How should I address a potential FERPA violation by a professor?

Go with option number 1. See what happens.

  1) Ask the professor - in private -

If you're just worried about your grade being posted, may be you can ask him to at least remove your grade from there and leave the rest for the students that want to know their grades as soon as possible. Either that, or may be he could just post people's student ids next to each grade. Or assign a random id himself once, and use that id to communicate future grade reports.

Do note that some online management systems are not all that user-friendly, especially compared to an excel spreadsheet. So do not mandate the way he should solve the problem, mention the problem, and discuss the kind of solutions that may be acceptable to you.

Also note that some grades only affect a tiny percentage of the entire course grade. So that is why some Professors are less worried about the privacy implications of releasing those grades publicly.

And yes, option 2 and 3 would work too, if option 1 doesn't work, but hopefully you won't need to escalate. As you can see from this Supreme Court decision regarding peer-grading, FERPA is not as absolute as you might believe. Furthermore, very few students would have the motivation or the tenacity to pursue this issue in a court of law.


When submitting a research paper as an independent researcher, is it advisable to have a professor look at it first?

I'll try to answer you two specific questions:

“Is it advisable to have a professor from a university look at your paper before you submit it?” — Yes, if you have no previous experience of publishing papers (as a principal author). Academic publication is a game with a set of written rules and some non-written expectations. You can find the rules indicated on the publisher's webpage (guidelines to authors, editorial policy, etc.). If you have read a good number of papers, including many papers from the specific journal (or conference, or …) you are submitting to, then you may have inferred some of the non-written expectations. But otherwise, having someone to help you with the more formal part of academic writing will enhance your paper's chances.
“Is it advisable to have a professor from a university look at your paper before you submit it?” — Yes again, if you do not have a very good understanding of the field, its advances and its directions. To be somewhat brutally honest (and in line with paul’s comment): from experience, newcomers to research, or to a specific field, have a natural tendency to reïnvent the wheel or overestimate the impact and novelty of their work. It's okay, judging these correctly involves a very good grasp of the overall field, both in-breadth and in-depth.
“Would it take the journal a longer time to referee your research paper if you have no affiliation?” — No. For two articles of the same quality, with an unknown author, I don't think the presence of an affiliation would impact review time.

Edit to answer question in comment: “Would a professor who reviews the paper want credit?” — It depends on the amount of work required and the ethics of the person you ask. If reviewing the paper requires significant amount of time, especially because there are many faults with the paper that need to be fixed, you could see that there must be incentive for the professor to invest in it. In all cases, discuss this issue upfront!


Six months have passed since paper has been accepted and it was not yet published - has the editor changed his mind?

It is very unlikely that the article has been "unaccepted", and as far as I know, most journals publish articles basically in order (modulo some special issues and things like that).

However most journals have backlogs, and can take a long time from submission of the final copy to getting the article to print.  I don't know how common that is in your field, but for math, in 2015, the AMS published some data on how long it takes math journals to publish an article; a quick glance shows that gaps of much longer than six months between acceptance and publication are common.


Is it ethical to apply for a short-term grant with a partner/spouse/girlfriend?

Provided you are qualified and intend to do a good job under the grant, I see no ethical considerations at all. Many people (most?) applying for grants in other countries have a variety of goals, not all of which are relevant to the position itself. Wanting to live in Paris is pretty common, I'd guess.

There would be an issue if she is the decision maker on who gets the grant. In such a case she should recuse from the decision and pass it to others, such as a superior. But otherwise, there should be no problem.


Does undergraduate course load matter in graduate admissions?

It's fine to spread things out a bit.  You might consider taking a gen ed requirement over the winter term, and some summer classes, to avoid extending things too much.

Taking a reasonable credit load per semester shows maturity.  It also helps prevent burnout.


How do I modify the title of a paper I submitted to ArXiv?

Short answer: I believe the only way is to submit a revision.

Long answer: As per this page:

It is not possible to make changes without generating a new version

Why? To allow authors to make changes to the comments and other metadata fields of publicly announced articles without generating a new version, and hence date stamp, would effectively mean that all changes would be backdated to the time the last version was submitted. This is open to abuse and thus not allowed.

The exceptions to this rule are the addition of journal reference and DOI information. The journal reference field may contain only full publication information for the article; the DOI field may contain only a DOI.

My suggestion: Although this replacement process would not be time consuming, it would be quite redundant and generate a new version of the paper. Since that would anyway happen whenever you revise your paper (say, after you incorporate the comments of referees), I would suggest -- under the assumption that the typo does not look glaringly bad -- to wait until you have a next version ready.


Should a PhD student be credited in supervisor’s article that is based on a book chapter by both?

Here are the relevant facts:

Copyright

The copyright of everything you create belongs to you by default (in any reasonable legislation).
In some legislations, your copyright or parts thereof may automatically be transferred to your employer upon creation.
Apart from that, any sort of copyright transfer can usually only happen due to a contract you signed, e.g., with your university, supervisor, or a publisher.
In the latter case, your co-authors (i.e., your supervisor) usually do not gain additional rights.
Publishing content to which you hold the copyright without your permission constitutes a copyright infringement.
The crucial question in case of a lawsuit will likely be what you can prove that you created.

Academic Ethics

If you creatively contributed to an article, which particularly includes conceptualising figures and writing paragraphs for a review articles, you have to be made a co-author according to academic authorship standards.
Even if Mary were the sole author of both articles involved, re-using material in the way you describe may constitute self-plagiarism.
This mostly depends on the publisher’s requirements regarding the absence of prior publication and the status of book articles in your field.
Submitting any content you created for publication without citation or similar considers a breach of academic ethics even if you are listed as an author or do not hold the copyright.

What you should do

Secure all evidence of which content you created.
Check your contracts and what has been published.
Talk to your supervisor.


How should I share (cite) my datasets and R analysis/code files in my thesis?

First, best compliments for your intent on open and reproducible research!

Your code and datasets ought to bring you better visibility for your research. GitHub is a good alternative to publish your code. If your datasets involve elements of machine learning you may donate it to the UCI Machine Learning Repository.


It seems that 77 journals use Editorial Express. Given that there are tens of thousands of scholarly journals, it does not seem to be immensely popular.
Anyway, one Editorial justifies the adoption of Editorial Express. It might answer parts of your question:

We have decided to use Editorial Express, developed by Professor John Rust at the University of Maryland. This software is very cost effective, and allows for much flexibility in how it is used. The software will send automatic reminders to reviewers, automatically save contact information provided by authors and reviewers, save all correspondence and manuscripts, and has many reporting functions. Editorial Express is Web-based, which allows the editors to use the software at any time, in any place. Ideally, this Web-based solution will allow us to coordinate the duties of John Mallinckrodt and myself, and might provide for some significant financial savings.

To examine the argument about cost-effectiveness further: The standard price of Editorial Express is $2000 per year, but can even be lower due to its "lowest price guarantee"-scheme. In comparison, one of its competitors, Manuscript Manager, has a graded pricing that may cost up to $8500 per year. Another one, ScholasticaHQ, offers a "peer review system" that costs $250 per year in addition to $10 per submitted manuscript (thus, if you have 200 submissions per year, it adds up to $2250).


One of the multiple submitted paper is published and others are withdrawn

Whatever you do in the future: do not submit the same manuscript to multiple (not even two) journals.

If you have managed to get the manuscript accepted in one journal you need to immediately withdraw all others. You state you have given "personal reasons" whereas in reality you should have provided a serious excuse to the journals for wasting their time.

If you have withdrawn all other manuscripts there should not be any further impact on the one accepted for publication. You should learn from the experience and perhaps acquaint yourself better with the publication process so as to avoid mistakes such as these again. If repeated, it may affect you adversely by gaining a bad reputation or possibly being "banned" from certain journals by their editors. So most negative impacts, if any, will fall on you.


Value of my prior publications when changing fields

I've had a somewhat similar experience, having done my Ph.D. in artificial intelligence / cognitive modeling and then later abandoning that area as I have moved into synthetic biology (my other line of research remained consistent, but that's a different story).

The good news is that you're at a perfect time in your career to make a field transition, and that a postdoc or two is the recommended way of doing so.  The bad news is that your prior publications count for pretty much nothing in the new field, and that this is further compounded by the fact that conference publications generally do not count in biomedical fields, only journals.

The reason that your prior publications don't count is simply that they are mostly not relevant evidence of what you can accomplish in the new field.  They are evidence of your fundamental technical skills, and since many of those are transferrable, that has no doubt helped with your current job applications.  A funding agency, however, will generally want a PI with a clear track record of accomplishment, particularly for highly competitive programs like Horizon 2020 (there's likely no problem including you as key personnel for your skills, though).  Likewise, after you've been in the field for a 2-3 years, people will expect you to start having some good journal publications in the new field, and it is these that you will be evaluated on in applying for future jobs, much more than your prior AI work.

Right now, then, the thing to do is buckle down and do good work, which can then fill up the future publication queue.  Making a transition is hard, but can be very rewarding, and all you likely need is a few solid mid-tier journal publications or one really high impact publication and you can bootstrap yourself nicely into your new chosen direction.


How does the teaching of biology differ from teaching physics?

See Eric Lander's introductory biology OCW course lecture videos for a refreshing take on biology from someone who was trained as a mathematician. The way Prof. Lander (and likely many others) teaches biology is similar to the 'hard sciences' (chemistry and physics), but the history of the science takes a larger role than it usually does in (say traditional introductory) physics and math courses.

Maybe a reason for this is that the ways that important biological processes take place are way too complicated for us to easily derive them from Newton's laws and some calculus, and so to bring people to speed in basic cell biology, one really needs to rely on a large amount of collected observations on non-intuitive, less widely observed phenomena than one does in classical physics to begin doing meaningful studies. One way to do this, is to just say such-and-such is the way things happen, now memorize it. Another approach however, is to explain how the existing models came to be. The second takes (much) more work.

At the most basic level, in either case one tests whether the conclusions/predictions that come from the models are consistent with what is observed, so the distinguishing of intro biology and intro physics on this point seems artificial. A real fundamental difference between the two again is that the type of things which are discussed in the intro biology course are much more complicated than those covered in a basic physics course, and so one must rely on more 'hand-waving' or historical references at certain points. To quote the famous mathematician von Neumann, 'If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is.'


Universities accepting non-cs background students to masters programs in cs

I would find it difficult even for a university in the US to accept a student for masters studies without, at least, data structures and algorithms. It is one of the most important courses in the curriculum and is where many people drop out of studies because of its difficulty and because it is a stepping stone into more theoretical CS (which is what graduate studies consists of!).

Basic C programming isn't really enough for a masters program. I am not an expert on the UK or European systems but from what I know I would say that your chances are very slim- though not impossible. If I were you- I would take more prereq courses that you see commonly listed on websites (especially data structures and algorithms- I'd also recommend an advanced algorithms course) and then apply as that would maximize your chances of admissions.

Good luck.


How to deal with students who are among the more ignorant but think the know everything because they worked hard and got straight "A"s in high school

I think this is an important issue, and wrestling with it has informed a lot of what I do as a community college lecturer in mathematics. Helping students make the transition from the BS they get in many K-12 programs, and getting to share real math with them for the first time, is a great challenge and responsibility.

What gets me a surprising amount of traction is to address this explicitly, as the first thing on my syllabus. Top goal: "Read and write math properly with variables." I verbally quiz them on this on day two. I touch back on it almost every day. I explicate how I'll be grading for this on tests, and show grading examples from old tests. Why? The professional writing (a) provides a shared language, (b) allows them to read any math book, (c) serves as an explanation to other students and colleagues, and (d) makes it easy to find and fix errors and disputes.

Example interaction from yesterday (day 9 of the fall semester): One student has garbled the writing of a polynomial multiplication; I point this out, and she does the "But I got the right answer" bit. I ask, "But what's the number one goal for the course?". She says, "I don't know" (which even she can tell is not a good response), and almost all the rest of the class calls out, "Reading and writing math properly".

So this makes the expectation very clear, and by talking about it as item #1, I get the majority of the class on my side, and the community standard (peer pressure) works greatly in my favor. There aren't many silver bullets in teaching, but I'm delighted at how effectively this one works for me.

(P.S.: While the above is math-specific, I think the basic idea of setting a reading/writing/justifying "top goal" can work in many classes. E.g., in my C++ programming course I start with a quote from Bjarne Stroustrup, "Design and programming are human activities; forget that and all is lost", and then likewise emphasize making one's code readable to other programmers via a common style. As Ken Bain writes in What the Best College Teachers Do, "Finally, the best educators often teach students how to read the materials..." [Ch. 4]).


Publishing a mathematical research article on research which is already done?

An article is not about you. It is not a reward of effort. In an article you try to communicate to the readers, so it needs to contain something that your readers want to read. If something is already done, then why would I want to read it? Maybe, you have variation, or a special case, or a more general case, that makes your equation or your derivation thereof different and interesting. But if that is not the case, then the answer is simply no.


Is a copied acknowledgements section considered plagiarism?

He recently realized that in the acknowledgements part the student has copied practically (word by word, line by line) the acknowledgements of another thesis available on the Internet by replacing the name of my colleague with the name of the supervisor of that thesis.

I'm slightly confused: I assume that in order to discover this, the advisor must have run the entire thesis through some plagiarism-detection software.  But the question indicates that this took place after the student's graduation.  I don't understand that: two reasonable times to run your student's thesis through plagiarism detection software are (i) at some point before you sign off on it and (ii) never.  Would one really do this after the fact out of idle curiosity, or did the advisor have some other reason to suspect that plagiarism took place?

Is line-by-line copying of someone else's acknowledgments a form of plagiarism?
Well, plagiarism has a sufficiently precise definition that I don't see how the answer can be "no".  The better question is whether this is viewed as unacceptable enough to do anything about.

I think that part of that question depends upon the writing quality and originality of the purloined acknowledgments.  As @Andreas Blass points out, if you've seen 10 different thesis acknowledgments, you've seen 1000 more: such acknowledgements are formally part of the thesis but they are not part of the academic / intellectual content of the thesis.  So they are not vetted in any way, and there is no expectation of intellectual originality.  There is more than one way to phrase "Thanks so much to my parents, my friends and my thesis advisor", but the number of standard ways to phrase that is so much smaller than the number of theses that the pigeonhole principle applies to show that many people are writing the same sentences in their acknowledgments.  If the purloined acknowledgments contained many clever and original turns of phrase, then it looks worse: the fact that what you stole has nothing to do with the intellectual content of the thesis cannot excuse the fact that you are taking credit for someone else's distinctive writing.  That's a really icky thing to do in acknowledgments to your own thesis.

Unless the purloined acknowledgments contained several paragraphs of poetry or something similarly egregious, I would not consider a formal plagiarism inquiry.  This runs the risk of getting the degree rescinded, which to me is clearly too harsh.  But there is a real problem here:

  He added that he was hurt by the fact that the student has not tried to say his 'thank you' words by his own words.

Ça y est.  The student's former advisor has discovered that the student has cut corners and compromised some academic integrity just to get out of thanking him in his own words.  What a slap in the face!  I think that if something like this happened to me, I would have to bring it up with the student (though it would be painfully awkward) just because I would feel like I have to be honest with them about the change in my opinion of them resulting from this discovery.  Without some kind of sincere apology / explanation of this, the future of this professional relationship is at risk.  The student, alas, may need to be informed that he should look elsewhere for future recommendation letters and so forth.

Added: A lot of people seem to be suggesting that parts of this answer are an overreaction.  I tried to make clear that I don't find the premise of the question completely plausible or understandable, but after discussing that I did what I think is the appropriate thing on Q&A sites like this one: I assumed the premise, in some form which made sense to me.  Yes, if the "word-by-word, line-by-line" copied acknowledgments constitute five lines thanking the student's family, friends and advisor, I see no problem at all -- and I  don't see it as a reason to run the text of the acknowledgment through an internet search.  Nor would such a search turn up a unique antecedent; it would turn up hundreds or thousands of cognate passages, as Andreas Blass pointed out. Thus to assume the premise I had to assume that the purloined text was much more substantial and distinctive. To be more specific, imagine the text was:

  I feel greatly honored to be able to add, in some small way, to a subject founded
  by so many [Field Xers] whose work I so deeply admire; among them are
  [My Advisor], [Person A], [Person B] and of course [Person Whose Name Appears in the Thesis Title], the richness of whose ideas seems undilutable by time.

  I thank [Professor C] and [Professor D] for suggestions directly relevant to the material appearing in this thesis. I thank [Fellow Student E] for helping me – quite a while ago now – with some results of [Somewhat Technical Theory] that appear in the appendix.

  I thank [Postdoc F] for helping me calculate a fistful of [Something] (I regret that none of these calculations appear in this thesis)
  and for generally being so free with his technical and [Field X-ical] insights.
  I am grateful to [Recent PhD G] for making his own as yet unpublished thesis
  work available to me.

  The graduate students in the [University Y Department of X] have been without
  exception intelligent and friendly, and it has been a pleasure to learn from them and with them over the years.

  Thanks to [Old Girlfriend H] for providing comfort in the sad days of [a few years ago]. Her kindness will never be forgotten.

  I am indebted to my thesis advisor [My Advisor] for more things than I can list
  here, but most recently for a careful reading of an early, ugly draft of a certain lengthy [Field X-ical] document.

  My father would have been proud of this thesis beyond all moderation. My
  mother has long made and continues to make me proud of her strength in the
  face of all the challenges life has to offer. I thank them both with all of my
  heart.

Imagine that the advisor read this the first time around and was happy to be thanked along with so many other people who made a difference in the student's life.  Then later, for whatever reason, he does an internet search on or including this text and discovers that it is lifted word-by-word, line-by-line from this 2003 PhD thesis.  The specificity of the stolen text would be downright creepy.  Is it really an overreaction if the advisor is upset by this??


Should you correct grammar mistakes during peer review?

In addition to the others answers given, I think that is it extremely important to state whether or not you consider the grammatical errors to affect the scientific substance of the paper.

Usually, grammatical errors don't actually effect your ability to evaluate the science in a paper.  Even when phrases are fairly tangled or when a missing word makes a sentence say the opposite of what is intended, you can usually sort out what the authors intended, and judge them on their science, not their presentation.

This is an extremely important responsibility: do not judge a paper based on grammar and language issues.

Whatever grammatical issues you point out, be explicit that they are not the reason for your recommendation.  Some reviewers will play language police, and recommend a paper be rejected because it is "sloppy."  This is, in my opinion, inexcusable: grammar, no matter how tangled, can always be cleaned up, and should only be held against an author if they refuse to do such cleanup.

In those rare cases that things are so badly presented that you cannot understand the science, however, state clearly that is what has happened, and that this is why you are judging the grammar to actually affect the acceptability of the paper.


How to deal with (ex-) supervisor not meeting promise to write reference letter

I'll guess you have done about all you can other than send a final notice very close to the deadline. The prof is probably targeting that "drop dead" date and continuous reminders may just get in the way. But a note on the next to last day would be good.

You might also start to think about other options. Who else might be able to do this for you?


Citing many map shapefiles from the same website

How to proceed probably depends on the number of files.

If it's just a handful, you could create individual listings for each file.
If there are a bunch of files with a similar naming structure, you could create a single bibliography entry for the main page, and then in a note in the citation identify the files used.
If there are hundreds of files or files with various naming conventions, it would probably be easiest to put this information in an appendix or supporting information document, and then provide a single citation to the web site.


What is the purpose of publishing in such journals?

There appears to be a mismatch between your view of "Math" and what math means to a broader community. Sure, there are those doing leading edge research, publishing bold new results, and so forth. But, there are also those who have a calling to do things like teach mathematics, including dedicated high school teachers. Why should there not be a journal for them to read? And if there is such a journal, somebody has to write for it, and those people are normally professionals closely engaged with teaching (remember that many professors, including in math, are at teaching-focused institutions).
In a non-math context, I would point to the American Association of Physics Teachers (aapt.org), associated with the American Physical Society. Their mission statement reads (AAPT Mission):

Mission:
AAPT's mission is to enhance the understanding and appreciation of physics through teaching.
When the organization was established in 1930, our goal was clear: "ensuring the dissemination of the knowledge of physics, particularly by way of teaching." Decades later, we remain committed to that core value, but with a new emphasis and meaning provided by our current mission statement.
Our vision is to be the leader in physics education. We are committed to providing the most current resources and up-to-date research needed to enhance a physics educator's professional development. The results are not only a deeper appreciation of the teaching profession, but most importantly, more enthusiastic involvement from their students.
The Association has identified four critical issues that will guide our future activities:
Increase AAPT's outreach to and impact on physics teachers
Increase the diversity and numbers of physics teachers and students
Improve the pedagogical skills and physics knowledge of teachers at all levels
Increase our understanding of physics learning and of ways to improve teaching effectiveness
The twenty-first century will provide the greatest opportunities and challenges for us as we take an active role in shaping the future. Our success will depend on the commitment, dedication, and continued input of our members and the physics education community. Join us in this journey to enhance the quality and effectiveness of physics education at all levels.

They publish several journals, the American Journal of Physics and The Physics Teacher, focused on slightly different audiences within their society. Frankly, some of their stuff is pretty interesting (in the spring there was a nice paper on the production of polonium in the Manhattan Project, physics included).


First, let me state that in my experience, there is no such thing as a formula for writing papers.  There are too many different types of results to be presented in too many different types of papers.

That said, however, there are most certainly patterns of presentation and argument that emerge as being particularly effective.  In my observation, many successful researchers have some form of such patterns that many of their papers adhere to.  Ultimately, for a researcher with integrity, this is not about chasing a metric, but about effective communication and about having an impact on their research community and, hopefully, the larger world.

That said, I think that the approach you propose of relating your work as though you were an independent observer, is not a good way of presenting, because you are not an independent observer.  An approach of "minimize the bad" is even worse, because then you are attempting to conceal the truth.  Instead, I recommend thinking of yourself as an "honest advocate" for your work.

You are a human being who believes the work you're doing is good and producing interesting results: in the introduction and related work section of the paper, you explain why you think the problem you're working on is interesting and how the results you've produced fit into the larger world.  You must, however, be honest with yourself and others about the strength of the results that you have found.  That means:

Be scrupulous about distinguishing between what your evidence shows and its relationship to your hypotheses: e.g., "the data is consistent with our model, though not strong enough to rule out the alternate hypothesis"
Don't value judge "good" and "bad," but instead report the circumstances under which statement is known to hold or fail.  It's OK if something only holds in a narrow case if that case is interesting and possibly important.
Publish early and often, so that you don't feel like your papers are so high stakes.  You might not get "glamour journal" papers, but you won't need to worry about being scooped, and you can get credit for the knowledge byproducts discovered during your search even if your ultimate goal is not achieved.

More important and more difficult than anything else, you need to be prepared for the fact that you may find your work has been going down an unproductive path and that you need to change your direction.


What should I do when a predatory conference will not listen to us and the journal might retract our paper?

The key statement in the above may be "Mr. C have powerful connections in government". That is an issue that may be impossible to overcome. If there is an ethics process in your profession generally, you can bring things to their attention. You can bring it to the attention of the conference committees and journal editors. Unfortunately you may be fighting powers that you can't overcome.

Given sufficient power and influence, yes, they can do whatever they want - ethical or not. If you can shine enough light on it you might get some satisfaction and it may come back to haunt Mr. C in the future, but making powerful enemies in some places isn't necessarily wise (or even healthy). Proceed cautiously. If you can build allies, it may help.


Parameter quantifying the number of publications expected from a good researcher

Note: I wrote this to answer the original question, which was less specific.

There's no a general answer to this question, because things change a lot by field.

If you want to have an idea of the extreme variability, you can look at this crazy table which reports the Italian minimum requirements to become tenured associate (II fascia) or full professor (I fascia), divided by field.

The third and the sixth columns of the linked tables report the minimum number of journal papers that should have been published in, respectively, the last ten and five years to be able to apply for the two positions. Then there are the number of citations and the h-index.

For instance, someone wanting to apply for a full professor position in mathematical logic is required to have at least 4 papers in the last 10 years, whereas an experimental particle physicist is required to have at least 164 publications if the average number of coauthors is between 501 and 1200.


Can I use the whole mathematical proof from references like books and reputed research papers for my own paper?

You certainly can, and should, use the equations (and theorems, etc.) that others have proved. Otherwise, you would have extremely hard time getting anything new done, as mathematics and physics research is quite cumulative in nature.

You use other results by citing the source. At least in mathematics, sometimes you just write "by the Lax-Milgram lemma we get...", if you are writing for an audience which knows what the Lax-Milgram lemma is. If you suppose not all of the audience knows this, then you provide a reference to the result: "by the Lax-Milgram lemma [1, theorem 4.7] we get..." (where the citation format may and does vary). If in doubt, err on the side of citing, as it will be helpful for beginners.

However, if you are writing a research paper and the concept of citations is unfamiliar to you, then it is a good idea to get some help from a scientist in the field (or any field). If you are at a research institute, find someone there. If not, it will be more difficult, maybe impossible, to find a contact, but you might still want to try. Publishing scientific articles is not a trivial task and there are some traps (predatory journals).

[1] Reputable source with bibliography info.


Is there advantage an for a student to know out of the course question in Ph.D. interview?

Saying you don't know the answer to a question is poor interview technique regardless of the situation.
Of course, you can't be expected to know or study every possible topic you might be asked questions about, but that's generally not the aim of these more difficult or esoteric questions. Instead, the interviewer wants to find out how you think and whether you are able to understand the question and reason your way to an answer even if you're unfamiliar with the subject matter.
After all, that's what research is all about: finding answers to questions that no one's studied before. The ability to apply previous reasoning to a new question is particularly important in physics, as we believe the same physical laws should hold anywhere in the Universe. Therefore, a good answer to a such a question would be "I'm not sure, but I would expect from my knowledge of X that Y might happen." And then go into detail as to why. It's also ok to ask for a moment to think before answering.
For what it's worth, PhD interviews are not typically like an exam, and you probably won't be aggressively grilled on your knowledge of a specific topic. More likely, the interviewers will get you to explain any previous research projects you might have done, and discuss your ideas for the future. That's not to say you shouldn't study topics outside your course, if you're interested in them and they're relevant to your intended PhD topic.


Research Grant - Difficulty in Obtaining and How?

Your question is very broad for this site. I will try to do my best to give you an overview, but you should really ask a more focused question if you hope for more specific answers.

Generally, what opportunities for research grants there are depends on many factors, but foremost where you are geographically and which career stage you are in. Geography matters because most basic research funds are national funds, that is they specifically fund research conducted e.g., in the US, in Switzerland, in the European Union, etc. The career stage matters as most "normal" project grants are available only to people in a certain career stage or position, typically faculty (sometimes also postdocs). For more early-career researchers, other special grant types are often available, such as PhD project funding, young investigator's grants, or similar. However, these usually differ from regular grants in that they often need to be applied for in collaboration with a faculty advisor, mentor, or host. One of the functions of this mentor is to make sure that the grant money is used correctly.

  I imagine being at the undergrad level is a problem, but I'm asking for general information - if I have to wait until I'm in a doctoral program or I've finished it, that's fine.

You are likely correct. As an undergrad there may be very few opportunities to apply for grants in your own name. Very few undergrads are academically mature and well-developed enough to form and implement their own research agenda, and giving out grants to students in such an early phase of their career will often be seen as too risky from a funding agency's point of view. Even being a doctoral student is already quite early to apply for project funding in your own name. Most grant opportunities open up for you when you are faculty at a research institution.

To give you one example from Switzerland: most funding provided by the SNSF (Swiss National Science Foundation) is given out through their individual project funding scheme. There are many restrictions on who can apply, but most importantly you need to be working at least 50% of your time in a research-active institution in Switzerland, and you need to hold a PhD degree since at least four years or hold an independent research position, e.g., be an assistant professor (Chapter 2, Article 4).

Your own salary cannot be funded by such a project grant, so it's only used to cover e.g., PhD students that you advise. This also clarifies why the SNSF largely restricts access to these funds to professors - the applicant needs to be somebody who can provide guidance and formal advisory to the staff employed in the project, and they assume more junior researchers will not be able to do that.

  In general, how difficult is it to get a research grant? There's relevant data that hasn't been explored and I'd be interested in doing it.

This depends on the grant, but in general it is very difficult. Most grants worth applying to have acceptance rates below 10%. Interestingly, the SNSF project funding scheme mentioned above is an exception, with acceptance rates in the 40% to 50% range

Further, and this is another reason why you may have to wait until you can run your own project, a large part of the grant evaluation procedure is usually an evaluation of the Principle Investigator. Quite frankly, a funding agency will look at grants by established senior researchers much less critically than by academically young or not yet established ones. While this may appear unfair, for the funding agency it is just much less risky to give money to a person that has already successfully conducted many projects than to somebody who hasn't.

  Also, how would I go about obtaining the grant? We can define what makes me a good candidate, but then where do I go?

This is not a question that can be answered with the detail that is provided. My suggestion is to keep your ideas in your head, maybe work on them in your free time or as a side project, and then revisit them once you are in the right career stage to apply for your own funding. This will also have the advantage that you then already have preliminary results during the application phase, which is another factor that you can use to tremendously increase the chances of your grant application.


How is sexism unknowingly perpetrated in academia?

And how can those of us who are well-meaning make sure to avoid doing so?

If you see something, say something.

You're correct that blatant sexism is mostly gone.  I'm a female computer engineer, and I have never been told that I can't do the job because I'm female.  What remains is "death by a thousand paper cuts" sexism.  For example, I was recently at a conference, and the small group I was in was discussing one of the presentations.  An older professor in the group remarked that the presentation was particularly good because the presenter was beautiful and wearing tight clothes.  Nobody called him on it: after all, he was trying to give her a compliment, mentioning it would be rude, he's older and things were different then, and so on.  And it's hard to blame them, because if that were the only sexist comment I heard that day, it wouldn't be such a big deal.  But shortly after that, someone jokingly said I should marry my PhD supervisor.  Then someone said a new tool is so user friendly that "even your mother could use it".

Each of these incidents on its own is fairly mild: most people probably don't even realize they're saying something exclusionary.  Unfortunately, if you're a woman, each one reminds you that you don't belong, so the cumulative effect is very discouraging.  However, if you correct every person who says something mildly sexist, you get a reputation as a bra-burning feminazi.  As a result, most women keep quiet, or only point out the particularly insensitive comments.  It would make an enormous difference if other men would call out the ones who make inappropriate comments.  You don't have to be dramatic or rude about it, but a quiet "I don't think that's appropriate" would take a lot of the burden off women.  And naturally, you can try to be more aware of the things you say to make sure you aren't accidentally discouraging women.  A lot of sexist ideas are so deeply ingrained that otherwise fair and open minded people will say them without a second thought (like the "even your mother" comment).

I don't want to downplay the other valuable things you can do, such as volunteering at math/science camps for girls, but if enough men followed this rule -- even part time -- 80% of the sexism I encounter would disappear. To modify Edmund Burke's quote a bit,

  All that is necessary for sexism to triumph is for good men to do nothing.

June 27, 2014: After a year of comment trolls, I think it's time to add a point about men's rights activists.  The key mistake that MRAs make is treating rights as a zero-sum game.  The fact is, gender stereotypes hurt everyone.  They hurt women who want to be engineers; they hurt men who want to be nurses.  They hurt women who don't want to have children; they hurt men who want to be stay-at-home dads.

Sometimes, these stereotypes result in a disadvantage for men.  For example, Doug Spoonwood points out that American men have to register with the selective service system to get student loans, while American women do not.  MRAs point to these cases and try to claim that feminism oppresses men.  This is, at best, willfully ignorant: all these inequalities come from the same outdated beliefs and stereotypes, which feminism opposes by definition.  The fact that these cases exist just indicates that gender equality is not a solved problem.  (Women in the American military were not allowed to be in units tasked with direct combat until 2013.)

My answer discusses a woman's point of view because that's what I know and that's what the question asked about.  I would be thrilled if a man in a predominantly female field added an answer discussing his experience.


My advisor said that I should be more modest, and we should meet more often. Should I tell him about my impostor syndrome? If yes, mail or personal?

My advisor sent me an e-mail that he thinks that I should be more modest and that we should meet more often.

Your prompt answer:

  Sounds good!

Nothing is gained by getting defensive.

(Do you know what meeting rhythm your advisor has in mind?  What often works well is a standing, weekly meeting.  If you have no progress to report, that's okay -- it can be helpful to establish a habit of meeting regularly, rain or shine.)


How to politely and logically explain that I don't want to receive notification at my private social media account?

I agree with Captain Emacs that you have a right to privacy. Private information(exam scores, contact information) should not be posted on Facebook but general seminar schedules can be.

I think the best course of action is to discuss this with the head of the department, and request in writing, that your information not be posted there. If that doesn't work then you will have to speak to someone above the him/her. If this is not an option see if there is someone you trust that you can ask for their help or advice to bring this issue to the right person's attention.


An interviewer has asked for a copy of an unpublished manuscript I'm writing, is it safe to do this?

There's no concrete, objective answer to this. My opinion is that it's fairly safe to give unpublished manuscripts to an academic interviewer. You definitely need specific permission from all the co-authors on the manuscript, though. If the interviewer is directly in the same field as you, and might be working on the same topic, you might be more hesitant, but it's not a definite "no".  Hopefully, if you're interviewing and considering working with this person, you've already decided that they are not a horrible human being, so you've already done a little of the due diligence.


My answer assumes the US university system, based on your stated location

Endowed funds (for positions or otherwise) are quite common at universities, so every University has an "Endowments Office" or "Office of Giving" or the like, which will most happily sit down with you to work out these sorts of details.

You will definitely need to sit down with that office to determine the details, however, because it will likely be different for every university. Factors influencing these details will likely include: public vs. private, overhead rates and structure, how the university manages its endowments, state and local tax laws, etc.

In short: get the university's experts involved.  The sorts of sums that you are considering will certainly get their attention.


What are the career prospects of doing a theoretical computer science PhD.?

If you truly have no country preference and are willing to go anywhere in the world, then there is a lot of potential opportunity.  In particular, I know there is a large amount of expansion in computer science in general (and thus likely theoretical as well) in the emerging universities of East and Southeast Asia, India, and the middle East.  Depending on your personal background and preferences, of course, you may find some cultural barriers to overcome.

I would also recommend considering the possibilities outside of traditional academia.  Theoretical computer science topics like you mention turn out to have a lot of applicability both in standard industry and in the in-between world of research institutes, national laboratories, startups, and non-traditional corporate environments that are not what people typically think of as "industry."

And then there's always just giving up academia altogether and making money, if your personal ethics would be OK with entering the financial world and playing hedge fund games...


Should I use recommendation letter from young professor I worked with or well-known professor I met in class?

Your REU evidence that X wrote you a weak letter is not very strong.  I run an REU, and we accept less than 3% of our applicants.  Our target participants are either legendary at small colleges (best in a decade), or excellent at top universities (top 25% this year at Harvard).  Plenty of excellent people get turned away for essentially random reasons.  Maybe one of your letters was submitted late.  Maybe you forgot to list a course on your application that was considered essential that year.  Maybe I had a bad burrito for lunch and hated your essay when I read it.  Maybe there were just lots of really good applicants that year.  And yes, maybe professor X (or professor Z, the other letter-writer) said or implied something negative about you.

In addition, Professor Y offering to write on your behalf after a one month course says more about her than it does about you.  This does not guarantee that she will write a strong letter, and if she does she may write strong letters for a lot of people, which might be known by the people reading her letters.

Here is my advice.  Go to Professor Y and tell her that you did research with Professor X and published a paper together.  Then, ask her whether you should ask for X's recommendation or hers.  If she really feels that you are spectacular, she will insist on writing the letter herself.


What does "awaiting EIC decision" mean when it occurs immediately after "awaiting reviewer selection"?

Sometimes tracking systems do not work very well and a change of status could mean nothing. Since I am a pessimist person I would give the same interpretation as you, but it is impossible to know. The wait is frightening but in this case is all what we have. Good luck!


what exactly does a research supervisor pay for PhD student funding?

Depending on your country, there may be different kinds of funding, including positions where you're an employee of the university/state/country. Such positions are usually owned by an individual professor. This is different from other funding sources that are not owned by individual professors, like stipends.

So, when you ask a professor if you can be her PhD student, without specifying a funding source, she may assume you're asking if she has a funded position readily available. In this situation, the answer is often no.

In addition, "no funding available" can also be a polite way of declining, if there are actually other reasons for saying no.


Yes, it is common and fairly reasonable.

So say you've implemented a new method for X.
And you submitted it as a PR on say github, as a new feature for
"SuperXdoerLibrary", and it was accepted.
Then you would, say something at the end of the Section where you describe your algorithm something like:

  This method for doing X is now available in SuperXdoerLibrary (V1.23)1.

And then in a footnote put a link to the SuperXdoerLibrary website, or github page. And probably also put a link on your website

It is very common to refer to what implementations of your algorithm referred to in your paper. And a "good thing".

As to if it is a stand alone implementation, or as a component in a larger library, I don't think it matters.
I would in-fact suggest it is even better if it is in a larger library as that will generally mean it is in a more usable state.


When to publish a journal article versus a scholarly book?

My observation is that in those disciplines one decides before hand to do research to write a book. So it is not a matter you have results and wait with publishing it, but as long as the book is not done, the research is not considered to be done.


How to protect my research rights when my proposal was stolen by my chair?

If you have been informed that your contract isn't being renewed, then the question is how badly you want to burn any bridges. However, I suspect that your chair is going to be of no use to you in any event.

The first thing you need to do is collect all of your records related to the grant. Any email, correspondence, etc.—anything that shows you were the real originator of the grant, and that she basically stole the work. I would also include the correspondence showing that your contract will not be renewed, as well as the visit of your future replacement. All of this shows dishonest intent on the part of your chair. This evidence should then be sent simultaneously to:

the dean of your college;
whoever is responsible for research across the university;
the chief administrative officer of the university;
the agent in charge of the section at the agency who awarded the grant; and
the office at the grant agency responsible for investigations into the grant.

The way you have been treated is reprehensible and the chair under no circumstances should be allowed to "skate free."

It also goes without saying that you should not do any further work related to this grant. You should also find a good lawyer.


What is the Minimum GPA for admission in a graduate school in a respectable science university in the US?

(In the US) in Physics, some programs will weight things like the physics subject GRE and research experience, especially publications, ahead of the GPA. However, some schools do have a GPA cut-off around 3.0, so it's possible some schools wouldn't get far enough into your application to read it.

If you want to apply to prestigious or highly-selective programs right now, I think you would need:

To have scored very well on the general and physics-subject GREs.
Very good letters of recommendation that speak directly to your ability to succeed in a graduate program.
An "explanation" for your GPA in your application. Was it because you worked a lot? Was it because you spent a lot of time doing research? Do your last couple semesters show a better GPA than your overall GPA? If so, you could make an argument that you addressed the issues that led to your lower GPA during the course of your undergraduate career, and these issues will not continue to impact your graduate performance.

If you don't fee you have documented supplementary support like that, you still have options:

Take a year off and gain experience
You can also take a year or two off and work a research/physics-related job or internship, and/or take a couple extra classes. Taking one class at a time while working a job or internship can push up your overall GPA that they will consider (and can go a long way to making your graduate career easier), and if you spend a year or so doing something else, there will be more focus on what else you were doing. If you can get a publication during that time, that's an excellent way to display that you do have the skills to succeed in a graduate program.

Apply to "Bridge" programs
Several universities have Bridge programs, meant to help students build a competitive background for graduate study. Often, these Bridge programs also grant your access to that institution's graduate program, if you finish 1-2 years of the bridge program in good standing. One example is The University of Chicago's Physics Bridge program. This is not a masters.

Apply to Masters programs
Many universities have Masters programs, which may include the opportunity of transferring into the university's graduate program, or to another university's graduate program.


Is Dean-hood largely irreversible, and if so why?

To become a dean at a research university, you have to have some prior administrative experience. So, chances are that you were department head for 4 or 8 years before you become dean. By the time you step down as dean, you've been an administrator for more than 10 years. You may have been able to keep up some kind of research program as a department head, but that's almost unheard of for deans -- certainly not at the level where you would be able to keep a lab running, write grants to support your lab staff, etc.

In other words, when you step down as dean, you're in a situation where you likely haven't kept up with the literature in the field for a good long time, where you don't have any current grants, where you no longer have grad students and postdocs, and where you haven't been to a lot of conferences to interact with the other people in your field. If your plan is to go back into research, it's going to take a while to make that happen -- and it does, and universities usually also give deans a year of no teaching after they step down to get back into their field. Or, you can decide that your many years of administrative experience are useful skills and continue to use them in other roles.


Some places in continental Europe can accept people with BSc but without MSc (but most - don't). In UK and US, MSc is a part of PhD, so typically you do don't need one to start.

But you ALWAYS need to consult a particular university/institute, as rules vary (and especially with treating foreign diplomas).

However, if your "GPA sucks" then, unless you have a strong research track (i.e. strong recommendation letters from your research internships, published papers) special exceptions may by unlikely.


Erratum, Rejoinder etc. in Article names: What are the differences?

Erratum/Corrigendum

These are corrections to an article after publication, perhaps due to mistakes during copyediting, or mistakes made by the authors while preparing the contents. The two terms are often used interchangeably, but some publishers (e.g. Elsevier) make the distinction that errata correct errors introduced by the publishers, and corrigenda correct errors introduced by the authors. Other publishers (e.g. APS) consider errata to be for nontrivial corrections by the authors. Basically, which term to use will depend on the journal in question.

Commentary / comment
Response to comment
Rejoinder

Sometimes you see a published paper and you have a criticism with its overall methodology, or conclusions. It should usually be about something central and important to the paper - something like a significant factor being overlooked in a statistical analysis. Then you can often submit a comment to the same journal detailing this criticism. Sometimes this is known as a commentary.

Smaller mistakes and errors are often better dealt with by letting the authors know, and hoping they'll submit a correction. Other times future papers (by you or them) can quietly correct simple typos in equations etc. After the comment, the original authors generally get to write a response to this comment. Sometimes the commenters can write a reply to this response, and this is often known as a rejoinder response.

  In which cases is/should an article be named one or the other?

As I hinted at above, this basically comes down to what the journal or publisher wants to call things.

  What other options do we have to discuss findings (other research articles) in journals?

The most important option is to write a new research article, in which it's a good idea to discuss past works as a motivation for your own work. Some journals also publish "letters to the editor".


Post-tenure move: Reference letter from institution to which I'm applying

A letter written by someone the reader knows is likely to be more credible than a letter written by someone unknown.  So it makes sense to get a letter from someone at X when you know the reader will be at X.

they might be seen as having a vested interest

Most letter writers have an interest in the success of the person they are recommending.  A writer who works at X will have additional knowledge of the interests of the whole university, which could result in a more useful letter.

would it be weird to draw on a reference from this collaborator when applying to the University of X?

No.


Research statement for professional versus research master's programs

You don't mention what field you're in or what country you want to apply to, but let me answer for computer science in the US.

  Is the evaluation of research statement done differently for professional masters and research masters? If so, what are these differences.

Professional masters programs won't ask for a research statement at all.

There are two types of computer science masters degrees in the US. One is the research masters, which requires a thesis in addition to advanced coursework.  The other is the professional masters, which is entirely based on coursework, with no research component.  Research masters students generally work with faculty advisors on a research project and may even be funded by teaching or research assistantships that include a tuition waiver.  Professional masters students pay full tuition (or get their employers to pay for them), and take classes and nothing else.

  can I take admission into professional degree first and then make a transition to research degree in order to increase my odds of admission?

In my experience, absolutely not!

Professional masters degrees are considered to be terminal degrees.  Because they lack a research component, they are not considered pathways to a research degree.

  I am an international applicant applying to US. So I do not with to go for PhD directly.

Why not?  At least in my department, a strong majority of PhD students are international, and most of them apply as undergraduates.  And I don't think my department is special in that regard.


Whether to quit PhD in psychology: overbearing post-doc, lack of passion for topic, not wanting to enter academia, lack of statistical support

I agree with you that, regarding 1) - difficult co-workers - you very well might quit and have just as overbearing a boss outside academia.  Although it is difficult, that shouldn't be a key driver in your decision.
(Note that pride is strongest within academia, so working with people who always think they're right is pretty normal!)

However, reasons #2) & 3) - having no passion because you don't think your work is useful to anyone, and being embarrassed about what you do - are very good reasons to seriously consider changing jobs.  This would probably be true in or out of the academic world.

Reason 4) - the fact that you have to learn something difficult all by yourself - may be pretty normal for many different research fields.  However, the thing that often propels people through these difficulties is a passion for what they're doing, either because it's enjoyable or because it feels like it'll be really useful later (to yourself or others).  If you don't feel either of those, then learning the new topics might be quite painful.

Depending on your situation, another option may exist - assuming you, at some point, were really excited about starting research in this field, perhaps  changing projects (or changing the particular aspect of your project that you pursue) could reinvigorate you?

It should be noted that just about every PhD goes through a time similar to what you're experiencing - the end not in sight, too many hurdles, just want it over, along with the constant fear that you're underperforming.  For me, I realized that at least I could say I loved my daily work, and thought it was really cool.  If I hadn't had that passion for what I was doing I wouldn't have been able to make it through the slump(s).


Cleaning up/Uniformize bibliography for long document

If you have the DOI codes, the best thing is to use the API and get the references yourself:

curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/[DOI code]

If you have them (and you should, for any modern article), parsing the bib to get them and getting the data can be done in a very simple script.


If it is included in the conference proceedings then sure, include it. It is important to make it clear that it is not a full paper so people have a separate section for listing things like posters or workshop papers.

But how much does it matter? For impressing a hiring committee, not much. It usually isn't very prestigious to present a poster and the acceptance rate is often very high

It is still your work though and was published, so I would list it mostly for completeness.

If it isn't included in the proceedings, then I probably wouldn't include it. The advice I have been told is that it will reduce the signal-to-noise ratio of my CV. Although, I have seen some of my friends in the humanities include such things so it might depend on your field.


How to format a large diagram with many formulas that does not easily fit on an A4 page?

First, I do not consider your diagram is too big unless your layout has ridiculously big margins. That does not mean that you cannot improve its layout such that the type is bigger and thus easier to read.

  What to do to make the diagram easier to read?

Your biggest problem is that the individual formulas are all horizontal and very close together, which forces you to make them rather small. Thus, I suggest to replace most of your straight lines by curved ones and rotate your formulas appropriately. Also, use more vertical space (which you should have). Finally, you can make your texts narrower by using more line breaks:

A quick sketch to illustrate this:

Note that I increased the size of all formulas while maintaining the width.

  Should I replace big formulas with numbers or letters to label the arrows with numbers or letters and describe the corresponding formulas below (or above) the diagram (so called, "legend")?

That sounds like a very bad idea to me. This way the reader would have to jump between diagram and legend all the time. The whole point of your diagram (as I understand it) is to have all these relation in one place. If you use a legend, you might as well skip the entire diagram and use text instead.


Applying to multiple fellowships simultaneously

I don't think there's any reason to fear "commitment" when you're applying for competitive fellowships. Because they're competitions, it's likely that the success rate will be exceedingly low, and then it makes sense that candidates will apply to multiple programs to improve their chances.

(I also would think it unlikely that the same reviewer accepts the same proposal for multiple fellowships, since doing so would represent a conflict of interest.)


Sending a thank you e-mail to a professor as an external intern

I think the proper answer is "Just Do It." She will be delighted to hear from you. Tell her about your current success. Open and close with "thanks". That's all it takes really.

Of course the things you say here would be excellent to include in your thank you.

However, sometimes a more formal letter is called for, sent by ordinary mail. That is up to you, of course.


I slept, how should I respond to the professor?

Students are allowed to sleep at night. In all likelihood the prof just forgot about the differences in timezone, or miscalculated the time difference.  Just answer something like :

Dear prof. XXX,

Sorry I missed your reply. It was 22:00 hours when I sent that message, and went to sleep immediately afterwards. Could we make another Skype appointment?

Best,
YYY


How to sell my current solution to my advisor?

In general trying to sell things to your advisor puts you on dangerous ground.
For example, the way you pitched your research in the question makes it seem like there are no problems that bar publication with your approach (as pointed out in the comments, fast approximations are generally publishable if they are novel). So I can't say why your advisor is hesitating. From the information given, it seems your advisor 1) is hesitating for no reason or 2) has a legitimate problem you didn't describe. If it's the 2nd case, be worried. Someone who brushes over and can't articulate legitimate problems with their approach is not someone who usually puts out high quality research. A big part of getting a PhD is learning how to be critical of your own work, and your advisor can't help you learn this if you don't listen to criticism.
Rather than sell to your advisor, I would open up more communication with them. Find out more about their reservations. Really try to get to the root of why the advisor doesn't want to publish. If your research has merit, that will come through in an honest investigation of its merits and its flaws. If your research has flaws, then listen to people who point them out, understand the flaws, and work on figuring out how to fix them.


I would assume that it is a fairly common practice as long as no conflicts of interest arise. But, to be sure, this is really a question to address to the editor. You might have to say a few words about the colleague.
Some situations, of course, require confidentiality. Most do not as long as the normal rules and expectations apply.


Should I use fancy paper for non-resume application materials?

Above some minimum quality threshold (like, it's actually a piece of paper that is roughly a uniform white), the fanciness of the paper has had no bearing on any hiring decision that I've been a part of.


Whom to cite when describing an argument in another paper that builds upon yet another paper?

I will use 'Johnson (2016)' and 'Smith (2015)' rather than 'Y' and 'X' in my examples:

Explicitly corroborating Smith's (2015) hypothesis that mice love cheese, Johnson (2016) demonstrated that mice ate cheese rather than carrots, when offered both.
Smith (2015) argued that mice love cheese. Johnson (2016), citing Smith, experimentally verified this hypothesis.
Johnson (2016) interpreted her experimental results using Smith's (2015) conjecture that mice love cheese.

If you want to be critical rather than 'mindless' about Johnson's interpretation of the result, just offer alternative interpretations (with additional citations). However, if the original interpretation is plausible, and if the issue is not the focus of your paper, it's okay just to follow Johnson (and thereby Smith).


What to do with seemingly fabricated data when researching a paper's citations

It seems like the Chart author was interpreting the Paper's research, and basically created a new chart while citing the Paper as the "source", but that actual chart nor data exists on Paper at all.

Maybe the author created the chart from the paper's data and cited the paper as the data's source. You've mentioned the Chart is useful, suggesting the author added value. (Whilst also suggesting the chart is not true, which seems contradictory.)

what exactly do I do with the knowledge that the chart seems to be fabricated?

You could email the author and ask for clarification.


Do you acknowledge someone mentioned in your paper/presentation that is in the audience?

If you're merely referring to someone's work who you don't know very well or haven't worked with, I wouldn't. If they are someone who is well known then it's likely that people will recognise that they are in the audience and that you are referencing their work.

If it is someone you have worked with or someone in your lab, then they usually get a shoutout. For example, a PI presenting work that is primarily done by a grad student or postdoc is likely to point this out and point out the person if they are in the audience. The reason for this is that it is beneficial to that person to be recognised. It encourages others to talk to/network with them because of the work they've done.


Removing an author from a future publication

Most authorship questions are a gray area: she did contribute to the paper, but was it a significant intellectual contribution (which is one usual criterion), with emphasis of both significant and intellectual (or scientific)? That's for you and her to decide, taking into account the customs of your field.

From her point of view, I can see two reasons why she might be consider a rightful co-author of the paper:

If the data collection was itself part of the scientific research, i.e. if it could not have been done by an unskilled worker following instructions. If so, then her data collection was significant (and it doesn't really ).
If the conclusions drawn from the preliminary analysis were useful in tuning your final analysis, i.e. if her work helped design a better analysis method.

Though by your description it seems like she may not pass the threshold, it is true that having her as a co-author on an earlier publication (conference abstract) gives her a stronger case than otherwise. If her contribution was deemed important enough for authorship at first, and you now publish work that includes this contribution, why shouldn't she be an author? I don't think that authorship “dilutes” because other larger contributions were added…

In conclusion: you maybe have good reasons not to make her a co-author, but if she feels like fighting it, she does have valid enough arguments that it could get messy. I'd advise discussing it openly with her, but being ready to have her as co-author if she feels strongly about it.


Planning to start a Bachelor's degree during my PhD: what to say to my advisor?

This is probably more of an opinion answer, but I would say you should say to your advisor either:

  I'm leaving my PhD because _________ and I am going to instead get a bachelor's degree in _______.

or

  I am not feeling good about my research progress and not enjoying research to the point that I am considering leaving the program - can you help?

To be blunt, your plan to do both at once sounds like a horrible blunder. If you are struggling in your PhD now, adding an additional set of responsibilities is not going to make that problem go away. I can't imagine your advisor giving you any different advice than I have.

Further, if you choose to not tell your advisor, I think this would be akin to what is described negatively as "ghosting" in the context of a personal relationship, which is considered to be incredibly rude towards anyone you have an established contact with. Slowly letting your performance decline while you stop paying attention to your PhD and start working on other things is just going to make everyone miserable, and probably destroy any chance you have of getting a good recommendation from your advisor in your future endeavors.

You suggested you've been looking for counseling, and indeed, if your mental health is suffering, that would be a good idea, much better than your plan to take on additional responsibilities.


If the interviewer says "We have other interviews to conduct and then back to you in few days", is it a bad sign to not get the job?

It's not a bad sign at all. If they have more interviews arranged, they wouldn't be doing their job if they didn't interview them. They don't just hire the first person suitable for the job. They hire the best person for the job! This may still be you - or it may be the next person to be interviewed.

Be patient, and they should let you know one way or the other!


The answer is a resounding Yes.

That is, it's not "either-or", but "both". On the one hand, as a postdoc, you will be expected to start coming up with your own research ideas and projects and take an active role in pitching your ideas to funding bodies, possibly even become PI on smaller grants yourself. Your supervisor will of course still play a major role.

On the other hand, your research should still tie in to your supervisor's area of expertise. Otherwise, why do you work with him and not someone else? And how should he help you with advice and contacts?

In the end, there will be a mixture between the two options you describe. When you join a group, you may respond to a job opening for a specific project, but even then, you will need to develop your own ideas in relation to this project and pursue your own interesting questions related to the project. Or you may have your own idea, possibly even your own funding, and more-or-less cold-call a potential supervisor, but even then, for the supervisor to accept you as a postdoc, you will need to explain to him how your idea ties in with his own work.


About to submit my PhD thesis in 4 months, feeling lost about my future and inadequate for any job. What should I do?

Your future prospects are not nearly as limited as you perceive them to be. Right now, you are trapped in the cult-like thinking of academia, which causes you to believe that the only measures of life success are high-octane research output and grant dollars. But these beliefs are false.

If things really are as you have described, then it may be true that you won't be competitive for academic jobs and postdocs. That's fine. Your training will make you an attractive candidate for other jobs in other fields. My guess is that you have a lot of coding skills, and perhaps a lot of experience in data analysis. These abilities are in high demand, and with time, you will be able to position yourself to compete for them.

My suggestion is to take some time away from your PhD studies, if this is possible, before you submit your dissertation. You need to get away from the cult and the patterns of thinking which are currently suffocating you. Visit family or friends, take time alone, play video games for a few weeks straight--whatever you do, clear your head. You will gain the perspective you need in order to identify goals you feel comfortable with and excited about, and once you understand what those are, you will be able to develop a plan to reach them.


In the words of Lichtfouse (2013) a research article is above all a communication tool and its purpose is to transfer scientific information from one individual to other individuals.

Publishing a paper is for me the way to show that I am doing research and sharing it with others. But, it is clear that I also am pressured into publishing because promotions and the ability to attract funding relies on publications as a primary evaluation tool. So although I do not publish with the expressed intent of attracting more funding or my own promotions, I am well aware of the spiralling development that is ongoing. I do want to mention that publishing something primarily gives me personally a sense of achievement, that my research is good enough to pass the scrutiny of peers etc. As with, I surmise, mostly everyone else, I thrive from doing a good job and getting a sense of accomplishment. Publishing does that for me.

Whether or not people read my research can be answered by yes and no. Everyone does not read my papers but some who do not should and some who reference my work, really ought to read it, again. On the whole, I think papers get the attention they deserve, some get more and some get less attention than I think is fair. But, since my work gets referenced reasonably often, I think over and under referenced papers average out.

The "pressure to publish" is definitely there and I believe that universities and funding agencies should try to improve the way they evaluate research so as to avoid "salami slicing" and other types of publishing effects. But, how such a system should look is difficult to say although many indices such as the h-index can be used. Since there are no perfect systems, it is perhaps more important to look at the ethical aspects of publishing and make awareness of and discssion on publishing issues better.

Lichtfouse, E., 2013. Scientific writing for impact factor journals. Nova Publishers, New York.


How to prepare for an online interview for a professorship position?

I interviewed candidates in the US for a similar position, the number one non-academic tip is to pay attention to how you appear on Zoom, and go for a professional setup. I was surprised how many candidates were speaking in a relatively dark room with a visible bed (even an unmade bed) behind them.

Look at the camera, not the screen
Find a relatively solid, professional, not distracting background
Light yourself from the front
Make sure the camera is raised to something approaching the level of your head

If possible, do a practice interview on Zoom first to prepare.


Should I postpone my MEXT scholarship application process until 2021 due coronavirus outbreak?

At this point there are no guarantees. Things could be fine in a year or not. There could be a vaccine or not. Japan could be doing well or not. The pool of applicants could be stronger then or not. Travel may be easier or not. There are just too many variables.

Under the circumstances you are probably best advised to continue on with an application until you reach a firm decision point (acceptance, say). Perhaps more will be known then. But expect chaos in the near term. Too many governments are behaving incompetently and making bad decisions. That could change or not.


On areas of overlap between Computer Science and Economics

There is a large and thriving community studying what is commonly known as Economics and Computation. This includes

Algorithmic Game Theory: the study of computational strategic agents. A good reference for this is the seminal Algorithmic Game Theory book. This subfield includes routing games (how selfish agents behave in network routing), mechanism design (auctions, such as spectrum auctions or Google ad auctions) and more.
Computational Fair Division: fair allocation of divisible/indivisible goods. This includes matching markets (college admissions, kidney exchanges) and assignment problems (course allocation, public housing assignment)
Computational Social Choice: efficient aggregation of opinions. This includes standard voting analysis as well as multi winner elections, opinion dynamics and more.


How much is expected to know before starting a PhD

The best way to respond to this specific question is to engage the potential supervisor about specific content in the articles.  You are not expected to know everything at this stage.  But it is important to show you are interested, can engage with the material, and (not least) actually took the time to read what they sent.

A response like "I read them but I didn't understand everything" doesn't give them any information about you.

Be specific, e.g.

I found the way authors applied X method in this paper to be really interesting.  I was familiar with this but didn't realize it could be used this way.
The authors did X but why didn't they use alternative approach Y?
I don't understand what this statement means...could you explain it?

Asking questions about things you don't understand can be one of the best ways to engage.


Conclusions section in a letter: To give a peek into new findings (not reported in letter) or not

It sounds like the depth of your findings are at odds with the letter format. If you want to talk about the full optimization across all parameters in detail I would consider an alternate format for publication.

That being said, one of the prominent journals in my field (JASA, whose full author guidelines can be found here) provides specific guidance for letters to the editor that supports your mentioning additional results that will be expanded on in future publications:

  The work should have a modicum of completeness, to the extent that the letter “tells a story” that is at least plausible to the reader, and it should have some nontrivial support for what is being related. Not all the loose strings need be tied together. Often there is an implicit promise that the publication of the letter will be followed up by a regular research article that fills in
  the gaps and that does all the things that a regular research article should do.

Note that this is just one journal in one field, and the expectations of the journal you are submitting to may differ.  I would recommend looking at your target journal's guidelines before proceeding one way or the other.


Acknowledgments in google scholar citations

Acceptable I'm not sure, but it really doesn't sound like a good idea.

The point of Google Scholar is to collect in one place the information on papers in which you are an author. If the paper in question was prominent enough in your profile to attract my attention, I would assume that something suspicious is going on, and there is no way for me to tell whose fault it is. Overall, it doesn't send the kind of signal you would probably want to send.


Is it reasonable to worry about lack of potential for dating in postdoc positions?

How is Academia different that any other job? You work for a number of hours a day, and then you are free to use your time solving jigsaws at home or socialising with other people.

Perhaps the academic environment has the advantage of multiculturalism. In most industries, the large majority of the people are from the country; but at universities you can find much more diversity, and thus, easier to find people you feel more comfortable with.

Lastly, in large cities there are, statistically, more potential "suitable partners", but they will be more difficult to find. As a mathematician, you may want to model it as an Erdős–Rényi graph, for the fun of it.

In the end, I think either path will have comparable a priori chances of finding love, so this should not be your main criteria to decide what to do with your life. Being happy with what you do will make you a nicer person, and have a larger impact that the city you are in.

And, to put at ease your concerns, most professors I know are married, and they certainly went down the postdoc path.


How often do good journals publish amusing little corollaries?

If other people share your enthusiasm for the observation and the proof, then it's of interest to journals. I would just contact one of the editors and see what they suggest. It's their job to be in charge of these questions.


Asking professor for recommendation after rejecting his PhD offer

I don't see any issue at all. Just ask and be honest. What was true in the past may not be true now. You don't need to go into all of the reasons that you refused in the past, but changing your mind about going abroad is not an issue.

If s/he supported you in the past, they are probably a good person to support you now. Don't let this hesitation work against taking advantage of an opportunity.


Who holds the copyright if I did research at one university and write a thesis at another?

You confuse two different things: The copyright attaches to the written work (in your case the thesis). The intellectual property attaches to the content of the contribution (in your case, the algorithm).

Likely (though I'm not qualified to give legal advice), the copyright for your thesis resides with you and/or university B, whereas the intellectual property in the algorithm resides with university A.


If you're writing a conference paper, put it in the same place as it appears in the conference papers you read.  If you're not reading any conference papers, you're not ready to write one.

If you're writing a journal paper, put it in the same place as it appears in the journal papers you read.  If you're not reading any journal papers, you're not ready to write one.

If you're writing a dissertation, put it in the same place as it appears in the dissertations you read.  If you're not reading any dissertations, you're not ready to write one.

If you're writing a $PAPER_TYPE, put it in the same place as it appears in the $PAPER_TYPEs that you read.  If you're not reading any $PAPER_TYPEs, you're not ready to write one.

Also: Ask your advisor.


What is the academic route to study Archaeology?

It is very difficult to answer with very little information. Archaeology is a very vast transversal field. It can be decomposed by techniques, by periods or by the targeted cultures. So the first question you need to ask yourself is whether you want to be an archaeologist (expertise in techniques) or a specialist of a period or culture (egyptologist for instance).

In the first case, scientific majors in high school is probably better than others, but this is not very important after all. However, be advise that excavation techniques are related to "dirt on the hands" techniques, but also to some top notch scientific techniques (specially for the analysis, where you may need knowledge of stats, paleontology, zoology, botany, chemistry, etc.).

In the second case, I would advise to start quickly to acquire a strong background in art history and ancient languages (starting with greek and latin). I will be easier to learn linguistic and semiology afterwards. I guess that both art history and ancient languages can be learned at the high school level in most countries.

At the university, students usually progress concurrently in archaeology techniques and culture specialization.


Does it makes sense to publish new math whose primary significance is its applicability to another field?

I'm an applied mathematician and I have written some papers with a focus similar to what you describe:

They don't include fundamentally new mathematics
They achieve new/faster/better results in some application, by applying mathematical techniques that are not known in the application field

This kind of work should usually be published in a journal of the application area, not a mathematics journal.  The application specialists are the ones who need to learn about what you've done, so they can use it.  You need to write your manuscript in a way that is accessible and convincing to application specialists.  This probably means not focusing on theorems and proofs, but on results.  It may require changing the vocabulary and notation you use.  It is often not easy, and you will need to spend time reading the literature of the application field.  It can be very helpful to find someone in that field you can talk to, or even get as a co-author.


I sent an unupdated version of my MSc. thesis to a supervisor of a PhD project I am applying for

Even final published theses can, and do, have errors.

Don’t worry, if the errors are typos etc you will be fine, however if there is a serious error in the theory or analysis then that may be different.


How to transition from lectures/exams to research/thesis?

Firstly, don't worry. This anxiety that you describe is extremely common and completely normal. You're right that it stems from the transition from very tightly-constrained styles of work to something that is much more open-ended. You are half-way there - you have recognised that you have many different possible paths to follow. But I get the impression that you are still thinking in terms of pass and fail. You talk about finding the "right decision", and that a given approach "might fail or not", but research is not so black-and-white.

Of the many different paths that you are considering, it's not that some of them contain death-traps where you will be forever doomed, whereas some are shining paths to glory. It is likely that you can make a success of any of them (just so long as you don't stay rooted to one spot for too long...). Even a "failure" to find a solution is useful. In the words of Thomas Edison:

  "I have not failed. I've just found 10,000 ways that won't work."

You might find inspiration for something else, or you might just be able to rule out one method - that is still progress.

You also talk about whether to pursue a single issue in depth, or take a radical change of direction. Both those approaches are valid, and it's up to you which style you prefer. Eventually, with experience, you will start to get a bit of a nose for what sorts of approach work best for you, and maybe be able to head in a slightly straighter line through your research. But even professors are not perfect in that regard. Until then, as @user37208 suggests in the comments, your advisor should be a great source of advice here and can help you to break down the problem into more manageable chunks, and give you a bit of direction when you feel you are wandering around without success.

You may be thinking "that's all very well, but at the end of the day, my thesis will pass or fail." While that's true, this will depend far more on how well you can explain what you have done, and whether you can demonstrate that you have made reasonable efforts to tackle one or more problems, than on whether you have actually found "an answer" or not.


Is there a chance for a new university in another country to accept my passed courses/classes?

Many universities/countries in europe have adopted the "bologna system" which mainly aims for comparability of degrees so that it gets easy to do masters studies in a different country than your bachelor. With this they also adopted the ECTS (European Credit Transfer System) which should make different courses comparable. There are definitely ambitions to make it possible to switch mid studies.

So much for theory. In the real world, at least here in Austria, it is definitely possible to finish your study at another university. However, they might not accept all your finished courses or not with that amount of credits. We even had cases where master/PhD students were required to do bachelor studies lab courses to get to a similar level.

All of this is usually handeled by the dean of studies who can decide if you are allowed to finish your studies at that university and what you have to do to reach that goal. What you should do is speak to the dean and ask them directly, only he/she can give you an answer if it works in your case.


What are the chances of getting into a PHD program even if your graduate research is completely different?

Completely possible!

You only need to argument your research as multi-field with an holistic approach, base your methods or the relation on technology and how it impacts the new field, or propose some innovative way to apply or relate computational sciences to biological systems (neural networks or Ai to learn how X works are always a good hit.)

As as example, my first career was in 'environmental improvement and diagnostics', then I went into 'informatique sciences' , specialization MBA into 'economy', then MBA into ' Computational Systems' but PHD in 'Organizations direction/Management'. It all comes down on how you relate everything.

As for how easy it would be to enter, well, you need to see which universities you want, go into their website's  and see their requirements for candidates. You can then tailor your proposal to them and contact the admissions department to say what they want. Even within the same country there are variants among the universities, more so between public and private ones.


google scholar has not listed me as coauthor

It is a bit difficult to speak on behalf of Google here. The best idea is probably to contact them directly [1].

Before you do that, however, I would encourage you to double check if the details on the websites where your paper is published are correct. Much of what Google Scholar does is just indexing those websites and taking their data from there. Google explicitly recommends to ask for corrections there and not on Google Scholar. They also say state that an update to any details might take quite a bit of time, in the order of months [2]. So any recent correction to details on the publisher's side might not be updated yet.

[1] https://support.google.com/scholar/contact/general

[2] https://scholar.google.com/intl/de/scholar/help.html#corrections


Apply for a cluster for scientific computing from a developing country for academic use?

This doesn't quite answer the question, but in case you have some funds available (but not enough to buy a cluster): Various cloud services - Amazon in particular but probably others - will let you "spin up" a temporary compute cluster on their servers. You pay for this by the minute, or sometimes by more complicated systems where the price is according to demand.

For small projects this approach can be quite economical, and so may be feasible in some circumstances where access to a dedicated system is unaffordable.


How to ask for a recommendation letter if no professor knows me in person?

Asking for a recommendation letter from a person who does not know you makes sense neither for you nor for a potential referee. The purpose of a reference letter is to let others know about your work habits, your motivation, your skills etc. A person who does not know you can not judge any of these things, thus even if you can convince a professor to write a letter about you it might not necessarily have a benefit for an application when it simply states that you have attended some courses.
You could try to contact a professor in a field you feel motivation for and whose work you are interested in and ask about potential student projects, irrespective of courses or credits. This can:

Help get to know a professor personally
Help you figure out if you enjoy working in an academic environment
Get you a personal recommendation letter


Can "Feel free to contact me if you are interested in a copy of any of my publications." cause legal issues?

This will likely vary from journal to journal, but the information should be available in the "authors" section on a journal's webpage. For example, Science provides the document "License to Publish—Information for Authors" document, which clearly states:

  Once the Work has been published in Science and provided the Work's first appearance in Science is properly cited, authors may:

  ...

  Distribute photocopies of the Work to colleagues for non-commercial purposes only (providing that recipients are informed that they may not further distribute or copy the Work). Authors may distribute photocopies or download and email the Science PDF to their colleagues for their colleagues' personal use provided the recipients understand that the copy may not be further distributed or reproduced without the approval of AAAS.

This license would allow what you described, as it's non-commercial.


I will be graduating a semester early, what schools have spring & summer intake?

check the list below for spring intake colleges. dates may be different as the list is for 2015

http://www.hotcoursesabroad.com/india/prepare-to-apply/how-to-apply-to-a-university/usas-spring-2015-admissions/


Consider teaching as a career. You don't have to do research then, but you do have to the understand the material. If you like learning about the material then this would suit you well; you might even be able to convey your love for the topic to future students.

Potential problem: chances you'll need an advanced degree to be able to teach at university level. With just a Bachelor's degree you can still teach at high school level and below.

Alternatively, consider publishing/science journalism. These two fields don't need you to do research too, but your output in both improve if you understand the material.

Potential problem: it's possible the physicists you'll be speaking to consider publishers a scam, and you by working in one are complicit in the scam. You'll have to decide for yourself if you can put up with that. Science journalism is relatively benign in this sense, but you'll be forced into confronting how something you find so wonderful, so interesting, and so amazing can be considered by others to be boring and pointless.