenheimer apparently named the Trinity nuclear test after a religious poem by John Donne, and he famously quoted two passages from the Bhagavad Gita to express his reaction to the first nuclear explosion:

  If the radiance of a thousand suns were to burst at once into the sky,
  that would be like the splendor of the mighty one.

  Now I am become Death, the destroyer of worlds.

Those passages are tremendously evocative and have been re-quoted many times. There's even a Linkin Park album named for the "thousand suns" line. I wouldn't consider it improper for a text on nuclear physics to include those quotes.


Choosing Writing Samples for Ph.D application

I'd suggest not to submit a whole thesis. Imagine the frantic look the admission committee members would have when they found out they just printed hundreds of pages.

Ultimately, they care if you can publish. So, definitely keep a and b, and focus on them heavily. For c, I'd suggest do a bit of curating and pick the most interesting chapter that does not overlap with a and b in contents. If none, then I'd suggest the literature review chapter. It's a good section to show your understanding of the field and your skill of information synthesis.

As for d, they only ask for three; course work (in my opinion) is not worth breaking the quota for. I'd, however, consider submitting if i) it features an extremely innovative idea which may become one of your study objectives, or ii) it acts as the foundation of your then Master's work and publication. It would show that you have the ability to carry and idea forward to fruition, and that's always a plus.

Good luck with the application!


Applying to state-side Graduate programs with European degree(s)

Usually a BSc would suffice. This is because PhDs in the US typically contain 2-3 years of lectures, coursework and exams before you do any research. This is the equivalent of doing a separate Master's (and indeed, many students pick up a Master's degree on the way to the PhD, almost by default). In the European system, PhD students start research from day one, so most will have a Master's degree already.

You could consider emailing the graduate admissions people at the universities you're interested in, to find out more about entry requirements specific to your own case.


What could/do applicants usually ask professors, and how does this reflect in a statement of purpose?

Can I ask more about what you research?

Don’t be so vague. You can find out for yourself what a professor is researching by reading some of their most recent publications. Think about the papers carefully and try and ask a pertinent question, for example:

  I was reading your paper X and have a question about Theorem Y. Is it related to Lemma Z as described in paper Q?

  Do you think I am a good fit for the university?

Instead of asking what the professor thinks, I would emphasise why I know I’m a good fit for that university. If you don’t like the look of the department, why bother contacting them in the first place?

  Would you consider taking me on as a PhD student?

I prefer “Will you be taking on a PhD student next year?”, although this may be just a cultural/ politeness thing.

  Do you think I am better suited for MS/MPhil than a PhD?

Again, I feel this is something you need to decide before contacting them. Look closely at the program requirements and think critically about your own skills and knowledge and where you will fit best. If you’re still in doubt, contact the admissions tutor with this question, not a potential supervisor.

Many of the PhDs I’ve been applying for lately strongly encourage inclusion of a potential supervisor's name in the statement of purpose, so they can direct the application to the relevant person. You could include a mention of the professor you contacted in the following way:

  My research interests lie in the field of pure maths, and more specifically how Lemma Z can be applied to Theorem Y. I would like to work with Professor A in research group B.

All of this is based on my own experience of applying to UK physics PhDs (which I am still in the process of doing).


emailing supervisor to ask about application status

It doesn't seem effective to ask the admissions office again if they have already said that you will hear only when decisions have been made.
But you could give the potential advisor an update that you haven't heard anything yet, asking if he has. But it seems unlikely that one of you would be notified and the other not.
Unless you have some actual reason for needing to know, such as replying about another opportunity, I'd suggest patience. You don't speed anything up by sending pointless emails.


In a manuscript, how do you know when you need to source the brand and location for materials?

It should be the case that material are not dependent on brand and location, but in many cases, especially the biological sciences, they are.  This is wrong and bad, but is also simply the state of the science at present, in areas that have not yet had standards and mechanisms for certifying those standards.  For example, something as apparently "simple" as DNA synthesis has no established quality control standards, so when somebody uses DNA supplied by an industrial supplier, which supplier can really make a difference!  The same is notoriously true for reagents as well---to the point where people will often put down not just the brand but the batch number.

So, how do you know when you need to reference the brand name?  There are two answers to this which are, unfortunately, somewhat contradictory:

Scientifically, you need to put it down whenever the expected variance in materials from supplier to supplier is might make a significant difference in the results that are observed.  If you don't know whether it will make a difference, you need to put it down.  Note that this is also strongly dependent on the size of the effect that you are measuring: if you predict and observe a function with high precision and minimal variance, then the materials are much less likely to matter than if you are observing a 10% variation in a noisy system and had to apply a significance test to determine that the result actually existed.
From a cultural perspective, you need to put the brand name down anywhere that reviewers in your field will expect to see a brand name, whether or not it is appropriate.  You can learn this by looking at papers, but it won't necessarily tell you what the scientific truth is, because there are often unsupported assumptions embedded in this cultural practice.

The conservative approach, of course, is to give brand for the union of both, and that's a reasonable strategy.  As methods progress, however, we should move toward the point where the mechanisms and experimental methods are well enough established that the effects of the incidental experimental circumstances can be minimized...


Weaker chance of admit if classmate has already been admitted to graduate program?

I am unaware of any graduate program that makes an active effort to diversify with respect to the undergraduate institutions of their students. If our top 10 applicants were all from UC Berkeley, for example, we'd have no qualms about admitting them in exclusion of applicants from any other school. Thus in a direct causal sense, it shouldn't hurt you at all that another applicant from your school has been accepted (other than the fact that there is now one fewer slots available in their incoming class).

However, knowing that a fellow student has been admitted already does change your conditional probability of being admitted, for the worse. Given that at least some acceptances have been sent out and you are not among them, it is now less likely than it was before that you will be accepted. But this logic applies equally well to any acceptance from any school; it is no more discouraging that the accepted student happens to be from your institution.