Finding a journal for specialised, interdisciplinary research

In which journals are the papers you are citing published? Which journals do these papers, in turn, cite? Which conferences and workshops have been around on your topic and where were the contributions to them published? These are all potential venues for your paper.

Also make sure to ask around among colleagues who work in the field and ask your supervisor.

You can always informally inquire with the editor of a potential journal outlet whether your paper falls within the scope of that journal. They might perhaps even be so kind as to suggest alternatives, in case they don't deem your paper pertinent.


Is it ethical for PhD advisor to collect ideas or even project description text from students/postdocs for his/her own funding proposal?

In many places, your stipend (including overhead) as well as the costs of running the lab, buying computers, publishing papers, and traveling to conferences all comes out of your PI's budget. That budget does not magically appear, but is funded through grants. Those grants have some leeway in what work they might support, but not infinite latitude.
So: going forward do you want to be supported? If so, would you not prefer to be supported to do something that you want to do, rather than whatever your advisor can get funding for without any help from you?
So, yes, it is entirely ethical for your professor/PI/advisor to ask you for ideas and even text to contribute to the grant application. Should you have no desire to help procure funding for the group to work on problems of interest to you, you really need to contemplate just how you are currently funded.


Being incorrectly assigned as a thesis reviewer?

You have a conflict of interest which is NOT your fault: declare it officially

You have been nominated for a duty in respect of which there is a conflict of interest of which the persons responsible for ratifying your nomination for said duty may be unaware. Given that you did not consent to the nomination, this is not your fault, but you have an ethical obligation to declare the conflict of interest officially and in writing. Once the conflict of interest has been declared and recorded officially, responsibility for adjudicating the appropriateness of your nomination rests with the persons responsible for ratifying your nomination.

Whether the conflict of interest is acceptable depends on local regulations and custom, but what you describe strikes me as problematic enough to disqualify you from being an external reviewer. But, based on how you describe things, the situation is not your fault. The professional response is to raise the issues with the person responsible for organising the review/examination/defence. I will address your four numbered points individually.

Re §1: being "from the same lab" strikes me as failing to meet the criterion of being "outside of the Students’ Educational Program" (but maybe the institution has a different interpretation? To be honest, I find their definition already very lax, since I would consider "external" to mean "not working at the same institution").
Re §2: in many places, the custom is for the external examiner/reviewer to be approached prior to being nominated, but this is not universal; at the same time, unless there is something in your contract about taking-up examining duties of this sort whenever requested, you should feel free to refuse.
Re §3: the short notice is not your problem, so you should feel free to refuse on that basis alone.
Re §4: this is the most serious issue, but it is not your fault, so you should be completely open about it.

Your questions

Q1: I would consider it dishonest if a reviewer/examiner failed to declare a conflict of interest, which is to what the problems you describe amount.

Q2: Contact the relevant office/convenor/official, and disclose the conflict of interest in writing. Explain that you did not agree to be nominated for the role of external assessor duty. Then:

option A (ask either to be excused or for confirmation to proceed)

Ask the office/convenor/official either

to excuse you from the assessment duty (this is the professional course of action if a conflict of interest is deemed unacceptable) or
confirm in writing that you can undertake the assessment duty despite your conflict of interest (if this happens, keep the relevant letter/message, and bring it to the defence -- that way, if you are challenged about acting as external assessor, you can show the letter/message and thus not be blamed for the situation).

option B (say you are excusing yourself on the grounds of conflict of interest)

If you feel strongly that the conflict of interest is unacceptable, you can, alternatively, simply notify the office/convenor/official that you refuse to act as external reviewer due to the conflict of interest. It is perfectly reasonable and professional to say this, unless you have misunderstood the nature of the role.

option C (say you cannot do it in the timeframe)

If you feel the institution does not take conflicts of interest seriously, you may wish to refuse due to the short notice of the examining engagement.

Finally

Do not keep quiet about the conflict of interest out of some desire to protect the Master's student. He/she may have acted inappropriately by nominating you; if so. it would be far better for him/her if this mistake is rectified before the defence, not after.

If you keep quiet and somebody else discovers this conflict of interest, it could have serious ramifications for the Master's student and you may be regarded as having behaved unprofessionally or even unethically. If, on the other hand, you declare the conflict of interest officially, then any blowback would be to the person/official who permitted you to serve as external assessor despite being told about the conflict of interest (because, when questioned about it, you would say, "yes, of course I was aware of the conflict of interest, and declared it accordingly to the dean and the rest of the panel; as you can see from this message dated ___, the dean confirmed that I can still act as external assessor; I was a bit uneasy about it, but I was not about to argue with the dean").


Can a letter from a professor not from my university but a high-ranking university carry extra weight?

Getting a good letter is more important than getting a letter from a professor at University B. So if the professor in question only knows you through your attendance of his course, he most likely won't be able to speak to your research potential. As that is the most important aspect of an application for graduate school, this would not work in your favour. (The points in this answer are excellent guidelines for who to ask for reference letters.)

If he is otherwise qualified to write a good letter for you, then the fact that he is from University B might work slightly in your favour, as admission committees tend to give greater weight to letters of recommendation from researchers that they know.


Has a doctoral degree any value outside of its main area?

Though the topic of your dissertation may be extremely narrow and focused, the process of acquiring a PhD teaches you the skills to attack virtually any problem very deeply, if given sufficient time.  Ultimately, the PhD is just a piece of paper.  The real value of it is the ability to produce something of value to others (i.e. research, a product, etc...).


How to choose the most worthwhile research papers to define my thesis?

I can answer this from the perspective of someone who did it poorly in retrospect, but from a different field (engineering). You will want to make sure that any papers you begin with are:

Accepted findings in the field. I made the mistake of basing much of my thesis work on a paper which was used a one-off paradigm, and was not replicated by anyone other than myself. This resulted in my needing to spend much more time validating my results than I otherwise would have needed to, because there was no other validation in the literature.
Simplicity over novelty. You're a graduate student, at the beginning of your career. You'll have tons of time to do awesome things as your career progresses. Unless you're working for Dr. Awesome BigName Researcher whose lab is known for doing cutting-edge work on X, be conservative... choose the less exciting but more likely to work research over the more exciting but very complex and/or more likely to fail.

Note that this post is completely irrelevant to anyone whose advisor effectively tells them what their thesis project is, as your criterion will be (1) the papers your advisor hands you. You have my sympathies :)


In my experience, different professors can have very different feelings about this. If you have any doubt, best to ask your primary adviser.


To include part of a published paper in a dissertation?

The copyright issues are the same as always. If you don't hold copyright on something, say you have given it to a publisher, then you need permission from the copyright holder to reproduce it for publication.

But you also need to be clear, if you just include copies of old work (copy paste) that you cite the original to avoid claims of self plagiarism. Claiming old work as new (or seeming to) is normally treated as an ethical lapse, similar to treating the work of others as your own. Cite and be safe.

To me, a "stapled dissertation" should be exactly that. An introduction, some material tying everything together, a conclusion, and literally stapling copies of the old papers. I doubt that very many would agree with me, but if that is what it is, then present it as such. Those places that permit such dissertations believe that a doctoral should be awarded for a body of work not necessarily for a single major work. The philosophy is sound, though I've never used it. That is to say, the "joke" isn't really a joke. It is fine if permitted by your committee and university.

Creative commons doesn't apply if you have all rights to your own work. Any license or no license would be fine. But it is the permission of the actual copyright holder that is needed. If they have licensed it generally under Creative Commons then it is likely that you can rely on the generally permissive nature of those licenses in your work. But if not, you can request permission (an individual license) to do what you want to do. I think that most reputable journals and conferences would be happy to give you back any required permissions, while they still hold the copyright.


Is there a website that shows current research strides in several academic fields?

I would not normally say Reddit is a good tool, and may get downvoted for suggesting such a maddening thing, but /r/science aka The Reddit Journal of Science provides a surprisingly high-level view of science research that is considered interesting, while also fitting your requirement that it splits information by field (the entire right side is dedicated to individual fields).

For example, these are some of the top articles from the past month.

Environment: NASA now says vast methane cloud over US southwest is for real
Social Sciences: The secret to raising well behaved teens? Maximise their sleep: While paediatricians warn sleep deprivation can stack the deck against teenagers, a new study reveals youth’s irritability and laziness aren’t down to attitude problems but lack of sleep
Health: Gut microbe found in people with eating disorders (bulimia, anorexia). Experiments show it produces a human hormone mimic that affects feeling of satisfaction, energy use, and mood. The severity of eating disorder symptoms is positively correlated with immune reaction to the mimic.
Neuroscience: Scientists have found “hidden” brain activity that can indicate if a vegetative patient is aware
Physics: Researchers have developed a new method for harvesting the energy carried by particles known as ‘dark’ spin-triplet excitons with close to 100% efficiency, clearing the way for hybrid solar cells which could far surpass current efficiency limits.

Obviously, you'll still have to do work of digging through potential garbage or low-quality sources and fact-checking. If it holds water, then you can dive into the related literature.


You mentioned the problem: "It needs to be something new". That's not only highly unspecific, but also extremely hard to gauge by a prospective PhD student.

Sure, you can start reading articles/conference proceedings and try to find interesting questions (e.g., what these authors mentioned as open questions). But in my experience, you need to be working in a domain/field to really get an idea which questions/problems are interesting and worth-while to answer/solve. After all, the research the papers are based on is usually at least a year old and conferences proceedings aren't that much up-to-date. So the person who likely can tell you whether something is new is your adviser, if s/he is actively doing research. A good adviser, who is part of the research community (visits conferences, works with other researchers, does peer-reviews for journals and conferences) should know what the other researchers work on (and thus reduce the risk that you get scooped half-way in your thesis) and guide you where you can make a contribution.

If you really want to work with this adviser, one way would be to check his/her publications and look for interesting topics/open questions. You could go from there and state your interest and ask him/her for possible directions where you can take his/her previous research. While the work has to be new and it must be your work, in my opinion it really helps to have a content expert to get started and to get good feedback. After all, I would consider a PhD an apprenticeship, not something you should do solo.


U.S. Government Shutdown -- potential effects for the upcoming Spring 2019 semester

The short answer is that the 2018-2019 US government shutdown shouldn't affect student loans for the vast majority of students, but some may have some issues.

Now, for the longer answer:

First, note that the Department of Education has contracted out loan services. In effect, the loan payouts (and repayments) are administered by non-government entities. These will still be disbursing grants and federal student loans. Second, I believe student aid programs are forward-funded to cover an academic year, rather than the calendar year, so the Spring semester should've been funded already. Third, the Department of Education is actually not affected by the 2018-2019 shutdown in the first place, as Congress has already approved the agency's spending bill.

That said, it turns out that the partial shutdown of the Internal Revenue Service (IRS) can cause issues for some. In particular, obtaining income documentation directly from the IRS does not appear to be possible at this time. This can affect both people repaying already incurred student loans, and students who applied for federal student aid during the shutdown - particularly lower income students, who are more likely to be flagged for income verification. So, to connect back to your question, the shutdown can affect students who didn't rely on federal loans or student aid during the Fall semester, but applied for the Spring semester, and who didn't have all necessary documentation available.

I don't know how many graduate students that would apply to, but it certainly applies to many undergraduate students. There have in fact been news stories about it. Now, I expect most universities will be flexible in how they handle these situations, perhaps accepting some forms of documentation they otherwise wouldn't have, or extending tuition deadlines. Students who find themselves in this mess should probably speak to their financial aid office.


How to prove that a student is plagiarizing with paraphrasing software like Spinbot?

I think you would need to know the particular source text that you believe it was modified from. In that case, demonstrating identical structure ought to be sufficient: a sentence-by-sentence comparison ought to show convincingly that the exact same ideas have been used in the same order. This absolutely falls under the definition of plagiarism (whether or not it was done in an automated way by a spinbot), and provided the text is of a decent length, it would be unreasonable for the student to claim that they happened upon the same structure by coincidence.

If you don't have the original text, I'm not aware of any tools you could use to search for it - that would seem to be a very complex (though maybe not insurmountable) AI problem. But if you don't know the source text, how would you suspect it in the first place (unless you'd caught the student in the act)?


Why is getting a PhD considered "financially irresponsible" by some people?

I don’t have experience in industry myself, but know several people who do (and have made the transition from industry to academia and vice versa).

Broadly speaking, getting a CS PhD in the USA with the intent of switching to industry after will result in about $500k in lost wages. This is accounting for about 5 years of PhD salary vs programming salary, raises, bonuses etc. The jobs that necessitate a PhD in industry are few and far between, and are highly competitive. Thus, starting a PhD with industry in mind, and assuming you’ll get that job is, statistically speaking, unrealistic. There are still many good reasons to still do it!

It’s a fun and fulfilling endeavor that offers you a chance to think freely about things you care about for 5 years!
If you are entrepreneurial then I know some people who start companies based in their PhD work.
If your undergraduate degree isn’t in computer science then your PhD can be treated as a semi vocational degree (though granted a masters will do as well)
If you’re interested in moving to the USA then a PhD offers a path to permanent residence.
You like research and want to leave the door open to academia. In that case a PhD is a must.


Math PhD after graduating with average grades

This is the sort of thing you won't know until you apply and someone with authority to decide evaluates your background. However, in general, your most recent work will weigh more heavily in a decision for most people who think about it for more than a minute.

However, you are in competition with others who don't have your "disadvantage" so you need to have some way to explain it. If your recent work overwhelms the past then you are more likely to be successful.

A doctoral advisor will be more interested in your potential for the future than in your past and will be looking for both deep knowledge and enthusiasm. Most likely the issue of getting funding or not depends on how much confidence he/she has in you rather then your past. But there will be competition, even there.

But if you don't ask, you don't get an answer.


Do schools/universities in EU prefer to appoint PhD graduates as teachers from their own student pools?

Each EU country has quite a different academic culture. Some are perceived as being quite insular, with a lot of hiring from within; some are considered "impenetrable" by outsiders; some are quite the opposite and offer significant perks to try to attract top notch scholars from outside. Each system has its quirks and it is impossible to talk about the differences without knowing which country you are speaking about here I'm afraid.

Speaking personally, I know that the Dutch university that I am about to move to has hired people in the same department as I will be in with degrees and research backgrounds in several other EU countries, but you can't really extrapolate that information out beyond the Netherlands.


Is using a similar experimental procedure and analysis structure to test something different considered plagiarism?

You are only building on the shoulders of giants, there is nothing wrong with that, as long as you cite the sources. Your hypothesis and your data are original, you are only applying a method that has the advantage of having been validated in the literature.
This might make your work less original, but what is the point of developing a new statistical analysis if a perfectly fitting one already exists?


Implications for the candidate if a contacted external evaluator declines

Chairs / deans / provosts will tell you that declining will have no effect. This is the official and morally as well as legally correct answer.

However, I've had the great pleasure (not) of serving on a committee (at a private, elite R1) where the promotion review chair did not like the candidate and raised the issue that there were a certain percentage of declines to strengthen their tenuous case against the scholar ("no one likes/respects this scholar thus they are declining to serve as reviewers).

This was counter to policy and in my mind immoral and possibly illegal depending on the circumstances.

If you do decline, please include a phrase that you are declining due to personal / workload reasons and that the committee must absolutely not use your declination to in anyway prejudice the candidate's case.

Now as to your subsidiary question as to whether you should feel obliged to write, this is more of a moral question. As a tenured full professor, I do feel an obligation to my discipline to do these reviews.

However, I will only do a review if I can do it well. If a candidate's work is out of my field of expertise or if my workload prevents me from doing a good job, I won't write. My first obligation is, after all, to my research agenda and my students.

Furthermore, there have been cases where I know too much about a candidate to write an objective review. In those cases, I ask to be relieved due to a conflict of interest.

There are varying opinions on whether one should write negative letters and this should really be a separate question. My own philosophy is that my letter is a third-person's neutral observation of the strength of the candidate's application for tenure. I thus write about the strengths that I see for this case, but whether the strengths are sufficient for tenure is ultimately a decision that should be made by the tenuring committees.


What simple events can a graduate student club organise to network with former students, companies, etc.?

Simple ideas:

Seminar where a professor gives a talk on his/her current research. Provide beer.
Invite an alum from one of the companies you're talking about to give a talk on something new from the company. Provide beer.
Simple cook-out, which includes beer (even better if this is a recurring event, monthly, once a semester, etc.).

More involved ideas:

Mini-poster conference, where a quorum of students have posters about their current research. Alum can act as judges, if you want to award prizes. Provide beer.
Invite a famous alumus to give a talk. This always involves more work than you're expecting, but can have big pay-offs. Might necessitate actual cocktails (and possibly pay for the speaker, but if you play it right you should find an alumnus willing to do it for free).
Field-trip to a local engineering firm that may have something interesting to look at (or a tour). Drinks at a local bar afterward.


I received an F32, how do I ask for more money?

I have worked as a research administrator in the Boston area for 8 years, and thus have seen all postdoc salaries in the areas I work (natural sciences, engineering, and computer science).  This is not how salary works for postdocs.

It is set by location.  Boston pays higher than other areas due to cost of living.  They have to set a rate that is sustainable to meet future commitments as well.
It is set by funding source.  NIH has minimums that must be adhered to.  If you don't receive NIH funding, you can pay less unless your institution says no.
It is set by field.  I work in a top research university, known for having high salaries in research positions, including graduate students.  Within the same building, there is a $30k disparity in pay between postdocs.  Econ CS folks pay $80k because the faculty have to compete with both finance and Silicon Valley stealing their postdocs.  Bio-engineering postdocs get the NIH minimum.  It's not personal--it has to do with the fields they are in and the competition for postdocs.

Of the hundreds of postdoc salaries I have personally managed, I have only seen PIs supplement if the fellowship pays below the department standard or NIH minimum.  If that's not the case here, I would not approach the PI.

The point of you getting an F32 is three-fold:

You learn how to write a grant on your own.
You can spend time on your own project, promoting independence in research.
You relieve the stress of procuring funding for the PI.

[Clarification on the compliance involved with this funding source:  F32s are highly regulated; the grants policy statement defines supplementation and additional compensation differently, and it's important to make sure we are explicit about which words we are using.

A supplement, is additional stipend funding that provides no benefit to the PI.  Because additional stipend funding must be consistent across the institution, frequently the policy is to use a department standard or NIH minimum as the policy to which a trainee is supplemented.  This is paid out as a stipend and is not certifiable effort.

Additional compensation, is essentially a part-time job which allows the postdoc to work on other projects up to a total of 10 hrs/week.  This is paid out as salary, and if on a federal grant is certifiable effort.

Unless they provide a part-time job for you (see policy statement), this leads to the conundrum of the PI spending more money on a postdoc who will not work on their grant.  Furthermore, you can't work on a grant that overlaps with your own.  This is probably why this method is less common than expected; if you request the raise of $15k, these additional funds (stipend, not salary) by definition must be of no benefit to the PI, because F32 Postdocs fall under the "trainee" definition of the Department of Labor.  If your salary is $58,500 and you received $15k in salary instead of stipend at the same hourly rate; NIH could cite your institution for non-compliance, because it's technically above the 25% figure that they allow for additional compensation.  The funding source is irrelevant.  Your institution should have guidance on how they handle F32s.  Here's one for UCSF.]

You are currently considered a bonus to the PI and a great relief. Startups don't last forever.  They are great for bridging funding when data and results are difficult to procure; funding new research that sponsors won't fund; paying for expenses that cannot be allocated to a grant (e.g., general lab supplies or travel).  She's not rich--there is plenty in her future to spend this money on, some of which could be on you (e.g., professional dues or travel).

Research funding is a rough game, so be supportive of her too.  There is some risk for her as well, as her future funding is not guaranteed.  Funding cliffs can be seriously painful for a PI, as they don't have personnel to procure data, do initial analysis, etc.  Everything comes to a crawl, and it's hard to get published or funded when you can't pay students or postdocs. Should this happen, she may become a ward of the department, which will cause her reputation to take a hit with her peers.

If you are still going to approach her, definitely consider how tough her situation is, even if she wants to give you everything you ask for.  In the end, you are both at the mercy of limited funds, and her responsibility is to make sure she has the funds to support everyone in her lab that she is committed to.


As a new faculty member, how do I avoid the Peter Principle?

Based on my experience with faculty, if you care about managing well, and don't want to be a bad manager, you are already doing better than many people. Again, in my experience, the worst offenders along these lines are those who think they are God's gift to their graduate students and postdocs, and cannot bear to hear any criticism.

So, if you want to do a good job managing:

Keep caring about doing a good job and encourage constructive
criticism/suggestions.
In particular, talk to the people you are managing, and find out
what they think. Lots of junior people are scared to even give
constructive advice to their seniors, because they don't know if it
will adversely affect them. It is obvious to say that you can often
learn a great deal from the people around you, but people sometimes
forget that this is very much true of the junior people you work
with as well.

This is only tangentially relevant, but this blog post by Matt Zimmerman is quite good.


I have found an error in a textbook. What can I do about it?

First of all, see if the book has a newer edition, and try to look at a copy and see if it corrects the error.

If not, then try to find:

The publisher's web page for the book
The author's professional web page, which hopefully has some mention of the book.
An unofficial errata list (google the book's title and "errata" or "corrections").

Check in both places for an errata list, which may already have a correction of the error.

If not, then it is worth trying to report it.  Writing the email is the easy part: just politely point out that you believe there is an error on page NNN, and explain as completely as possible why you believe it is incorrect.  If you think you know how it could be corrected, you could explain that as well, but it isn't strictly necessary.

The hard part is figuring out where to send it; publishers and authors should make this obvious, but often they do not.

For a major established textbook (which I assume this is), I would focus on the publisher, since the original author may well not be actively involved with the book anymore.  See if there is any contact or feedback information on the book's web page.

If you are a faculty member, the publisher probably has assigned a representative for your institution.  You may get a better response by contacting your rep directly and asking them to forward your report to the appropriate person.  If you are a student and this is your course text, you could ask your professor to contact the publisher's rep.

If there is an unofficial errata list, it should include contact information for the person who's maintaining it; send a report to them.

For a text or monograph with a smaller audience, you will probably do better to contact the author directly; look for contact info on their professional web page.

It's a good service to the community to report errors in books so they can eventually be fixed, so thanks for doing this.  However, if the publisher/author make it a huge pain to do so, that is ultimately their problem.  Make a reasonable effort to report it to an appropriate person, but if you don't succeed, there's no need for heroic efforts.


Salary and Rank Discrepency: assistant profs with better records than associates in the same dept

Position in a university, and consequently salary, is not simply a function of being "hot and young", grant funding, and publications. But there are many other factors you may be missing. For example, the associate professors in your department may be teaching larger classes (under the assumption that the department tries to give the assistants smaller classes while they build a resume for their tenure decision); they may also, with more experience, be better teachers. And they will almost certainly have far higher service loads -- sitting on committees, mentoring, reviewing duties, etc. All of these are things that are valuable to a department and that is worth a certain amount of salary. But it's hardly visible from the outside, even though it definitely diminishes your ability to do research and publish a lot.

Finally, the associate professors have one less promotion to look forward to, and consequently a lower salary potential. For example, an assistant professor paid 5% less than an associate will earn 5% more after promotion, which translates into a quite significant sum over the remaining work life.

I do get your point, and there definitely are departments that have significantly improved and where the young crop is better than the old, and should expect to be paid better when comparing at the same stage in their careers. But it's hard to determine a "fair salary" between different ranks if all you reduce things to is grants & publications.


Graduate school holding a diversity committee meeting. What do I need to do to be effective?

We (and indeed you) clearly cannot read the minds of those who have called the meeting, however I'd like to suggest a third option:

Someone in the administration is definitely trying to do something, but because universities are large and cumbersome organizations, change takes time.

The best things you can do are heading to that meeting prepared (which you appear to have done) and with an open mind. Assume the intent is to have a productive meeting, but also one that likely won't have a great deal of actionable things come out of it. First meetings rarely do. Express that you've got ideas, and are willing to work with them. And find out who the people are who you should be talking to - if the meeting does seem like it's sincere, try to finish by identifying at the very least who you should talk to about "next steps".

In terms of leverage? Almost none. But that doesn't mean you can't get things done - university administrators are human beings, and they too care about things. For example, at my university, the problems of first generation students are taken quite seriously and we still struggle at times.


Working with a Ph.D. supervisor that may have to take medical leave?

I'm a big fan of saying "donkey" when it's a donkey, rather than beating around the bush and calling it a grey-colored, short-legged horse.

The thing is: Everyone, including the professor, understands that any leave of absence he's going to take will affect you in a number of important ways. It's not like anyone can be mad at you for wanting to bring this up. So that's what I would do, acknowledging the awkwardness of the situation, in a personal conversation:

  Professor, I would really like to work with you, but I have one last, awkward topic I'd like to ask you. When talking to others in the department over the past couple of weeks, someone mentioned that you may take an extended leave of absence for personal reasons. It's really none of my business to ask you about this, or the reasons for this, but if I signed up with you, it would be something that clearly affects me as a graduate student. So I wanted to bring it up and see whether that was true or not.

That gives the professor an opportunity to tell you how it is. He will understand why you ask, and tell you about as much as he chooses to share. If there really are medical reasons, you're not likely going to get any better answer by going around his back and asking others in the department.

I'll also mention that over your career as a grad student, you're likely going to have a number of awkward conversations with your adviser anyway. You may have to talk about money issues (grant runs out and it's not clear if the follow-up grant will be approved), breaking up with your girlfriend and falling into a hole for a number of months, being sick for an extended time, etc. Professors have awkward conversations with students all the time, and the better ones have figured out how to have them without it being that big a deal. So talking about something you have a legitimate concern about should be par for the course.


When reviewing a manuscript for the second time, is it fair to comment on aspects I did not realise the first time?

I believe that it is entirely reasonable to make major requests of a manuscript on second review, as long as it is maintaining your basic standard for acceptance rather than moving the goalposts.

For example, I have had the experience where things about a paper were very unclear to me in the initial review because of shortcomings in the authors' presentation.  Upon revision, those things became much clearer---but not in a good way.  The extra information shed light on serious flaws in the authors' work, which has led me to in some cases recommend further major revision and in other cases recommend rejection.

On the other hand, some reviewers seem to like asking authors to do entirely new work, not because it is necessary for publication, but because the reviewer wants to know the answer or thinks it will make "a more interesting paper."  This happens most frequently with "glamour" journals.  I believe this sort of "moving the goalposts" on publication is not appropriate even in the first review, and doubly so in a revision review.


Can I change my master thesis topic and supervisor under following scenario?

Additional time is trivial compared to how you manage the relationships with faculty.
Ideally, you would go to your existing advisor, explain your dilemma/issue and he/she would be understanding and recommend that you pursue you new interest with faculty X.  That would allow you to maintain a positive relationship with the existing faculty advisor and avoid him/her communicating erroneously with other faculty.  This process is important to the extent that you wish to maintain a positive disposition of many faculty, not just him/her.  Will you need their recommendations any time in the future?
a
If you have an extremely tenuous relationship with your existing thesis advisor, xtent that you may need recommendations from any faculty for future employment, these steps are critical.  If you feel that your relationship with the existing advisor is weak, you might approach the department chairperson--but only if you are something more than a stranger to him/her.


Supervisor keeps "showstopping" defense with nit-picky grammar errors

The things you call "nitpicky grammar errors" are often (in my experience) symptoms of a deeper problem:

that the student has stopped caring about raising the thesis to a suitably high standard, and has not grasped what "completed" means in the context. An unfinished thesis simply can't be marked.

First, get your own proof-reader, and get help in getting all of these problems fixed - your supervisor is too busy to be a proof-reader, and it's an inefficient use of limited supervisory time.

Why is the grammar sloppy?

For different students, the underlying cause will differ; some won't be writing in their native language; some are careless; some have weak language skills; some haven't grasped the importance of good grammar and spelling to clear communication and to academic publishing. I've no idea which of these is true in your case, or if it's something else - that's between you and your supervisor.

Whose problem is it anyway?

You don't care about your grammar errors. That is your problem, not your supervisor's. You are angry. Again, that's your problem. Trying to make it your supervisor's problem, will make an enemy of someone who you need on your side. You think your supervisor's comments on content are trivial, and that is also your problem, not your supervisor's problem.

And now this post has maybe made you angry too. And that would also be your problem, not my problem.

I say all this, because accepting that they are your problems, is the first step to fixing them.

Collaboration not conflict

The problem that I am trying to help you fix, is that your supervisor is telling you what you need to finish, and you seem to resent doing it.  Supervision has to be a collaborative partnership, not a battle. Now, in theory, it's your supervisor's job to make it such. However, in some cases, in academia as well as in the real world, you often need to manage your manager - and that can mean you taking responsibility for ensuring that it is is a collaborative relationship.

So, find out what incentivises your supervisor, and try to put those incentives in place. Is it publishing papers? Esteem within the department? Conference papers? Get your supervisor on your side.

The worst case

And (take a deep breath): sometimes, when a thesis is genuinely bad, it's not apparent at first. All one sees on the first couple of readings, are a few errors here, and a few errors there; but when they're corrected, new problems appear.

It gets to be like "Star Wars the Phantom Menace" - the East Coast of the US produced one homebrew re-edit of it, to fix some problems; the West Coast produced a different homebrew re-edit, to fix other problems; but in the end, both re-edits and the original are pretty awful films: fixing the most obvious problems just exposed other problems.

I really really hope that's not the case in your case; but as this answer will hopefully be read by many people in your shoes, then at some point, it will be true for one of them. And at that point, that person and their supervisor need to think about a radical rewrite, or walking away from it as a lost cause.

Where to go from here

But for almost all cases, it's just a matter of getting your supervisor onside, getting a definitive list of the problems, and then you doing what your supervisor says is required to fix them. With them, write a checklist, and then return the checklist to them, with a note next to each one, stating how and where you've fixed it, or how you're defending it.

And finally - this post will inevitably contain spelling and grammar errors - it's Muphry's law in action. But that doesn't invalidate the advice in any way. With language, context is everything. This post is not academic scholarship; your thesis is.


How do I remove an article from Scopus indexing?

I would suggest you contact them directly

And explain why they should remove the article, with actual proof that it's no longer available in the journal in question.


We don't know the specific situation of the paper or your thesis, but as a general rule, you should be an author if (i) you participated in the intellectual development of the research in question, and (ii) you participated in the work that needed to be done.

So, if the paper is about determining the isotopic structure and age analysis of a bone that you collected and for which you had previously done archaeological analyses (i.e., the paper and your study look at different things), then you probably do not deserve to be an author because you only provided a bone, but did not participate in the research as reported on in the paper.

On the other hand, if the paper does not only do some isotope analysis, but also describes the archaeological setting as an important part of the paper (i.e., your work; rather than just quote your previous work to provide a setting for the paper), then you should be an author on the paper.

In the end, we cannot tell you whether or not you should have been an author because we don't know what exactly the paper contains, and how that relates to your work.


What's the difference between a degree in Mathematics and in Mathematical Sciences?

Short answer:

You should consult the specific programs you are interested in to find what they cover and how they differ at that particular institution, and the advantages of one versus the other depend on your interests and goals.

Longer answer:

"Mathematical sciences" suggests a potentially broader focus of study to include math-adjacent subjects like statistics, mathematical approaches to computer science, actuarial science, etc.

The specific focus of a given program depends on that particular program; a particular program awarding a degree in Mathematics could include study in 'mathematical sciences' as well as more of a 'pure math' approach, or it could not, and vice versa: a program in 'mathematical sciences' could include mathematics itself alongside other related topics. A program in 'mathematical sciences' in one institution might include mathematical statistics; in another institution there might be a clear separation with another program specifically in statistics and no overlap.

In summary: you should consult the specific programs at institutions you are interested in, most likely starting from their website (for example, for Oxford's MSc in mathematical sciences).

Advantages of one versus the other depend on your interests and goals, and can't be answered here.


Etiquette in difficult situation with colleague

Threatening is always manipulation. Usually there is talk than walk behind it.

it is not option to conform to his threatening behavior, and you certainly do not want to work with such a person. You owe nothing to that person if verbally abused you. So you should minimize interaction with such a person. Can you pull out from those collaborations?

There might be anti-discrimination institutions that -could- be helpful, depending on circumstances.


What kind of video conference software do academics use?

I use Skype and Google Hangouts all the time. No stigma attached. Go for whatever is convenient for everyone.


Should all voluntary self-identification forms for faculty positions be filled?

The forms generally help HR departments comply with legal requirements and might be used to alert departments about bias in either the advertising or hiring process. There is no harm in filling out the forms since any university you want to work for keeps the responses confidential. The forms are generally pretty short, so filing them out is not a big deal. That said, a strategy where you only fill out forms when the application process is reasonable might be productive. If the HR department cannot be bothered to acknowledge your application or doesn't allow uploading a CV, then maybe you should make their job a little harder too.


My co-authors don't want to help get our manuscripts published anymore. What should I do?

Parts of your question are too circumstance-specific to really be answerable without more details, but a couple of the final points can be answered a bit.

  Is it worth it to keep fighting these battles all by myself if they still benefit?

You sound like you resent the fact that they still benefit.  That’s the wrong thing to be focusing on: the question is, do you (and your field!) benefit enough for it to be worth your time and energy pushing the work through to completion/publication?  If so, then do it — and if they benefit, then that’s a bonus, and with luck they’ll even be grateful to you for it later.

If you feel a third authorship isn’t worth the effort it’d take, but e.g. a first or second authorship would be, then discuss this with your co-workers as honestly as you can.  Say something like: “I think this work is worth the effort to get published, and I would be happy to do the main share of the work from here; but given the amount of work needed, I think in that case we should consider changing the author ordering to reflect it.  Would you be willing to consider that?”

  I don't want to give up, but it's demotivating to have co-authors who don't care.

It’s not necessarily that they “don’t care”.  They may feel as frustrated and torn as you — caring about the work and wanting to see it published, but feeling dispirited about the chances of that, and that at this point their time and energy are better spent on other things.


Hypothesis incorrectly stated and submitted

I'm hoping to be correct here, but this depends partially on personalities. Since you found the error, you should immediately inform everyone involved of the error and offer to supply a corrected version immediately. If people are reasonable they should act reasonably, of course. If you wait, and someone else notices it, you will have difficulties.

Getting things absolutely backwards is likely more common than you imagine. Also, when you write and then proofread your own writing, you are very likely to see what you want to see, what you think you wrote, rather than what you actually wrote. Most reasonable people will recognize that, have a bit of a chuckle and move on.

But you have to be the one to raise the flag.

You raise this issue on a week end. If at all possible, don't wait for the new week to inform at least your professor.

One of the reasons that books have editors and journals assign reviewers is to catch these kind of errors of inattention. Sometimes an advisor will perform that function for a student, but not always.


Is it appropriate to send the abstract to the editor and ask him if my paper is a good fit with the journal?

Sure.  The benefit is really not to get wrapped up with a long review cycle for something that doesn't make it in anyways when you could have gone elsewhere.

That said, I think the very top journals (in science at least) like Science, Nature, PRL are pretty up front about weeding out stuff that is not notable and also committed to some speed in publishing.  So you might just get a fast answer on notability, regardless by running through the regular submissions process.  "We just don't publish cuprates that don't superconduct" was an actual editor communication from one of those magazines.


How does a University tackle admissions for Master's Degree from students that come from a different college?

There is probably a small overall effect. But most universities are interested in diversity, and many universities encourage their students to move on after graduation. The reason is that, if the faculty in a (sub) field is small, then you will benefit from wider exposure to ideas. You may have learned about as much as you can from a given faculty.

Some places will have strict rules that every applicant is to be treated similarly.

But the effect that I suspect is there is that some students develop a research association with a faculty member or group and there is reluctance on both sides to break it. Those students may have an advantage in continuing due to the letters of recommendation etc. that they bring.

But there are forces pulling both ways. And you need to do well, in any case, to take advantage of any asymmetry.

Students, on the other hand, often want to continue at the same institution. There may be geographical associations and a feeling of comfort. "BA, MA, PhD, University of Michigan" is a pretty common sort of thing to see.


How much guidance should I reasonably expect from an MSc Thesis Supervisor

I'm not sure how much of your issue is related to the specific field—mathematicians are known for being somewhat more independent than graduate students in, say, engineering.

That said, your advisor should at least show signs of being interested in your research. If you feel like you need help, and aren't getting any, then you need to make arrangements to get it. At first, I'd recommend talking to other graduate students and postdocs under your advisor. Next, I'd talk to other students outside the group; finally, I'd move on to other faculty.

It really depends on how easy or difficult it is to change advisors. If it's relatively easy, then in the end, it might be necessary as a last resort. If not, you'll need to make do with a rather unfortunate situation.

Ultimately, this is a case-by-case kind of situation: you'll need to talk to more people in your department and find out how widespread this is. Some advisors are completely hands-off, and expect their students to be self-motivating. Others are hands-on to the point of micromanagement. In math, my impression from conversations with colleagues is that the tendency is towards being hands-off, but it's impossible to say what will be the case in your specific department.


Busy professor failed to finish recommendation letters

First of all, find out if December 15th is too late to send the letters. If it's not too late, then you don't have a problem as long as the professor writes you a letter when he has more time.

Assuming the 15th is too late: Was the professor aware of the deadline when he offered to write you the letter? Did he have sufficient time to write the letter (I always erred on the side of at least a month, if not two)? If so, then he has a very real obligation to fulfill that promise. Writing letters of recommendation is not a favor that professors do for their students, it is a key part of their jobs as academics. Letters of recommendation is one of the key metrics by which institutions determine who they should accept. They help shape the landscape of the research community that the professors themselves are a part of. It is unfortunate for the professor that he has to spend a lot of his time writing a grant proposal to save his lab, but that does not excuse him from his other responsibilities.

Unfortunately, that doesn't necessarily mean that you should poke the professor every day and/or try to force the professor to write you the letter. Though he is the one at fault for failing to provide you the service that he should, you are likely the one who will suffer; either by not having a letter of recommendation, or having a haphazardly written letter that lacks attention to detail and fails to highlight your skills as a researcher. Normally I would tell you to find someone else to write you the letter, but given that you're out of time, I think your only option is to respectfully remind the professor that this is extremely important for your career, and that you require his letter of recommendation in order for your application to be considered valid. If he refuses to write it, then I would honestly consider that an ethical violation and encourage you to bring it up with your dean.

However, if you gave the professor 2 weeks notice to write the letter and/or did not make him aware of the deadline, then it may be hard to "force" him to fulfill his obligation as you did not perform your due diligence in lining up your letters early. That being said, most institutions have deadlines in December so I would assume that the professor was aware of the general timeline of when the recommendation would be due.


Double blinded review but the appendix contains author's name

When in doubt: yes.  Let them know when and how you found this potentially compromising information.  Especially if you think this may impact your objectivity (e.g. "I don't recognize this name, so I'm not going to trust him as much and may/will be more critical than I otherwise would"). But even if you think your evaluation will be unaltered, you should let the editor know.  They need to be the one to decide if the review process can still meet the necessary criteria, if the authors should be notified and asked to alter the file to eliminate the metadata, etc.

In your case it sounds like you did the entire review under appropriate double blinding, fully unaware of the authors while making the evaluation, and then at the very end of the process you gleaned a potential clue about the author name. If so, then the editor may accept that no actual problem has arisen, and may simply try to take steps to ensure such metadata is no longer visible to reviewers.

Things get more complicated if there are multiple reviewers for this paper: it now becomes possible that one or more of them saw this data early in the process, and it potentially compromised their review, but yet this went unacknowledged. This makes it all the more important to inform the editor.


How do I cite a result that I've only seen stated without a proof, and I prove myself?

If it's a textbook-level result, you could just cite a textbook. Otherwise, if you derived it yourself or with colleagues, no citation is required unless you published that proof earlier (not likely if it's a minor one). But you should definitely thank the people who helped in acknowledgments.

Finally, note that there is a threshold for citation: if a result is trivial, and as such is likely to have been independently demonstrated by many people over time, with no clear historical/seminal work, then you do not need to cite it.


When applying for a new job or fellowship, how to protect your ideas from being stolen by the lab you are applying to?

I wouldn't worry about this, unless you have some reason to think you are particularly at risk for having an idea stolen.

Ideas are generally not the bottleneck in research.  Any experienced researcher will have many more ideas than there is time to investigate, and the hard part is actually carrying out the research well.  This means there is little or no incentive to steal untested ideas, especially in comparison with the risk of professional embarrassment from an accusation of theft.

When I've seen impressive ideas in graduate school or job applications, I've admired the applicant more than the idea.  Sometimes there have been cases where it would be exciting to work on this topic with the applicant, but
I've never seen a case where an initial idea was so obviously great in isolation that I wish I could take it up myself without involving the applicant.

That's not to say theft can't happen, but I don't think it's a likely or worrisome threat.  There's also not much you can do to prevent it in this scenario.  You can create enough documentation to prove that you had the idea yourself, but it's much harder to prove that the other person hadn't already had the same idea independently (which does happen on occasion).  You might be able to prove that someone behaved like a jerk by not telling you that they were competing with you, but you probably can't prove that they stole your idea.

Given that it's not a big risk and isn't easy to address, I'd recommend not worrying about it.


apply for faculty while working in industry

I would think that you should consider a somewhat different question. What is the best path for me, now, to obtain a faculty position later? You probably have several options and each of them takes some time to implement. Which is the best path if the goal is to become a productive faculty member?

The two main pathways would, perhaps, be more education and some time in industry. Either can probably be good, but I would suggest that further/deeper education is probably going to be more valued than industry experience, with one exception.

If you were to find a unique, cutting-edge, industry position that puts you in contact with top-level research and development in an area that is seen as vital at the time, then that would be a nice thing to brag about on your CV. But working as a drudge in some mid-level outfit won't really help you advance in academia. These top-level positions are pretty rare, and may not be open to you with your current background.

Note that the top-level industry experience I'm mentioning is the sort of thing that you can bring back to the university to build a research program an/or give important advantages to students.

I think it is easier to find a way to stand out in the educational realm if that is where you want to be eventually, than it is to go and then transition back with the same level of excellence. But that is more opinion than fact, of course.


How and why do references in academic papers work?

But how does this work in practice? When a reviewer gets a paper, how can they check if the references are reliable? There are so many potential obstacles in the way - many authors and papers will be unknown (so now you need to review those articles as well); articles can be taken from obscure, out-of-print books and journals that are nowhere to be found; paywalls that the reviewer would have to pay out of their own pocket; etc.
It seems to me so impractical as to be almost impossible. How is it done in practice?

A properly chosen referee should be familiar with some of the cited references, but probably won't be familiar with all of them. If you're not familiar with any of the references, that's a red flag that you either should decline the referee request, or that the manuscript authors have little knowledge of the field. Leaving that case aside, most referees are probably more trusting of already published papers - at least ones published in reputable avenues. This is mostly reasonable, as they passed some kind of review already, hopefully from a knowledgeable and diligent referee. However, you shouldn't rely on that. Even when true, mistakes can be overlooked.
When you need to read another paper to understand a point/claim made in a manuscript you are reviewing there are some "smell tests" worth using (valuable for any paper you read, really):

Does the manuscript represent the cited paper fairly and without misunderstandings?
Do the results of the cited paper seem plausible?
Are they supported by good arguments?
How has the paper been cited (outside the paper you're reviewing)? After all, someone building on certain results is the person most likely to scrutinize them, so you may find additional support, counterevidence, or limitations in the literature. (Sometimes you can also find a better or more understandable exposition of the results.)

Depending on the specifics of the situation and the standards of the field, it may take more or less time to convince yourself that this paper is probably correct. However, fully "re-reviewing" the cited paper is (usually) not required or expected. If it is central for the manuscript you're reviewing then you might have to, but in that case the manuscript likely already retells the main argument, so it might be less additional work than you envision. What is much more common is to ask/suggest that the authors of the manuscript clarify, support, justify, qualify or hedge their statements as required. That is, you don't have to do the authors' work for them - they're supposed to convince you that their results are valid given the starting points. If they can't explain why the sources they build on are correct, well, they should at a minimum state their limits of their understanding clearly.
So ask if the approximations are justified under the current conditions, or if some external factors were accounted for in an experiment. Point out that technique X has some shortcomings that could affect the result, or if the validity of theory Y hasn't been established in the current regime. Doing so not only helps you figuring out if you trust the results, but also improves the paper for a less expert audience.
As for paywalls, you can ask the editor of the journal to provide you with a copy of papers you need for the review. If that doesn't work, or if the reference is an out-of-print book, inter-library loans can help you out. Ultimately, if the source is nowhere to be found (e.g. a unique original manuscript), or if the referee is unqualified to judge some aspect of the work, they should state so in the report.

The above is largely a description of how a referee could check if the references are reliable, and how they ideally should behave. In practice, however, corners will be cut in a number of places. Some people just aren't very meticulous, others don't want to spend too much time on working for free - especially if the manuscript is incremental, or maybe not all that interesting. Some people might see a famous name in the author list and conclude that the results are probably fine. Any reader should be aware that there are flaws in the reviewing process, and not trust papers blindly - especially when building on them.


The answer depends on what you mean by "count". If we consider whether they should be counted as citations: yes definitely. Afer all, the citations reflect how your science is read and then cited by others. It is then clear that these "count".

A problem occurs when using the citation counts provided by different services such as Researcher ID through Web of Science. Then it is not certain that the "in press" version is counted. I, for example have papers where in press citations exist. In Web of Science, I can actually see them but the connection is not automatically done so I would have to add them to the appropriate paper count manually. I know it is possible to write to Web Of Science and have references corrected or coupled. I, for example have another paper that occurs in four posts because people have written the wrong volume number, the wrong year of publication etc. Since I am senior and these extra citations are not critical to me I have not tried to get them corrected but they can of course be more important in an early career case.

Other services such as Google Scholar may work differently. I have opted for providing measures from services to which I can link and thereby have others verify my numbers. So in the end this becomes a technical problem, the citations certainly count.


How did authors prepare figures in their publications before the advent of computers?

I believe many of them did the drawing themselves with ink pen, for example. Graphs can be drawn using pins and a metal ruler: you put pins (or small nails) in a measured points of a graph, and then bend a ruler to pass through all nails. The ruler will eventually form a curve, known as a B-spline interpolant of a given set of points.


Requested *contact information of two references* in application for a PhD

You have to supply the contact information.
So:
Address (postal)
Email address
Telephone number(s) landline definitely, mobile not always
This is so that the admissions / adjudicating committee can get a reference according to their policy. That could be a 5 minute chat or asking the referee for a personal letter, or sending the referee a particular form to be completed.
Whatever they want, you need to supply the contact information. Be sure that if you don't then it will negatively affect your application, even to the point that it gets binned immediately. They have too many to waste time coming back to you "oh, you forgot the contact info for 2 referees"...


Co-authors on a study have cut communication, what can be done?

Ultimately, you can't make someone collaborate or communicate with you if they don't want to.  I think your only option is to either abandon the project, or rewrite it to remove the parts that your collaborator contributed and then publish it as solo work.  I don't see how union representation could help in any way.

I'm pretty surprised that this would happen twice, and would wonder if there's something about your interactions that might be causing it.  People usually don't voluntarily drop all contact with a collaborator unless something has happened that makes them uncomfortable to continue working with them - ethical concerns, abusive behavior, severe inability to communicate, etc.  If you have a colleague who works in the field, and you trust them to be honest with you, you might want to show them the history of your communications and see if they observe any red flags which you might not be aware of.

If you have any common acquaintances with this collaborator, they might also be able to give you some idea as to what is going on.

Normally I'd wonder if there is some involuntary reason for lack of communication - illness, personal problems, death, spam filters - but here it sounds like you've ruled those out.

Regardless of what initially caused the breakdown, I don't think your strategy of "weekly emails/calls for a year" was a good one.  I would probably send a maximum of about three messages / calls, with longer periods in between each, and the last one being an ultimatum of sorts: "if I don't hear back from you by date X, then I am going to do Y" (where Y could be stopping work on the project, or removing their contributions and proceeding, or whatever).  And then if they don't respond, you do Y, and move on with your life.  Persistence can be a virtue, but in this case I'm reminded of the saying about how insanity is when you keep doing the same thing and expect different results.

Another tip for the future is to have multiple projects going on with multiple different collaborators, so that if one of them falls apart (either for scientific or interpersonal reasons) you still have some publications.


Can I lie about my GRE score to get a better letter of recommendation?

I am tempted to say: "Never ever lie on an issue like that." Actually, I say: Never ever lie on an issue like that. First of all, it's wrong, plain and simple. Second, from a more practical point of view, you never know how it's going to bite you back.

It can taint you forever, even if here you are downplaying your achievement. It will be difficult for people to believe that you actually did that, and they will start believing that you are untruthful in other aspects, too. Frankly, it will raise more than a few question marks if it should come out.

You'll have to live with the exaggerating letters, or else to find someone else to write you a sensible one.


I submitted a paper to a journal one week ago. What does "Awaiting ME Processing" mean?

The acronym ME most likely stands for "Managing Editor" or "Manuscript Editor", and so the message says that the paper is awaiting processing by this person.  As shown in this question on the process for journals, that initial "processing" step usually involves an initial assessment by that initial editor, and if it passes that hurdle it will then be sent out for peer review by referees.


What is reasonable expenditure on meals during a conference?

Ask your advisor. Your university is likely to have a maximum allowable per diem that is based on the city that the conference is in. It varies from university to university, but mine just pays the per diem for that city regardless of how much you actually spend. Many universities do it this way. It saves time and money processing expenses on a meal-by-meal and receipt-by-receipt basis. If your university does this, then it doesn't matter how much you spend on yourself.

Also, given that the per diem is likely capped in the $40-$50/day range anyway, you are unlikely to blow your advisor's travel budget on food even if you hit the max every day.


Is it better to submit a paper to an important journal without the supervisor name or to a less important journal with the supervisor name?

In my view, using authorship as a bargaining chip like this is ethically inappropriate.

Either the supervisor's contributions to the paper warrant including him as an author, or they don't.

If they do, then he needs to be listed as a co-author no matter where you publish, and you need his agreement on where the paper is to be submitted.

If they don't, then he should not be listed as a co-author, no matter where you publish, and you and the remaining authors can make your own decision about where to submit (though you still might value his input).


How to report GPA, if minimum letter grade credits not reached?

It seems the National Defense Science and Engineering Graduate (NDSEG) Fellowship states:

  What GPA do I enter for my school if I just started attending? You can
  enter 0.0 as your GPA – reviewers will understand that you have not
  yet received a GPA for that school and will not view it negatively.
  Link: https://ndseg.asee.org/faq/academic_background_section

Will follow-up if I receive any formal statement from the UCSC Office of the Registrar.


Should graduate study be done when you are not fully interested in the subject matter?

An unmotivated graduate student will usually be a lackluster student at best. These students will be more likely to be distracted by whatever their true interests are.

Moreover, in a program like the one you are describing, you will be making a very significant career detour. You would be advised not to make such a move unless you are absolutely sure that it's something you'll want to do for the next four years, since you will have a payback requirement. If you're not sure about it, this is the kind of move that can wreak havoc on your career—particularly if you (re-)discover your dissatisfaction after the classwork is complete, and the service period begins.


Reviving a Rejected Proposal -- Question on Ethical Considerations

In the background that you have presented, I see only one half of the question being asked: "Will you join on this proposal?"

The clear next step is to query again with the other half, in order to make disinterest explicit, writing something along the lines of:

  Since you have not responded to my emails asking whether you would like to join this proposal, my understanding is that you are not interested.  I am intending to go ahead with this proposal, so unless I hear otherwise from you, I will assume you have no objection.

This places the question squarely with the other person.  If they respond one way or another, it resolves the question.  If they do not respond, you are free to assume that they are accepting that you submit without them.

Do, however, make certain to do due diligence to determine that the other person hasn't changed institution or email, such that your communications are not being received.  You may also want to try a phone call before giving up on contact.


The rationale behind academic and industry salary difference

I highly doubt university salary policies are based on "economic incentive", especially in European countries where universities are directly funded by the ministry of education. Generally, political, not economic reasons prevail.

That aside, competition for academic positions is already fierce - there is simply no need to offer higher salaries to attract candidates. Currently, candidates are attracted by reputation, the thirst for knowledge, and similar non-monetary considerations. It is by no means clear that higher salaries would attract better candidates: you would have to argue that someone who simply follows the money would make a better researcher than someone who is willing to put in long hours at low pay for the dream of someday being allowed to put "Prof. Dr." in front of their name!


budget allocation in research grant applications

Apart from asking your institution's research support unit (if there is one) as suggested in other answers, try to get in touch with colleagues with grants similar to yours (in terms of grant call, scale of the funding and scientific area) and see if they can show you their budget. In my experience when I was new to grant requests, this was the single most helpful thing that helped me tune my budget.


What are the key features of a short (15 min) conference presentation?

How can I balance the details of research without losing the audience on key points?

From my perspective, the key to giving a 15 minute talk is to omit all of the details.  Many audience members don't care, the few who do can read your paper, and in any case it's impossible to convey any serious details clearly and correctly in such a short time.  If you try, then much of the audience will stop paying attention; you'll end up wasting their time and missing a great opportunity to present your work.  Instead, your goal should be to ensure that everyone leaves with some understanding of what you've done, and that some of them are inspired to learn more.

This means you should focus on the big picture.  What did you do, how and why did you do it, and what have we learned from it?  In mathematics, I'd focus on context, motivation, definitions, theorem statements, examples, and intuition.  It's OK to give a brief proof outline or sketch, but nothing detailed or complicated.  If you can't summarize it in a few sentences, it's too complicated.

There are various ways short talks can go wrong.  For example, some of them try to compress 30 minutes of content into 15 minutes by talking fast and barely explaining anything, while others simply omit the background and context needed to understand the presentation.  However, there's a common difficulty behind many bad talks: they focus on the speaker's desires and goals rather than the audience's.  Ultimately, you need to design your presentation to fit the background and interests of the audience and the time available, rather than what you wish you could tell them.


I don't mean to be rude but JeffE's answer (which I cannot comment on-site as I don't have the necessary reputation)

  Whatever.
  Your major won't matter as much as your demonstrated potential for research in applied mathematics, which you can develop in almost(?) any engineering discipline.

is so off-base, it's like saying that majoring in English gives you license to do a PhD in any field that involves writing in the English language.

Engineering is certainly not a substitute for applied mathematics, and the transition can be very harsh.

First of all, you need to localize yourself. Applied mathematics in the US is different from applied mathematics in the UK, which is different from applied mathematics in France. Similarly, applied mathematics at Harvard (which would not be with mathematics, but SEAS) would be different from applied mathematics at Courant at NYU or in the Mathematics department at Princeton (who don't have an applied mathematics department, but rather a Program)
In any case, you will be expected to know all the core mathematics curriculum that pure mathematicians take in their first two years. From here, it will depend on what subfield of applied mathematics you're interested in. For example, if you are applying to a subfield that involves the classical mathematical physics (like solid or fluid mechanics), then you would need classes on those.
Engineering classes are vastly different from mathematics classes in almost all the mathematical topics. There might be some overlap in terms of, for example, fluid mechanics, but even then there is a big distinction between engineering fluid mechanics and mathematical fluid mechanics. For instance, mathematical fluid mechanics would involve more rigorous reductions and derivations of the Navier-Stokes equations (exploring techniques in asymptotic analysis, for instance).
There is some possibility of jumping from an engineering degree to an applied mathematics PhD, but again, this would depend on the country and the university and the department. If you want to examine the difference, look at the applied mathematics department at Cambridge University and compare to the applied mathematics group at the Courant Institute in NYU. Also, examine the PhDs of current faculty.


Dropping "acknowledgement section" in thesis

You would of course need to check with your university/department specifically, but I can't imagine anyone requiring it.

That said, consider what part of your thesis people will actually bother to read.  Bachelor theses (and even masters theses) will rarely, if ever, be read for their content except by your advisors.  Maybe someone will glance at your conclusions or use your bibliography as a jumping off point.

If your family or friends were to take a look at it, they're going to see your Vita (they probably know that already) and your Acknowledgements.  And they are far more likely to glance at your thesis than anyone else (just being honest).

I've on occasion, though, found the acknowledgments section very useful.  It will often point out scholars who have helped out, libraries that have manuscripts, funding sources etc. and while technically that's probably mentioned somewhere in the paper and/or bibliography, but frankly seeing something like this

  Much thanks to the Mr. I, the rare book collections specialist at J Library for having given me such wide access and assistance in research, and to the J Fund for Study which so graciously enabled me to spend the summer at K Library, and to Prof. L from M university, whom I met during that time, for her constant insights to N things.

can, in one paragraph, give more information that can help a young scholar interested in a similar field than the entirety of the thesis.


How to stay motivated during the final year of the PhD program?

The mistake that people make when "unmotivated" is to "take breaks." Of course, you need breaks from time to time, but doing nothing while hoping to later to be able to do something is a recipe for disaster. The best ways to stay motivated, at the end of a PhD program, or otherwise, has XXX keys:

Establish a system for accomplishing tasks.
Set your work calendar and stick to it.
Have a plan for when you are unmotivated, and use it.
Ward off distractions.

Establish a System

There are many programs for accomplishing tasks, and most involve creating a task list and checking off those tasks. Popular ones that I like included the Pomodoro Technique and the Getting Things Done methodology. Regardless which method you choose, follow it. This not only helps you complete your tasks on time, it also prevents you missing your graduation because of a failure to file the 1000 forms that all universities seem to require in your final year.

Stick to a Work Calendar

This is easier if you are teaching, but make sure that you have work days and 'off' days (usually weekends). It is important to work on the work days, but it is just as important to take off days off. If you don't all of your days blur together, and it becomes even harder to get 'up' for the work days. On every work day, you must do some work.

Have a plan for unmotivation

Everyone has days that they just aren't ready to go, so plan for that. For me, I go through old articles and re-read them, update my notes on things relevant to my research, or refine my programing. That usually gets me out of a funk, and I sometimes get good ideas from it. You should always have a 'backstop' for these tasks, too, so they don't become your primary objective, which leads to...

Ward off distractions

Everyone fights distractions, but the two that are killers at this point are: new project ideas and ankle biters. It seems like everyone who is working on a Dissertation suddenly has 1 billion ideas at the end for what to do next. The temptation is to stop working on the dissertation and start on a new project, because it is all shiny and new. Instead, write it down in a notebook of file you keep for that purpose and accept that you will come back to it when you have more time. If you always keep such a notebook, you will never run out of research ideas.

Ankle-biters can take over any life, mostly because they are necessary. Most important is that you you prioritize your work first. Be aware of the deadlines, and don't do any of them until you are done with your actual work, or until they are due. Your research is your job; filling our paperwork isn't. If you treat it that way, you will better be able to stay motivated.


The etiquette of leaving a faculty position

The following rules are pretty standard:

It's not reasonable to quit in the middle of a class except in a dire emergency (for example, a serious health problem).  In practice this means you can quit only between semesters, unless you aren't currently teaching.  Many universities plan their teaching one year at a time, in which case quitting in between the fall and spring semesters may be a problem.
You should try hard to leave enough time for your university to find a replacement for your future teaching.  For example, for a US-style semester system, announcing in January that you will leave as of the next academic year (starting in September) is probably reasonable.  Announcing it in April is more problematic, but it might be OK if you have to.  Announcing it in June is a serious problem, and announcing it in August is a disaster.
It's common for tenured, and sometime tenure-track, faculty to go on leave for a year or two rather than immediately resigning, even if they are sure they won't return.  If your chair offers you that option, then you should definitely take it.  Turning it down (and resigning instead) comes across as an insult: you are effectively saying that your new job is so much better that you can't imagine ever wanting to return.


Chapter in printed thesis vs. journal article

(Note: This answer doesn't apply to hard-copy theses provided to your university library as part of your degree requirements. These count as theses for the paragraph on exceptions.)

You're dealing with two separate issues here. The scholarly ethics of duplicate publication and the copyright issues. Let's tackle them one by one.

Scholarly Ethics

Most academic journals will not consider for publication work that his previously been published elsewhere (or is being considered for publication elsewhere); furthermore, the submitting author will usually be required to explicitly confirm that the work is not published (nor being considered for publication) during submission. This is known as the Ingelfinger rule. Subject to a few exceptions, discussed momentarily, the mode of publication doesn't matter: peer-reviewed paper, conference proceeding, book/book chapter, newspaper article, blog post, vanity publisher or predatory journal, it's been published. This doesn't simply apply to the manuscript, it applies to the work (So you can't rewrite the same analysis of the same data and claim the rule doesn't apply). You can read the reasons for (and against) this on Wikipedia.

Now, as I mentioned, there are some widespread exceptions, principally for things that happen in the normal course of academia. So inclusion in a thesis, even one that is made available online, is not usually considered publishing; similarly for conference presentations where no proceedings paper has been published. Expansion of communications into full papers is typically allowed. Increasingly, the use of pre-print servers is becoming permitted. Some journals/fields will permit submission of journal articles that heavily expand a conference proceeding, but in other fields this is a no-no.

Specific policies are set by individual journals/publishers. For example, Nature, Science and Elsevier.*

This means, when publishing, you should publish the peer-reviewed academic version first, then, subject to copyright, you can publish your book.

Minor consideration: (self) plagiarism. You should always reference the first publication of your work in any later re-publication, to avoid accusations of plagiarism (with a possible exception for publications derived from PhD theses). So even if a publisher allowed you to submit a journal article after you published your book, you would still have to cite your book.

*Interestingly, I did once inform Elsevier that a paper in one of their journals seemed to have been previously published elsewhere, and got ignored.

Copyright

Your options for republishing the paper as a book will vary depending on the copyright status of your publication. Here are some possible scenarios (not all will be available with all journals):

Open access publication that leaves copyright with the authors

You can do what you want to republish the article, including republishing it as-is, since you hold the copyright
You probably can't reuse the publisher PDFs for republication, as they will probably have trademarked logos on them
You will need to appropriately reference your original paper to avoid self-plagiarism

Open access publication that leaves copyright with the journal

You may be able to republish the paper under the open access license. This will depend on the license chosen by you/the journal.
You will need to consider whether there are clauses restricting things such as commercial use and the preparation of derivative works
You may find the license too restrictive, in which case proceed as for a non-open-access publication

Publication is not open access, copyright is with the journal

You cannot reuse the article without permission from the journal
You could try contacting the publisher, or using the Copyright Clearance Center to obtain permission
Otherwise, you will need to ensure that your book is different enough from the publication that it is not an infringement of copyright
Typically, this would require completely rewriting it from scratch (not merely paraphrasing), ideally restructuring it and re-drawing all the figures (trying to make them as different as reasonably possible from the journal version)
You may be able to obtain permission for specific components of the paper (e.g. figures) individually via the Copyright Clearance Center. In that case, you could use them as is, with appropriate acknowledgements
Academic ethics still dictates that you cite that your source is your original paper

Summary

Publish the paper first, then the book. You state that the book is merely "customary" - it can wait. Consider the copyright issues before publishing the book - this may mean you have to either seek permission from your publisher or modify your thesis chapter, if it is too close to the published paper. Protect yourself against allegations of self-plagiarism - ensure that your paper is very clearly listed as a source in your book.


Is it wise to mention any personal struggle in a statement of purpose (for doctrate program)?

I think a quick examination of human psychology suggests that being specific about this stuff is a terrible idea.  Even people who want to be neutral would associate you with murder (unfairly, of course).  Better to never put the idea in their head.


What to do when a prospective PhD supervisor doesn't follow up after an initial positive response?

The professor encouraged you to apply --- so that's what he expects you to do next. It is nothing wrong in your attempt to establish a more substantial connection with him and to promote yourself in his eyes, it increases your chances to get selected. However, imagine that at the same time there are probably 100+ other candidates, trying to do exactly the same --- sending him several smart research questions, involving him in some discussion, and expecting to chat over Skype with him in a few days. How would you feel in his shoes?

Of course, professors want to be available for their potential PhD students, TAs and colleagues, and of course, they want to participate in the selection process. But many of them do not want to carry out all the communication themselves --- that's what secretariat, admissions, and HRs are for! I assume there is a formal route to submit your application, and I suggest exactly what your professor suggested --- prepare your application and submit as instructed.

If in a meantime you receive a message from him --- go forth and suggest a Skype meeting. If not --- assume that the professor is busy, and submit your application before the deadline anyway.


Is it reasonable for an author to withdraw an accepted paper because they have since done better work?

No, this is not reasonable. It's up to you to determine that your paper meets an acceptable standard before you submit it, and stand by that determination unless you find a critical error in the work. Maybe it's not as good as what you're working on now, or maybe you're just overthinking things out of perfectionism, but it doesn't matter. Not every paper is a breakthrough, and that's alright.

Practically speaking, one less-than-exciting paper isn't going to give you a reputation as a salami slicer, and even if it did, this is much less bad (think several orders of magnitude less bad) than having a reputation for wasting editors' and referees' time because you won't stand behind your own work.

I'm not sure about the legal fine points, but you might not even be able to retract the paper at this stage without the editor's agreement (and why would the editor agree if there's nothing wrong with the paper?).


As Nate Eldredge has already mentioned, you should check your university's thesis guide if there is anything specific about code. If not, contact your thesis/dissertation office to see if they can help out.

I'll now speak from my own experience working at my university. I suggest to students that code be placed in the appendix material. Why? So it doesn't clutter the body.

If you're writing in LaTeX, be sure to read the documentation of any package you use to import your code. If you wish to leave it as a link, be sure to follow your university's instructions on that.


How to approach student in lab with very bad English?

As an adviser or mentor it can be interesting to learn how the person you are advising/mentoring is feeling. Based on the response, you might gain a clearer idea on how to approach finding a solution. It seems that the individual in question understands written English quite well given you mention you have chosen to communicate via email. I would suggest sending them a message asking them how they are feeling with the program so far and with their work in the lab, and what are some challenges he has faced or is facing. You could ask whether he feels his English proficiency has been problematic so far, and add a couple of other items to like working with the equipment and colleagues, for example. This opens a space for conversation that is minimally face-threatening to the individual and invites them to seek advice and guidance to help their better functioning in the lab.


Is it appropriate to ask the professor a trick question?

Asking it as a "trick", where you pretend it is a real question and you don't  know the answer, could certainly be annoying depending on the professor's mood.  So don't try to be tricky.

  Hi Professor, if you have a few minutes, I came across an interesting puzzle that I thought you might appreciate.  I thought the answer was pretty surprising.  [if invited to continue:] Look at this program; can you guess what it would output?

You should make it clear that this is a "riddle" to which you already know the answer.  If the professor isn't interested in spending time thinking about it, he can always ask you to tell him the answer, or just say he is too busy right now.

Also, you know your professor better than we do; use your own judgment as to whether he is someone that would find this sort of thing interesting.

Some commenters have raised the question of whether this is an appropriate use of office hours at all.  My view is that it is, since it is at least somewhat related to the content of the course (same programming language).  It also has the potential to lead to a technical discussion in which you might learn something.  I personally would be happy to have this kind of conversation with a  student during my office hours.

Of course, it should be low priority. If there are other students waiting with questions that are directly about the course (homework, lecture, etc), then this is not a good time to ask your puzzle; go away and come back another time.

I am assuming that your honest goal in all this is simply to share something that you think the professor will find technically interesting, and/or to learn more about it yourself.  If your intention is actually to "test" the professor, or to impress him with your obscure technical knowledge, or make him think you are smart so that you get a better grade, then please don't; that would be rude and disrespectful, and professors tend to be pretty good at seeing through things like that.


Can I get a postdoc in China more than 3 years after having received my PhD?

There are two kinds of post-doctoral fellowships available in China. The more traditional Chinese post-doctoral fellowship offers you a government-recognised certificate at the end of training. The more "Western" style does not. There are additional differences having to do with employment, benefits and such that are too individual to list here. Regardless, both are two year contractual commitments.

In general, the more traditional route is very strict in its requirements. You must meet age and graduation requirements and register through a common government portal. The strictness is due, in part, to closely aligned visa requirements. Thus, even if the institution to which you are applying is willing to allow you to attend four years after your PhD, the visa bureau is likely to decline this application.

The more "Western" style of fellowship is much more fluid because it is, in part, more structured like an employment contract and less a training scheme. In addition, there is no need for the academic institute to issue you a government-recognised training certificate. Under this route, there is more flexibility in entry requirements. However, this route is much, much less popular in China. It may not exist in some fields of research.

Good luck.


Doing a PhD or starting an industrial career?

Doing a PhD is a wonderful experience. It requires from you to become monomaniacal and obsessive with a very narrow topic in your discipline. There are many highs and many lows while you work on your doctorate. But the motivation should be your very own desire to learn and deeply engage in our discipline. Doing a doctorate for any other reason (e.g. professional opportunity,social status), will not keep you motivated enough -- let alone guarantee professional attainment. If your Master's thesis or your understanding of how academia works ("publish or perish") did not invigorate you to go for a doctorate, I would discourage you from spending your time and effort in pursuing it. Whatever you decide, good luck!


Can I publish research in a peer-reviewed journal if parts of it have previously been published in a self published book?

I didn't find any formal policies addressing this specific case, but my intuition is that it would probably be all right.  It could be analogous to publishing sections of a thesis, which is generally accepted.

If you have a journal in mind for the paper, you could contact the editors and ask their position on the issue.  If and when you eventually submit the paper, you should include a note to the editor explaining the situation, and probably mention this in the text of the paper as well.  If you disclose everything, there won't be any ethical issue; the editor can make the decision, and I expect there would be some good journals that won't have a problem with it.

Factors that might be relevant:

Was the book offered for sale publicly, or distributed privately among colleagues?
How many copies were produced/sold?
Did you retain the copyright on the book?


Creating compound alerts with Google Scholar

I think what you're looking for is a Google Scholar Alert for

  +"robot" +("deep learning" OR "neural network") +("navigation" OR "localisation")

Google search operators include "OR", "-" and "+", and permit brackets, but do not use "AND".

Fun fact: The order of the terms will change the order of results (and content of previews). That matters if the hits exceed the number permitted by your alert.