Proposing research as Ph.D. thesis in Sweden

When it comes to PhD and postdoc positions there is essentially two types of positions, and some partially overlapping ones. The critical element here is where the money for the actual research is coming from. That is way more important than whatever idea you might have for a project.

So if the money is coming from:

a specific grant with certain goals and deadlines, then the PI (the principle investigator, i.e. the group leader) will have to show some results. S/He will want to have someone work on that project and nothing else
alternatively if it's core funding (from the faculty/university/private funding etc) then the money is not "earmarked" and the PI can pursue interesting ideas more freely.

So assuming you are not bringing your own research funds, if you really want to work on your own idea from day 1, and not willing to compromise on that, then your only option is to find someone that has plenty of money and not many ideas.

Not to sound too grim but you should know that it's a tall order


My professor keeps opening my office door without knocking at the door

Ethical yes. Polite no, it is not. I do not see what ethics (resolving human morality) have to do with opening the door.

On a philosophical level, ethics and manners are kind of incompatible since they deal with a different nature of question.


Faculty or industry applications without phd advisor's letter

As someone who has served on academic search committees, I would say that you certainly raise a red flag about your application if you don't have your Ph.D. advisor as one of your references.  Not having your advisor as a reference is not a deal-breaker, but it does raise questions.

A couple thoughts for you:
1) Your advisor may have a much different (i.e., higher) opinion of you than you might expect.  They did choose to work with you, after all, and most advisors want their advisees to be successful.  Unless you've done something to cause your advisor to actively dislike you, I'd suggest reconsidering asking your advisor.  Even if the review isn't glowing, it could still be quite positive.  [For example -- I wasn't sure how positive a reference from my advisor would be, but it turned out that he was able to say positive things about my grad-school experience and training that I had neglected to highlight in my application.  His mentioning of those additional skills helped me get my first academic position.]

2) If your relationship with your Ph.D. advisor is especially strained, you may want to address your reasons for not including him/her in your reference list in your cover letter, CV, or some other document that you'd send in with your application.  As an application reviewer, I value honesty -- if you state why you didn't choose your advisor as a recommender from the get-go, it sets a tone that you're not trying to hide anything.  (We've all had tough colleagues and heard horror stories about advisors from friends, so we can understand.)  Be careful not to disparage your advisor too much if you go this route, though -- you never know who on the other end might know your advisor.

Good luck with your applications!


Share copyrighted stimulus material with collaborator

Non-profit research is one of the typical "fair use" exceptions to copyright law, so if it's OK for you to be using them for research, it's probably OK for you to share them with your collaborator as well.

Every country has its own particular regulations around copyright, so it's definitely worth confirming with them. If you're just using short excerpts as user stimulus and not publicly distributing, though, that should be pretty well protected in most jurisdictions.

That bit about "not publicly distributing", however, is quite important. As such, if you want to share with your collaborator, make sure you do it with some sort of access-controlled sharing system like Google Drive, DropBox, BitBucket, or even your own FTP server rather than just posting it openly on a webpage somewhere.


Being asked to pay penalty if fail PhD qualifying exam

In the United States, I have never heard of such a policy, and would consider it somewhat strange and vindictive on the part of the university.  Yes, it can be frustrating for professors when a student drops out with a Masters, but it's better to lose an unwilling or unable student early than to attempt to cudgel them along toward an ill-deserved doctorate.

In terms of "free rides" and "paying back," in most cases that I am aware of, a Ph.D. student who is supported by the department or their advisor is not just given money, but is working as a teaching assistant or research assistant.

Perhaps if one was supported by an external fellowship it might include such a term.  If I were a student, however, I would be very leery of accepting such an offer.


Nominating my Supervisor as a Speaker in a Workshop Conference

Why don't you simply ask her about her willingness to be a speaker? If you explain it properly to her, I think she might see it as a nice gesture (especially if she is as helpful and intelligent as you describe). However, I personally wouldn't nominate her as a speaker without her approval, since that gives off a vibe of you deciding over her head, which you should avoid.


How to attribute subfigures from other sources ? / Does cropping a figure consitute a change?

I don't see anything special.
A caption fitting the journal style but saying something like "taken from fig. 2e in ref #" seems perfect to me.
You are not cropping the subfigure.
But even in that case, and even if the figure would be data, you just add "spectrum, plot, whatever cropped" from....
Obviously what you let out should not contradict or shouldn't be much related to the point that you actually discuss.


submitting pre-prints at Tenure-track faculty application

Seems to me that (b) would be best.

"Preprint" usually means something that is ready to be published, so don't send something that isn't of publishable quality. You'll likely be asked to submit a research statement or something similar, in which you can describe what you're currently working on.

If you have at least 3 papers (or preprints) that you feel represent quality work, then there's no reason to send fewer than 3.  Obviously focus on the newest and best ones, but even an older paper gives an indication of the depth, breadth and quality of your research program.


How should I refer to non-permanent Web Pages, via Web Pages saved in PDF format?

I think that there are three main cases to consider here:

The web pages are aggregated data, e.g., in your example of a study that quantifies change over time.  Collecting web pages as data is routinely done in scientific studies, such as complexity studies that track a lot of pages.  In this case, the pages are not generally cited (and any data from them is likely to be at least partially abstracted and de-identified, to deal with a variety of legal issues).
An individual web page is a subject of study, e.g., for literary or intellectual criticism.  In this case, the standard references to the URL with time accessed is appropriate, along with block quoting of critical passages as part of your analysis.  You should save full copies yourself, and share them upon request, but likely cannot publish them unless you obtain permission or unless the source has explicitly adopted a copyright that allows republication (e.g., Wikipedia).
The web page is being cited as a scientific work (some overlap with the last case).  In this case also, the standard reference of URL with time accessed is appropriate.  This is unusual, since most scientific works go into archival papers of some form, but does happen---I've certainly done so, when that is actually the right document to cite.  This should still be a document with some expectation of longevity, e.g., a blog post on a scientist's established site, the archives of a mailing list or discussion group, a manual from a piece of software's distribution site.


Correct formatting of step-by-step equation demonstrations in papers

I don't believe there is a correct way to do this, because you shouldn't put them together.

Writing i = i + 1 fully contains everything the reader should need to know about the statement.  If you really want to lay out both a theoretical pseudocode notation and walk through an iteration, I would do them separately.  One way might be something like:

for i in range(0, 10):
    i = i + 1
    print i

  In this step we print to the screen the numbers 1 through 10.  For example, in the first iteration i takes on the value 0 from the first line, then has 1 added to itself.  The third line then prints 1 to the screen.

This way your pseudocode is treated like a mathematical equation in a paper, indented or otherwise separate from regular text, then examples as you go are just included in the text.  Depending on your audience and the complexity of the statements, you might also trust your audience to be able to parse your pseudocode without the need for filling in sample values.  Feeling like you need to walk through an example with numbers might be a sign that your pseudocode needs improving.

In short, trying to mash them together as you're suggesting just seems confusing to me.

The huge, important caveat to what I suggest: look through the literature specific to your field and see how this is done elsewhere.  If you can't find any examples of someone doing what you're asking about (which I assume to be the case since you're asking here rather than just emulating that), then don't do it.  Conversely, if you do find examples of it being done, copy that method.


Are you permitted to forward the reviews from a rejected manuscript when submitting to a new journal?

I have done this a couple of times (but not always going down in the journal hierarchy). In my cover letter I indicated that "the paper was previously submitted to [blah], but was rejected because [...]. A copy of the report can be obtained by writing to [editor name]."

The motivation for not including the copy of the report is that it keeps me honest. I can't just select the bits I like.

I have never had any problems with this approach, and I believe it to be the right thing to do. It saves editors' and referees' work.


Latex submission template: keep figures to margin size?

I strongly advise complying with the formatting guidelines that you are provided.

Organizations like Elsevier give you a template an submission instructions for a reason, and in many cases the final formatted version will look nearly identical to a submission that follows their template. You can push your luck by violating the formatting guidelines, but this will make you look unprofessional and may annoy the editor and reviewers.  Do you really want to take that risk?

More to the point: most visual material can be readily organized into a number of formats.  Are you certain that you must have massive landscape images?


Are there any professors with PhDs in Humanities from Asian Universities working outside of Asia?

Update

I found at least one. Hikari Hori currently teaches at Department of East Asian languages and Culture of Columbia University. She received her Ph. D. in gender studies and Japanese visual cultural studies from Gakushuin University, Tokyo, in 2004

End of Update

I am no expert in Asian studies. Please take my opinion as a grain of salt. However, being a native Chinese speaker and having read some academic papers about politics and economics in Asian Studies recently, I feel that I want to say something about your question.

  getting a degree from Japan would be more or less "career suicide"

This may have some truth in it if you study one of the STEM fields because many good schools in STEM fields are not in Asia. So, you have fewer choices if you pursue PhD in Asia.

But, you study in an Asian-studies related field and you go to North America or Europe to study it? This does not make sense to me. Let's say your topic is related to social economics in Japan. You don't want to study Japanese and live in Japan to observe its social economics by yourself? You go to US and read papers about Japanese social economics without seeing the recent developments in Japan and then write your own papers?

On the behalf of all Asians, I certainly welcome you to stay in Asia, speak Asian languages and then study Asia. We would all appreciate it! Thank you.


Possible pitfalls of taking a year off to travel following a PhD instead of immediately starting with a post-doc position?

Although I envy a PhD graduate who has the funds left after obtaining a doctorate to pursue a year of travel, I don't think this is a good idea (unless your degree is in anthropology, in which case it's probably a great idea!) Some thoughts:

You are at a tenuous position in your career -- you've reached a peak (not necessarily the top-most peak), and you are very prepared for academia (although possibly not mentally, as you allude). Your degree has a half-life of sorts -- others will continue to do research in your field while you jet-set the world, and your own work will start to get stale. Now is the best chance you're going to have to convince people who may want to hire you that you're a candidate at the tip of the spear, so to speak.
While a year is not too long, your letter-writers aren't going to have as fresh a picture of you from which to paint their glowing recommendations. You can mitigate this by asking for letters now, but you'll want them to review the letters a year from now (and change the date!) when they do submit them for applications.
Academia can be a fierce environment, as you've probably learned during your candidate years, and possibly why you don't feel you're ready. But, removing yourself from the process for a year doesn't help your case in academia, except to possibly calm your spirits in order to be reinvigorated in a year. Although not universal, the people working the hardest get the best jobs.

All of that said: do what you feel is best for you. If you're not ready for academia, by all means remove yourself from the process for as much time as you need. Better to have a harder time getting a post-doc in a year than to spend a year burning out on something you're not prepared to do.


How strange is it (as an undergrad) to email a professor from another institution about possibly working in their lab?

Not strange at all, just don't expect a quick response!

A plan of attack can be summarised in the following way:

1) Be specific

Make sure your email is brief, polite and clearly outlines why you want to work in their lab in particular.

I would recommend searching for a few different labs that do the specific research you're interested in, which you can find out by looking for recent publications or on the websites of the relevant institutions. Perhaps someone in your current department can recommend a lab- they may have connections, or would be willing to write you a reference letter.

2) Be persistent

If you don't get a reply within a few weeks, follow up once and then let it lie. Try asking someone else.

Most importantly, don't give up- it took me nearly three months of emailing back and forth with ten different people when I was in a similar situation last year.

3) Be enthusiastic

Remember professors are generally happy when someone expresses an interest in their niche field and shouldn't just dismiss you offhand.

Good luck!


How to extend and convert a conference paper into a journal submission?

This varies from journal to journal. For example, in some subfields of CS (where this comes up all the time), the informal rule is that the journal version should have at least 30% new content (including new experiments, new algorithms and so on), and this new content should be identified clearly in a cover letter. In other subfields (like in theory) the expectation is that all proofs will be presented in full detail (no sketches), but new results are not necessary.

So it depends greatly on the subfield and the journal. As always, when in doubt, ask the editor of the journal, or colleagues who've submitted there before.


Peer review in Computer Science Journals

In computer science, unlike in the majority of other academic fields, most research is published as articles in conference proceedings, and conferences do follow a quick review process. I imagine that the pressure on journals to provide a quick review process is thus less strong.


I think that you may experience what can be characterized as Frustration.

  frustration is a common emotional response to opposition, related to
  anger, annoyance and disappointment.

As you're reading scientific papers, you're on higher level of scientific work than is expected from graduate student - I did not read too much papers during my MSc.
And it depends also what is expected of you by your colleagues, so compare whether your frustration is not combined with Imposter syndrome mentioned in comments.

E.g. Authors usually spent several months or years to produce some results and to write a paper. So understanding the paper may take also some time to readers. Other problem is that some papers are so brief thus it's rather a problem of the authors if they can't explain their scientific problem or solution to somebody outside their domain niche.

I have been experiencing frustration personally many times during my MSc, PhD and my current postdocs projects. When it happened I gave myself a time limit. So during that time limit it's good to consult the problem with somebody else. If I don't make any progress and frustration continues after the time limit, I give up and move to somewhere else.

The limit and tolerance to frustration is very subjective. Nobody should expect you to grasp all problems and in short time. My oppinion is that mental health is more important than scientific achievements.


Found an error in a paper that I already presented at a student engineering conference; what should I do now?

For a paper published in a journal you would go for errata if the mistake is minor and does not invalidate the conclusions of the paper, or for retraction if the mistake invalidates the conclusions. In your case I would contact the organizers of the conference and ask what you should do.

You may feel ashamed about making a mistake that goes into publication (I talk from experience) but acknowledging it and trying to fix it is laudable (not everyone does it), is the ethical alternative and it will give you some peace of mind afterwards.


PhD in the Netherlands: Can I negotiate the starting step in my salary scale?

Short answer, no.
Every PhD student starts at the same level, I have never heard of anyone negotiating a higher salary (I did my PhD in the Netherlands). The only two exceptions I am aware of are a) medical doctors doing a PhD - they start at a higher salary - and b) people funded by an outside source like a foreign government or company, where the outside source stipulates and pays the salary.
But a higher salary based on work experience: no. I don't suppose there's any harm in asking if you have already accepted the PhD position, but don't get your hopes up. I actually know one PhD student who has tried it, but she got shut down fast by HR.


What is your paper for? I think figures (for example in journal articles or thesis) usuaully have a caption below them, in addition to their number:

  Figure 1.  Cumulative food intake in rats during intragastric treatment

But typically there is no "title", unless you have a "list of figures" somewhere in the beginning of the document: then it is ok to use the same phrase as caption and title, because they are not written at the same place.


I uploaded a transcript in my online application for grad school but did not include the back side (transcript legend), should I worry?

Unless your undergraduate university has an uncommon or very different grading system than that of your prospective graduate university, this should not be a big deal. Your prospective graduate university will most likely ask you for originals or certified copies of your documents when you are admitted.

The uploaded documents have no official value and are used by the committee to decide on your aptitude for the program. As long as no important information is missing, you should be fine.

That said, there is nothing against sending them the full document now, so go ahead if you are worried. The worst that can happen is that they ignore your email.


Finding the total number of papers published in a given journal, for a given year

If the journal is indexed in Web of Science, this can be easily searched for. You mention it doesn't seem to help, but I don't understand why. In the main search window, search for 1) publication name = [name of journal] and 2) published in whichever year you're interested in.


Is it a good academic practice to tell the reader in the introduction what the essay is about directly?

I'm not sure what you mean by "essay", but for an academic paper in general, the reader should be told a minimum of four times what the paper is about and what your contribution is. This should be stated in (1) the title, (2) the abstract, (3) the introduction, and (4) the conclusion.

That is a typical North American style. In some academic cultures, such as Northern Europe where I'm sitting, it's common to not do any of that. In a typical paper here, you can read all of the four parts mentioned above and still have no idea what the author is bringing to the table. You're guaranteed to annoy many readers that way.

So my answer to your question is: Tell the reader as soon as possible what the point and punchline of your paper is. The reader doesn't want a mystery novel, he wants to know as soon as possible whether your paper is worth reading.


Writing a recommendation letter for PhD advisor

Because you're being asked for a letter of recommendation for an award given to a faculty member for good mentoring, this letter is going to look very different from the kinds of letters of recommendation written for students applying to graduate programs, faculty applicants, etc.

For your letter, the goal should be to show that this faculty member has been a good mentor to you and other students.  You can best make the case for this by describing in detail how the faculty member has mentored you.  How does he or she interact with you?  What do they say when you're struggling with something in your research?   Do they ask you to discuss your long term goals as well as your short term plans?


There are a wide variety of postdocs available, which makes summarization challenging.  Typically, the goal of a postdoctoral fellowship is to broaden your research experience and better prepare you for a career in academia immediately after your graduation with a PhD.  Postdocs are extremely common in the sciences.  (Perhaps they are a bit too common.)  As mentioned by Andreas Blass in the comments, many positions are advertised seeking recent (i.e., within 2-4 years) PhD grads.

It is possible to do multiple postdocs sequentially, though anything beyond two is a bit of a red flag for being hired in academia.  It's probably best to think of your PhD graduation as starting a clock for academic positions.  If you haven't gotten an academic position within five years, then the application process becomes quite different.  If you are planning on waiting this long, you would likely be better off working in industry or at a research lab and attempting to make the transition back to academia without doing a postdoc.  (I'm not familiar with this process, so I won't comment on it.)

If you're interested in more information about postdocs, I can recommend the following sources:

The National Postdoctoral Association has terrible web design, but there's lots of good information there if you can dig for it.
Georgia Tech's Office of Postdoctoral Services has a lot of great information, albeit targeted towards GT Postdocs.  You should also look to see if the places you're applying have a similar organization.
Peter Feibelman's A PhD is Not Enough!: A Guide to Survival in Science is a relatively short book on how to succeed as a postdoc.  It was recently updated, and is probably the best generic introduction to life as a postdoc available.
The CRA's Postdoc Best Practices Guide is intended for postdocs in computing, but I don't see why it wouldn't be valuable to a broader audience.  It's much shorter than Feibelman's book, and covers some of the same ground.


How to create an environment in which students can report teacher-student sexual harassment?

I refer you to the Student Conduct Administration & Title IX:
Gold Standard Practices for Resolution of Allegations
of Sexual Misconduct on College Campuses report from the Association for Student Conduct Administration. While this report is specifically about responding to complaints about student-on-student sexual harassment, many of the "best practices" described there apply more generally.

Some specifics from that document:

To better understand the climate on your campus, there is a list of "Questions to Ask Your Campus" on page 19 of the document mentioned above. These questions may help you identify the problems and a way forward for your specific college. (There is no one-size-fits all resolution to this problem.)
Find out if it is possible (e.g. for your Office of Institutional Research, if you have one) to conduct campus-wide climate surveys to understand whether existing efforts to inform students of sexual harassment policies and procedures are effective. If (as you suspect) they are not, this survey will serve as a baseline against which to judge the effectiveness of changes in how you present and disseminate these policies.
How comprehensible are your policies to your student body? Would your students feel the need to involve a attorney or a parent in order to understand the policies and procedures related to filing a sexual harassment claim?
Make it easy to report sexual harassment. A campus should have several avenues through which students can report (phone, in-person, email, and online form, for example).

To reduce the barrier to making a "formal complaint," make the student's first interaction as simple as possible:

  For example, if the first conversation includes something like, “You’re not going to want to go before a hearing board of three
  older faculty members that you might later have as instructors and discuss intimate details of your sex life,” that student is not likely to file a formal complaint.

Help students understand that even if they are not prepared to make a formal complaint, they can still get some relief from the situation (with "supportive measures" as they are known in Title IX). For example, in your scenario, the student should be allowed to change classes (and she should understand that she can transfer to another class) even if she is not ready to proceed with a formal complaint.
According to the April 2014 Q&A Guidance on Title IX from the OCR, the school's written Title IX grievance procedures should explicitly include "sources of counseling, advocacy, and support" for students. Does your school's policies include these? Are they adequate?

Another useful document is How to Protect Students from Sexual Harassment: A Primer for Schools, from the National Women's Law Center.


How to use MeSH Qualifiers in a PubMed search string?

MeSH terms are divided into descriptors (or main headings) and qualifiers (or subheadings). Each descriptor can have zero or more qualifiers. A qualifier cannot exist without being attached to a descriptor.

The difference in the number of search results you have observed is because in your second search "locomotion/physiology" [mh] you are searching for entries which have the locomotion descriptor and physiology as a qualifier of the locomotion descriptor. In your first search "locomotion"[mh] AND "physiology"[sh] you are searching for entries with the locomotion descriptor and physiology as a qualifier to any of the MeSH terms attached to the entry.

For example PM28410594 is matched by your first search, but not your second.


It may be GPA. It may be rank in your class. It may be your percentile on the graduate exams. I agree with @GrotesqueSI: The answer is to email the professor again and request clarification.


Should I include salary information on my CV?

This is not standard in any academic or industry context I am familiar with.

Typically salary negotiations (if they exist and a position is not simply funded at a fixed salary) occur after a hiring decision is made, that is, a step past when someone is reading your CV.

I would find it odd to see salary information in a CV.


Pursuing a Masters, trying to figure out the potential effects of my undergraduate transcript on PhD admissions

You're right to be concerned. Some places will be scared off—or more accurately, won't even see your application—because of your undergraduate record. But some won't. Some will see your strong record in computer science, in graduate classes, and in research, at the expense of other classes as a sign of passion/focus/geekery (which is a strong advantage in research) combined with immaturity (which most people grow out of).

PhD admission is a random process, a numbers game.  You have a high-variance record, so to be reasonably confident of admission, you should apply to a wider spectrum of places than someone with a more consistent record with the same average.

I strongly recommend discussing your concerns directly with your letter writers.  They have to make the case that the admissions committee should ignore the black marks in your record and focus on your considerable strengths—good performance in graduate classes, excellence in your chosen field, strong research ability, and so on.  (You can't really make that case yourself.) Your references may also be willing to contact colleagues directly, to convince them to pull strings on your behalf.

Also: PUBLISH!

Best of luck!


Should a letter of recommendation be customised for each university when applying for a masters program?

Never hold your own recommendation letter (looks unethical), let your current lecturers send the recommendation letter to the universities directly (via email for example), that you applied for.

Most universities, ask for two recommendation letters, by asking the information of the lecturers (e.g., email, address, phone, etc.) who do that for you. So the recommendation letters will be sent by your lecturers (e.g., email, mail, online form, etc.) to the universities you applied for; without you seeing/holding the letter.


Is it appropriate for a journal to cancel an accepted review request before the deadline?

Is it ethical for journal to cancel accepted review request before deadline?

In some circumstances, it would be ethically required to cancel the review request.  The editor has avoided wasting more of your time by cancelling the request.

"Unforseen circumstances" probably means the authors withdrew the manuscript.

Canceling a review request can also occur when another reviewer has submitted a review which ensures the manuscript cannot be published.


Given that a correct and satisfactory proof exists in the literature, you would not be providing "research results" per se, so a full research article probably is not worth writing at this stage, unless you can devise a more elegant or straightforward or otherwise "improved" proof.

If you are unable to provide that, it would certainly be appropriate to comment on the difficulty of correctly proving the theorem, and do a "comparative" study in the form of a letter to indicate the challenges and make them known to a wider audience.

But, as you said, it's certainly a matter worth talking about—it really is a question about the appropriate "form" of writing your results up.


Graduating with a PhD in May, should I take a good offer in an undesired location?

If you care about your career, be prepared to move to wherever you find the best opportunity.


Why might researchers distinguish their interests between applied math and computational math?

"Applied" math is in opposition to "pure" mathematics: that is, applied mathematics is used for a specific ("real-world") problem, such as fluid mechanics, statistical physics, or even the biosciences. This need not be computational: in many cases, it involves the study of differential equations and other analytical tools (expansions and other techniques).

In contrast, "computational" mathematics implies mathematics that cannot be solved by "pen and paper" techniques but instead require the use of a computer—either desktop or cluster—to solve.


Found a severe error in a conference paper after presentation but before the proceedings

Let's see:

You wrote a paper of sufficient writing quality that it was chosen for presentation at a conference and publication.
None of the peer reviewers noticed anything wrong with it.
None of the people in the audience questioned it.
Your supervisor saw nothing wrong with it.
You gave an excellent presentation.
You found a flaw in a paper that had already been accepted for publication.
You had the integrity to withdraw your paper from publication.

That's a long list of things to put on your "plus" list.
Most undergrads don't achieve even one of them.
None of them should be seen as a negative.

Be warned that you'll become more jaded as you progress.

I remember as a grad student being asked by my supervisor to review a paper that had been sent for him to review.  It was well written and obviously the result of a lot of hard work, but I found a fundamental oversight that would have allowed the entire problem to be reduced to something very trivial.

We told the publishers about this, and they wrote back requesting that we recommend it for publication anyway.  My supervisor said that the author could publish another paper later that would re-analyze the problem and present it differently.

That's one (of many) reasons I eventually didn't bother finishing my own PhD.


Postdoc positions: turning down alternative offers safely and timely

Here are some important points to consider:

Are you a bad person to take strategy x rather than y: no. You are fighting for your life here, while other institutions are fighting over having a nice person to talk to and some very minor travel allowance. Your needs take priority. Maximize your utility and don't think of anything else.
Will people or institutions remember any action or inaction on your part and hold a grudge forever? yes. people do that. it's a game theory thing that was set through natural selection. So, whatever you do is ok, but others may still get mad, to the point of even acting against their own interest just to hurt you. So even though you are morally allowed to do anything you want, acting in a way that will get people mad is not in your interest (and that's why we have the mechanism discussed above, to make other scared of making us mad).
Is the offer from institution B a sure thing: NO. Stuff does happen sometimes. You should not assume it will be ok.

So what can you do? First, you should let B know that you have other offers. You can also ask them if getting an offer from them is a sure thing or if instead you should pursue other possibilities for the time being. If nothing else, it will make them want you more.. If they say it's a sure thing and that you can stop looking elsewhere, and they respected people from a respectable institution, it's probably ok. But just to be sure, once you get such a response make sure to announce it to the world. Write on your homepage that you were promised an offer from them, put a copy of the letter on Facebook, do whatever you need to make sure that if they back out their image will suffer. Of course, in that case you should tell prof. A about your offer, explain that you would still be happy to visit and collaborate, and all the other yada yada.

If you don't get a firm commitment from B, then you should act accordingly. You can let Prof. A know that you have information from B that they may make you an offer (make him want you more..), but don't let him know that you will definitely go there once an offer is finalized. If he has any decency he will not ask: travel money is small change and he is making a new connection, this is beneficial for all parties anyway. If he does ask, simply say that you have not made a final decision and you prefer to only decide once you have a firm offer in your hand. If you then get an offer from B before the trip to A you can let A know that you got the offer and it fits you for oh so many reasons that you doubt that you would eventually choose A. But you would of course be happy to collaborate in the future, or visit to give a talk, and yada yada.


How can I find an expert to help review my PhD thesis?

After your supervisor, your best bet is to ask people in your research lab/team if they can review your thesis. A PhD thesis usually talks about specific and sometimes complex scientific concepts. Therefore, even PhD students from other research groups won't have the necessary background to review it. Alternatively, you can ask someone you trust from outside your research lab/team who's research is closely matched to your own.

Note: I didn't include "asking other faculty" because that would be an irrational request (it is not their job and you already have an advisor) unless your current advisor formally suggests this approach.


Contact professors regarding a not registered invention idea

You can always contact professors in order to team up, however it will probably be the case that they will provide PhD students to team up with you. This is just a matter of communication and I don't think that is the real problem here.

The idea not being registered yet raises the real issue, because if you start to emailing everybody to try find a team someone may find the idea interesting and start working on it. Then comes the question is it possible to register the idea like in a patent or something? If not, is it possible to publish a paper about it on a conference, this would be a way to turn the idea public but with an authorship kept.

Another thing related to the team item is that you should first get an adviser and be accepted for a PhD program and then you should worry with the team up for the implementation, maybe even with your adviser help.


I can't find a masters thesis advisor. Can I publish independently in a math journal and get my MSc degree that way?

Publishing an article and getting a degree are two different things.  One can do either of them without the other.

At least at the Ph.D. level, the thesis should be of "publishable quality" but in some exceptional cases may not be published.  And of course many get masters degrees without publishing.

You can publish without an advisor.  But it seems unlikely you will get a degree without one.  (Some Ph.D. programs may have a masters degree by coursework and examinations that you receive during the course of your Ph.D. work.)

Generally, the work for your degree is done after you have an advisor, in consultation with that advisor.  It is rare that you have the work done before you have an advisor.


Why are there so few MOOCs for the core college curriculum for a BS in Math?

I feel that this is heavily driven by the job-market. Topics in academic mathematics do not possess the necessary buzzword status to make MOOCs profitable. Very few job postings ever ask for competency in abstract algebra, real and complex analysis, basic calculus, etc. Many job postings want machine learning, "big data," "artificial intelligence," virtual reality, etc.

When a MOOC advertises its wares, very few people are going to click on an ad that tells them they can learn abstract algebra and category theory. A MOOC teaching Python and "data science" intrigues a number of people who believe that if they can just learn a little Python, all of the sudden Facebook will pay them $150k a year to do data science.


Doubt regarding uploading Tables and Figures for the accepted manuscript

In my opinion, the guideline regarding tables is outdated, and one can safely ignore it. If you submit your manuscript in LaTeX, put your tables in the main text. This is a current mainstream in (STEM-related) journals, and it is good to delicately push IEEE towards it. In case if they insist on doing this the other way (which I seriously doubt), you can address the questions to their production team.


I would normally choose the two-year program, for exactly the reasons that you cite. One of the few reasons why I would consider the one-year program is if there is a particular individual you want to work with, or if it is your first-choice school for the PhD program and it offers a path of lower resistance to already be a student there.

Otherwise, as JeffE points out, you won't really save much time by going to the one-year program over the two-year program. (Besides, if it's a coursework-based program, you'll probably get more out of the two-year deal!)


Is a good PhD student or researcher expected to spend some part of their day/week regularly reading new research papers/pre-prints?

There are pages like http://www.arxiv-sanity.com/ to filter the mass of papers on arXiv and give you the chance to read what interests you most. Furthermore, you can also go through all recent papers on your phone (instead of browsing instagram, reddit or whatever), read the abstract and mark everything that might be interesting to later read. I'm not sure if it is expected, that might strongly depend on your institute, group or advisor, but it is surely possible to do it in nicer ways than by simply clicking through arXiv directly.

I know good researchers who check arXiv daily, I know other just as good ones that haven't looked at it in months, so there also is no general rule there for after the PhD it seems.

Btw, if anyone knows of other nice ways to filter the arXiv feed, feel free to share/add, I'm not yet 100% happy with the ones mentioned that I currently know.


Should I ask the instructor for a make-up exam for attending a PhD interview at another university (and risk my standing)?

You don't have to tell your instructor why you want to reschedule your exam.  Just tell her you have a conflict with a personal matter and ask if it is possible to take the exam on a different date.

She might say no, but if she does, then she would probably have said no even if you had told her the real reason.  Usually exam makeup policies are either "flexible" or "no makeups except for medical reasons or conflict with another course".  Attending an admissions event at another university isn't any more compelling as an excuse than "generic personal business".

If she does say no, then you're going to have to choose between the two.  It probably makes the most sense to attend the interview and then come back for your exam, skipping the second day of the event.  It's probably not wise to skip the exam - you don't want to get bad grades if you are looking to apply elsewhere.


Where to use MLA in-text citations for Computer Science paper

Would I place an in-text citation citing the book at the end of the paragraph?

Right after the paraphase. If it took a whole paragraph, so at the end of it.

  ... does every fact need to be cited?

Generally, you do not need to cite information that is considered common knowledge. For instance, facts found in many sources or facts easily observed.

  if I were to say a PTM is a type of NTM, would this alone need to be cited with an in-text citation?

I would say no. Even Wikipedia is already aware of such. But be aware that it is an arbitrary choice. Expert audience will have different expectations of what constitutes common knowledge. If you have an adviser ask for his help.

Further, your argument might be stronger by using supporting evidence from other sources. Additional information related to the topic you're discussing would help to verify your claims. Hence, cite others work if such statement is crucial to your argumentation.


Will bad grades in non-math classes affect admission?

I'm not in your discipline, so I'm not sure how much this is similar...When we evaluate doctoral and master-level students for admission, we first check if their GPA meets the minimum criteria. If it does, then we look to see how well they did in courses that would help them succeed in our graduate programs. If your GPA hasn't suffered too badly because of the non-math courses, they might not hurt you.  However, I would caution not to mention to admissions personnel/reviewers that you believe the non-math courses were "useless" so you blew them off. That doesn't sound very professional- if asked, I would say that you focused more on the math courses to prepare for your graduate studies, which took time away from your other coursework.


Is it more difficult for teetotalers to develop academic contacts?

No. What really helps in building academic contacts is not beer, wine or any other alcohol, but the ability to generate informal discussions in relaxed settings. Fortunately, there are many ways to achieve that goal that do not require the intake of alcohol!

Even without going very far from drinking, sharing a nice lunch or dinner in an appropriate setting is one good way to establish contacts.


Do I need to wait for a journal to "consent" to paper withdrawal before submitting elsewhere?

I'd recommend waiting a week or two to see whether you get a response to your withdrawal.  At this stage it can't be urgent to resubmit immediately, and having their reply would guarantee that they are aware that you have withdrawn the paper.  (By contrast, I don't think an e-mail read receipt means much.  For all you know, an administrative assistant opened the e-mail and then mistakenly deleted it without realizing what it said.)  I wouldn't go so far as to say you are required to wait for a response, but better safe than sorry.

I think you've got a much bigger issue to worry about, though, and that's why you withdrew the paper after acceptance.  At least in mathematics, withdrawing an accepted paper is extremely unusual.  To a first approximation, it typically means there's something seriously wrong with either the paper or the journal.  You can certainly do it, but given the effort that has gone into handling and refereeing the paper, you will cause offense if you don't have a very good reason.

If you inadvertently submitted the paper to a junk or predatory journal, then you don't need to worry about causing offense.  (Offending the editors of predatory journals is not a bad thing.)  In that case, withdrawing the paper is certainly the right decision.

If you dreadfully screwed up in your choice of journal, for example by submitting a brilliant breakthrough to a respectable but not impressive journal without realizing how good the paper was, then you should apologize profusely for wasting everyone's time.  Hopefully they'll understand that it was a genuine mistake on your part, and they'll sympathize with the awkward position you are in and give their blessing to resubmitting elsewhere.

If the paper is seriously flawed, then that's a respectable reason to withdraw it.  You might look bad for having submitted it, but then again, the referee didn't find the mistake either.  But this isn't a compelling reason to submit elsewhere soon: if you don't check whether the original journal is willing to publish the revised paper, then it looks like the changes were just an excuse to withdraw the paper.

Under normal circumstances, it will cause offense if people think you are withdrawing an accepted paper just to try your luck at a more prestigious journal.  In particular, this is a dangerous impression to leave if you ever hope to submit to this journal again.  As an editor, I would certainly not be happy to see a new submission from an author who had previously withdrawn an accepted paper without a compelling excuse.

All this gives you another reason to move slowly and wait for a reply.  If you have a good reason for withdrawal, then it's worth making sure you have communicated it clearly.  In any case, you are doing something rather unusual and serious, and it's best not to give the impression you are treating it lightly or casually.


Referencing literature review in discussion

Just cite the author again. It should be clear what your source is every time you use a source.


Is it wrong to call yourself Dr First_Name Last_Name when you have a Professional Doctorate such as DTech or DBA and not a PhD or MBBS?

This is highly dependant on legislation (of the country where you are when you are calling yourself). In germany (AFAIK, one of the more picky legislations wrt what you can call yourself):

Let's assume you move to Germany with a proper DTech from South Africa, Australia, UK or Sweden. Proper meaning: scientific thesis, degree from a university (or similar recognied highest level institution), honorary degrees have separate rules, bought degrees cannot be used in Germany.

For South Africa, the most general rules apply: you are Firstname Lastname, DTech (University of ...)* you can also add a translation: (Doktor der Technologie).
If the country doesn't use the latin alphabet, you can transliterate. And long form or usual abbreviation are both fine.

* Whether you put the degree before or after the name doesn't matter.
For Australia, there is a treaty on equivalency of degrees and in consequence (legal text in German) you are Dr. Firstname Lastname. Not Dr.-Ing., though.
Since Sweden is member of EU (same for EWR), with a Swedish DTech, you have the choice. You can either be Firstname Lastname, DTech or Dr. Firstname Lastname. Again, not Dr.-Ing. even though that is the German degree corresponding to the Swedish DTech.

This does not apply to so-called Berufsdoktorate where the doctor is awarded not for a research thesis but automatically when finishing a Master level education.
UK used to be in the EU until recently and the offical texts have not yet caught up with Brexit. I saw a note somewhere that UK degrees are still treated like EU.

German doctorate degrees are mostly of the form Dr. ... ..., e.g. I'm Dr. rer. nat. (doctor in natural things [sciences], in my case chemistry).

When addressing a person, usually at most the "doctor" is pronounced, the type/field only if that is considered important for the specific occasion.
I could ask to have the doctor put into my ID card where it would appear as DR (the line is all uppercase) only, without specifying what kind of doctor I am.
I could also put the doctor to my doorbell, either as Dr. rer. nat. C. Beleites (sounds very arrogant, unless it is part of the professional doorbell Chemometric Consulting Dr. rer. nat. C. Beleites where I'd think it only a bit stuffy -  as it is, the office door bell actually reads Chemometric Consulting C. Beleites) or as Dr. C. Beleites (slightly arrogant). Only my business card contains in small print the information that I'm Dr. rer. nat. and Dipl.-Chem. (since one cannot know from Dr. rer. nat. that I'm chemist).

  BAppSci (Chiropractor), BAppSci (Osteopathy) that call themselves Dr.

This is not allowed in Germany. Even a physician can call themselves Dr. only if they actually obtained a doctor degree. Otherwise, they are
Firstname Lastname, Arzt (physician, meaning they passed their state exams and got approbated) or Firstname Lastname, Facharzt für ... (meaning they also passed the specialization exam for field ...).

If they also did their doctorate, they are Dr. med. Firstname Lastname, Facharzt für ....

  whether having a DTech allows one to formally/officially to be designated as a Dr. P.S.

Not in Germany.

In some faculties, the candidate can ask to get e.g. a Ph. D. rather than the usual Dr. rer. nat.. But once that degree is awarded, one has to stick with it.


I don't really see the point. I agree with a PhD being a license to do research. If you are interested in astrophysics and want to get a strong profile for future work there, make sure your publications are related. That's much more convincing than two PhDs.


I suspect that even if the TERM is not defined, that knowing the JOB will help you make a proper submission.  Is it a postdoc or lecutureship or tenure track? Even if the job description is scanty (but why would you invest time in a detailed submission for a job that you don't know what it is), you can make some guesses based on the school, group, etc.  Is the school a teaching or research university?

So, I really don't understand coming at this thing with a "can you explain this term to me" versus giving more context, clues.  This is both you might answer the question yourself or how we might help you.

Also, I would reach out say you are interested and ask for guidance.


When do I need permission from website owners before data mining their pages for research?

When do I need consent from websites owners?

Under U.S.-like laws - you need this every time. In layman's terms, by default, you can look at public site areas and only look, no duplicating or storing, etc. Despite that even your browser does it freely, laws are convoluted here. If in a special agreement published on a site or in some other explicit form is not stated a permission for this usage, you should not do it. There also may be an explicit mark about public domain or a standard open-source license. But, even this public agreement isn't enough for your purposes.

Few of the potential problems:

Use protected by legal rights data isn't legal. (may be covered by a public
agreement or a written permission)
If you interfering with sites' availability via additional load, this may be a hostile act as well. (not only an admin's ban, this is a potential legal issue)
Even if the site owner allow it, you can break some    federal laws -
about personal data collection or something else, this is a question for a licensed lawyer. Also, more information needed for answer from this point of view.

So, yes, the written permission is the only legal way to dig somewhere and even this could be insufficient. People do sometimes their own similar projects without any permissions, maybe, because they think, this is too boring and slow to write some letters and do a legality research. However, you want to publish the results about work with thousands of thousands web pages. So, "cover your back" isn't a meaningless paranoidal phrase in your case. And this is only a few obvious legal concerns, also there're more ethical and technical problems with using web resources in not allowed by their owners ways.

If you just lightly ping every few seconds for checking availability of some serious sites, some of them just ban your bot after a while. Others log your activity and use the log if this will becomes a problem. I'd personally banned many harmful crawlers and filled a bunch of complains about unclear automatic requests which was loading resources dedicated for clients.


How to deal with premature student questions during a lecture which will be covered in a subsequent slide?

Another option that I saw once and I thought was, frankly, pretty great:

In my Introduction to Logic class my professor taught from Powerpoint slides, and the slide was divided into two sections, the main section on the left, and a small column on the right. The column on the right was titled "Questions You Probably Have" and was exactly that. Underneath each question in bold it either said "Next slide!" or "Ask me!"  And so, inevitably, people would ask the "Ask Me!" questions and he would click the "Ask me!" link and it would jump to a tangential slide and he would go into the details.

And if someone asked him something not on the slide, he would always say, "Great question!", give the questioner a bonus point on the next exam (even though he did this no one abused it, I'm sure he had a plan if they had, but it was another amazing thing he did), And as he answered it he would scribble a few notes. Before the next class, he would show us the new slide he'd created (or the new text in the next slide) for that question and ask us if it made sense now.

Basically, as a shortcut method it covered all three of the core issues this sort of thing entails:

"Here's what's coming up next."
"Yes, yes, you are very clever for thinking of that."
Getting a coherent lesson together that encourages feedback.

Also, it was kind of meta and spooky when the slides really would predict questions I'd have, when really it was just the material presented itself the same to hundreds of other people before me.


How do professors get to apply and work on industry projects?

Reputation, personal contacts, and open calls for proposals.

Academics who publish important papers relevant to industry problems are likely to draw the attention of people in those industries who may reach out to the professor to find out more about their research. These kinds of contacts may turn into invitations to come speak, collaborate, or even a contract project to get paid to do research for the company.

Similarly, not everyone who gets a PhD goes into academia, so it's likely that a professor will have former labmates from grad school or postdocing or recent advisees who have gone into industry. These connections, if maintained, can be invaluable for finding out about the needs of industry and may lead to funded research projects.

Finally, some companies run research programs more or less just like government research programs. If you want to work with Microsoft Research or Google or Pfizer, you may simply go to their website, discover what research funding programs they are funding, and apply.

There are certainly other possibilities (incubators, university-level liaison offices, etc), but these three are among the most common.


Can you get statistical data on research paper submissions and publications?

IMHO, this is unlikely to fly. Some journals might give you statistics on the number of submitted and accepted publications. But submission to a journal is typically confidential and as an author, I would be pretty upset if Nature revealed this information to someone else.

Where you might be able to do similar analysis is a site like arXiv.org. It's used heavily in physics in other fields as a preprint service, and there are usually notes where and when a submission is accepted to a journal. Keywords are also included. The difference is that not everyone submitting to Phys Rev necessarily uses arXiv.org.


Is "because it's fun" an acceptable justification for choosing a certain research path (when communicating to peers/colleagues)?

There is a difference between the personal motivation of a person to work on a subject, and motivating why a subject is worth working on. We should always be able justify the later, both from an ethical and practical point of view ("because it is fun" will not convince anybody to pay you to do it).

In practice most researchers (certainly the successful ones), can provide a detailed motivation of why their work is relevant to the furtherment of their field and humanity as a whole.

However, this motivation might differ quite significantly from their personal reason(s) for wanting to work on the subject. In particular, they typically will have reasons for working on this specific thing, rather the long list of other things that are also worth doing. (In this category "because it's fun" is probably preferable over  the much more cynical "because we can".)


Is a tree/graph visualization of methods literature a useful addition to lit review?

I'm a little bit cautious about diagrams like this. The reason is that often the relationship between different pieces of work is much more messy and partial than is readily captured by such a diagram, and systematizing onto a diagram can cause one to unintentionally leave out or "neaten up" some of the most interesting pieces of hybrid work.

That said, sometimes diagrams are appropriate---consider, for example, some of the wonderful diagrams for relationships between computational complexity classes.  In this case, a diagram is a wonderful aid to comprehension, and as such, if the work in your field really does organize so nicely, I think that using a diagram is a good use of space, particularly in a document like a thesis or thesis proposal where you are not facing tight space constraints.


Is it acceptable to ask a professor to write a reccomendation letter now to save for later?

It's certainly acceptable to ask. But:

In the US, at least, most universities require the professors to electronically upload their letters directly. So, having him write a letter and hand it to you might not be all that helpful -- you'll still need him to upload it when you apply to grad school. If you're worried about him dying, you might be able to get another professor to upload his letter on his behalf...but that gets a little tricky.
A lot of students have plans to go to grad school N years after graduation -- but at least anecdotally, it seems like the vast majority of those students change their plans and never end up in grad school. So, he may be reluctant to write a letter that has a good chance (at least statistically) of never being used.

I would just discuss this openly with him -- tell him that you plan to ask for a letter in 2 years, and want to make sure that all the details aren't forgotten before then (it is not necessary to suggest that he is senile or at risk of dying).

He may write some notes to help himself write it, or he may agree to write the entire letter now.
If not, this conversation gives you an opening to write your notes and e-mail them to him -- including some bullets that summarize your work and others that record any subjective evaluations he's shared with you. Then, two years from now, all you have to do is reply to this message and tell him you need the letter.


Bibliography format with multiple citations from same book? (APA)

Normally duplicates are avoided. Also, your duplicates do not have a page reference and are therefore useless in this respect.

Whether or not you have to specify the page number, I would personally check with your supervisor to avoid misunderstandings.


American universities - where does all the money go?

The answer is completely different at different types of schools. At state schools in California, the increases in tuition have gone to offset decreases in state funding. At some private schools with big endowments, e.g., Princeton, it's simply not true that tuition has gone up dramatically. (Princeton is now about the same price as Berkeley for a kid from an affluent family.) At other private schools, the increased tuition may be paying for amenities like rock-climbing walls, or it may simply have increased because parents perceive high tuition as a sign of status and quality.


Is PhD worth it when considering your career in industry

You haven't really defined what you mean by "...when considering your career" in the subject of this post.  On the one hand, you say,

  I would like to deepen my understanding on my field.

If your goal is to deepen your understanding, one way to do that is to get a PhD. You can also do this on your own, without getting a PhD, but you'll find a more structured path and (possibly) more resources if you go down the PhD route.

On the other hand, you say,

  I am interested for a career on industry.

Are you interested in industry because of the money?  If that is the case, you're most likely better off earning a full income and "moving up the ladder" during the time you would spend in graduate school, which means you should forego getting a PhD to concentrate on the money.

If you're interested in a career in industry because of reasons outside of financial considerations, then you have to think about what kinds of jobs you're looking to take in industry. If you're satisfied that your current skills and educational level will make you competitive for the jobs you want, you should probably reconsider the PhD, and to "deepen your understanding" in a different way. Then again, a certain percentage of people want to get a PhD for the challenge and for strictly personal reasons, removed from the job details themselves.

If the jobs you want to get are generally given to PhDs, then you have your answer already -- get the PhD to make yourself competitive for those positions.

I suggest writing down all of your long-term goals, and then weighing them against the time and cost (and opportunity costs) of getting your PhD. If after all that you still don't have a good answer, you might consider continuing with your program for another year and just postponing the decision until then.  Eventually, either you will get your PhD, or you will be convinced that it is better off that you stop the program (but the decision may get harder the closer you are to finishing).


Is it ok to use "and/or" in my dissertation?

The construction "and/or" generally betrays a weak sentence construction. It's almost always possible to replace the use of "and/or" with a more satisfactory construction (such as "either . . . or" or "at least one of").

So while you are allowed to use it (unless your style manual tells you otherwise!), I think it's always better to avoid it in such writing. (One sign that it has not really gained widespread acceptance is the fact that most style manuals still tell you to eliminate "and/or" constructions entirely.)


What to write about in a master thesis that's mostly software applying common knowledge?

How do I come up with content?

The first thing to do is ask yourself why your supervisor instructed you to perform this work in the first place. Unless they wanted to give you completely meaningless work for no reason (unlikely), they are likely interested in whether the system you are building demonstrates some interesting and non-trivial result. For example, perhaps they are interested in how different types of hardware interact with each other using this library. Perhaps they think that this setup might make x protocol go more quickly. Who knows, the point is that you should find out what their motivation was, and then write your thesis as an analysis of the result they were trying to measure.

I feel like an upaid software developer disguised as a thesis student

You're not going to like this, but in my opinion, what you've described does not qualify as a master's thesis. A master's thesis is essentially a doctoral dissertation of (much) smaller scope. It is by definition a research endeavor. What you have described sounds like just a very basic software project that should take no more than a few days to hook up and measure.

I don't blame you for not knowing this, I blame your supervisor for not making this clear. Some of the main motivations for doing a master's thesis are typically to give a master's student experience with research, and to get them published so as to help them in applying to PhD programs or other research positions. In this case, I think you are justified in being confused about what content to discuss in your thesis because it doesn't sound like your supervisor has directed you to do any research whatsoever.

If you were planning on using this thesis as a boost to your career (be it for PhD applications, or in industry), it may be worth sitting down with your supervisor to figure out how to actually get you involved with research. If the supervisor is giving this kind of work to do as a thesis, then in my opinion it means that they're taking advantage of you as free labor rather than doing what they should be doing, which is guiding you as you learn how to perform research.


How detailed should one be in writing the referee's report?

When I write a report I try to be as detailed as possible in my response to the authors. This is important as they will need my comments to improve the manuscript, and if the comments are vague they will fail to do so. However, many of the journals I have experience with in my field (life sciences and bioinformatics) ask referees to avoid including comments regarding the suitability for publication in the letter to the authors. For that purpose they provide the score sheet that needs to be filled when submitting the report (at least for journals using electronic systems).

However, those score sheets cannot convey all the information about the impressions of the referee after reading the paper. Therefore, there is always a section with comments to the editors. In this section you should add any relevant information that is not clearly represented in the score sheet. Personally, I always try to add specific comments to the editors. For example, I may have complained in my report about the poor description of the statistical methods. Then I will let know the editor that that is, in my opinion, a mandatory change for the suitability of the manuscript for publication. Finally, when writing my comments to the editor, I try to be as brief as possible (but never just 'yes' or 'no'), so that I do not overwhelm the editor's likely busy inbox with unnecessary comments.

In summary, the comments to the editor should include any information that is not properly represented in the score sheet, cannot go into the response to the authors, and may be relevant for the editor in order to make an appropriate decision on the manuscript.


How to change to Mathematics PhD program following M.S. in Computer Science?

Take a look at Is it easy to change your major after starting your PhD or masters, if it is necessary?, which is somewhat similar.

In particular, unfortunately, it sounds like your current mathematics background is very far from what would be needed to enter a math PhD program - it's maybe 1/4 of the coursework that would be expected. You would need to have preparation equivalent to that of a BS in mathematics, and that sounds like it would be the equivalent of 2-3 more years of full time coursework for you.

To be honest, I don't think that the coursework you describe can even have given you much of a sense of what pure mathematics is, much less what it is like to do research in the area.  One needs rigorous proof-based classes such as real analysis and abstract algebra.

I would not really advise you, or anyone, to even think about grad school in mathematics before they have enough of a background to reasonably understand what it involves.


This is perfectly acceptable.

Caveats:
I would be wary about asking questions you should know the answer to.
I would also avoid anything that might be interpreted as a criticism. I know this sounds obvious but its an easy mistake to make. If you are not a tiny bit careful, "Please clarify X" can easily be read as "X wasn't clear".

If your advisor isn't clear you're covered that it's not a 'trivial' or stupid question.
If you are careful about how you word the question, you shouldn't be in any danger of offending anyone. Explaining things can be tricky and if you are outside the immediate field, it doesn't look bad for anyone that you didn't follow.

Conversely not asking could end up reflecting badly on you. He will in all likelihood: understand the issue, see how it applies to your situation, and will be interested in your response/use of his results. If you don't follow it will probably be clear. If on top of that you missed (what he will see as) an easy step to rectify the situation - ask, exactly as you suggest - he may well see it in a negative light.

Finally if for some nuanced reason - and I really can't think what this would be - there was a reason he wouldn't be happy to discuss this with you: if you ask in a way that doesn't demand or expect an answer no harm will have been done.


How to deal with GPA-related questions in standardized job application forms, if you have no GPA for graduate studies

As noted in the comments, the first thing to do is to contact the company HR department.

If you don't get a rapid response, however, then I would recommend filling in the form with as obvious a nonsense number as it will let you (e.g., -1, 9000), or if it won't let you do that, then fill in whatever it thinks is a perfect GPA (you passed all your classes, right?).  Then explain the form problem and your true situation in text.  The best place to do this is, in order of preference:

A free-text "Comments" or "Other Information" field on the application form, since that will typically be seen at the same time a person is seeing the GPA.
Your cover letter
Your resume

Note, however, that you are not very likely to get a positive response in any case from this type of completely generic application form, since it is likely getting filled to the brim with pseudo-spam from a vast number of recent graduates worldwide.  HR departments often put such a "catch-all" form out in order to satisfy formal requirements, rather than because they expect to actually do much hiring in this manner.


Show examples of public dataset in master thesis

In principle it depends on the permissions given to you by the owners of the data. Any open source licence would give you permission to share elements of the dataset with attribution (though I am not a lawyer). If it's listed on GitHub there's usually a licence shown on the repository's main page (see screenshot). If not, you can contact the authors to ask them to be 100% above board.

A screenshot of a GitHub repository header

Copying a figure from a paper might be somewhat shakier, as the publisher may own the rights to images as published in the final version. Your country may have "fair use" or "fair dealing" exemptions from copyright requirements for educational uses of certain materials, but it could be complicated to ensure you are following these rules. A university librarian may be able to help you further.

In practice, I think it's very unlikely that there would be a problem with what you're planning to do.


Prior thesis examiners as potential future journal article referees?

Is seems to me that what you are caught on is one of the key tensions in reviewing:

The more knowledgeable the reviewer, the more likely they are to have some sort of conflict of interest regarding a manuscript.
The more independent a reviewer, the less qualified they are likely to be for a deep review of a manuscript.

Different journals and different editors have different places where they draw the line on the range of acceptable tradeoffs between knowledge and conflict of interest.

As such, I would recommend simply providing the information to the editor in your list of recommended referees, along the lines of what you have suggested but with less assumptions regarding the appropriate course of action:

  X would be a good reviewer, but was one of the reviewers of my thesis.

The editor will then be able to make the call as best they judge (which they will do in any case), and will not be likely to feel that you are pushing them to either use or not use the person as a reviewer.


I know of no university that advises you to take a sabbatical. Lucky people have departments that allow them to take a sabbatical every once in a while. Sabbaticals don't generally result in a change in research focus.

I think there are three indicators about when it is time to change research focus.

You are bored and want to change
You can no longer publish in your area and receive rejections along the lines of "This is no longer a relevant area"
You can no longer get funding in you area and receive rejections along the lines of "This is no longer a relevant area"


How to write something which is already written?

Do not try to rearrange or paraphrase, but write in your own words.

How do you do it:

Read what you need to read.
Think about it.
Write it down again (without looking at the original source).

It takes more time than paraphrasing/rearranging, but it is worth the effort. You see if you really understood the topic and also you may discover that you have something new to say.


Can the university cut the notice period short?

I suspect (but have no legal standing) that they are obligated to pay you through the notice period even if they ask you to leave early.

But it also seems like they still are bound by a six month notice period rather than suddenly getting a shorter one because of your action.

But suspect and seems are pretty dangerous to rely on from someone who is just speculating. And, no one here can give you legal advice even with full information. We can only guess and hope we are correct. But you are the one on the line here.

I worry, also, that you have an adversarial attitude about HR. I suspect (that word again) that they are legally obligated to give you proper advice. They probably don't require all of the details of your situation to do so.


Does one get academic credit towards a degree for open online courses?

Most of the courses that I've seen explicitly state that you obtain no credit for doing the course. More explicitly, they may offer certificates of completion, but these certificates do not convey academic credit. For example, from Coursea's Term's of Service:

  This Letter of Completion, if provided to you, would be from Coursera and/or from the instructors. You acknowledge that the Letter of Completion, if provided to you, may not be affiliated with Coursera or any college or university. Further, Coursera offers the right to offer or not offer any such Letter of Completion for a class. You acknowledge that the Letter of Completion, and Coursera’s Online Courses, will not stand in the place of a course taken at an accredited institution, and do not convey academic credit.

So the short answer is that you will be unlikely to obtain such credit. Certainly, read the terms of service to be sure. Nevertheless, you could add such things to your CV to demonstrate your interest in a particular field.


Is it worthwhile to publish short paper as graduate student?

There are many reasons why it is helpful to publish. The usual reason is that it enhances your standing in the community of scholars and professionals. But another important reason, in my view, is just for the experience of it. You force yourself to bring your ideas into an understandable and maybe usable form. That is good for your mind and publishing is just the goad to get it done.

Submitting to a conference or journal will also get you independent feedback on both your ideas and your writing. That is valuable also.

In CS, however, most of the work is presented in conferences, so you might look for a suitable one and submit there.

If you want a career in academia, publishing is essential, and starting early gives you more experience for when the more important results are ready.

It is also usually good advice to follow your advisor's lead.

Good luck and see you at the conference.


Are there any metrics considering how heavily cited a paper is within another paper?

As far as I know, no.  The problem is that what you want to measure is impossible to accurately automate (even standard citation counts that Google Scholar automates are not 100% accurate) without hard-coding such information into the paper, as in Dirk's comment.  This of course has some issues, in addition to being a paradigm shift for the way citations are made (just as there are pressures now to include a citation, there would be pressures with such a system to make something an "important" citation).

The suggestion you made, about counting the number of times a paper is cited, crossed my mind in the past (along with some other ideas) but the problem is that it doesn't directly measure what you're asking.  There are different reasons to cite a paper, and the number of times you explicitly cite something in a given work depends on too many different factors, a large one being the author's writing style.

Remember the current paradigm: references are just that, references, which put the work in context for the reader and supply details that one uses.  Their purpose is not to provide a measure of the value of paper or researcher.  Once you go down the path of twisting things to measure worth and assign prestige (even if that is not your purpose), you just make things into a competitive game.


What is the difference between letter, communication and journal paper?

In physics, each category has a different length limit.  Often "paper" has no limit.  Typically the shorter the length limit, the more prestigious it is and the tougher the acceptance criteria.  The subject matter covered by the journal is the same for all categories.  Some journals also have a "review" category which includes papers which are not original research.  Often a review is by invitation only.


Should I (student) share my data with a researcher I don't know directly?

TL;DR - talk to your supervisor (which to be honest is the answer to about 90% of the questions on here, but hopefully this answer helps structure that discussion).

First of all, you might need to check whether you are even in a position to make this decision. The ownership of intellectual property arising from student projects can be a complex subject and you might want to check with your Knowledge Exchange and Commercialisation office or equivalent before sending a large dataset to an external partner. In most cases this is likely to be a formality and there will be no issues unless the dataset might be used commercially, but they may want to put a simple Material Transfer Agreement in place to define how the recipient can use or further distribute the dataset.

Assuming it's up to you, essentially you have three options:

give them the data without restriction. Best-case scenario: co-authorship, worst-case: nothing.
refuse to give them the data. Best case scenario: nothing. Worst-case scenario: you and your supervisor look bad and you damage a potential future relationship with a collaborator or employer.
give them the data after taking some actions to increase the likelihood of acknowledgement. There are three real options here:

3a) (mentioned by @gvgramazio) upload the data to a public repository. The preferred repository varies by field but I'd use an academic data repository like Figshare. You get a citeable DOI but this is not a publication, so if you're looking for publications, this doesn't help (it should, but that's another discussion).

3b) publish the dataset in a data journal like Nature Scientific Data; then everyone can use it but has to acknowledge you by citing the source.

3c) set up a material transfer agreement that defines how the recipient can use the data and what you get in return, which can formally include the option of coauthorship in some form if a manuscript is produced.

With option 1, the most likely outcome depends on their character. Are they a good person to collaborate with? Do they have a good reputation as a collaborator? This is probably the most important question, since if they're a good person to work with then I honestly can't see them not including you as a co-author anyway in this situation, although this could vary by field. Another, related consideration is whether might you potentially be working with (or for) them in the future, and if so if this might increase your visibility or chance of a job. If you don't know them, the only real way to assess this is by asking your supervisor, who knows them and also has an interest in supporting you.

Option 2 - refusing outright - really isn't likely to end well.

Option (3a) - a data repository - guarantees acknowledgement but not necessarily in a form that's useful to you, and option (3b) - a data paper - is the most work and guarantees acknowledgement in a form that's likely to be useful to you, but both (3a) and (3b) mean you're less likely to get a co-authorship.

Option (3c) is trickier. In my field MTAs are increasingly common but also very unpopular with some researchers. As the provider of the data, having it covered by an MTA is the safest option but negotiating one can be intimidating. Fortunately, most institutions have offices to handle this sort of thing.

You also need to consider a few other questions:

how helpful are the different possible outcomes going to be for your career? In my field you are assessed primarily on publications in peer-reviewed journals so 3b is preferable to 3a. However, if the friend is able to acknowledge the data by citing it, they are less likely to include you as a co-author unless you make further substantial contributions to the analysis (which they don't have to give you the opportunity to do).
Does their proposed analysis sound exciting? If it has a good chance of resulting in a really, really good paper and relies heavily on your dataset, then a chance of a co-authorship on a really high impact paper might be better than a lead authorship on a data-only paper.

Ultimately, most of these questions will be things your supervisor is able to help you with. So I'd arrange to talk to your supervisor, explain your concerns, and ask which option they suggest.


Is software developed by publicly funded research groups legally public domain?

No, in general they are not.

It is true that works prepared by US federal government employees as part of their official duties are in the public domain.  This applies, for instance, to journal articles by scientists at DOE or DOD laboratories.  It does not apply to public university employees (they work for state/local governments) and, as far as I know, it does not apply to computer code.


What is the significance of the corresponding author?

As Faheem pointed out there are other questions that deal with what a corresponding author is. You second question is not covered by those questions though.

The corresponding author should be an author that will be easy to find again after a few years. Ph.D students are not great choices since they are almost by definition not going to have the same contact information by the time most people read the article. In mathematics this is a serious concern because the backlog in articles can be multiple years and the student can already have graduated and moved across the world by the time the article is officially published.

As the other questions point out in some fields corresponding author is used to indicate contribution to some degree. But the old fashioned use of "the author you can find an address for" is still a worthwhile thing.


Google Scholar: Will having HTML and PDF in different subdirectories lead to incorrect indexing?

Google Scholar is pretty smart about these things.  On all of the websites I'm involved with, we keep the PDFs in a separate directory from the page that links to them, and Scholar finds them just fine.  Of course, we also don't us the citation_pdf_url tag, so maybe we're fine because we're low-tech and Scholar does the inference for us...

I recommend doing it the easy way, and trusting Scholar to be smart.  If it doesn't do the right thing, then you can always go back and drop the tag and wait for a refresh.  And then if that doesn't work, you can do it the hard way.


What should I do when the recommender is not replying?

I would do a couple of things.
First, see if you can quickly organize a different recommender. Maybe futile, but it might work. Long term it might be useful to have a backup in any case.
Second, but simultaneously, inform the university to which you are applying that you can't reach the recommender and that Covid may be the reason. Tell them you have a copy of another letter from this person and ask for their advice on how to proceed. Give the name and email of your recommender, I think.
I suspect that people will be reasonable, given the general disruption. It shouldn't reflect badly on you if you do due diligence in getting recommendations. They may even be a bit "soft" about deadlines for such things. Note that admissions to doctoral programs is normally handled by people, not machines, and the people are all facing various kinds of disruption.
Finally, note that you not getting feedback from the recommender doesn't necessarily mean that they aren't otherwise doing their part. There may be a lot of reasons for not replying, many of them valid.


Signed up for a talk, not enough material

Twenty minutes is not long for a talk.  Moreover, most students drastically overestimate how much material you can put in a short talk.  Giving a short introduction to the field and how it came about will be more than adequate to fill that amount of time, and would be a perfectly reasonable topic for an incoming PhD student with only four months in the program.  Time permitting, it might also be nice to mention your research question and the general avenues of inquiry you are going to use to solve it.  You should also leave a few minutes for questions and comments, particularly since this will give researchers in the audience an opportunity to offer suggestions on your research idea.
So no --- you didn't make a mistake signing up for this talk.  Don't bother trying to cram out new research results for it --- just stick with your plan to give a short introduction to your field and a brief outline of your research question.  That should be enough to hold people's interest and solicit some questions, and the twenty minutes will go by in a flash.  I doubt a short talk like this is really going to help your CV all that much, but it will be good practice for giving conference talks, and if you are lucky, it might precipitate a longer conversation on your research idea with one or more of the researchers in the audience.
(And as Buffy points out in the comments below, no one will be upset with you if you don't use all your time --- running over time is bad, but having time to spare is fine.)


If you want the option of going to grad school for math, you should apply regardless. By not applying, you are voting no on your admission. Rather than self-selecting out, let them tell you no.


How can an undergraduate be recognized for work done on a paper, with a fellow PhD student and a professor?

The best thing you can do to ensure your work is recognized and credited is to have honest, open communications with the other people you’re working with. So long as everybody’s clear on who is doing what, and everybody is acting ethically, you shouldn’t run into problems.


Re-asking a professor if I can write my thesis after I chose another one

All you should admit is "a discrepancy, strictly on a personal level, not subject-related". That must be sufficient. You might add you made an error in your first judgment (probably due to the limited time-frame for decision) - which actually seems to be the case: so don't lay the blame on prof. A.

Even if prof. B knows everything about the conduct/character or prof. A (which is more than likely!), he or she will probably appreciate integrity - coexisting with your ability and willingness to admit a mistake and to revise your decisions in order to find a solution.

Please, don't get prof. B into a situation where he has to (or could feel obliged to) comment on the actions of prof. A. They have to get along on a professional level until retirement (while students come and go, in a manner of speaking).


Should I do Master or PhD to teach in community college?

A large portion of the community college workforce is part-time.  When there are full time job openings, they are quite competitive.  I will assume you are looking for full time work.  I have observed that many community college job advertisements say that a PhD is desirable, and I think that the applicant pool will typically contain many PhDs.  So I would suggest getting a PhD.

Be sure that during your PhD, you demonstrate that you know how to teach.  You can find quite a bit of information about how to obtain a job at a community college in columns on Inside Higher Ed.  If you earn a masters in the course of earning your PhD, teaching part-time at a community college during your PhD could be a good strategy.


The 2008 study entitled Peer Review in Scholarly Journals - Perspective of the Scholarly Community:  An International Study aimed "to measure the attitudes and behaviour of the academic community with regard to peer review."  Some quotes from the summary:

  Double-blind review was preferred. Although the normal experience of researchers in most fields was of single-blind review, when asked which was their preferred option, there was a preference for double-blind review, with 56% selecting this, followed by 25% for single-blind, 13% for open and 5% for post-publication review. Open peer review was an active discouragement for many reviewers, with 49% saying that disclosing their name to the author would make them less likely to review.

and

  Double-blind review was seen as the most effective. Double-blind review had the most respondents (71%) who perceived it to be effective, followed (in declining order) by single-blind (52%), post-publication (37%) and open peer review (27%).

A 2008 article in Nature (and a correction) discusses the above study but the article is about double-blind review versus single-blind review, and not about blind review versus open review.


getting a job with a PhD in (pure) mathematics

Your supervisor is honest, blunt, and very helpful because by ruling out the academic path he's saving you a lot of time.

The bad news is it sounds like you screwed up your PhD. Not getting strong research results, not having diversified your PhD experience (e.g. lack of teaching experience makes it harder for you to get a teaching job), and not having a firm idea of what you want to do after the PhD means you sound lost right now. The good news is, chances are you learned more than you think you did, and those things are applicable to the job market.

First: don't think you have to do research. It is what you've been doing for the PhD, but it's not what you have to do in the future. Just consider this: if you like research + are good at it, why didn't you do better in the PhD? Why weren't you able to complete the initial research proposals, why weren't you able to get publishable results, why weren't you able to impress your supervisor such that he can write a strong letter of recommendation? You might have good reasons for these, and it's up to you to convince yourself that yes, you still want to do research, and yes, you are talented + motivated enough to succeed in it.

If I were you, I'd start examining the possibility that I am not actually good at research and / or it is not what I want to do. Do some serious soul-searching here. You are making a life-altering decision. If it makes you feel bad that by leaving academia you are "failing", don't worry too much about it: there's a good chance that by leaving academia you'll have a more successful life (in terms of material possessions).

Second: go to your local jobs portal (use Google if you don't know what these are) and search for jobs that require a PhD in mathematics. Do you find anything that catches your fancy? For example searching on indeed.com for "phd math", I get this job among many others. Note the requirements:

  Preferred qualifications:
  MBA, Master's or PhD degree in a quantitative field.

  Experience with stakeholder management and ability to influence senior stakeholders.
  Demonstrated knowledge of statistics and data analysis including R programming or other statistical software packages.

I highlighted the most relevant parts. You say you are familiar with R. That means you are in business! You can potentially do this job! If you further have experience with statistics and data analysis (do you?) you're in an even better position.

It's up to you to search the jobs portal for jobs you can do, and then it's up to you to apply. It's true that visa issues might sink your candidacy, but it's also true that because PhDs are relatively rare, you might have skills nobody else will have and therefore the employer is willing to sponsor you. You will not know unless you try.

Do remember that even if you can't find a US employer, you can still work elsewhere. It's a big world out there, and it's not true that third-world countries don't need your skills. Example of such a job in India (admittedly they're not looking for PhD-level candidates, but you could still apply).

Third: once you have an idea about what the options in industry are like, then you can start thinking about what you want to do. Are you sure you still want to do math research? If so I'd talk to your supervisor again about what options are available to you. He's already told you your prospects are not good, so you'll need all the help you can get from him. For example, perhaps you could find a position as a teaching assistant somewhere and do research in your spare time. This will not be easy - doing research while holding a full-time job is very difficult - and it's not likely to be well-paid, but if it's what you want to do, you can try.

On the other hand if you think industry will serve you better, then finish up your thesis & defense and start applying for jobs. Be sure to visit your university's career center as well; they'll be able to help you a lot.


How much help with coursework is acceptable?

It depends. Some teachers want all the work to be that of the student and disallow any assistance. Some allow assistance only from teacher or TA (to control amount of help). Some have liberal allowance for collaboration.

Just ask the teacher what is allowed.

I would just be rather strict with yourself.  Like don't call it "help" when you are just copying.


How to avoid identifying myself in a review?

If you believe that there are papers that the author should cite, list them in your review.  Yes, I mean the specific papers, with complete bibliographic information.  If you include some of your own papers in that list, the author of the refereed paper may suspect that you're the referee, but so what?

On the other hand, if you believe that the only papers that the author should cite were written by you, you're probably wrong.  Look harder.


Can you submit an abstract that was accepted to a conference but not presented, for a different conference?

In my field, and I think in other traditional disciplines as well, is pretty common to present talks or posters more than once.
Thus, your doubt has no ground. Presentations aren't papers, they are dedicated to an actual audience, so you could resubmit the "basically the same" work even attending this conference you cannot in fact attend.

(How many times it makes sense to present the same core depends on many factors I am not going to list here) .

I recommend you to explain to the current organizing committee, or the branch in charge of the scientific content of the event, about your impossibility and why. Let them know you will try to submit and attend the next conference.

Also, in case the current accepted abstracts go printed, try to reformulate it at least a bit. This has nothing to do with copyright or self-plagiarism but it something I always do not to convey the idea of laziness or that I and my coworkers are prone to sloppy copy and paste.